Actual source code: mpiov.c

      1: /*
      2:    Routines to compute overlapping regions of a parallel MPI matrix
      3:   and to find submatrices that were shared across processors.
      4: */
      5: #include <../src/mat/impls/aij/seq/aij.h>
      6: #include <../src/mat/impls/aij/mpi/mpiaij.h>
      7: #include <petscbt.h>
      8: #include <petscsf.h>

     10: static PetscErrorCode MatIncreaseOverlap_MPIAIJ_Once(Mat,PetscInt,IS*);
     11: static PetscErrorCode MatIncreaseOverlap_MPIAIJ_Local(Mat,PetscInt,char**,PetscInt*,PetscInt**,PetscTable*);
     12: static PetscErrorCode MatIncreaseOverlap_MPIAIJ_Receive(Mat,PetscInt,PetscInt**,PetscInt**,PetscInt*);
     13: extern PetscErrorCode MatGetRow_MPIAIJ(Mat,PetscInt,PetscInt*,PetscInt**,PetscScalar**);
     14: extern PetscErrorCode MatRestoreRow_MPIAIJ(Mat,PetscInt,PetscInt*,PetscInt**,PetscScalar**);

     16: static PetscErrorCode MatIncreaseOverlap_MPIAIJ_Once_Scalable(Mat,PetscInt,IS*);
     17: static PetscErrorCode MatIncreaseOverlap_MPIAIJ_Local_Scalable(Mat,PetscInt,IS*);
     18: static PetscErrorCode MatIncreaseOverlap_MPIAIJ_Send_Scalable(Mat,PetscInt,PetscMPIInt,PetscMPIInt *,PetscInt *, PetscInt *,PetscInt **,PetscInt **);
     19: static PetscErrorCode MatIncreaseOverlap_MPIAIJ_Receive_Scalable(Mat,PetscInt,IS*,PetscInt,PetscInt *);

     21: PetscErrorCode MatIncreaseOverlap_MPIAIJ(Mat C,PetscInt imax,IS is[],PetscInt ov)
     22: {
     23:   PetscInt       i;

     26:   for (i=0; i<ov; ++i) {
     27:     MatIncreaseOverlap_MPIAIJ_Once(C,imax,is);
     28:   }
     29:   return 0;
     30: }

     32: PetscErrorCode MatIncreaseOverlap_MPIAIJ_Scalable(Mat C,PetscInt imax,IS is[],PetscInt ov)
     33: {
     34:   PetscInt       i;

     37:   for (i=0; i<ov; ++i) {
     38:     MatIncreaseOverlap_MPIAIJ_Once_Scalable(C,imax,is);
     39:   }
     40:   return 0;
     41: }

     43: static PetscErrorCode MatIncreaseOverlap_MPIAIJ_Once_Scalable(Mat mat,PetscInt nidx,IS is[])
     44: {
     45:   MPI_Comm       comm;
     46:   PetscInt       *length,length_i,tlength,*remoterows,nrrows,reducednrrows,*rrow_ranks,*rrow_isids,i,j;
     47:   PetscInt       *tosizes,*tosizes_temp,*toffsets,*fromsizes,*todata,*fromdata;
     48:   PetscInt       nrecvrows,*sbsizes = NULL,*sbdata = NULL;
     49:   const PetscInt *indices_i,**indices;
     50:   PetscLayout    rmap;
     51:   PetscMPIInt    rank,size,*toranks,*fromranks,nto,nfrom,owner;
     52:   PetscSF        sf;
     53:   PetscSFNode    *remote;

     55:   PetscObjectGetComm((PetscObject)mat,&comm);
     56:   MPI_Comm_rank(comm,&rank);
     57:   MPI_Comm_size(comm,&size);
     58:   /* get row map to determine where rows should be going */
     59:   MatGetLayouts(mat,&rmap,NULL);
     60:   /* retrieve IS data and put all together so that we
     61:    * can optimize communication
     62:    *  */
     63:   PetscMalloc2(nidx,(PetscInt ***)&indices,nidx,&length);
     64:   for (i=0,tlength=0; i<nidx; i++) {
     65:     ISGetLocalSize(is[i],&length[i]);
     66:     tlength += length[i];
     67:     ISGetIndices(is[i],&indices[i]);
     68:   }
     69:   /* find these rows on remote processors */
     70:   PetscCalloc3(tlength,&remoterows,tlength,&rrow_ranks,tlength,&rrow_isids);
     71:   PetscCalloc3(size,&toranks,2*size,&tosizes,size,&tosizes_temp);
     72:   nrrows = 0;
     73:   for (i=0; i<nidx; i++) {
     74:     length_i  = length[i];
     75:     indices_i = indices[i];
     76:     for (j=0; j<length_i; j++) {
     77:       owner = -1;
     78:       PetscLayoutFindOwner(rmap,indices_i[j],&owner);
     79:       /* remote processors */
     80:       if (owner != rank) {
     81:         tosizes_temp[owner]++; /* number of rows to owner */
     82:         rrow_ranks[nrrows]  = owner; /* processor */
     83:         rrow_isids[nrrows]   = i; /* is id */
     84:         remoterows[nrrows++] = indices_i[j]; /* row */
     85:       }
     86:     }
     87:     ISRestoreIndices(is[i],&indices[i]);
     88:   }
     89:   PetscFree2(*(PetscInt***)&indices,length);
     90:   /* test if we need to exchange messages
     91:    * generally speaking, we do not need to exchange
     92:    * data when overlap is 1
     93:    * */
     94:   MPIU_Allreduce(&nrrows,&reducednrrows,1,MPIU_INT,MPIU_MAX,comm);
     95:   /* we do not have any messages
     96:    * It usually corresponds to overlap 1
     97:    * */
     98:   if (!reducednrrows) {
     99:     PetscFree3(toranks,tosizes,tosizes_temp);
    100:     PetscFree3(remoterows,rrow_ranks,rrow_isids);
    101:     MatIncreaseOverlap_MPIAIJ_Local_Scalable(mat,nidx,is);
    102:     return 0;
    103:   }
    104:   nto = 0;
    105:   /* send sizes and ranks for building a two-sided communcation */
    106:   for (i=0; i<size; i++) {
    107:     if (tosizes_temp[i]) {
    108:       tosizes[nto*2]  = tosizes_temp[i]*2; /* size */
    109:       tosizes_temp[i] = nto; /* a map from processor to index */
    110:       toranks[nto++]  = i; /* processor */
    111:     }
    112:   }
    113:   PetscMalloc1(nto+1,&toffsets);
    114:   toffsets[0] = 0;
    115:   for (i=0; i<nto; i++) {
    116:     toffsets[i+1]  = toffsets[i]+tosizes[2*i]; /* offsets */
    117:     tosizes[2*i+1] = toffsets[i]; /* offsets to send */
    118:   }
    119:   /* send information to other processors */
    120:   PetscCommBuildTwoSided(comm,2,MPIU_INT,nto,toranks,tosizes,&nfrom,&fromranks,&fromsizes);
    121:   nrecvrows = 0;
    122:   for (i=0; i<nfrom; i++) nrecvrows += fromsizes[2*i];
    123:   PetscMalloc1(nrecvrows,&remote);
    124:   nrecvrows = 0;
    125:   for (i=0; i<nfrom; i++) {
    126:     for (j=0; j<fromsizes[2*i]; j++) {
    127:       remote[nrecvrows].rank    = fromranks[i];
    128:       remote[nrecvrows++].index = fromsizes[2*i+1]+j;
    129:     }
    130:   }
    131:   PetscSFCreate(comm,&sf);
    132:   PetscSFSetGraph(sf,nrecvrows,nrecvrows,NULL,PETSC_OWN_POINTER,remote,PETSC_OWN_POINTER);
    133:   /* use two-sided communication by default since OPENMPI has some bugs for one-sided one */
    134:   PetscSFSetType(sf,PETSCSFBASIC);
    135:   PetscSFSetFromOptions(sf);
    136:   /* message pair <no of is, row>  */
    137:   PetscCalloc2(2*nrrows,&todata,nrecvrows,&fromdata);
    138:   for (i=0; i<nrrows; i++) {
    139:     owner = rrow_ranks[i]; /* processor */
    140:     j     = tosizes_temp[owner]; /* index */
    141:     todata[toffsets[j]++] = rrow_isids[i];
    142:     todata[toffsets[j]++] = remoterows[i];
    143:   }
    144:   PetscFree3(toranks,tosizes,tosizes_temp);
    145:   PetscFree3(remoterows,rrow_ranks,rrow_isids);
    146:   PetscFree(toffsets);
    147:   PetscSFBcastBegin(sf,MPIU_INT,todata,fromdata,MPI_REPLACE);
    148:   PetscSFBcastEnd(sf,MPIU_INT,todata,fromdata,MPI_REPLACE);
    149:   PetscSFDestroy(&sf);
    150:   /* send rows belonging to the remote so that then we could get the overlapping data back */
    151:   MatIncreaseOverlap_MPIAIJ_Send_Scalable(mat,nidx,nfrom,fromranks,fromsizes,fromdata,&sbsizes,&sbdata);
    152:   PetscFree2(todata,fromdata);
    153:   PetscFree(fromsizes);
    154:   PetscCommBuildTwoSided(comm,2,MPIU_INT,nfrom,fromranks,sbsizes,&nto,&toranks,&tosizes);
    155:   PetscFree(fromranks);
    156:   nrecvrows = 0;
    157:   for (i=0; i<nto; i++) nrecvrows += tosizes[2*i];
    158:   PetscCalloc1(nrecvrows,&todata);
    159:   PetscMalloc1(nrecvrows,&remote);
    160:   nrecvrows = 0;
    161:   for (i=0; i<nto; i++) {
    162:     for (j=0; j<tosizes[2*i]; j++) {
    163:       remote[nrecvrows].rank    = toranks[i];
    164:       remote[nrecvrows++].index = tosizes[2*i+1]+j;
    165:     }
    166:   }
    167:   PetscSFCreate(comm,&sf);
    168:   PetscSFSetGraph(sf,nrecvrows,nrecvrows,NULL,PETSC_OWN_POINTER,remote,PETSC_OWN_POINTER);
    169:   /* use two-sided communication by default since OPENMPI has some bugs for one-sided one */
    170:   PetscSFSetType(sf,PETSCSFBASIC);
    171:   PetscSFSetFromOptions(sf);
    172:   /* overlap communication and computation */
    173:   PetscSFBcastBegin(sf,MPIU_INT,sbdata,todata,MPI_REPLACE);
    174:   MatIncreaseOverlap_MPIAIJ_Local_Scalable(mat,nidx,is);
    175:   PetscSFBcastEnd(sf,MPIU_INT,sbdata,todata,MPI_REPLACE);
    176:   PetscSFDestroy(&sf);
    177:   PetscFree2(sbdata,sbsizes);
    178:   MatIncreaseOverlap_MPIAIJ_Receive_Scalable(mat,nidx,is,nrecvrows,todata);
    179:   PetscFree(toranks);
    180:   PetscFree(tosizes);
    181:   PetscFree(todata);
    182:   return 0;
    183: }

    185: static PetscErrorCode MatIncreaseOverlap_MPIAIJ_Receive_Scalable(Mat mat,PetscInt nidx, IS is[], PetscInt nrecvs, PetscInt *recvdata)
    186: {
    187:   PetscInt         *isz,isz_i,i,j,is_id, data_size;
    188:   PetscInt          col,lsize,max_lsize,*indices_temp, *indices_i;
    189:   const PetscInt   *indices_i_temp;
    190:   MPI_Comm         *iscomms;

    192:   max_lsize = 0;
    193:   PetscMalloc1(nidx,&isz);
    194:   for (i=0; i<nidx; i++) {
    195:     ISGetLocalSize(is[i],&lsize);
    196:     max_lsize = lsize>max_lsize ? lsize:max_lsize;
    197:     isz[i]    = lsize;
    198:   }
    199:   PetscMalloc2((max_lsize+nrecvs)*nidx,&indices_temp,nidx,&iscomms);
    200:   for (i=0; i<nidx; i++) {
    201:     PetscCommDuplicate(PetscObjectComm((PetscObject)is[i]),&iscomms[i],NULL);
    202:     ISGetIndices(is[i],&indices_i_temp);
    203:     PetscArraycpy(indices_temp+i*(max_lsize+nrecvs),indices_i_temp, isz[i]);
    204:     ISRestoreIndices(is[i],&indices_i_temp);
    205:     ISDestroy(&is[i]);
    206:   }
    207:   /* retrieve information to get row id and its overlap */
    208:   for (i=0; i<nrecvs;) {
    209:     is_id     = recvdata[i++];
    210:     data_size = recvdata[i++];
    211:     indices_i = indices_temp+(max_lsize+nrecvs)*is_id;
    212:     isz_i     = isz[is_id];
    213:     for (j=0; j< data_size; j++) {
    214:       col = recvdata[i++];
    215:       indices_i[isz_i++] = col;
    216:     }
    217:     isz[is_id] = isz_i;
    218:   }
    219:   /* remove duplicate entities */
    220:   for (i=0; i<nidx; i++) {
    221:     indices_i = indices_temp+(max_lsize+nrecvs)*i;
    222:     isz_i     = isz[i];
    223:     PetscSortRemoveDupsInt(&isz_i,indices_i);
    224:     ISCreateGeneral(iscomms[i],isz_i,indices_i,PETSC_COPY_VALUES,&is[i]);
    225:     PetscCommDestroy(&iscomms[i]);
    226:   }
    227:   PetscFree(isz);
    228:   PetscFree2(indices_temp,iscomms);
    229:   return 0;
    230: }

    232: static PetscErrorCode MatIncreaseOverlap_MPIAIJ_Send_Scalable(Mat mat,PetscInt nidx, PetscMPIInt nfrom,PetscMPIInt *fromranks,PetscInt *fromsizes, PetscInt *fromrows, PetscInt **sbrowsizes, PetscInt **sbrows)
    233: {
    234:   PetscLayout       rmap,cmap;
    235:   PetscInt          i,j,k,l,*rows_i,*rows_data_ptr,**rows_data,max_fszs,rows_pos,*rows_pos_i;
    236:   PetscInt          is_id,tnz,an,bn,rstart,cstart,row,start,end,col,totalrows,*sbdata;
    237:   PetscInt         *indv_counts,indvc_ij,*sbsizes,*indices_tmp,*offsets;
    238:   const PetscInt   *gcols,*ai,*aj,*bi,*bj;
    239:   Mat               amat,bmat;
    240:   PetscMPIInt       rank;
    241:   PetscBool         done;
    242:   MPI_Comm          comm;

    244:   PetscObjectGetComm((PetscObject)mat,&comm);
    245:   MPI_Comm_rank(comm,&rank);
    246:   MatMPIAIJGetSeqAIJ(mat,&amat,&bmat,&gcols);
    247:   /* Even if the mat is symmetric, we still assume it is not symmetric */
    248:   MatGetRowIJ(amat,0,PETSC_FALSE,PETSC_FALSE,&an,&ai,&aj,&done);
    250:   MatGetRowIJ(bmat,0,PETSC_FALSE,PETSC_FALSE,&bn,&bi,&bj,&done);
    252:   /* total number of nonzero values is used to estimate the memory usage in the next step */
    253:   tnz  = ai[an]+bi[bn];
    254:   MatGetLayouts(mat,&rmap,&cmap);
    255:   PetscLayoutGetRange(rmap,&rstart,NULL);
    256:   PetscLayoutGetRange(cmap,&cstart,NULL);
    257:   /* to find the longest message */
    258:   max_fszs = 0;
    259:   for (i=0; i<nfrom; i++) max_fszs = fromsizes[2*i]>max_fszs ? fromsizes[2*i]:max_fszs;
    260:   /* better way to estimate number of nonzero in the mat??? */
    261:   PetscCalloc5(max_fszs*nidx,&rows_data_ptr,nidx,&rows_data,nidx,&rows_pos_i,nfrom*nidx,&indv_counts,tnz,&indices_tmp);
    262:   for (i=0; i<nidx; i++) rows_data[i] = rows_data_ptr+max_fszs*i;
    263:   rows_pos  = 0;
    264:   totalrows = 0;
    265:   for (i=0; i<nfrom; i++) {
    266:     PetscArrayzero(rows_pos_i,nidx);
    267:     /* group data together */
    268:     for (j=0; j<fromsizes[2*i]; j+=2) {
    269:       is_id                       = fromrows[rows_pos++];/* no of is */
    270:       rows_i                      = rows_data[is_id];
    271:       rows_i[rows_pos_i[is_id]++] = fromrows[rows_pos++];/* row */
    272:     }
    273:     /* estimate a space to avoid multiple allocations  */
    274:     for (j=0; j<nidx; j++) {
    275:       indvc_ij = 0;
    276:       rows_i   = rows_data[j];
    277:       for (l=0; l<rows_pos_i[j]; l++) {
    278:         row    = rows_i[l]-rstart;
    279:         start  = ai[row];
    280:         end    = ai[row+1];
    281:         for (k=start; k<end; k++) { /* Amat */
    282:           col = aj[k] + cstart;
    283:           indices_tmp[indvc_ij++] = col;/* do not count the rows from the original rank */
    284:         }
    285:         start = bi[row];
    286:         end   = bi[row+1];
    287:         for (k=start; k<end; k++) { /* Bmat */
    288:           col = gcols[bj[k]];
    289:           indices_tmp[indvc_ij++] = col;
    290:         }
    291:       }
    292:       PetscSortRemoveDupsInt(&indvc_ij,indices_tmp);
    293:       indv_counts[i*nidx+j] = indvc_ij;
    294:       totalrows            += indvc_ij;
    295:     }
    296:   }
    297:   /* message triple <no of is, number of rows, rows> */
    298:   PetscCalloc2(totalrows+nidx*nfrom*2,&sbdata,2*nfrom,&sbsizes);
    299:   totalrows = 0;
    300:   rows_pos  = 0;
    301:   /* use this code again */
    302:   for (i=0;i<nfrom;i++) {
    303:     PetscArrayzero(rows_pos_i,nidx);
    304:     for (j=0; j<fromsizes[2*i]; j+=2) {
    305:       is_id                       = fromrows[rows_pos++];
    306:       rows_i                      = rows_data[is_id];
    307:       rows_i[rows_pos_i[is_id]++] = fromrows[rows_pos++];
    308:     }
    309:     /* add data  */
    310:     for (j=0; j<nidx; j++) {
    311:       if (!indv_counts[i*nidx+j]) continue;
    312:       indvc_ij = 0;
    313:       sbdata[totalrows++] = j;
    314:       sbdata[totalrows++] = indv_counts[i*nidx+j];
    315:       sbsizes[2*i]       += 2;
    316:       rows_i              = rows_data[j];
    317:       for (l=0; l<rows_pos_i[j]; l++) {
    318:         row   = rows_i[l]-rstart;
    319:         start = ai[row];
    320:         end   = ai[row+1];
    321:         for (k=start; k<end; k++) { /* Amat */
    322:           col = aj[k] + cstart;
    323:           indices_tmp[indvc_ij++] = col;
    324:         }
    325:         start = bi[row];
    326:         end   = bi[row+1];
    327:         for (k=start; k<end; k++) { /* Bmat */
    328:           col = gcols[bj[k]];
    329:           indices_tmp[indvc_ij++] = col;
    330:         }
    331:       }
    332:       PetscSortRemoveDupsInt(&indvc_ij,indices_tmp);
    333:       sbsizes[2*i]  += indvc_ij;
    334:       PetscArraycpy(sbdata+totalrows,indices_tmp,indvc_ij);
    335:       totalrows += indvc_ij;
    336:     }
    337:   }
    338:   PetscMalloc1(nfrom+1,&offsets);
    339:   offsets[0] = 0;
    340:   for (i=0; i<nfrom; i++) {
    341:     offsets[i+1]   = offsets[i] + sbsizes[2*i];
    342:     sbsizes[2*i+1] = offsets[i];
    343:   }
    344:   PetscFree(offsets);
    345:   if (sbrowsizes) *sbrowsizes = sbsizes;
    346:   if (sbrows) *sbrows = sbdata;
    347:   PetscFree5(rows_data_ptr,rows_data,rows_pos_i,indv_counts,indices_tmp);
    348:   MatRestoreRowIJ(amat,0,PETSC_FALSE,PETSC_FALSE,&an,&ai,&aj,&done);
    349:   MatRestoreRowIJ(bmat,0,PETSC_FALSE,PETSC_FALSE,&bn,&bi,&bj,&done);
    350:   return 0;
    351: }

    353: static PetscErrorCode MatIncreaseOverlap_MPIAIJ_Local_Scalable(Mat mat,PetscInt nidx, IS is[])
    354: {
    355:   const PetscInt   *gcols,*ai,*aj,*bi,*bj, *indices;
    356:   PetscInt          tnz,an,bn,i,j,row,start,end,rstart,cstart,col,k,*indices_temp;
    357:   PetscInt          lsize,lsize_tmp;
    358:   PetscMPIInt       rank,owner;
    359:   Mat               amat,bmat;
    360:   PetscBool         done;
    361:   PetscLayout       cmap,rmap;
    362:   MPI_Comm          comm;

    364:   PetscObjectGetComm((PetscObject)mat,&comm);
    365:   MPI_Comm_rank(comm,&rank);
    366:   MatMPIAIJGetSeqAIJ(mat,&amat,&bmat,&gcols);
    367:   MatGetRowIJ(amat,0,PETSC_FALSE,PETSC_FALSE,&an,&ai,&aj,&done);
    369:   MatGetRowIJ(bmat,0,PETSC_FALSE,PETSC_FALSE,&bn,&bi,&bj,&done);
    371:   /* is it a safe way to compute number of nonzero values ? */
    372:   tnz  = ai[an]+bi[bn];
    373:   MatGetLayouts(mat,&rmap,&cmap);
    374:   PetscLayoutGetRange(rmap,&rstart,NULL);
    375:   PetscLayoutGetRange(cmap,&cstart,NULL);
    376:   /* it is a better way to estimate memory than the old implementation
    377:    * where global size of matrix is used
    378:    * */
    379:   PetscMalloc1(tnz,&indices_temp);
    380:   for (i=0; i<nidx; i++) {
    381:     MPI_Comm iscomm;

    383:     ISGetLocalSize(is[i],&lsize);
    384:     ISGetIndices(is[i],&indices);
    385:     lsize_tmp = 0;
    386:     for (j=0; j<lsize; j++) {
    387:       owner = -1;
    388:       row   = indices[j];
    389:       PetscLayoutFindOwner(rmap,row,&owner);
    390:       if (owner != rank) continue;
    391:       /* local number */
    392:       row  -= rstart;
    393:       start = ai[row];
    394:       end   = ai[row+1];
    395:       for (k=start; k<end; k++) { /* Amat */
    396:         col = aj[k] + cstart;
    397:         indices_temp[lsize_tmp++] = col;
    398:       }
    399:       start = bi[row];
    400:       end   = bi[row+1];
    401:       for (k=start; k<end; k++) { /* Bmat */
    402:         col = gcols[bj[k]];
    403:         indices_temp[lsize_tmp++] = col;
    404:       }
    405:     }
    406:    ISRestoreIndices(is[i],&indices);
    407:    PetscCommDuplicate(PetscObjectComm((PetscObject)is[i]),&iscomm,NULL);
    408:    ISDestroy(&is[i]);
    409:    PetscSortRemoveDupsInt(&lsize_tmp,indices_temp);
    410:    ISCreateGeneral(iscomm,lsize_tmp,indices_temp,PETSC_COPY_VALUES,&is[i]);
    411:    PetscCommDestroy(&iscomm);
    412:   }
    413:   PetscFree(indices_temp);
    414:   MatRestoreRowIJ(amat,0,PETSC_FALSE,PETSC_FALSE,&an,&ai,&aj,&done);
    415:   MatRestoreRowIJ(bmat,0,PETSC_FALSE,PETSC_FALSE,&bn,&bi,&bj,&done);
    416:   return 0;
    417: }

    419: /*
    420:   Sample message format:
    421:   If a processor A wants processor B to process some elements corresponding
    422:   to index sets is[1],is[5]
    423:   mesg [0] = 2   (no of index sets in the mesg)
    424:   -----------
    425:   mesg [1] = 1 => is[1]
    426:   mesg [2] = sizeof(is[1]);
    427:   -----------
    428:   mesg [3] = 5  => is[5]
    429:   mesg [4] = sizeof(is[5]);
    430:   -----------
    431:   mesg [5]
    432:   mesg [n]  datas[1]
    433:   -----------
    434:   mesg[n+1]
    435:   mesg[m]  data(is[5])
    436:   -----------

    438:   Notes:
    439:   nrqs - no of requests sent (or to be sent out)
    440:   nrqr - no of requests received (which have to be or which have been processed)
    441: */
    442: static PetscErrorCode MatIncreaseOverlap_MPIAIJ_Once(Mat C,PetscInt imax,IS is[])
    443: {
    444:   Mat_MPIAIJ     *c = (Mat_MPIAIJ*)C->data;
    445:   PetscMPIInt    *w1,*w2,nrqr,*w3,*w4,*onodes1,*olengths1,*onodes2,*olengths2;
    446:   const PetscInt **idx,*idx_i;
    447:   PetscInt       *n,**data,len;
    448: #if defined(PETSC_USE_CTABLE)
    449:   PetscTable     *table_data,table_data_i;
    450:   PetscInt       *tdata,tcount,tcount_max;
    451: #else
    452:   PetscInt       *data_i,*d_p;
    453: #endif
    454:   PetscMPIInt    size,rank,tag1,tag2,proc = 0;
    455:   PetscInt       M,i,j,k,**rbuf,row,nrqs,msz,**outdat,**ptr;
    456:   PetscInt       *ctr,*pa,*tmp,*isz,*isz1,**xdata,**rbuf2;
    457:   PetscBT        *table;
    458:   MPI_Comm       comm;
    459:   MPI_Request    *s_waits1,*r_waits1,*s_waits2,*r_waits2;
    460:   MPI_Status     *recv_status;
    461:   MPI_Comm       *iscomms;
    462:   char           *t_p;

    464:   PetscObjectGetComm((PetscObject)C,&comm);
    465:   size = c->size;
    466:   rank = c->rank;
    467:   M    = C->rmap->N;

    469:   PetscObjectGetNewTag((PetscObject)C,&tag1);
    470:   PetscObjectGetNewTag((PetscObject)C,&tag2);

    472:   PetscMalloc2(imax,(PetscInt***)&idx,imax,&n);

    474:   for (i=0; i<imax; i++) {
    475:     ISGetIndices(is[i],&idx[i]);
    476:     ISGetLocalSize(is[i],&n[i]);
    477:   }

    479:   /* evaluate communication - mesg to who,length of mesg, and buffer space
    480:      required. Based on this, buffers are allocated, and data copied into them  */
    481:   PetscCalloc4(size,&w1,size,&w2,size,&w3,size,&w4);
    482:   for (i=0; i<imax; i++) {
    483:     PetscArrayzero(w4,size); /* initialise work vector*/
    484:     idx_i = idx[i];
    485:     len   = n[i];
    486:     for (j=0; j<len; j++) {
    487:       row = idx_i[j];
    489:       PetscLayoutFindOwner(C->rmap,row,&proc);
    490:       w4[proc]++;
    491:     }
    492:     for (j=0; j<size; j++) {
    493:       if (w4[j]) { w1[j] += w4[j]; w3[j]++;}
    494:     }
    495:   }

    497:   nrqs     = 0;              /* no of outgoing messages */
    498:   msz      = 0;              /* total mesg length (for all proc */
    499:   w1[rank] = 0;              /* no mesg sent to intself */
    500:   w3[rank] = 0;
    501:   for (i=0; i<size; i++) {
    502:     if (w1[i])  {w2[i] = 1; nrqs++;} /* there exists a message to proc i */
    503:   }
    504:   /* pa - is list of processors to communicate with */
    505:   PetscMalloc1(nrqs,&pa);
    506:   for (i=0,j=0; i<size; i++) {
    507:     if (w1[i]) {pa[j] = i; j++;}
    508:   }

    510:   /* Each message would have a header = 1 + 2*(no of IS) + data */
    511:   for (i=0; i<nrqs; i++) {
    512:     j      = pa[i];
    513:     w1[j] += w2[j] + 2*w3[j];
    514:     msz   += w1[j];
    515:   }

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

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

    524:   /* Allocate Memory for outgoing messages */
    525:   PetscMalloc4(size,&outdat,size,&ptr,msz,&tmp,size,&ctr);
    526:   PetscArrayzero(outdat,size);
    527:   PetscArrayzero(ptr,size);

    529:   {
    530:     PetscInt *iptr = tmp,ict  = 0;
    531:     for (i=0; i<nrqs; i++) {
    532:       j         = pa[i];
    533:       iptr     +=  ict;
    534:       outdat[j] = iptr;
    535:       ict       = w1[j];
    536:     }
    537:   }

    539:   /* Form the outgoing messages */
    540:   /* plug in the headers */
    541:   for (i=0; i<nrqs; i++) {
    542:     j            = pa[i];
    543:     outdat[j][0] = 0;
    544:     PetscArrayzero(outdat[j]+1,2*w3[j]);
    545:     ptr[j]       = outdat[j] + 2*w3[j] + 1;
    546:   }

    548:   /* Memory for doing local proc's work */
    549:   {
    550:     PetscInt M_BPB_imax = 0;
    551: #if defined(PETSC_USE_CTABLE)
    552:     PetscIntMultError((M/PETSC_BITS_PER_BYTE+1),imax, &M_BPB_imax);
    553:     PetscMalloc1(imax,&table_data);
    554:     for (i=0; i<imax; i++) {
    555:       PetscTableCreate(n[i],M,&table_data[i]);
    556:     }
    557:     PetscCalloc4(imax,&table, imax,&data, imax,&isz, M_BPB_imax,&t_p);
    558:     for (i=0; i<imax; i++) {
    559:       table[i] = t_p + (M/PETSC_BITS_PER_BYTE+1)*i;
    560:     }
    561: #else
    562:     PetscInt Mimax = 0;
    563:     PetscIntMultError(M,imax, &Mimax);
    564:     PetscIntMultError((M/PETSC_BITS_PER_BYTE+1),imax, &M_BPB_imax);
    565:     PetscCalloc5(imax,&table, imax,&data, imax,&isz, Mimax,&d_p, M_BPB_imax,&t_p);
    566:     for (i=0; i<imax; i++) {
    567:       table[i] = t_p + (M/PETSC_BITS_PER_BYTE+1)*i;
    568:       data[i]  = d_p + M*i;
    569:     }
    570: #endif
    571:   }

    573:   /* Parse the IS and update local tables and the outgoing buf with the data */
    574:   {
    575:     PetscInt n_i,isz_i,*outdat_j,ctr_j;
    576:     PetscBT  table_i;

    578:     for (i=0; i<imax; i++) {
    579:       PetscArrayzero(ctr,size);
    580:       n_i     = n[i];
    581:       table_i = table[i];
    582:       idx_i   = idx[i];
    583: #if defined(PETSC_USE_CTABLE)
    584:       table_data_i = table_data[i];
    585: #else
    586:       data_i  = data[i];
    587: #endif
    588:       isz_i   = isz[i];
    589:       for (j=0; j<n_i; j++) {   /* parse the indices of each IS */
    590:         row  = idx_i[j];
    591:         PetscLayoutFindOwner(C->rmap,row,&proc);
    592:         if (proc != rank) { /* copy to the outgoing buffer */
    593:           ctr[proc]++;
    594:           *ptr[proc] = row;
    595:           ptr[proc]++;
    596:         } else if (!PetscBTLookupSet(table_i,row)) {
    597: #if defined(PETSC_USE_CTABLE)
    598:           PetscTableAdd(table_data_i,row+1,isz_i+1,INSERT_VALUES);
    599: #else
    600:           data_i[isz_i] = row; /* Update the local table */
    601: #endif
    602:           isz_i++;
    603:         }
    604:       }
    605:       /* Update the headers for the current IS */
    606:       for (j=0; j<size; j++) { /* Can Optimise this loop by using pa[] */
    607:         if ((ctr_j = ctr[j])) {
    608:           outdat_j        = outdat[j];
    609:           k               = ++outdat_j[0];
    610:           outdat_j[2*k]   = ctr_j;
    611:           outdat_j[2*k-1] = i;
    612:         }
    613:       }
    614:       isz[i] = isz_i;
    615:     }
    616:   }

    618:   /*  Now  post the sends */
    619:   PetscMalloc1(nrqs,&s_waits1);
    620:   for (i=0; i<nrqs; ++i) {
    621:     j    = pa[i];
    622:     MPI_Isend(outdat[j],w1[j],MPIU_INT,j,tag1,comm,s_waits1+i);
    623:   }

    625:   /* No longer need the original indices */
    626:   PetscMalloc1(imax,&iscomms);
    627:   for (i=0; i<imax; ++i) {
    628:     ISRestoreIndices(is[i],idx+i);
    629:     PetscCommDuplicate(PetscObjectComm((PetscObject)is[i]),&iscomms[i],NULL);
    630:   }
    631:   PetscFree2(*(PetscInt***)&idx,n);

    633:   for (i=0; i<imax; ++i) {
    634:     ISDestroy(&is[i]);
    635:   }

    637:   /* Do Local work */
    638: #if defined(PETSC_USE_CTABLE)
    639:   MatIncreaseOverlap_MPIAIJ_Local(C,imax,table,isz,NULL,table_data);
    640: #else
    641:   MatIncreaseOverlap_MPIAIJ_Local(C,imax,table,isz,data,NULL);
    642: #endif

    644:   /* Receive messages */
    645:   PetscMalloc1(nrqr,&recv_status);
    646:   MPI_Waitall(nrqr,r_waits1,recv_status);
    647:   MPI_Waitall(nrqs,s_waits1,MPI_STATUSES_IGNORE);

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

    653:   PetscMalloc1(nrqr,&xdata);
    654:   PetscMalloc1(nrqr,&isz1);
    655:   MatIncreaseOverlap_MPIAIJ_Receive(C,nrqr,rbuf,xdata,isz1);
    656:   PetscFree(rbuf[0]);
    657:   PetscFree(rbuf);

    659:   /* Send the data back */
    660:   /* Do a global reduction to know the buffer space req for incoming messages */
    661:   {
    662:     PetscMPIInt *rw1;

    664:     PetscCalloc1(size,&rw1);

    666:     for (i=0; i<nrqr; ++i) {
    667:       proc = recv_status[i].MPI_SOURCE;

    670:       rw1[proc] = isz1[i];
    671:     }
    672:     PetscFree(onodes1);
    673:     PetscFree(olengths1);

    675:     /* Determine the number of messages to expect, their lengths, from from-ids */
    676:     PetscGatherMessageLengths(comm,nrqr,nrqs,rw1,&onodes2,&olengths2);
    677:     PetscFree(rw1);
    678:   }
    679:   /* Now post the Irecvs corresponding to these messages */
    680:   PetscPostIrecvInt(comm,tag2,nrqs,onodes2,olengths2,&rbuf2,&r_waits2);

    682:   /* Now  post the sends */
    683:   PetscMalloc1(nrqr,&s_waits2);
    684:   for (i=0; i<nrqr; ++i) {
    685:     j    = recv_status[i].MPI_SOURCE;
    686:     MPI_Isend(xdata[i],isz1[i],MPIU_INT,j,tag2,comm,s_waits2+i);
    687:   }

    689:   /* receive work done on other processors */
    690:   {
    691:     PetscInt    is_no,ct1,max,*rbuf2_i,isz_i,jmax;
    692:     PetscMPIInt idex;
    693:     PetscBT     table_i;

    695:     for (i=0; i<nrqs; ++i) {
    696:       MPI_Waitany(nrqs,r_waits2,&idex,MPI_STATUS_IGNORE);
    697:       /* Process the message */
    698:       rbuf2_i = rbuf2[idex];
    699:       ct1     = 2*rbuf2_i[0]+1;
    700:       jmax    = rbuf2[idex][0];
    701:       for (j=1; j<=jmax; j++) {
    702:         max     = rbuf2_i[2*j];
    703:         is_no   = rbuf2_i[2*j-1];
    704:         isz_i   = isz[is_no];
    705:         table_i = table[is_no];
    706: #if defined(PETSC_USE_CTABLE)
    707:         table_data_i = table_data[is_no];
    708: #else
    709:         data_i  = data[is_no];
    710: #endif
    711:         for (k=0; k<max; k++,ct1++) {
    712:           row = rbuf2_i[ct1];
    713:           if (!PetscBTLookupSet(table_i,row)) {
    714: #if defined(PETSC_USE_CTABLE)
    715:             PetscTableAdd(table_data_i,row+1,isz_i+1,INSERT_VALUES);
    716: #else
    717:             data_i[isz_i] = row;
    718: #endif
    719:             isz_i++;
    720:           }
    721:         }
    722:         isz[is_no] = isz_i;
    723:       }
    724:     }

    726:     MPI_Waitall(nrqr,s_waits2,MPI_STATUSES_IGNORE);
    727:   }

    729: #if defined(PETSC_USE_CTABLE)
    730:   tcount_max = 0;
    731:   for (i=0; i<imax; ++i) {
    732:     table_data_i = table_data[i];
    733:     PetscTableGetCount(table_data_i,&tcount);
    734:     if (tcount_max < tcount) tcount_max = tcount;
    735:   }
    736:   PetscMalloc1(tcount_max+1,&tdata);
    737: #endif

    739:   for (i=0; i<imax; ++i) {
    740: #if defined(PETSC_USE_CTABLE)
    741:     PetscTablePosition tpos;
    742:     table_data_i = table_data[i];

    744:     PetscTableGetHeadPosition(table_data_i,&tpos);
    745:     while (tpos) {
    746:       PetscTableGetNext(table_data_i,&tpos,&k,&j);
    747:       tdata[--j] = --k;
    748:     }
    749:     ISCreateGeneral(iscomms[i],isz[i],tdata,PETSC_COPY_VALUES,is+i);
    750: #else
    751:     ISCreateGeneral(iscomms[i],isz[i],data[i],PETSC_COPY_VALUES,is+i);
    752: #endif
    753:     PetscCommDestroy(&iscomms[i]);
    754:   }

    756:   PetscFree(iscomms);
    757:   PetscFree(onodes2);
    758:   PetscFree(olengths2);

    760:   PetscFree(pa);
    761:   PetscFree(rbuf2[0]);
    762:   PetscFree(rbuf2);
    763:   PetscFree(s_waits1);
    764:   PetscFree(r_waits1);
    765:   PetscFree(s_waits2);
    766:   PetscFree(r_waits2);
    767:   PetscFree(recv_status);
    768:   if (xdata) {
    769:     PetscFree(xdata[0]);
    770:     PetscFree(xdata);
    771:   }
    772:   PetscFree(isz1);
    773: #if defined(PETSC_USE_CTABLE)
    774:   for (i=0; i<imax; i++) {
    775:     PetscTableDestroy((PetscTable*)&table_data[i]);
    776:   }
    777:   PetscFree(table_data);
    778:   PetscFree(tdata);
    779:   PetscFree4(table,data,isz,t_p);
    780: #else
    781:   PetscFree5(table,data,isz,d_p,t_p);
    782: #endif
    783:   return 0;
    784: }

    786: /*
    787:    MatIncreaseOverlap_MPIAIJ_Local - Called by MatincreaseOverlap, to do
    788:        the work on the local processor.

    790:      Inputs:
    791:       C      - MAT_MPIAIJ;
    792:       imax - total no of index sets processed at a time;
    793:       table  - an array of char - size = m bits.

    795:      Output:
    796:       isz    - array containing the count of the solution elements corresponding
    797:                to each index set;
    798:       data or table_data  - pointer to the solutions
    799: */
    800: static PetscErrorCode MatIncreaseOverlap_MPIAIJ_Local(Mat C,PetscInt imax,PetscBT *table,PetscInt *isz,PetscInt **data,PetscTable *table_data)
    801: {
    802:   Mat_MPIAIJ *c = (Mat_MPIAIJ*)C->data;
    803:   Mat        A  = c->A,B = c->B;
    804:   Mat_SeqAIJ *a = (Mat_SeqAIJ*)A->data,*b = (Mat_SeqAIJ*)B->data;
    805:   PetscInt   start,end,val,max,rstart,cstart,*ai,*aj;
    806:   PetscInt   *bi,*bj,*garray,i,j,k,row,isz_i;
    807:   PetscBT    table_i;
    808: #if defined(PETSC_USE_CTABLE)
    809:   PetscTable         table_data_i;
    810:   PetscTablePosition tpos;
    811:   PetscInt           tcount,*tdata;
    812: #else
    813:   PetscInt           *data_i;
    814: #endif

    816:   rstart = C->rmap->rstart;
    817:   cstart = C->cmap->rstart;
    818:   ai     = a->i;
    819:   aj     = a->j;
    820:   bi     = b->i;
    821:   bj     = b->j;
    822:   garray = c->garray;

    824:   for (i=0; i<imax; i++) {
    825: #if defined(PETSC_USE_CTABLE)
    826:     /* copy existing entries of table_data_i into tdata[] */
    827:     table_data_i = table_data[i];
    828:     PetscTableGetCount(table_data_i,&tcount);

    831:     PetscMalloc1(tcount,&tdata);
    832:     PetscTableGetHeadPosition(table_data_i,&tpos);
    833:     while (tpos) {
    834:       PetscTableGetNext(table_data_i,&tpos,&row,&j);
    835:       tdata[--j] = --row;
    837:     }
    838: #else
    839:     data_i  = data[i];
    840: #endif
    841:     table_i = table[i];
    842:     isz_i   = isz[i];
    843:     max     = isz[i];

    845:     for (j=0; j<max; j++) {
    846: #if defined(PETSC_USE_CTABLE)
    847:       row   = tdata[j] - rstart;
    848: #else
    849:       row   = data_i[j] - rstart;
    850: #endif
    851:       start = ai[row];
    852:       end   = ai[row+1];
    853:       for (k=start; k<end; k++) { /* Amat */
    854:         val = aj[k] + cstart;
    855:         if (!PetscBTLookupSet(table_i,val)) {
    856: #if defined(PETSC_USE_CTABLE)
    857:           PetscTableAdd(table_data_i,val+1,isz_i+1,INSERT_VALUES);
    858: #else
    859:           data_i[isz_i] = val;
    860: #endif
    861:           isz_i++;
    862:         }
    863:       }
    864:       start = bi[row];
    865:       end   = bi[row+1];
    866:       for (k=start; k<end; k++) { /* Bmat */
    867:         val = garray[bj[k]];
    868:         if (!PetscBTLookupSet(table_i,val)) {
    869: #if defined(PETSC_USE_CTABLE)
    870:           PetscTableAdd(table_data_i,val+1,isz_i+1,INSERT_VALUES);
    871: #else
    872:           data_i[isz_i] = val;
    873: #endif
    874:           isz_i++;
    875:         }
    876:       }
    877:     }
    878:     isz[i] = isz_i;

    880: #if defined(PETSC_USE_CTABLE)
    881:     PetscFree(tdata);
    882: #endif
    883:   }
    884:   return 0;
    885: }

    887: /*
    888:       MatIncreaseOverlap_MPIAIJ_Receive - Process the received messages,
    889:          and return the output

    891:          Input:
    892:            C    - the matrix
    893:            nrqr - no of messages being processed.
    894:            rbuf - an array of pointers to the received requests

    896:          Output:
    897:            xdata - array of messages to be sent back
    898:            isz1  - size of each message

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

    905: */
    906: static PetscErrorCode MatIncreaseOverlap_MPIAIJ_Receive(Mat C,PetscInt nrqr,PetscInt **rbuf,PetscInt **xdata,PetscInt * isz1)
    907: {
    908:   Mat_MPIAIJ     *c = (Mat_MPIAIJ*)C->data;
    909:   Mat            A  = c->A,B = c->B;
    910:   Mat_SeqAIJ     *a = (Mat_SeqAIJ*)A->data,*b = (Mat_SeqAIJ*)B->data;
    911:   PetscInt       rstart,cstart,*ai,*aj,*bi,*bj,*garray,i,j,k;
    912:   PetscInt       row,total_sz,ct,ct1,ct2,ct3,mem_estimate,oct2,l,start,end;
    913:   PetscInt       val,max1,max2,m,no_malloc =0,*tmp,new_estimate,ctr;
    914:   PetscInt       *rbuf_i,kmax,rbuf_0;
    915:   PetscBT        xtable;

    917:   m      = C->rmap->N;
    918:   rstart = C->rmap->rstart;
    919:   cstart = C->cmap->rstart;
    920:   ai     = a->i;
    921:   aj     = a->j;
    922:   bi     = b->i;
    923:   bj     = b->j;
    924:   garray = c->garray;

    926:   for (i=0,ct=0,total_sz=0; i<nrqr; ++i) {
    927:     rbuf_i =  rbuf[i];
    928:     rbuf_0 =  rbuf_i[0];
    929:     ct    += rbuf_0;
    930:     for (j=1; j<=rbuf_0; j++) total_sz += rbuf_i[2*j];
    931:   }

    933:   if (C->rmap->n) max1 = ct*(a->nz + b->nz)/C->rmap->n;
    934:   else max1 = 1;
    935:   mem_estimate = 3*((total_sz > max1 ? total_sz : max1)+1);
    936:   if (nrqr) {
    937:     PetscMalloc1(mem_estimate,&xdata[0]);
    938:     ++no_malloc;
    939:   }
    940:   PetscBTCreate(m,&xtable);
    941:   PetscArrayzero(isz1,nrqr);

    943:   ct3 = 0;
    944:   for (i=0; i<nrqr; i++) { /* for easch mesg from proc i */
    945:     rbuf_i =  rbuf[i];
    946:     rbuf_0 =  rbuf_i[0];
    947:     ct1    =  2*rbuf_0+1;
    948:     ct2    =  ct1;
    949:     ct3   += ct1;
    950:     for (j=1; j<=rbuf_0; j++) { /* for each IS from proc i*/
    951:       PetscBTMemzero(m,xtable);
    952:       oct2 = ct2;
    953:       kmax = rbuf_i[2*j];
    954:       for (k=0; k<kmax; k++,ct1++) {
    955:         row = rbuf_i[ct1];
    956:         if (!PetscBTLookupSet(xtable,row)) {
    957:           if (!(ct3 < mem_estimate)) {
    958:             new_estimate = (PetscInt)(1.5*mem_estimate)+1;
    959:             PetscMalloc1(new_estimate,&tmp);
    960:             PetscArraycpy(tmp,xdata[0],mem_estimate);
    961:             PetscFree(xdata[0]);
    962:             xdata[0]     = tmp;
    963:             mem_estimate = new_estimate; ++no_malloc;
    964:             for (ctr=1; ctr<=i; ctr++) xdata[ctr] = xdata[ctr-1] + isz1[ctr-1];
    965:           }
    966:           xdata[i][ct2++] = row;
    967:           ct3++;
    968:         }
    969:       }
    970:       for (k=oct2,max2=ct2; k<max2; k++) {
    971:         row   = xdata[i][k] - rstart;
    972:         start = ai[row];
    973:         end   = ai[row+1];
    974:         for (l=start; l<end; l++) {
    975:           val = aj[l] + cstart;
    976:           if (!PetscBTLookupSet(xtable,val)) {
    977:             if (!(ct3 < mem_estimate)) {
    978:               new_estimate = (PetscInt)(1.5*mem_estimate)+1;
    979:               PetscMalloc1(new_estimate,&tmp);
    980:               PetscArraycpy(tmp,xdata[0],mem_estimate);
    981:               PetscFree(xdata[0]);
    982:               xdata[0]     = tmp;
    983:               mem_estimate = new_estimate; ++no_malloc;
    984:               for (ctr=1; ctr<=i; ctr++) xdata[ctr] = xdata[ctr-1] + isz1[ctr-1];
    985:             }
    986:             xdata[i][ct2++] = val;
    987:             ct3++;
    988:           }
    989:         }
    990:         start = bi[row];
    991:         end   = bi[row+1];
    992:         for (l=start; l<end; l++) {
    993:           val = garray[bj[l]];
    994:           if (!PetscBTLookupSet(xtable,val)) {
    995:             if (!(ct3 < mem_estimate)) {
    996:               new_estimate = (PetscInt)(1.5*mem_estimate)+1;
    997:               PetscMalloc1(new_estimate,&tmp);
    998:               PetscArraycpy(tmp,xdata[0],mem_estimate);
    999:               PetscFree(xdata[0]);
    1000:               xdata[0]     = tmp;
    1001:               mem_estimate = new_estimate; ++no_malloc;
    1002:               for (ctr =1; ctr <=i; ctr++) xdata[ctr] = xdata[ctr-1] + isz1[ctr-1];
    1003:             }
    1004:             xdata[i][ct2++] = val;
    1005:             ct3++;
    1006:           }
    1007:         }
    1008:       }
    1009:       /* Update the header*/
    1010:       xdata[i][2*j]   = ct2 - oct2; /* Undo the vector isz1 and use only a var*/
    1011:       xdata[i][2*j-1] = rbuf_i[2*j-1];
    1012:     }
    1013:     xdata[i][0] = rbuf_0;
    1014:     if (i+1<nrqr) xdata[i+1]  = xdata[i] + ct2;
    1015:     isz1[i]     = ct2; /* size of each message */
    1016:   }
    1017:   PetscBTDestroy(&xtable);
    1018:   PetscInfo(C,"Allocated %" PetscInt_FMT " bytes, required %" PetscInt_FMT " bytes, no of mallocs = %" PetscInt_FMT "\n",mem_estimate,ct3,no_malloc);
    1019:   return 0;
    1020: }
    1021: /* -------------------------------------------------------------------------*/
    1022: extern PetscErrorCode MatCreateSubMatrices_MPIAIJ_Local(Mat,PetscInt,const IS[],const IS[],MatReuse,Mat*);
    1023: /*
    1024:     Every processor gets the entire matrix
    1025: */
    1026: PetscErrorCode MatCreateSubMatrix_MPIAIJ_All(Mat A,MatCreateSubMatrixOption flag,MatReuse scall,Mat *Bin[])
    1027: {
    1028:   Mat            B;
    1029:   Mat_MPIAIJ     *a = (Mat_MPIAIJ*)A->data;
    1030:   Mat_SeqAIJ     *b,*ad = (Mat_SeqAIJ*)a->A->data,*bd = (Mat_SeqAIJ*)a->B->data;
    1031:   PetscMPIInt    size,rank,*recvcounts = NULL,*displs = NULL;
    1032:   PetscInt       sendcount,i,*rstarts = A->rmap->range,n,cnt,j;
    1033:   PetscInt       m,*b_sendj,*garray = a->garray,*lens,*jsendbuf,*a_jsendbuf,*b_jsendbuf;

    1035:   MPI_Comm_size(PetscObjectComm((PetscObject)A),&size);
    1036:   MPI_Comm_rank(PetscObjectComm((PetscObject)A),&rank);
    1037:   if (scall == MAT_INITIAL_MATRIX) {
    1038:     /* ----------------------------------------------------------------
    1039:          Tell every processor the number of nonzeros per row
    1040:     */
    1041:     PetscMalloc1(A->rmap->N,&lens);
    1042:     for (i=A->rmap->rstart; i<A->rmap->rend; i++) {
    1043:       lens[i] = ad->i[i-A->rmap->rstart+1] - ad->i[i-A->rmap->rstart] + bd->i[i-A->rmap->rstart+1] - bd->i[i-A->rmap->rstart];
    1044:     }
    1045:     PetscMalloc2(size,&recvcounts,size,&displs);
    1046:     for (i=0; i<size; i++) {
    1047:       recvcounts[i] = A->rmap->range[i+1] - A->rmap->range[i];
    1048:       displs[i]     = A->rmap->range[i];
    1049:     }
    1050:     MPI_Allgatherv(MPI_IN_PLACE,0,MPI_DATATYPE_NULL,lens,recvcounts,displs,MPIU_INT,PetscObjectComm((PetscObject)A));
    1051:     /* ---------------------------------------------------------------
    1052:          Create the sequential matrix of the same type as the local block diagonal
    1053:     */
    1054:     MatCreate(PETSC_COMM_SELF,&B);
    1055:     MatSetSizes(B,A->rmap->N,A->cmap->N,PETSC_DETERMINE,PETSC_DETERMINE);
    1056:     MatSetBlockSizesFromMats(B,A,A);
    1057:     MatSetType(B,((PetscObject)a->A)->type_name);
    1058:     MatSeqAIJSetPreallocation(B,0,lens);
    1059:     PetscCalloc1(2,Bin);
    1060:     **Bin = B;
    1061:     b     = (Mat_SeqAIJ*)B->data;

    1063:     /*--------------------------------------------------------------------
    1064:        Copy my part of matrix column indices over
    1065:     */
    1066:     sendcount  = ad->nz + bd->nz;
    1067:     jsendbuf   = b->j + b->i[rstarts[rank]];
    1068:     a_jsendbuf = ad->j;
    1069:     b_jsendbuf = bd->j;
    1070:     n          = A->rmap->rend - A->rmap->rstart;
    1071:     cnt        = 0;
    1072:     for (i=0; i<n; i++) {
    1073:       /* put in lower diagonal portion */
    1074:       m = bd->i[i+1] - bd->i[i];
    1075:       while (m > 0) {
    1076:         /* is it above diagonal (in bd (compressed) numbering) */
    1077:         if (garray[*b_jsendbuf] > A->rmap->rstart + i) break;
    1078:         jsendbuf[cnt++] = garray[*b_jsendbuf++];
    1079:         m--;
    1080:       }

    1082:       /* put in diagonal portion */
    1083:       for (j=ad->i[i]; j<ad->i[i+1]; j++) {
    1084:         jsendbuf[cnt++] = A->rmap->rstart + *a_jsendbuf++;
    1085:       }

    1087:       /* put in upper diagonal portion */
    1088:       while (m-- > 0) {
    1089:         jsendbuf[cnt++] = garray[*b_jsendbuf++];
    1090:       }
    1091:     }

    1094:     /*--------------------------------------------------------------------
    1095:        Gather all column indices to all processors
    1096:     */
    1097:     for (i=0; i<size; i++) {
    1098:       recvcounts[i] = 0;
    1099:       for (j=A->rmap->range[i]; j<A->rmap->range[i+1]; j++) {
    1100:         recvcounts[i] += lens[j];
    1101:       }
    1102:     }
    1103:     displs[0] = 0;
    1104:     for (i=1; i<size; i++) {
    1105:       displs[i] = displs[i-1] + recvcounts[i-1];
    1106:     }
    1107:     MPI_Allgatherv(MPI_IN_PLACE,0,MPI_DATATYPE_NULL,b->j,recvcounts,displs,MPIU_INT,PetscObjectComm((PetscObject)A));
    1108:     /*--------------------------------------------------------------------
    1109:         Assemble the matrix into useable form (note numerical values not yet set)
    1110:     */
    1111:     /* set the b->ilen (length of each row) values */
    1112:     PetscArraycpy(b->ilen,lens,A->rmap->N);
    1113:     /* set the b->i indices */
    1114:     b->i[0] = 0;
    1115:     for (i=1; i<=A->rmap->N; i++) {
    1116:       b->i[i] = b->i[i-1] + lens[i-1];
    1117:     }
    1118:     PetscFree(lens);
    1119:     MatAssemblyBegin(B,MAT_FINAL_ASSEMBLY);
    1120:     MatAssemblyEnd(B,MAT_FINAL_ASSEMBLY);

    1122:   } else {
    1123:     B = **Bin;
    1124:     b = (Mat_SeqAIJ*)B->data;
    1125:   }

    1127:   /*--------------------------------------------------------------------
    1128:        Copy my part of matrix numerical values into the values location
    1129:   */
    1130:   if (flag == MAT_GET_VALUES) {
    1131:     const PetscScalar *ada,*bda,*a_sendbuf,*b_sendbuf;
    1132:     MatScalar         *sendbuf,*recvbuf;

    1134:     MatSeqAIJGetArrayRead(a->A,&ada);
    1135:     MatSeqAIJGetArrayRead(a->B,&bda);
    1136:     sendcount = ad->nz + bd->nz;
    1137:     sendbuf   = b->a + b->i[rstarts[rank]];
    1138:     a_sendbuf = ada;
    1139:     b_sendbuf = bda;
    1140:     b_sendj   = bd->j;
    1141:     n         = A->rmap->rend - A->rmap->rstart;
    1142:     cnt       = 0;
    1143:     for (i=0; i<n; i++) {
    1144:       /* put in lower diagonal portion */
    1145:       m = bd->i[i+1] - bd->i[i];
    1146:       while (m > 0) {
    1147:         /* is it above diagonal (in bd (compressed) numbering) */
    1148:         if (garray[*b_sendj] > A->rmap->rstart + i) break;
    1149:         sendbuf[cnt++] = *b_sendbuf++;
    1150:         m--;
    1151:         b_sendj++;
    1152:       }

    1154:       /* put in diagonal portion */
    1155:       for (j=ad->i[i]; j<ad->i[i+1]; j++) {
    1156:         sendbuf[cnt++] = *a_sendbuf++;
    1157:       }

    1159:       /* put in upper diagonal portion */
    1160:       while (m-- > 0) {
    1161:         sendbuf[cnt++] = *b_sendbuf++;
    1162:         b_sendj++;
    1163:       }
    1164:     }

    1167:     /* -----------------------------------------------------------------
    1168:        Gather all numerical values to all processors
    1169:     */
    1170:     if (!recvcounts) {
    1171:       PetscMalloc2(size,&recvcounts,size,&displs);
    1172:     }
    1173:     for (i=0; i<size; i++) {
    1174:       recvcounts[i] = b->i[rstarts[i+1]] - b->i[rstarts[i]];
    1175:     }
    1176:     displs[0] = 0;
    1177:     for (i=1; i<size; i++) {
    1178:       displs[i] = displs[i-1] + recvcounts[i-1];
    1179:     }
    1180:     recvbuf = b->a;
    1181:     MPI_Allgatherv(MPI_IN_PLACE,0,MPI_DATATYPE_NULL,recvbuf,recvcounts,displs,MPIU_SCALAR,PetscObjectComm((PetscObject)A));
    1182:     MatSeqAIJRestoreArrayRead(a->A,&ada);
    1183:     MatSeqAIJRestoreArrayRead(a->B,&bda);
    1184:   }  /* endof (flag == MAT_GET_VALUES) */
    1185:   PetscFree2(recvcounts,displs);

    1187:   if (A->symmetric) {
    1188:     MatSetOption(B,MAT_SYMMETRIC,PETSC_TRUE);
    1189:   } else if (A->hermitian) {
    1190:     MatSetOption(B,MAT_HERMITIAN,PETSC_TRUE);
    1191:   } else if (A->structurally_symmetric) {
    1192:     MatSetOption(B,MAT_STRUCTURALLY_SYMMETRIC,PETSC_TRUE);
    1193:   }
    1194:   return 0;
    1195: }

    1197: PetscErrorCode MatCreateSubMatrices_MPIAIJ_SingleIS_Local(Mat C,PetscInt ismax,const IS isrow[],const IS iscol[],MatReuse scall,PetscBool allcolumns,Mat *submats)
    1198: {
    1199:   Mat_MPIAIJ     *c = (Mat_MPIAIJ*)C->data;
    1200:   Mat            submat,A = c->A,B = c->B;
    1201:   Mat_SeqAIJ     *a = (Mat_SeqAIJ*)A->data,*b = (Mat_SeqAIJ*)B->data,*subc;
    1202:   PetscInt       *ai=a->i,*aj=a->j,*bi=b->i,*bj=b->j,nzA,nzB;
    1203:   PetscInt       cstart = C->cmap->rstart,cend = C->cmap->rend,rstart = C->rmap->rstart,*bmap = c->garray;
    1204:   const PetscInt *icol,*irow;
    1205:   PetscInt       nrow,ncol,start;
    1206:   PetscMPIInt    rank,size,tag1,tag2,tag3,tag4,*w1,*w2,nrqr;
    1207:   PetscInt       **sbuf1,**sbuf2,i,j,k,l,ct1,ct2,ct3,**rbuf1,row,proc;
    1208:   PetscInt       nrqs=0,msz,**ptr,*req_size,*ctr,*pa,*tmp,tcol,*iptr;
    1209:   PetscInt       **rbuf3,*req_source1,*req_source2,**sbuf_aj,**rbuf2,max1,nnz;
    1210:   PetscInt       *lens,rmax,ncols,*cols,Crow;
    1211: #if defined(PETSC_USE_CTABLE)
    1212:   PetscTable     cmap,rmap;
    1213:   PetscInt       *cmap_loc,*rmap_loc;
    1214: #else
    1215:   PetscInt       *cmap,*rmap;
    1216: #endif
    1217:   PetscInt       ctr_j,*sbuf1_j,*sbuf_aj_i,*rbuf1_i,kmax,*sbuf1_i,*rbuf2_i,*rbuf3_i;
    1218:   PetscInt       *cworkB,lwrite,*subcols,*row2proc;
    1219:   PetscScalar    *vworkA,*vworkB,*a_a,*b_a,*subvals=NULL;
    1220:   MPI_Request    *s_waits1,*r_waits1,*s_waits2,*r_waits2,*r_waits3;
    1221:   MPI_Request    *r_waits4,*s_waits3 = NULL,*s_waits4;
    1222:   MPI_Status     *r_status1,*r_status2,*s_status1,*s_status3 = NULL,*s_status2;
    1223:   MPI_Status     *r_status3 = NULL,*r_status4,*s_status4;
    1224:   MPI_Comm       comm;
    1225:   PetscScalar    **rbuf4,**sbuf_aa,*vals,*sbuf_aa_i,*rbuf4_i;
    1226:   PetscMPIInt    *onodes1,*olengths1,idex,end;
    1227:   Mat_SubSppt    *smatis1;
    1228:   PetscBool      isrowsorted,iscolsorted;

    1233:   MatSeqAIJGetArrayRead(A,(const PetscScalar**)&a_a);
    1234:   MatSeqAIJGetArrayRead(B,(const PetscScalar**)&b_a);
    1235:   PetscObjectGetComm((PetscObject)C,&comm);
    1236:   size = c->size;
    1237:   rank = c->rank;

    1239:   ISSorted(iscol[0],&iscolsorted);
    1240:   ISSorted(isrow[0],&isrowsorted);
    1241:   ISGetIndices(isrow[0],&irow);
    1242:   ISGetLocalSize(isrow[0],&nrow);
    1243:   if (allcolumns) {
    1244:     icol = NULL;
    1245:     ncol = C->cmap->N;
    1246:   } else {
    1247:     ISGetIndices(iscol[0],&icol);
    1248:     ISGetLocalSize(iscol[0],&ncol);
    1249:   }

    1251:   if (scall == MAT_INITIAL_MATRIX) {
    1252:     PetscInt *sbuf2_i,*cworkA,lwrite,ctmp;

    1254:     /* Get some new tags to keep the communication clean */
    1255:     tag1 = ((PetscObject)C)->tag;
    1256:     PetscObjectGetNewTag((PetscObject)C,&tag2);
    1257:     PetscObjectGetNewTag((PetscObject)C,&tag3);

    1259:     /* evaluate communication - mesg to who, length of mesg, and buffer space
    1260:      required. Based on this, buffers are allocated, and data copied into them */
    1261:     PetscCalloc2(size,&w1,size,&w2);
    1262:     PetscMalloc1(nrow,&row2proc);

    1264:     /* w1[proc] = num of rows owned by proc -- to be requested */
    1265:     proc = 0;
    1266:     nrqs = 0; /* num of outgoing messages */
    1267:     for (j=0; j<nrow; j++) {
    1268:       row  = irow[j];
    1269:       if (!isrowsorted) proc = 0;
    1270:       while (row >= C->rmap->range[proc+1]) proc++;
    1271:       w1[proc]++;
    1272:       row2proc[j] = proc; /* map row index to proc */

    1274:       if (proc != rank && !w2[proc]) {
    1275:         w2[proc] = 1; nrqs++;
    1276:       }
    1277:     }
    1278:     w1[rank] = 0;  /* rows owned by self will not be requested */

    1280:     PetscMalloc1(nrqs,&pa); /*(proc -array)*/
    1281:     for (proc=0,j=0; proc<size; proc++) {
    1282:       if (w1[proc]) { pa[j++] = proc;}
    1283:     }

    1285:     /* Each message would have a header = 1 + 2*(num of IS) + data (here,num of IS = 1) */
    1286:     msz = 0;              /* total mesg length (for all procs) */
    1287:     for (i=0; i<nrqs; i++) {
    1288:       proc      = pa[i];
    1289:       w1[proc] += 3;
    1290:       msz      += w1[proc];
    1291:     }
    1292:     PetscInfo(0,"Number of outgoing messages %" PetscInt_FMT " Total message length %" PetscInt_FMT "\n",nrqs,msz);

    1294:     /* Determine nrqr, the number of messages to expect, their lengths, from from-ids */
    1295:     /* if w2[proc]=1, a message of length w1[proc] will be sent to proc; */
    1296:     PetscGatherNumberOfMessages(comm,w2,w1,&nrqr);

    1298:     /* Input: nrqs: nsend; nrqr: nrecv; w1: msg length to be sent;
    1299:        Output: onodes1: recv node-ids; olengths1: corresponding recv message length */
    1300:     PetscGatherMessageLengths(comm,nrqs,nrqr,w1,&onodes1,&olengths1);

    1302:     /* Now post the Irecvs corresponding to these messages */
    1303:     PetscPostIrecvInt(comm,tag1,nrqr,onodes1,olengths1,&rbuf1,&r_waits1);

    1305:     PetscFree(onodes1);
    1306:     PetscFree(olengths1);

    1308:     /* Allocate Memory for outgoing messages */
    1309:     PetscMalloc4(size,&sbuf1,size,&ptr,2*msz,&tmp,size,&ctr);
    1310:     PetscArrayzero(sbuf1,size);
    1311:     PetscArrayzero(ptr,size);

    1313:     /* subf1[pa[0]] = tmp, subf1[pa[i]] = subf1[pa[i-1]] + w1[pa[i-1]] */
    1314:     iptr = tmp;
    1315:     for (i=0; i<nrqs; i++) {
    1316:       proc        = pa[i];
    1317:       sbuf1[proc] = iptr;
    1318:       iptr       += w1[proc];
    1319:     }

    1321:     /* Form the outgoing messages */
    1322:     /* Initialize the header space */
    1323:     for (i=0; i<nrqs; i++) {
    1324:       proc      = pa[i];
    1325:       PetscArrayzero(sbuf1[proc],3);
    1326:       ptr[proc] = sbuf1[proc] + 3;
    1327:     }

    1329:     /* Parse the isrow and copy data into outbuf */
    1330:     PetscArrayzero(ctr,size);
    1331:     for (j=0; j<nrow; j++) {  /* parse the indices of each IS */
    1332:       proc = row2proc[j];
    1333:       if (proc != rank) { /* copy to the outgoing buf*/
    1334:         *ptr[proc] = irow[j];
    1335:         ctr[proc]++; ptr[proc]++;
    1336:       }
    1337:     }

    1339:     /* Update the headers for the current IS */
    1340:     for (j=0; j<size; j++) { /* Can Optimise this loop too */
    1341:       if ((ctr_j = ctr[j])) {
    1342:         sbuf1_j        = sbuf1[j];
    1343:         k              = ++sbuf1_j[0];
    1344:         sbuf1_j[2*k]   = ctr_j;
    1345:         sbuf1_j[2*k-1] = 0;
    1346:       }
    1347:     }

    1349:     /* Now post the sends */
    1350:     PetscMalloc1(nrqs,&s_waits1);
    1351:     for (i=0; i<nrqs; ++i) {
    1352:       proc = pa[i];
    1353:       MPI_Isend(sbuf1[proc],w1[proc],MPIU_INT,proc,tag1,comm,s_waits1+i);
    1354:     }

    1356:     /* Post Receives to capture the buffer size */
    1357:     PetscMalloc4(nrqs,&r_status2,nrqr,&s_waits2,nrqs,&r_waits2,nrqr,&s_status2);
    1358:     PetscMalloc3(nrqs,&req_source2,nrqs,&rbuf2,nrqs,&rbuf3);

    1360:     if (nrqs) rbuf2[0] = tmp + msz;
    1361:     for (i=1; i<nrqs; ++i) rbuf2[i] = rbuf2[i-1] + w1[pa[i-1]];

    1363:     for (i=0; i<nrqs; ++i) {
    1364:       proc = pa[i];
    1365:       MPI_Irecv(rbuf2[i],w1[proc],MPIU_INT,proc,tag2,comm,r_waits2+i);
    1366:     }

    1368:     PetscFree2(w1,w2);

    1370:     /* Send to other procs the buf size they should allocate */
    1371:     /* Receive messages*/
    1372:     PetscMalloc1(nrqr,&r_status1);
    1373:     PetscMalloc3(nrqr,&sbuf2,nrqr,&req_size,nrqr,&req_source1);

    1375:     MPI_Waitall(nrqr,r_waits1,r_status1);
    1376:     for (i=0; i<nrqr; ++i) {
    1377:       req_size[i] = 0;
    1378:       rbuf1_i        = rbuf1[i];
    1379:       start          = 2*rbuf1_i[0] + 1;
    1380:       MPI_Get_count(r_status1+i,MPIU_INT,&end);
    1381:       PetscMalloc1(end,&sbuf2[i]);
    1382:       sbuf2_i        = sbuf2[i];
    1383:       for (j=start; j<end; j++) {
    1384:         k            = rbuf1_i[j] - rstart;
    1385:         ncols        = ai[k+1] - ai[k] + bi[k+1] - bi[k];
    1386:         sbuf2_i[j]   = ncols;
    1387:         req_size[i] += ncols;
    1388:       }
    1389:       req_source1[i] = r_status1[i].MPI_SOURCE;

    1391:       /* form the header */
    1392:       sbuf2_i[0] = req_size[i];
    1393:       for (j=1; j<start; j++) sbuf2_i[j] = rbuf1_i[j];

    1395:       MPI_Isend(sbuf2_i,end,MPIU_INT,req_source1[i],tag2,comm,s_waits2+i);
    1396:     }

    1398:     PetscFree(r_status1);
    1399:     PetscFree(r_waits1);

    1401:     /* rbuf2 is received, Post recv column indices a->j */
    1402:     MPI_Waitall(nrqs,r_waits2,r_status2);

    1404:     PetscMalloc4(nrqs,&r_waits3,nrqr,&s_waits3,nrqs,&r_status3,nrqr,&s_status3);
    1405:     for (i=0; i<nrqs; ++i) {
    1406:       PetscMalloc1(rbuf2[i][0],&rbuf3[i]);
    1407:       req_source2[i] = r_status2[i].MPI_SOURCE;
    1408:       MPI_Irecv(rbuf3[i],rbuf2[i][0],MPIU_INT,req_source2[i],tag3,comm,r_waits3+i);
    1409:     }

    1411:     /* Wait on sends1 and sends2 */
    1412:     PetscMalloc1(nrqs,&s_status1);
    1413:     MPI_Waitall(nrqs,s_waits1,s_status1);
    1414:     PetscFree(s_waits1);
    1415:     PetscFree(s_status1);

    1417:     MPI_Waitall(nrqr,s_waits2,s_status2);
    1418:     PetscFree4(r_status2,s_waits2,r_waits2,s_status2);

    1420:     /* Now allocate sending buffers for a->j, and send them off */
    1421:     PetscMalloc1(nrqr,&sbuf_aj);
    1422:     for (i=0,j=0; i<nrqr; i++) j += req_size[i];
    1423:     if (nrqr) PetscMalloc1(j,&sbuf_aj[0]);
    1424:     for (i=1; i<nrqr; i++) sbuf_aj[i] = sbuf_aj[i-1] + req_size[i-1];

    1426:     for (i=0; i<nrqr; i++) { /* for each requested message */
    1427:       rbuf1_i   = rbuf1[i];
    1428:       sbuf_aj_i = sbuf_aj[i];
    1429:       ct1       = 2*rbuf1_i[0] + 1;
    1430:       ct2       = 0;

    1433:       kmax = rbuf1[i][2];
    1434:       for (k=0; k<kmax; k++,ct1++) { /* for each row */
    1435:         row    = rbuf1_i[ct1] - rstart;
    1436:         nzA    = ai[row+1] - ai[row];
    1437:         nzB    = bi[row+1] - bi[row];
    1438:         ncols  = nzA + nzB;
    1439:         cworkA = aj + ai[row]; cworkB = bj + bi[row];

    1441:         /* load the column indices for this row into cols*/
    1442:         cols = sbuf_aj_i + ct2;

    1444:         lwrite = 0;
    1445:         for (l=0; l<nzB; l++) {
    1446:           if ((ctmp = bmap[cworkB[l]]) < cstart) cols[lwrite++] = ctmp;
    1447:         }
    1448:         for (l=0; l<nzA; l++) cols[lwrite++] = cstart + cworkA[l];
    1449:         for (l=0; l<nzB; l++) {
    1450:           if ((ctmp = bmap[cworkB[l]]) >= cend) cols[lwrite++] = ctmp;
    1451:         }

    1453:         ct2 += ncols;
    1454:       }
    1455:       MPI_Isend(sbuf_aj_i,req_size[i],MPIU_INT,req_source1[i],tag3,comm,s_waits3+i);
    1456:     }

    1458:     /* create column map (cmap): global col of C -> local col of submat */
    1459: #if defined(PETSC_USE_CTABLE)
    1460:     if (!allcolumns) {
    1461:       PetscTableCreate(ncol,C->cmap->N,&cmap);
    1462:       PetscCalloc1(C->cmap->n,&cmap_loc);
    1463:       for (j=0; j<ncol; j++) { /* use array cmap_loc[] for local col indices */
    1464:         if (icol[j] >= cstart && icol[j] <cend) {
    1465:           cmap_loc[icol[j] - cstart] = j+1;
    1466:         } else { /* use PetscTable for non-local col indices */
    1467:           PetscTableAdd(cmap,icol[j]+1,j+1,INSERT_VALUES);
    1468:         }
    1469:       }
    1470:     } else {
    1471:       cmap     = NULL;
    1472:       cmap_loc = NULL;
    1473:     }
    1474:     PetscCalloc1(C->rmap->n,&rmap_loc);
    1475: #else
    1476:     if (!allcolumns) {
    1477:       PetscCalloc1(C->cmap->N,&cmap);
    1478:       for (j=0; j<ncol; j++) cmap[icol[j]] = j+1;
    1479:     } else {
    1480:       cmap = NULL;
    1481:     }
    1482: #endif

    1484:     /* Create lens for MatSeqAIJSetPreallocation() */
    1485:     PetscCalloc1(nrow,&lens);

    1487:     /* Compute lens from local part of C */
    1488:     for (j=0; j<nrow; j++) {
    1489:       row  = irow[j];
    1490:       proc = row2proc[j];
    1491:       if (proc == rank) {
    1492:         /* diagonal part A = c->A */
    1493:         ncols = ai[row-rstart+1] - ai[row-rstart];
    1494:         cols  = aj + ai[row-rstart];
    1495:         if (!allcolumns) {
    1496:           for (k=0; k<ncols; k++) {
    1497: #if defined(PETSC_USE_CTABLE)
    1498:             tcol = cmap_loc[cols[k]];
    1499: #else
    1500:             tcol = cmap[cols[k]+cstart];
    1501: #endif
    1502:             if (tcol) lens[j]++;
    1503:           }
    1504:         } else { /* allcolumns */
    1505:           lens[j] = ncols;
    1506:         }

    1508:         /* off-diagonal part B = c->B */
    1509:         ncols = bi[row-rstart+1] - bi[row-rstart];
    1510:         cols  = bj + bi[row-rstart];
    1511:         if (!allcolumns) {
    1512:           for (k=0; k<ncols; k++) {
    1513: #if defined(PETSC_USE_CTABLE)
    1514:             PetscTableFind(cmap,bmap[cols[k]]+1,&tcol);
    1515: #else
    1516:             tcol = cmap[bmap[cols[k]]];
    1517: #endif
    1518:             if (tcol) lens[j]++;
    1519:           }
    1520:         } else { /* allcolumns */
    1521:           lens[j] += ncols;
    1522:         }
    1523:       }
    1524:     }

    1526:     /* Create row map (rmap): global row of C -> local row of submat */
    1527: #if defined(PETSC_USE_CTABLE)
    1528:     PetscTableCreate(nrow,C->rmap->N,&rmap);
    1529:     for (j=0; j<nrow; j++) {
    1530:       row  = irow[j];
    1531:       proc = row2proc[j];
    1532:       if (proc == rank) { /* a local row */
    1533:         rmap_loc[row - rstart] = j;
    1534:       } else {
    1535:         PetscTableAdd(rmap,irow[j]+1,j+1,INSERT_VALUES);
    1536:       }
    1537:     }
    1538: #else
    1539:     PetscCalloc1(C->rmap->N,&rmap);
    1540:     for (j=0; j<nrow; j++) {
    1541:       rmap[irow[j]] = j;
    1542:     }
    1543: #endif

    1545:     /* Update lens from offproc data */
    1546:     /* recv a->j is done */
    1547:     MPI_Waitall(nrqs,r_waits3,r_status3);
    1548:     for (i=0; i<nrqs; i++) {
    1549:       proc    = pa[i];
    1550:       sbuf1_i = sbuf1[proc];
    1552:       ct1     = 2 + 1;
    1553:       ct2     = 0;
    1554:       rbuf2_i = rbuf2[i]; /* received length of C->j */
    1555:       rbuf3_i = rbuf3[i]; /* received C->j */

    1558:       max1   = sbuf1_i[2];
    1559:       for (k=0; k<max1; k++,ct1++) {
    1560: #if defined(PETSC_USE_CTABLE)
    1561:         PetscTableFind(rmap,sbuf1_i[ct1]+1,&row);
    1562:         row--;
    1564: #else
    1565:         row = rmap[sbuf1_i[ct1]]; /* the row index in submat */
    1566: #endif
    1567:         /* Now, store row index of submat in sbuf1_i[ct1] */
    1568:         sbuf1_i[ct1] = row;

    1570:         nnz = rbuf2_i[ct1];
    1571:         if (!allcolumns) {
    1572:           for (l=0; l<nnz; l++,ct2++) {
    1573: #if defined(PETSC_USE_CTABLE)
    1574:             if (rbuf3_i[ct2] >= cstart && rbuf3_i[ct2] <cend) {
    1575:               tcol = cmap_loc[rbuf3_i[ct2] - cstart];
    1576:             } else {
    1577:               PetscTableFind(cmap,rbuf3_i[ct2]+1,&tcol);
    1578:             }
    1579: #else
    1580:             tcol = cmap[rbuf3_i[ct2]]; /* column index in submat */
    1581: #endif
    1582:             if (tcol) lens[row]++;
    1583:           }
    1584:         } else { /* allcolumns */
    1585:           lens[row] += nnz;
    1586:         }
    1587:       }
    1588:     }
    1589:     MPI_Waitall(nrqr,s_waits3,s_status3);
    1590:     PetscFree4(r_waits3,s_waits3,r_status3,s_status3);

    1592:     /* Create the submatrices */
    1593:     MatCreate(PETSC_COMM_SELF,&submat);
    1594:     MatSetSizes(submat,nrow,ncol,PETSC_DETERMINE,PETSC_DETERMINE);

    1596:     ISGetBlockSize(isrow[0],&i);
    1597:     ISGetBlockSize(iscol[0],&j);
    1598:     MatSetBlockSizes(submat,i,j);
    1599:     MatSetType(submat,((PetscObject)A)->type_name);
    1600:     MatSeqAIJSetPreallocation(submat,0,lens);

    1602:     /* create struct Mat_SubSppt and attached it to submat */
    1603:     PetscNew(&smatis1);
    1604:     subc = (Mat_SeqAIJ*)submat->data;
    1605:     subc->submatis1 = smatis1;

    1607:     smatis1->id          = 0;
    1608:     smatis1->nrqs        = nrqs;
    1609:     smatis1->nrqr        = nrqr;
    1610:     smatis1->rbuf1       = rbuf1;
    1611:     smatis1->rbuf2       = rbuf2;
    1612:     smatis1->rbuf3       = rbuf3;
    1613:     smatis1->sbuf2       = sbuf2;
    1614:     smatis1->req_source2 = req_source2;

    1616:     smatis1->sbuf1       = sbuf1;
    1617:     smatis1->ptr         = ptr;
    1618:     smatis1->tmp         = tmp;
    1619:     smatis1->ctr         = ctr;

    1621:     smatis1->pa           = pa;
    1622:     smatis1->req_size     = req_size;
    1623:     smatis1->req_source1  = req_source1;

    1625:     smatis1->allcolumns  = allcolumns;
    1626:     smatis1->singleis    = PETSC_TRUE;
    1627:     smatis1->row2proc    = row2proc;
    1628:     smatis1->rmap        = rmap;
    1629:     smatis1->cmap        = cmap;
    1630: #if defined(PETSC_USE_CTABLE)
    1631:     smatis1->rmap_loc    = rmap_loc;
    1632:     smatis1->cmap_loc    = cmap_loc;
    1633: #endif

    1635:     smatis1->destroy     = submat->ops->destroy;
    1636:     submat->ops->destroy = MatDestroySubMatrix_SeqAIJ;
    1637:     submat->factortype   = C->factortype;

    1639:     /* compute rmax */
    1640:     rmax = 0;
    1641:     for (i=0; i<nrow; i++) rmax = PetscMax(rmax,lens[i]);

    1643:   } else { /* scall == MAT_REUSE_MATRIX */
    1644:     submat = submats[0];

    1647:     subc    = (Mat_SeqAIJ*)submat->data;
    1648:     rmax    = subc->rmax;
    1649:     smatis1 = subc->submatis1;
    1650:     nrqs        = smatis1->nrqs;
    1651:     nrqr        = smatis1->nrqr;
    1652:     rbuf1       = smatis1->rbuf1;
    1653:     rbuf2       = smatis1->rbuf2;
    1654:     rbuf3       = smatis1->rbuf3;
    1655:     req_source2 = smatis1->req_source2;

    1657:     sbuf1     = smatis1->sbuf1;
    1658:     sbuf2     = smatis1->sbuf2;
    1659:     ptr       = smatis1->ptr;
    1660:     tmp       = smatis1->tmp;
    1661:     ctr       = smatis1->ctr;

    1663:     pa         = smatis1->pa;
    1664:     req_size   = smatis1->req_size;
    1665:     req_source1 = smatis1->req_source1;

    1667:     allcolumns = smatis1->allcolumns;
    1668:     row2proc   = smatis1->row2proc;
    1669:     rmap       = smatis1->rmap;
    1670:     cmap       = smatis1->cmap;
    1671: #if defined(PETSC_USE_CTABLE)
    1672:     rmap_loc   = smatis1->rmap_loc;
    1673:     cmap_loc   = smatis1->cmap_loc;
    1674: #endif
    1675:   }

    1677:   /* Post recv matrix values */
    1678:   PetscMalloc3(nrqs,&rbuf4, rmax,&subcols, rmax,&subvals);
    1679:   PetscMalloc4(nrqs,&r_waits4,nrqr,&s_waits4,nrqs,&r_status4,nrqr,&s_status4);
    1680:   PetscObjectGetNewTag((PetscObject)C,&tag4);
    1681:   for (i=0; i<nrqs; ++i) {
    1682:     PetscMalloc1(rbuf2[i][0],&rbuf4[i]);
    1683:     MPI_Irecv(rbuf4[i],rbuf2[i][0],MPIU_SCALAR,req_source2[i],tag4,comm,r_waits4+i);
    1684:   }

    1686:   /* Allocate sending buffers for a->a, and send them off */
    1687:   PetscMalloc1(nrqr,&sbuf_aa);
    1688:   for (i=0,j=0; i<nrqr; i++) j += req_size[i];
    1689:   if (nrqr) PetscMalloc1(j,&sbuf_aa[0]);
    1690:   for (i=1; i<nrqr; i++) sbuf_aa[i] = sbuf_aa[i-1] + req_size[i-1];

    1692:   for (i=0; i<nrqr; i++) {
    1693:     rbuf1_i   = rbuf1[i];
    1694:     sbuf_aa_i = sbuf_aa[i];
    1695:     ct1       = 2*rbuf1_i[0]+1;
    1696:     ct2       = 0;

    1699:     kmax = rbuf1_i[2];
    1700:     for (k=0; k<kmax; k++,ct1++) {
    1701:       row = rbuf1_i[ct1] - rstart;
    1702:       nzA = ai[row+1] - ai[row];
    1703:       nzB = bi[row+1] - bi[row];
    1704:       ncols  = nzA + nzB;
    1705:       cworkB = bj + bi[row];
    1706:       vworkA = a_a + ai[row];
    1707:       vworkB = b_a + bi[row];

    1709:       /* load the column values for this row into vals*/
    1710:       vals = sbuf_aa_i + ct2;

    1712:       lwrite = 0;
    1713:       for (l=0; l<nzB; l++) {
    1714:         if ((bmap[cworkB[l]]) < cstart) vals[lwrite++] = vworkB[l];
    1715:       }
    1716:       for (l=0; l<nzA; l++) vals[lwrite++] = vworkA[l];
    1717:       for (l=0; l<nzB; l++) {
    1718:         if ((bmap[cworkB[l]]) >= cend) vals[lwrite++] = vworkB[l];
    1719:       }

    1721:       ct2 += ncols;
    1722:     }
    1723:     MPI_Isend(sbuf_aa_i,req_size[i],MPIU_SCALAR,req_source1[i],tag4,comm,s_waits4+i);
    1724:   }

    1726:   /* Assemble submat */
    1727:   /* First assemble the local rows */
    1728:   for (j=0; j<nrow; j++) {
    1729:     row  = irow[j];
    1730:     proc = row2proc[j];
    1731:     if (proc == rank) {
    1732:       Crow = row - rstart;  /* local row index of C */
    1733: #if defined(PETSC_USE_CTABLE)
    1734:       row = rmap_loc[Crow]; /* row index of submat */
    1735: #else
    1736:       row = rmap[row];
    1737: #endif

    1739:       if (allcolumns) {
    1740:         /* diagonal part A = c->A */
    1741:         ncols = ai[Crow+1] - ai[Crow];
    1742:         cols  = aj + ai[Crow];
    1743:         vals  = a_a + ai[Crow];
    1744:         i     = 0;
    1745:         for (k=0; k<ncols; k++) {
    1746:           subcols[i]   = cols[k] + cstart;
    1747:           subvals[i++] = vals[k];
    1748:         }

    1750:         /* off-diagonal part B = c->B */
    1751:         ncols = bi[Crow+1] - bi[Crow];
    1752:         cols  = bj + bi[Crow];
    1753:         vals  = b_a + bi[Crow];
    1754:         for (k=0; k<ncols; k++) {
    1755:           subcols[i]   = bmap[cols[k]];
    1756:           subvals[i++] = vals[k];
    1757:         }

    1759:         MatSetValues_SeqAIJ(submat,1,&row,i,subcols,subvals,INSERT_VALUES);

    1761:       } else { /* !allcolumns */
    1762: #if defined(PETSC_USE_CTABLE)
    1763:         /* diagonal part A = c->A */
    1764:         ncols = ai[Crow+1] - ai[Crow];
    1765:         cols  = aj + ai[Crow];
    1766:         vals  = a_a + ai[Crow];
    1767:         i     = 0;
    1768:         for (k=0; k<ncols; k++) {
    1769:           tcol = cmap_loc[cols[k]];
    1770:           if (tcol) {
    1771:             subcols[i]   = --tcol;
    1772:             subvals[i++] = vals[k];
    1773:           }
    1774:         }

    1776:         /* off-diagonal part B = c->B */
    1777:         ncols = bi[Crow+1] - bi[Crow];
    1778:         cols  = bj + bi[Crow];
    1779:         vals  = b_a + bi[Crow];
    1780:         for (k=0; k<ncols; k++) {
    1781:           PetscTableFind(cmap,bmap[cols[k]]+1,&tcol);
    1782:           if (tcol) {
    1783:             subcols[i]   = --tcol;
    1784:             subvals[i++] = vals[k];
    1785:           }
    1786:         }
    1787: #else
    1788:         /* diagonal part A = c->A */
    1789:         ncols = ai[Crow+1] - ai[Crow];
    1790:         cols  = aj + ai[Crow];
    1791:         vals  = a_a + ai[Crow];
    1792:         i     = 0;
    1793:         for (k=0; k<ncols; k++) {
    1794:           tcol = cmap[cols[k]+cstart];
    1795:           if (tcol) {
    1796:             subcols[i]   = --tcol;
    1797:             subvals[i++] = vals[k];
    1798:           }
    1799:         }

    1801:         /* off-diagonal part B = c->B */
    1802:         ncols = bi[Crow+1] - bi[Crow];
    1803:         cols  = bj + bi[Crow];
    1804:         vals  = b_a + bi[Crow];
    1805:         for (k=0; k<ncols; k++) {
    1806:           tcol = cmap[bmap[cols[k]]];
    1807:           if (tcol) {
    1808:             subcols[i]   = --tcol;
    1809:             subvals[i++] = vals[k];
    1810:           }
    1811:         }
    1812: #endif
    1813:         MatSetValues_SeqAIJ(submat,1,&row,i,subcols,subvals,INSERT_VALUES);
    1814:       }
    1815:     }
    1816:   }

    1818:   /* Now assemble the off-proc rows */
    1819:   for (i=0; i<nrqs; i++) { /* for each requested message */
    1820:     /* recv values from other processes */
    1821:     MPI_Waitany(nrqs,r_waits4,&idex,r_status4+i);
    1822:     proc    = pa[idex];
    1823:     sbuf1_i = sbuf1[proc];
    1825:     ct1     = 2 + 1;
    1826:     ct2     = 0; /* count of received C->j */
    1827:     ct3     = 0; /* count of received C->j that will be inserted into submat */
    1828:     rbuf2_i = rbuf2[idex]; /* int** received length of C->j from other processes */
    1829:     rbuf3_i = rbuf3[idex]; /* int** received C->j from other processes */
    1830:     rbuf4_i = rbuf4[idex]; /* scalar** received C->a from other processes */

    1833:     max1 = sbuf1_i[2];             /* num of rows */
    1834:     for (k=0; k<max1; k++,ct1++) { /* for each recved row */
    1835:       row = sbuf1_i[ct1]; /* row index of submat */
    1836:       if (!allcolumns) {
    1837:         idex = 0;
    1838:         if (scall == MAT_INITIAL_MATRIX || !iscolsorted) {
    1839:           nnz  = rbuf2_i[ct1]; /* num of C entries in this row */
    1840:           for (l=0; l<nnz; l++,ct2++) { /* for each recved column */
    1841: #if defined(PETSC_USE_CTABLE)
    1842:             if (rbuf3_i[ct2] >= cstart && rbuf3_i[ct2] <cend) {
    1843:               tcol = cmap_loc[rbuf3_i[ct2] - cstart];
    1844:             } else {
    1845:               PetscTableFind(cmap,rbuf3_i[ct2]+1,&tcol);
    1846:             }
    1847: #else
    1848:             tcol = cmap[rbuf3_i[ct2]];
    1849: #endif
    1850:             if (tcol) {
    1851:               subcols[idex]   = --tcol; /* may not be sorted */
    1852:               subvals[idex++] = rbuf4_i[ct2];

    1854:               /* We receive an entire column of C, but a subset of it needs to be inserted into submat.
    1855:                For reuse, we replace received C->j with index that should be inserted to submat */
    1856:               if (iscolsorted) rbuf3_i[ct3++] = ct2;
    1857:             }
    1858:           }
    1859:           MatSetValues_SeqAIJ(submat,1,&row,idex,subcols,subvals,INSERT_VALUES);
    1860:         } else { /* scall == MAT_REUSE_MATRIX */
    1861:           submat = submats[0];
    1862:           subc   = (Mat_SeqAIJ*)submat->data;

    1864:           nnz = subc->i[row+1] - subc->i[row]; /* num of submat entries in this row */
    1865:           for (l=0; l<nnz; l++) {
    1866:             ct2 = rbuf3_i[ct3++]; /* index of rbuf4_i[] which needs to be inserted into submat */
    1867:             subvals[idex++] = rbuf4_i[ct2];
    1868:           }

    1870:           bj = subc->j + subc->i[row]; /* sorted column indices */
    1871:           MatSetValues_SeqAIJ(submat,1,&row,nnz,bj,subvals,INSERT_VALUES);
    1872:         }
    1873:       } else { /* allcolumns */
    1874:         nnz  = rbuf2_i[ct1]; /* num of C entries in this row */
    1875:         MatSetValues_SeqAIJ(submat,1,&row,nnz,rbuf3_i+ct2,rbuf4_i+ct2,INSERT_VALUES);
    1876:         ct2 += nnz;
    1877:       }
    1878:     }
    1879:   }

    1881:   /* sending a->a are done */
    1882:   MPI_Waitall(nrqr,s_waits4,s_status4);
    1883:   PetscFree4(r_waits4,s_waits4,r_status4,s_status4);

    1885:   MatAssemblyBegin(submat,MAT_FINAL_ASSEMBLY);
    1886:   MatAssemblyEnd(submat,MAT_FINAL_ASSEMBLY);
    1887:   submats[0] = submat;

    1889:   /* Restore the indices */
    1890:   ISRestoreIndices(isrow[0],&irow);
    1891:   if (!allcolumns) {
    1892:     ISRestoreIndices(iscol[0],&icol);
    1893:   }

    1895:   /* Destroy allocated memory */
    1896:   for (i=0; i<nrqs; ++i) {
    1897:     PetscFree(rbuf4[i]);
    1898:   }
    1899:   PetscFree3(rbuf4,subcols,subvals);
    1900:   if (sbuf_aa) {
    1901:     PetscFree(sbuf_aa[0]);
    1902:     PetscFree(sbuf_aa);
    1903:   }

    1905:   if (scall == MAT_INITIAL_MATRIX) {
    1906:     PetscFree(lens);
    1907:     if (sbuf_aj) {
    1908:       PetscFree(sbuf_aj[0]);
    1909:       PetscFree(sbuf_aj);
    1910:     }
    1911:   }
    1912:   MatSeqAIJRestoreArrayRead(A,(const PetscScalar**)&a_a);
    1913:   MatSeqAIJRestoreArrayRead(B,(const PetscScalar**)&b_a);
    1914:   return 0;
    1915: }

    1917: PetscErrorCode MatCreateSubMatrices_MPIAIJ_SingleIS(Mat C,PetscInt ismax,const IS isrow[],const IS iscol[],MatReuse scall,Mat *submat[])
    1918: {
    1919:   PetscInt       ncol;
    1920:   PetscBool      colflag,allcolumns=PETSC_FALSE;

    1922:   /* Allocate memory to hold all the submatrices */
    1923:   if (scall == MAT_INITIAL_MATRIX) {
    1924:     PetscCalloc1(2,submat);
    1925:   }

    1927:   /* Check for special case: each processor gets entire matrix columns */
    1928:   ISIdentity(iscol[0],&colflag);
    1929:   ISGetLocalSize(iscol[0],&ncol);
    1930:   if (colflag && ncol == C->cmap->N) allcolumns = PETSC_TRUE;

    1932:   MatCreateSubMatrices_MPIAIJ_SingleIS_Local(C,ismax,isrow,iscol,scall,allcolumns,*submat);
    1933:   return 0;
    1934: }

    1936: PetscErrorCode MatCreateSubMatrices_MPIAIJ(Mat C,PetscInt ismax,const IS isrow[],const IS iscol[],MatReuse scall,Mat *submat[])
    1937: {
    1938:   PetscInt       nmax,nstages=0,i,pos,max_no,nrow,ncol,in[2],out[2];
    1939:   PetscBool      rowflag,colflag,wantallmatrix=PETSC_FALSE;
    1940:   Mat_SeqAIJ     *subc;
    1941:   Mat_SubSppt    *smat;

    1943:   /* Check for special case: each processor has a single IS */
    1944:   if (C->submat_singleis) { /* flag is set in PCSetUp_ASM() to skip MPI_Allreduce() */
    1945:     MatCreateSubMatrices_MPIAIJ_SingleIS(C,ismax,isrow,iscol,scall,submat);
    1946:     C->submat_singleis = PETSC_FALSE; /* resume its default value in case C will be used for non-single IS */
    1947:     return 0;
    1948:   }

    1950:   /* Collect global wantallmatrix and nstages */
    1951:   if (!C->cmap->N) nmax=20*1000000/sizeof(PetscInt);
    1952:   else nmax = 20*1000000 / (C->cmap->N * sizeof(PetscInt));
    1953:   if (!nmax) nmax = 1;

    1955:   if (scall == MAT_INITIAL_MATRIX) {
    1956:     /* Collect global wantallmatrix and nstages */
    1957:     if (ismax == 1 && C->rmap->N == C->cmap->N) {
    1958:       ISIdentity(*isrow,&rowflag);
    1959:       ISIdentity(*iscol,&colflag);
    1960:       ISGetLocalSize(*isrow,&nrow);
    1961:       ISGetLocalSize(*iscol,&ncol);
    1962:       if (rowflag && colflag && nrow == C->rmap->N && ncol == C->cmap->N) {
    1963:         wantallmatrix = PETSC_TRUE;

    1965:         PetscOptionsGetBool(((PetscObject)C)->options,((PetscObject)C)->prefix,"-use_fast_submatrix",&wantallmatrix,NULL);
    1966:       }
    1967:     }

    1969:     /* Determine the number of stages through which submatrices are done
    1970:        Each stage will extract nmax submatrices.
    1971:        nmax is determined by the matrix column dimension.
    1972:        If the original matrix has 20M columns, only one submatrix per stage is allowed, etc.
    1973:     */
    1974:     nstages = ismax/nmax + ((ismax % nmax) ? 1 : 0); /* local nstages */

    1976:     in[0] = -1*(PetscInt)wantallmatrix;
    1977:     in[1] = nstages;
    1978:     MPIU_Allreduce(in,out,2,MPIU_INT,MPI_MAX,PetscObjectComm((PetscObject)C));
    1979:     wantallmatrix = (PetscBool)(-out[0]);
    1980:     nstages       = out[1]; /* Make sure every processor loops through the global nstages */

    1982:   } else { /* MAT_REUSE_MATRIX */
    1983:     if (ismax) {
    1984:       subc = (Mat_SeqAIJ*)(*submat)[0]->data;
    1985:       smat = subc->submatis1;
    1986:     } else { /* (*submat)[0] is a dummy matrix */
    1987:       smat = (Mat_SubSppt*)(*submat)[0]->data;
    1988:     }
    1989:     if (!smat) {
    1990:       /* smat is not generated by MatCreateSubMatrix_MPIAIJ_All(...,MAT_INITIAL_MATRIX,...) */
    1991:       wantallmatrix = PETSC_TRUE;
    1992:     } else if (smat->singleis) {
    1993:       MatCreateSubMatrices_MPIAIJ_SingleIS(C,ismax,isrow,iscol,scall,submat);
    1994:       return 0;
    1995:     } else {
    1996:       nstages = smat->nstages;
    1997:     }
    1998:   }

    2000:   if (wantallmatrix) {
    2001:     MatCreateSubMatrix_MPIAIJ_All(C,MAT_GET_VALUES,scall,submat);
    2002:     return 0;
    2003:   }

    2005:   /* Allocate memory to hold all the submatrices and dummy submatrices */
    2006:   if (scall == MAT_INITIAL_MATRIX) {
    2007:     PetscCalloc1(ismax+nstages,submat);
    2008:   }

    2010:   for (i=0,pos=0; i<nstages; i++) {
    2011:     if (pos+nmax <= ismax) max_no = nmax;
    2012:     else if (pos >= ismax) max_no = 0;
    2013:     else                   max_no = ismax-pos;

    2015:     MatCreateSubMatrices_MPIAIJ_Local(C,max_no,isrow+pos,iscol+pos,scall,*submat+pos);
    2016:     if (!max_no) {
    2017:       if (scall == MAT_INITIAL_MATRIX) { /* submat[pos] is a dummy matrix */
    2018:         smat = (Mat_SubSppt*)(*submat)[pos]->data;
    2019:         smat->nstages = nstages;
    2020:       }
    2021:       pos++; /* advance to next dummy matrix if any */
    2022:     } else pos += max_no;
    2023:   }

    2025:   if (ismax && scall == MAT_INITIAL_MATRIX) {
    2026:     /* save nstages for reuse */
    2027:     subc = (Mat_SeqAIJ*)(*submat)[0]->data;
    2028:     smat = subc->submatis1;
    2029:     smat->nstages = nstages;
    2030:   }
    2031:   return 0;
    2032: }

    2034: /* -------------------------------------------------------------------------*/
    2035: PetscErrorCode MatCreateSubMatrices_MPIAIJ_Local(Mat C,PetscInt ismax,const IS isrow[],const IS iscol[],MatReuse scall,Mat *submats)
    2036: {
    2037:   Mat_MPIAIJ     *c = (Mat_MPIAIJ*)C->data;
    2038:   Mat            A  = c->A;
    2039:   Mat_SeqAIJ     *a = (Mat_SeqAIJ*)A->data,*b = (Mat_SeqAIJ*)c->B->data,*subc;
    2040:   const PetscInt **icol,**irow;
    2041:   PetscInt       *nrow,*ncol,start;
    2042:   PetscMPIInt    rank,size,tag0,tag2,tag3,tag4,*w1,*w2,*w3,*w4,nrqr;
    2043:   PetscInt       **sbuf1,**sbuf2,i,j,k,l,ct1,ct2,**rbuf1,row,proc=-1;
    2044:   PetscInt       nrqs=0,msz,**ptr=NULL,*req_size=NULL,*ctr=NULL,*pa,*tmp=NULL,tcol;
    2045:   PetscInt       **rbuf3=NULL,*req_source1=NULL,*req_source2,**sbuf_aj,**rbuf2=NULL,max1,max2;
    2046:   PetscInt       **lens,is_no,ncols,*cols,mat_i,*mat_j,tmp2,jmax;
    2047: #if defined(PETSC_USE_CTABLE)
    2048:   PetscTable     *cmap,cmap_i=NULL,*rmap,rmap_i;
    2049: #else
    2050:   PetscInt       **cmap,*cmap_i=NULL,**rmap,*rmap_i;
    2051: #endif
    2052:   const PetscInt *irow_i;
    2053:   PetscInt       ctr_j,*sbuf1_j,*sbuf_aj_i,*rbuf1_i,kmax,*lens_i;
    2054:   MPI_Request    *s_waits1,*r_waits1,*s_waits2,*r_waits2,*r_waits3;
    2055:   MPI_Request    *r_waits4,*s_waits3,*s_waits4;
    2056:   MPI_Comm       comm;
    2057:   PetscScalar    **rbuf4,*rbuf4_i,**sbuf_aa,*vals,*mat_a,*imat_a,*sbuf_aa_i;
    2058:   PetscMPIInt    *onodes1,*olengths1,end;
    2059:   PetscInt       **row2proc,*row2proc_i,ilen_row,*imat_ilen,*imat_j,*imat_i,old_row;
    2060:   Mat_SubSppt    *smat_i;
    2061:   PetscBool      *issorted,*allcolumns,colflag,iscsorted=PETSC_TRUE;
    2062:   PetscInt       *sbuf1_i,*rbuf2_i,*rbuf3_i,ilen;

    2064:   PetscObjectGetComm((PetscObject)C,&comm);
    2065:   size = c->size;
    2066:   rank = c->rank;

    2068:   PetscMalloc4(ismax,&row2proc,ismax,&cmap,ismax,&rmap,ismax+1,&allcolumns);
    2069:   PetscMalloc5(ismax,(PetscInt***)&irow,ismax,(PetscInt***)&icol,ismax,&nrow,ismax,&ncol,ismax,&issorted);

    2071:   for (i=0; i<ismax; i++) {
    2072:     ISSorted(iscol[i],&issorted[i]);
    2073:     if (!issorted[i]) iscsorted = issorted[i];

    2075:     ISSorted(isrow[i],&issorted[i]);

    2077:     ISGetIndices(isrow[i],&irow[i]);
    2078:     ISGetLocalSize(isrow[i],&nrow[i]);

    2080:     /* Check for special case: allcolumn */
    2081:     ISIdentity(iscol[i],&colflag);
    2082:     ISGetLocalSize(iscol[i],&ncol[i]);
    2083:     if (colflag && ncol[i] == C->cmap->N) {
    2084:       allcolumns[i] = PETSC_TRUE;
    2085:       icol[i] = NULL;
    2086:     } else {
    2087:       allcolumns[i] = PETSC_FALSE;
    2088:       ISGetIndices(iscol[i],&icol[i]);
    2089:     }
    2090:   }

    2092:   if (scall == MAT_REUSE_MATRIX) {
    2093:     /* Assumes new rows are same length as the old rows */
    2094:     for (i=0; i<ismax; i++) {
    2096:       subc = (Mat_SeqAIJ*)submats[i]->data;

    2099:       /* Initial matrix as if empty */
    2100:       PetscArrayzero(subc->ilen,submats[i]->rmap->n);

    2102:       smat_i   = subc->submatis1;

    2104:       nrqs        = smat_i->nrqs;
    2105:       nrqr        = smat_i->nrqr;
    2106:       rbuf1       = smat_i->rbuf1;
    2107:       rbuf2       = smat_i->rbuf2;
    2108:       rbuf3       = smat_i->rbuf3;
    2109:       req_source2 = smat_i->req_source2;

    2111:       sbuf1     = smat_i->sbuf1;
    2112:       sbuf2     = smat_i->sbuf2;
    2113:       ptr       = smat_i->ptr;
    2114:       tmp       = smat_i->tmp;
    2115:       ctr       = smat_i->ctr;

    2117:       pa          = smat_i->pa;
    2118:       req_size    = smat_i->req_size;
    2119:       req_source1 = smat_i->req_source1;

    2121:       allcolumns[i] = smat_i->allcolumns;
    2122:       row2proc[i]   = smat_i->row2proc;
    2123:       rmap[i]       = smat_i->rmap;
    2124:       cmap[i]       = smat_i->cmap;
    2125:     }

    2127:     if (!ismax) { /* Get dummy submatrices and retrieve struct submatis1 */
    2129:       smat_i = (Mat_SubSppt*)submats[0]->data;

    2131:       nrqs        = smat_i->nrqs;
    2132:       nrqr        = smat_i->nrqr;
    2133:       rbuf1       = smat_i->rbuf1;
    2134:       rbuf2       = smat_i->rbuf2;
    2135:       rbuf3       = smat_i->rbuf3;
    2136:       req_source2 = smat_i->req_source2;

    2138:       sbuf1       = smat_i->sbuf1;
    2139:       sbuf2       = smat_i->sbuf2;
    2140:       ptr         = smat_i->ptr;
    2141:       tmp         = smat_i->tmp;
    2142:       ctr         = smat_i->ctr;

    2144:       pa          = smat_i->pa;
    2145:       req_size    = smat_i->req_size;
    2146:       req_source1 = smat_i->req_source1;

    2148:       allcolumns[0] = PETSC_FALSE;
    2149:     }
    2150:   } else { /* scall == MAT_INITIAL_MATRIX */
    2151:     /* Get some new tags to keep the communication clean */
    2152:     PetscObjectGetNewTag((PetscObject)C,&tag2);
    2153:     PetscObjectGetNewTag((PetscObject)C,&tag3);

    2155:     /* evaluate communication - mesg to who, length of mesg, and buffer space
    2156:      required. Based on this, buffers are allocated, and data copied into them*/
    2157:     PetscCalloc4(size,&w1,size,&w2,size,&w3,size,&w4);   /* mesg size, initialize work vectors */

    2159:     for (i=0; i<ismax; i++) {
    2160:       jmax   = nrow[i];
    2161:       irow_i = irow[i];

    2163:       PetscMalloc1(jmax,&row2proc_i);
    2164:       row2proc[i] = row2proc_i;

    2166:       if (issorted[i]) proc = 0;
    2167:       for (j=0; j<jmax; j++) {
    2168:         if (!issorted[i]) proc = 0;
    2169:         row = irow_i[j];
    2170:         while (row >= C->rmap->range[proc+1]) proc++;
    2171:         w4[proc]++;
    2172:         row2proc_i[j] = proc; /* map row index to proc */
    2173:       }
    2174:       for (j=0; j<size; j++) {
    2175:         if (w4[j]) { w1[j] += w4[j];  w3[j]++; w4[j] = 0;}
    2176:       }
    2177:     }

    2179:     nrqs     = 0;              /* no of outgoing messages */
    2180:     msz      = 0;              /* total mesg length (for all procs) */
    2181:     w1[rank] = 0;              /* no mesg sent to self */
    2182:     w3[rank] = 0;
    2183:     for (i=0; i<size; i++) {
    2184:       if (w1[i])  { w2[i] = 1; nrqs++;} /* there exists a message to proc i */
    2185:     }
    2186:     PetscMalloc1(nrqs,&pa); /*(proc -array)*/
    2187:     for (i=0,j=0; i<size; i++) {
    2188:       if (w1[i]) { pa[j] = i; j++; }
    2189:     }

    2191:     /* Each message would have a header = 1 + 2*(no of IS) + data */
    2192:     for (i=0; i<nrqs; i++) {
    2193:       j      = pa[i];
    2194:       w1[j] += w2[j] + 2* w3[j];
    2195:       msz   += w1[j];
    2196:     }
    2197:     PetscInfo(0,"Number of outgoing messages %" PetscInt_FMT " Total message length %" PetscInt_FMT "\n",nrqs,msz);

    2199:     /* Determine the number of messages to expect, their lengths, from from-ids */
    2200:     PetscGatherNumberOfMessages(comm,w2,w1,&nrqr);
    2201:     PetscGatherMessageLengths(comm,nrqs,nrqr,w1,&onodes1,&olengths1);

    2203:     /* Now post the Irecvs corresponding to these messages */
    2204:     PetscObjectGetNewTag((PetscObject)C,&tag0);
    2205:     PetscPostIrecvInt(comm,tag0,nrqr,onodes1,olengths1,&rbuf1,&r_waits1);

    2207:     /* Allocate Memory for outgoing messages */
    2208:     PetscMalloc4(size,&sbuf1,size,&ptr,2*msz,&tmp,size,&ctr);
    2209:     PetscArrayzero(sbuf1,size);
    2210:     PetscArrayzero(ptr,size);

    2212:     {
    2213:       PetscInt *iptr = tmp;
    2214:       k    = 0;
    2215:       for (i=0; i<nrqs; i++) {
    2216:         j        = pa[i];
    2217:         iptr    += k;
    2218:         sbuf1[j] = iptr;
    2219:         k        = w1[j];
    2220:       }
    2221:     }

    2223:     /* Form the outgoing messages. Initialize the header space */
    2224:     for (i=0; i<nrqs; i++) {
    2225:       j           = pa[i];
    2226:       sbuf1[j][0] = 0;
    2227:       PetscArrayzero(sbuf1[j]+1,2*w3[j]);
    2228:       ptr[j]      = sbuf1[j] + 2*w3[j] + 1;
    2229:     }

    2231:     /* Parse the isrow and copy data into outbuf */
    2232:     for (i=0; i<ismax; i++) {
    2233:       row2proc_i = row2proc[i];
    2234:       PetscArrayzero(ctr,size);
    2235:       irow_i = irow[i];
    2236:       jmax   = nrow[i];
    2237:       for (j=0; j<jmax; j++) {  /* parse the indices of each IS */
    2238:         proc = row2proc_i[j];
    2239:         if (proc != rank) { /* copy to the outgoing buf*/
    2240:           ctr[proc]++;
    2241:           *ptr[proc] = irow_i[j];
    2242:           ptr[proc]++;
    2243:         }
    2244:       }
    2245:       /* Update the headers for the current IS */
    2246:       for (j=0; j<size; j++) { /* Can Optimise this loop too */
    2247:         if ((ctr_j = ctr[j])) {
    2248:           sbuf1_j        = sbuf1[j];
    2249:           k              = ++sbuf1_j[0];
    2250:           sbuf1_j[2*k]   = ctr_j;
    2251:           sbuf1_j[2*k-1] = i;
    2252:         }
    2253:       }
    2254:     }

    2256:     /*  Now  post the sends */
    2257:     PetscMalloc1(nrqs,&s_waits1);
    2258:     for (i=0; i<nrqs; ++i) {
    2259:       j    = pa[i];
    2260:       MPI_Isend(sbuf1[j],w1[j],MPIU_INT,j,tag0,comm,s_waits1+i);
    2261:     }

    2263:     /* Post Receives to capture the buffer size */
    2264:     PetscMalloc1(nrqs,&r_waits2);
    2265:     PetscMalloc3(nrqs,&req_source2,nrqs,&rbuf2,nrqs,&rbuf3);
    2266:     if (nrqs) rbuf2[0] = tmp + msz;
    2267:     for (i=1; i<nrqs; ++i) {
    2268:       rbuf2[i] = rbuf2[i-1]+w1[pa[i-1]];
    2269:     }
    2270:     for (i=0; i<nrqs; ++i) {
    2271:       j    = pa[i];
    2272:       MPI_Irecv(rbuf2[i],w1[j],MPIU_INT,j,tag2,comm,r_waits2+i);
    2273:     }

    2275:     /* Send to other procs the buf size they should allocate */
    2276:     /* Receive messages*/
    2277:     PetscMalloc1(nrqr,&s_waits2);
    2278:     PetscMalloc3(nrqr,&sbuf2,nrqr,&req_size,nrqr,&req_source1);
    2279:     {
    2280:       PetscInt   *sAi = a->i,*sBi = b->i,id,rstart = C->rmap->rstart;
    2281:       PetscInt   *sbuf2_i;

    2283:       MPI_Waitall(nrqr,r_waits1,MPI_STATUSES_IGNORE);
    2284:       for (i=0; i<nrqr; ++i) {
    2285:         req_size[i] = 0;
    2286:         rbuf1_i        = rbuf1[i];
    2287:         start          = 2*rbuf1_i[0] + 1;
    2288:         end            = olengths1[i];
    2289:         PetscMalloc1(end,&sbuf2[i]);
    2290:         sbuf2_i        = sbuf2[i];
    2291:         for (j=start; j<end; j++) {
    2292:           id              = rbuf1_i[j] - rstart;
    2293:           ncols           = sAi[id+1] - sAi[id] + sBi[id+1] - sBi[id];
    2294:           sbuf2_i[j]      = ncols;
    2295:           req_size[i] += ncols;
    2296:         }
    2297:         req_source1[i] = onodes1[i];
    2298:         /* form the header */
    2299:         sbuf2_i[0] = req_size[i];
    2300:         for (j=1; j<start; j++) sbuf2_i[j] = rbuf1_i[j];

    2302:         MPI_Isend(sbuf2_i,end,MPIU_INT,req_source1[i],tag2,comm,s_waits2+i);
    2303:       }
    2304:     }

    2306:     PetscFree(onodes1);
    2307:     PetscFree(olengths1);
    2308:     PetscFree(r_waits1);
    2309:     PetscFree4(w1,w2,w3,w4);

    2311:     /* Receive messages*/
    2312:     PetscMalloc1(nrqs,&r_waits3);
    2313:     MPI_Waitall(nrqs,r_waits2,MPI_STATUSES_IGNORE);
    2314:     for (i=0; i<nrqs; ++i) {
    2315:       PetscMalloc1(rbuf2[i][0],&rbuf3[i]);
    2316:       req_source2[i] = pa[i];
    2317:       MPI_Irecv(rbuf3[i],rbuf2[i][0],MPIU_INT,req_source2[i],tag3,comm,r_waits3+i);
    2318:     }
    2319:     PetscFree(r_waits2);

    2321:     /* Wait on sends1 and sends2 */
    2322:     MPI_Waitall(nrqs,s_waits1,MPI_STATUSES_IGNORE);
    2323:     MPI_Waitall(nrqr,s_waits2,MPI_STATUSES_IGNORE);
    2324:     PetscFree(s_waits1);
    2325:     PetscFree(s_waits2);

    2327:     /* Now allocate sending buffers for a->j, and send them off */
    2328:     PetscMalloc1(nrqr,&sbuf_aj);
    2329:     for (i=0,j=0; i<nrqr; i++) j += req_size[i];
    2330:     if (nrqr) PetscMalloc1(j,&sbuf_aj[0]);
    2331:     for (i=1; i<nrqr; i++) sbuf_aj[i] = sbuf_aj[i-1] + req_size[i-1];

    2333:     PetscMalloc1(nrqr,&s_waits3);
    2334:     {
    2335:       PetscInt nzA,nzB,*a_i = a->i,*b_i = b->i,lwrite;
    2336:       PetscInt *cworkA,*cworkB,cstart = C->cmap->rstart,rstart = C->rmap->rstart,*bmap = c->garray;
    2337:       PetscInt cend = C->cmap->rend;
    2338:       PetscInt *a_j = a->j,*b_j = b->j,ctmp;

    2340:       for (i=0; i<nrqr; i++) {
    2341:         rbuf1_i   = rbuf1[i];
    2342:         sbuf_aj_i = sbuf_aj[i];
    2343:         ct1       = 2*rbuf1_i[0] + 1;
    2344:         ct2       = 0;
    2345:         for (j=1,max1=rbuf1_i[0]; j<=max1; j++) {
    2346:           kmax = rbuf1[i][2*j];
    2347:           for (k=0; k<kmax; k++,ct1++) {
    2348:             row    = rbuf1_i[ct1] - rstart;
    2349:             nzA    = a_i[row+1] - a_i[row];
    2350:             nzB    = b_i[row+1] - b_i[row];
    2351:             ncols  = nzA + nzB;
    2352:             cworkA = a_j + a_i[row];
    2353:             cworkB = b_j + b_i[row];

    2355:             /* load the column indices for this row into cols */
    2356:             cols = sbuf_aj_i + ct2;

    2358:             lwrite = 0;
    2359:             for (l=0; l<nzB; l++) {
    2360:               if ((ctmp = bmap[cworkB[l]]) < cstart) cols[lwrite++] = ctmp;
    2361:             }
    2362:             for (l=0; l<nzA; l++) cols[lwrite++] = cstart + cworkA[l];
    2363:             for (l=0; l<nzB; l++) {
    2364:               if ((ctmp = bmap[cworkB[l]]) >= cend) cols[lwrite++] = ctmp;
    2365:             }

    2367:             ct2 += ncols;
    2368:           }
    2369:         }
    2370:         MPI_Isend(sbuf_aj_i,req_size[i],MPIU_INT,req_source1[i],tag3,comm,s_waits3+i);
    2371:       }
    2372:     }

    2374:     /* create col map: global col of C -> local col of submatrices */
    2375:     {
    2376:       const PetscInt *icol_i;
    2377: #if defined(PETSC_USE_CTABLE)
    2378:       for (i=0; i<ismax; i++) {
    2379:         if (!allcolumns[i]) {
    2380:           PetscTableCreate(ncol[i],C->cmap->N,&cmap[i]);

    2382:           jmax   = ncol[i];
    2383:           icol_i = icol[i];
    2384:           cmap_i = cmap[i];
    2385:           for (j=0; j<jmax; j++) {
    2386:             PetscTableAdd(cmap[i],icol_i[j]+1,j+1,INSERT_VALUES);
    2387:           }
    2388:         } else cmap[i] = NULL;
    2389:       }
    2390: #else
    2391:       for (i=0; i<ismax; i++) {
    2392:         if (!allcolumns[i]) {
    2393:           PetscCalloc1(C->cmap->N,&cmap[i]);
    2394:           jmax   = ncol[i];
    2395:           icol_i = icol[i];
    2396:           cmap_i = cmap[i];
    2397:           for (j=0; j<jmax; j++) {
    2398:             cmap_i[icol_i[j]] = j+1;
    2399:           }
    2400:         } else cmap[i] = NULL;
    2401:       }
    2402: #endif
    2403:     }

    2405:     /* Create lens which is required for MatCreate... */
    2406:     for (i=0,j=0; i<ismax; i++) j += nrow[i];
    2407:     PetscMalloc1(ismax,&lens);

    2409:     if (ismax) {
    2410:       PetscCalloc1(j,&lens[0]);
    2411:     }
    2412:     for (i=1; i<ismax; i++) lens[i] = lens[i-1] + nrow[i-1];

    2414:     /* Update lens from local data */
    2415:     for (i=0; i<ismax; i++) {
    2416:       row2proc_i = row2proc[i];
    2417:       jmax = nrow[i];
    2418:       if (!allcolumns[i]) cmap_i = cmap[i];
    2419:       irow_i = irow[i];
    2420:       lens_i = lens[i];
    2421:       for (j=0; j<jmax; j++) {
    2422:         row = irow_i[j];
    2423:         proc = row2proc_i[j];
    2424:         if (proc == rank) {
    2425:           MatGetRow_MPIAIJ(C,row,&ncols,&cols,NULL);
    2426:           if (!allcolumns[i]) {
    2427:             for (k=0; k<ncols; k++) {
    2428: #if defined(PETSC_USE_CTABLE)
    2429:               PetscTableFind(cmap_i,cols[k]+1,&tcol);
    2430: #else
    2431:               tcol = cmap_i[cols[k]];
    2432: #endif
    2433:               if (tcol) lens_i[j]++;
    2434:             }
    2435:           } else { /* allcolumns */
    2436:             lens_i[j] = ncols;
    2437:           }
    2438:           MatRestoreRow_MPIAIJ(C,row,&ncols,&cols,NULL);
    2439:         }
    2440:       }
    2441:     }

    2443:     /* Create row map: global row of C -> local row of submatrices */
    2444: #if defined(PETSC_USE_CTABLE)
    2445:     for (i=0; i<ismax; i++) {
    2446:       PetscTableCreate(nrow[i],C->rmap->N,&rmap[i]);
    2447:       irow_i = irow[i];
    2448:       jmax   = nrow[i];
    2449:       for (j=0; j<jmax; j++) {
    2450:       PetscTableAdd(rmap[i],irow_i[j]+1,j+1,INSERT_VALUES);
    2451:       }
    2452:     }
    2453: #else
    2454:     for (i=0; i<ismax; i++) {
    2455:       PetscCalloc1(C->rmap->N,&rmap[i]);
    2456:       rmap_i = rmap[i];
    2457:       irow_i = irow[i];
    2458:       jmax   = nrow[i];
    2459:       for (j=0; j<jmax; j++) {
    2460:         rmap_i[irow_i[j]] = j;
    2461:       }
    2462:     }
    2463: #endif

    2465:     /* Update lens from offproc data */
    2466:     {
    2467:       PetscInt *rbuf2_i,*rbuf3_i,*sbuf1_i;

    2469:       MPI_Waitall(nrqs,r_waits3,MPI_STATUSES_IGNORE);
    2470:       for (tmp2=0; tmp2<nrqs; tmp2++) {
    2471:         sbuf1_i = sbuf1[pa[tmp2]];
    2472:         jmax    = sbuf1_i[0];
    2473:         ct1     = 2*jmax+1;
    2474:         ct2     = 0;
    2475:         rbuf2_i = rbuf2[tmp2];
    2476:         rbuf3_i = rbuf3[tmp2];
    2477:         for (j=1; j<=jmax; j++) {
    2478:           is_no  = sbuf1_i[2*j-1];
    2479:           max1   = sbuf1_i[2*j];
    2480:           lens_i = lens[is_no];
    2481:           if (!allcolumns[is_no]) cmap_i = cmap[is_no];
    2482:           rmap_i = rmap[is_no];
    2483:           for (k=0; k<max1; k++,ct1++) {
    2484: #if defined(PETSC_USE_CTABLE)
    2485:             PetscTableFind(rmap_i,sbuf1_i[ct1]+1,&row);
    2486:             row--;
    2488: #else
    2489:             row = rmap_i[sbuf1_i[ct1]]; /* the val in the new matrix to be */
    2490: #endif
    2491:             max2 = rbuf2_i[ct1];
    2492:             for (l=0; l<max2; l++,ct2++) {
    2493:               if (!allcolumns[is_no]) {
    2494: #if defined(PETSC_USE_CTABLE)
    2495:                 PetscTableFind(cmap_i,rbuf3_i[ct2]+1,&tcol);
    2496: #else
    2497:                 tcol = cmap_i[rbuf3_i[ct2]];
    2498: #endif
    2499:                 if (tcol) lens_i[row]++;
    2500:               } else { /* allcolumns */
    2501:                 lens_i[row]++; /* lens_i[row] += max2 ? */
    2502:               }
    2503:             }
    2504:           }
    2505:         }
    2506:       }
    2507:     }
    2508:     PetscFree(r_waits3);
    2509:     MPI_Waitall(nrqr,s_waits3,MPI_STATUSES_IGNORE);
    2510:     PetscFree(s_waits3);

    2512:     /* Create the submatrices */
    2513:     for (i=0; i<ismax; i++) {
    2514:       PetscInt    rbs,cbs;

    2516:       ISGetBlockSize(isrow[i],&rbs);
    2517:       ISGetBlockSize(iscol[i],&cbs);

    2519:       MatCreate(PETSC_COMM_SELF,submats+i);
    2520:       MatSetSizes(submats[i],nrow[i],ncol[i],PETSC_DETERMINE,PETSC_DETERMINE);

    2522:       MatSetBlockSizes(submats[i],rbs,cbs);
    2523:       MatSetType(submats[i],((PetscObject)A)->type_name);
    2524:       MatSeqAIJSetPreallocation(submats[i],0,lens[i]);

    2526:       /* create struct Mat_SubSppt and attached it to submat */
    2527:       PetscNew(&smat_i);
    2528:       subc = (Mat_SeqAIJ*)submats[i]->data;
    2529:       subc->submatis1 = smat_i;

    2531:       smat_i->destroy          = submats[i]->ops->destroy;
    2532:       submats[i]->ops->destroy = MatDestroySubMatrix_SeqAIJ;
    2533:       submats[i]->factortype   = C->factortype;

    2535:       smat_i->id          = i;
    2536:       smat_i->nrqs        = nrqs;
    2537:       smat_i->nrqr        = nrqr;
    2538:       smat_i->rbuf1       = rbuf1;
    2539:       smat_i->rbuf2       = rbuf2;
    2540:       smat_i->rbuf3       = rbuf3;
    2541:       smat_i->sbuf2       = sbuf2;
    2542:       smat_i->req_source2 = req_source2;

    2544:       smat_i->sbuf1       = sbuf1;
    2545:       smat_i->ptr         = ptr;
    2546:       smat_i->tmp         = tmp;
    2547:       smat_i->ctr         = ctr;

    2549:       smat_i->pa           = pa;
    2550:       smat_i->req_size     = req_size;
    2551:       smat_i->req_source1  = req_source1;

    2553:       smat_i->allcolumns  = allcolumns[i];
    2554:       smat_i->singleis    = PETSC_FALSE;
    2555:       smat_i->row2proc    = row2proc[i];
    2556:       smat_i->rmap        = rmap[i];
    2557:       smat_i->cmap        = cmap[i];
    2558:     }

    2560:     if (!ismax) { /* Create dummy submats[0] for reuse struct subc */
    2561:       MatCreate(PETSC_COMM_SELF,&submats[0]);
    2562:       MatSetSizes(submats[0],0,0,PETSC_DETERMINE,PETSC_DETERMINE);
    2563:       MatSetType(submats[0],MATDUMMY);

    2565:       /* create struct Mat_SubSppt and attached it to submat */
    2566:       PetscNewLog(submats[0],&smat_i);
    2567:       submats[0]->data = (void*)smat_i;

    2569:       smat_i->destroy          = submats[0]->ops->destroy;
    2570:       submats[0]->ops->destroy = MatDestroySubMatrix_Dummy;
    2571:       submats[0]->factortype   = C->factortype;

    2573:       smat_i->id          = 0;
    2574:       smat_i->nrqs        = nrqs;
    2575:       smat_i->nrqr        = nrqr;
    2576:       smat_i->rbuf1       = rbuf1;
    2577:       smat_i->rbuf2       = rbuf2;
    2578:       smat_i->rbuf3       = rbuf3;
    2579:       smat_i->sbuf2       = sbuf2;
    2580:       smat_i->req_source2 = req_source2;

    2582:       smat_i->sbuf1       = sbuf1;
    2583:       smat_i->ptr         = ptr;
    2584:       smat_i->tmp         = tmp;
    2585:       smat_i->ctr         = ctr;

    2587:       smat_i->pa           = pa;
    2588:       smat_i->req_size     = req_size;
    2589:       smat_i->req_source1  = req_source1;

    2591:       smat_i->allcolumns  = PETSC_FALSE;
    2592:       smat_i->singleis    = PETSC_FALSE;
    2593:       smat_i->row2proc    = NULL;
    2594:       smat_i->rmap        = NULL;
    2595:       smat_i->cmap        = NULL;
    2596:     }

    2598:     if (ismax) PetscFree(lens[0]);
    2599:     PetscFree(lens);
    2600:     if (sbuf_aj) {
    2601:       PetscFree(sbuf_aj[0]);
    2602:       PetscFree(sbuf_aj);
    2603:     }

    2605:   } /* endof scall == MAT_INITIAL_MATRIX */

    2607:   /* Post recv matrix values */
    2608:   PetscObjectGetNewTag((PetscObject)C,&tag4);
    2609:   PetscMalloc1(nrqs,&rbuf4);
    2610:   PetscMalloc1(nrqs,&r_waits4);
    2611:   for (i=0; i<nrqs; ++i) {
    2612:     PetscMalloc1(rbuf2[i][0],&rbuf4[i]);
    2613:     MPI_Irecv(rbuf4[i],rbuf2[i][0],MPIU_SCALAR,req_source2[i],tag4,comm,r_waits4+i);
    2614:   }

    2616:   /* Allocate sending buffers for a->a, and send them off */
    2617:   PetscMalloc1(nrqr,&sbuf_aa);
    2618:   for (i=0,j=0; i<nrqr; i++) j += req_size[i];
    2619:   if (nrqr) PetscMalloc1(j,&sbuf_aa[0]);
    2620:   for (i=1; i<nrqr; i++) sbuf_aa[i] = sbuf_aa[i-1] + req_size[i-1];

    2622:   PetscMalloc1(nrqr,&s_waits4);
    2623:   {
    2624:     PetscInt    nzA,nzB,*a_i = a->i,*b_i = b->i, *cworkB,lwrite;
    2625:     PetscInt    cstart = C->cmap->rstart,rstart = C->rmap->rstart,*bmap = c->garray;
    2626:     PetscInt    cend   = C->cmap->rend;
    2627:     PetscInt    *b_j   = b->j;
    2628:     PetscScalar *vworkA,*vworkB,*a_a,*b_a;

    2630:     MatSeqAIJGetArrayRead(A,(const PetscScalar**)&a_a);
    2631:     MatSeqAIJGetArrayRead(c->B,(const PetscScalar**)&b_a);
    2632:     for (i=0; i<nrqr; i++) {
    2633:       rbuf1_i   = rbuf1[i];
    2634:       sbuf_aa_i = sbuf_aa[i];
    2635:       ct1       = 2*rbuf1_i[0]+1;
    2636:       ct2       = 0;
    2637:       for (j=1,max1=rbuf1_i[0]; j<=max1; j++) {
    2638:         kmax = rbuf1_i[2*j];
    2639:         for (k=0; k<kmax; k++,ct1++) {
    2640:           row    = rbuf1_i[ct1] - rstart;
    2641:           nzA    = a_i[row+1] - a_i[row];
    2642:           nzB    = b_i[row+1] - b_i[row];
    2643:           ncols  = nzA + nzB;
    2644:           cworkB = b_j + b_i[row];
    2645:           vworkA = a_a + a_i[row];
    2646:           vworkB = b_a + b_i[row];

    2648:           /* load the column values for this row into vals*/
    2649:           vals = sbuf_aa_i+ct2;

    2651:           lwrite = 0;
    2652:           for (l=0; l<nzB; l++) {
    2653:             if ((bmap[cworkB[l]]) < cstart) vals[lwrite++] = vworkB[l];
    2654:           }
    2655:           for (l=0; l<nzA; l++) vals[lwrite++] = vworkA[l];
    2656:           for (l=0; l<nzB; l++) {
    2657:             if ((bmap[cworkB[l]]) >= cend) vals[lwrite++] = vworkB[l];
    2658:           }

    2660:           ct2 += ncols;
    2661:         }
    2662:       }
    2663:       MPI_Isend(sbuf_aa_i,req_size[i],MPIU_SCALAR,req_source1[i],tag4,comm,s_waits4+i);
    2664:     }
    2665:     MatSeqAIJRestoreArrayRead(A,(const PetscScalar**)&a_a);
    2666:     MatSeqAIJRestoreArrayRead(c->B,(const PetscScalar**)&b_a);
    2667:   }

    2669:   /* Assemble the matrices */
    2670:   /* First assemble the local rows */
    2671:   for (i=0; i<ismax; i++) {
    2672:     row2proc_i = row2proc[i];
    2673:     subc      = (Mat_SeqAIJ*)submats[i]->data;
    2674:     imat_ilen = subc->ilen;
    2675:     imat_j    = subc->j;
    2676:     imat_i    = subc->i;
    2677:     imat_a    = subc->a;

    2679:     if (!allcolumns[i]) cmap_i = cmap[i];
    2680:     rmap_i = rmap[i];
    2681:     irow_i = irow[i];
    2682:     jmax   = nrow[i];
    2683:     for (j=0; j<jmax; j++) {
    2684:       row  = irow_i[j];
    2685:       proc = row2proc_i[j];
    2686:       if (proc == rank) {
    2687:         old_row = row;
    2688: #if defined(PETSC_USE_CTABLE)
    2689:         PetscTableFind(rmap_i,row+1,&row);
    2690:         row--;
    2691: #else
    2692:         row = rmap_i[row];
    2693: #endif
    2694:         ilen_row = imat_ilen[row];
    2695:         MatGetRow_MPIAIJ(C,old_row,&ncols,&cols,&vals);
    2696:         mat_i    = imat_i[row];
    2697:         mat_a    = imat_a + mat_i;
    2698:         mat_j    = imat_j + mat_i;
    2699:         if (!allcolumns[i]) {
    2700:           for (k=0; k<ncols; k++) {
    2701: #if defined(PETSC_USE_CTABLE)
    2702:             PetscTableFind(cmap_i,cols[k]+1,&tcol);
    2703: #else
    2704:             tcol = cmap_i[cols[k]];
    2705: #endif
    2706:             if (tcol) {
    2707:               *mat_j++ = tcol - 1;
    2708:               *mat_a++ = vals[k];
    2709:               ilen_row++;
    2710:             }
    2711:           }
    2712:         } else { /* allcolumns */
    2713:           for (k=0; k<ncols; k++) {
    2714:             *mat_j++ = cols[k];  /* global col index! */
    2715:             *mat_a++ = vals[k];
    2716:             ilen_row++;
    2717:           }
    2718:         }
    2719:         MatRestoreRow_MPIAIJ(C,old_row,&ncols,&cols,&vals);

    2721:         imat_ilen[row] = ilen_row;
    2722:       }
    2723:     }
    2724:   }

    2726:   /* Now assemble the off proc rows */
    2727:   MPI_Waitall(nrqs,r_waits4,MPI_STATUSES_IGNORE);
    2728:   for (tmp2=0; tmp2<nrqs; tmp2++) {
    2729:     sbuf1_i = sbuf1[pa[tmp2]];
    2730:     jmax    = sbuf1_i[0];
    2731:     ct1     = 2*jmax + 1;
    2732:     ct2     = 0;
    2733:     rbuf2_i = rbuf2[tmp2];
    2734:     rbuf3_i = rbuf3[tmp2];
    2735:     rbuf4_i = rbuf4[tmp2];
    2736:     for (j=1; j<=jmax; j++) {
    2737:       is_no     = sbuf1_i[2*j-1];
    2738:       rmap_i    = rmap[is_no];
    2739:       if (!allcolumns[is_no]) cmap_i = cmap[is_no];
    2740:       subc      = (Mat_SeqAIJ*)submats[is_no]->data;
    2741:       imat_ilen = subc->ilen;
    2742:       imat_j    = subc->j;
    2743:       imat_i    = subc->i;
    2744:       imat_a    = subc->a;
    2745:       max1      = sbuf1_i[2*j];
    2746:       for (k=0; k<max1; k++,ct1++) {
    2747:         row = sbuf1_i[ct1];
    2748: #if defined(PETSC_USE_CTABLE)
    2749:         PetscTableFind(rmap_i,row+1,&row);
    2750:         row--;
    2751: #else
    2752:         row = rmap_i[row];
    2753: #endif
    2754:         ilen  = imat_ilen[row];
    2755:         mat_i = imat_i[row];
    2756:         mat_a = imat_a + mat_i;
    2757:         mat_j = imat_j + mat_i;
    2758:         max2  = rbuf2_i[ct1];
    2759:         if (!allcolumns[is_no]) {
    2760:           for (l=0; l<max2; l++,ct2++) {
    2761: #if defined(PETSC_USE_CTABLE)
    2762:             PetscTableFind(cmap_i,rbuf3_i[ct2]+1,&tcol);
    2763: #else
    2764:             tcol = cmap_i[rbuf3_i[ct2]];
    2765: #endif
    2766:             if (tcol) {
    2767:               *mat_j++ = tcol - 1;
    2768:               *mat_a++ = rbuf4_i[ct2];
    2769:               ilen++;
    2770:             }
    2771:           }
    2772:         } else { /* allcolumns */
    2773:           for (l=0; l<max2; l++,ct2++) {
    2774:             *mat_j++ = rbuf3_i[ct2]; /* same global column index of C */
    2775:             *mat_a++ = rbuf4_i[ct2];
    2776:             ilen++;
    2777:           }
    2778:         }
    2779:         imat_ilen[row] = ilen;
    2780:       }
    2781:     }
    2782:   }

    2784:   if (!iscsorted) { /* sort column indices of the rows */
    2785:     for (i=0; i<ismax; i++) {
    2786:       subc      = (Mat_SeqAIJ*)submats[i]->data;
    2787:       imat_j    = subc->j;
    2788:       imat_i    = subc->i;
    2789:       imat_a    = subc->a;
    2790:       imat_ilen = subc->ilen;

    2792:       if (allcolumns[i]) continue;
    2793:       jmax = nrow[i];
    2794:       for (j=0; j<jmax; j++) {
    2795:         mat_i = imat_i[j];
    2796:         mat_a = imat_a + mat_i;
    2797:         mat_j = imat_j + mat_i;
    2798:         PetscSortIntWithScalarArray(imat_ilen[j],mat_j,mat_a);
    2799:       }
    2800:     }
    2801:   }

    2803:   PetscFree(r_waits4);
    2804:   MPI_Waitall(nrqr,s_waits4,MPI_STATUSES_IGNORE);
    2805:   PetscFree(s_waits4);

    2807:   /* Restore the indices */
    2808:   for (i=0; i<ismax; i++) {
    2809:     ISRestoreIndices(isrow[i],irow+i);
    2810:     if (!allcolumns[i]) {
    2811:       ISRestoreIndices(iscol[i],icol+i);
    2812:     }
    2813:   }

    2815:   for (i=0; i<ismax; i++) {
    2816:     MatAssemblyBegin(submats[i],MAT_FINAL_ASSEMBLY);
    2817:     MatAssemblyEnd(submats[i],MAT_FINAL_ASSEMBLY);
    2818:   }

    2820:   /* Destroy allocated memory */
    2821:   if (sbuf_aa) {
    2822:     PetscFree(sbuf_aa[0]);
    2823:     PetscFree(sbuf_aa);
    2824:   }
    2825:   PetscFree5(*(PetscInt***)&irow,*(PetscInt***)&icol,nrow,ncol,issorted);

    2827:   for (i=0; i<nrqs; ++i) {
    2828:     PetscFree(rbuf4[i]);
    2829:   }
    2830:   PetscFree(rbuf4);

    2832:   PetscFree4(row2proc,cmap,rmap,allcolumns);
    2833:   return 0;
    2834: }

    2836: /*
    2837:  Permute A & B into C's *local* index space using rowemb,dcolemb for A and rowemb,ocolemb for B.
    2838:  Embeddings are supposed to be injections and the above implies that the range of rowemb is a subset
    2839:  of [0,m), dcolemb is in [0,n) and ocolemb is in [N-n).
    2840:  If pattern == DIFFERENT_NONZERO_PATTERN, C is preallocated according to A&B.
    2841:  After that B's columns are mapped into C's global column space, so that C is in the "disassembled"
    2842:  state, and needs to be "assembled" later by compressing B's column space.

    2844:  This function may be called in lieu of preallocation, so C should not be expected to be preallocated.
    2845:  Following this call, C->A & C->B have been created, even if empty.
    2846:  */
    2847: PetscErrorCode MatSetSeqMats_MPIAIJ(Mat C,IS rowemb,IS dcolemb,IS ocolemb,MatStructure pattern,Mat A,Mat B)
    2848: {
    2849:   /* If making this function public, change the error returned in this function away from _PLIB. */
    2850:   Mat_MPIAIJ     *aij;
    2851:   Mat_SeqAIJ     *Baij;
    2852:   PetscBool      seqaij,Bdisassembled;
    2853:   PetscInt       m,n,*nz,i,j,ngcol,col,rstart,rend,shift,count;
    2854:   PetscScalar    v;
    2855:   const PetscInt *rowindices,*colindices;

    2857:   /* Check to make sure the component matrices (and embeddings) are compatible with C. */
    2858:   if (A) {
    2859:     PetscObjectBaseTypeCompare((PetscObject)A,MATSEQAIJ,&seqaij);
    2861:     if (rowemb) {
    2862:       ISGetLocalSize(rowemb,&m);
    2864:     } else {
    2865:       if (C->rmap->n != A->rmap->n) {
    2866:         SETERRQ(PETSC_COMM_SELF,PETSC_ERR_PLIB,"Diag seq matrix is row-incompatible with the MPIAIJ matrix");
    2867:       }
    2868:     }
    2869:     if (dcolemb) {
    2870:       ISGetLocalSize(dcolemb,&n);
    2872:     } else {
    2874:     }
    2875:   }
    2876:   if (B) {
    2877:     PetscObjectBaseTypeCompare((PetscObject)B,MATSEQAIJ,&seqaij);
    2879:     if (rowemb) {
    2880:       ISGetLocalSize(rowemb,&m);
    2882:     } else {
    2883:       if (C->rmap->n != B->rmap->n) {
    2884:         SETERRQ(PETSC_COMM_SELF,PETSC_ERR_PLIB,"Off-diag seq matrix is row-incompatible with the MPIAIJ matrix");
    2885:       }
    2886:     }
    2887:     if (ocolemb) {
    2888:       ISGetLocalSize(ocolemb,&n);
    2890:     } else {
    2892:     }
    2893:   }

    2895:   aij = (Mat_MPIAIJ*)C->data;
    2896:   if (!aij->A) {
    2897:     /* Mimic parts of MatMPIAIJSetPreallocation() */
    2898:     MatCreate(PETSC_COMM_SELF,&aij->A);
    2899:     MatSetSizes(aij->A,C->rmap->n,C->cmap->n,C->rmap->n,C->cmap->n);
    2900:     MatSetBlockSizesFromMats(aij->A,C,C);
    2901:     MatSetType(aij->A,MATSEQAIJ);
    2902:     PetscLogObjectParent((PetscObject)C,(PetscObject)aij->A);
    2903:   }
    2904:   if (A) {
    2905:     MatSetSeqMat_SeqAIJ(aij->A,rowemb,dcolemb,pattern,A);
    2906:   } else {
    2907:     MatSetUp(aij->A);
    2908:   }
    2909:   if (B) { /* Destroy the old matrix or the column map, depending on the sparsity pattern. */
    2910:     /*
    2911:       If pattern == DIFFERENT_NONZERO_PATTERN, we reallocate B and
    2912:       need to "disassemble" B -- convert it to using C's global indices.
    2913:       To insert the values we take the safer, albeit more expensive, route of MatSetValues().

    2915:       If pattern == SUBSET_NONZERO_PATTERN, we do not "disassemble" B and do not reallocate;
    2916:       we MatZeroValues(B) first, so there may be a bunch of zeros that, perhaps, could be compacted out.

    2918:       TODO: Put B's values into aij->B's aij structure in place using the embedding ISs?
    2919:       At least avoid calling MatSetValues() and the implied searches?
    2920:     */

    2922:     if (B && pattern == DIFFERENT_NONZERO_PATTERN) {
    2923: #if defined(PETSC_USE_CTABLE)
    2924:       PetscTableDestroy(&aij->colmap);
    2925: #else
    2926:       PetscFree(aij->colmap);
    2927:       /* A bit of a HACK: ideally we should deal with case aij->B all in one code block below. */
    2928:       if (aij->B) {
    2929:         PetscLogObjectMemory((PetscObject)C,-aij->B->cmap->n*sizeof(PetscInt));
    2930:       }
    2931: #endif
    2932:       ngcol = 0;
    2933:       if (aij->lvec) {
    2934:         VecGetSize(aij->lvec,&ngcol);
    2935:       }
    2936:       if (aij->garray) {
    2937:         PetscFree(aij->garray);
    2938:         PetscLogObjectMemory((PetscObject)C,-ngcol*sizeof(PetscInt));
    2939:       }
    2940:       VecDestroy(&aij->lvec);
    2941:       VecScatterDestroy(&aij->Mvctx);
    2942:     }
    2943:     if (aij->B && B && pattern == DIFFERENT_NONZERO_PATTERN) {
    2944:       MatDestroy(&aij->B);
    2945:     }
    2946:     if (aij->B && B && pattern == SUBSET_NONZERO_PATTERN) {
    2947:       MatZeroEntries(aij->B);
    2948:     }
    2949:   }
    2950:   Bdisassembled = PETSC_FALSE;
    2951:   if (!aij->B) {
    2952:     MatCreate(PETSC_COMM_SELF,&aij->B);
    2953:     PetscLogObjectParent((PetscObject)C,(PetscObject)aij->B);
    2954:     MatSetSizes(aij->B,C->rmap->n,C->cmap->N,C->rmap->n,C->cmap->N);
    2955:     MatSetBlockSizesFromMats(aij->B,B,B);
    2956:     MatSetType(aij->B,MATSEQAIJ);
    2957:     Bdisassembled = PETSC_TRUE;
    2958:   }
    2959:   if (B) {
    2960:     Baij = (Mat_SeqAIJ*)B->data;
    2961:     if (pattern == DIFFERENT_NONZERO_PATTERN) {
    2962:       PetscMalloc1(B->rmap->n,&nz);
    2963:       for (i=0; i<B->rmap->n; i++) {
    2964:         nz[i] = Baij->i[i+1] - Baij->i[i];
    2965:       }
    2966:       MatSeqAIJSetPreallocation(aij->B,0,nz);
    2967:       PetscFree(nz);
    2968:     }

    2970:     PetscLayoutGetRange(C->rmap,&rstart,&rend);
    2971:     shift = rend-rstart;
    2972:     count = 0;
    2973:     rowindices = NULL;
    2974:     colindices = NULL;
    2975:     if (rowemb) {
    2976:       ISGetIndices(rowemb,&rowindices);
    2977:     }
    2978:     if (ocolemb) {
    2979:       ISGetIndices(ocolemb,&colindices);
    2980:     }
    2981:     for (i=0; i<B->rmap->n; i++) {
    2982:       PetscInt row;
    2983:       row = i;
    2984:       if (rowindices) row = rowindices[i];
    2985:       for (j=Baij->i[i]; j<Baij->i[i+1]; j++) {
    2986:         col  = Baij->j[count];
    2987:         if (colindices) col = colindices[col];
    2988:         if (Bdisassembled && col>=rstart) col += shift;
    2989:         v    = Baij->a[count];
    2990:         MatSetValues(aij->B,1,&row,1,&col,&v,INSERT_VALUES);
    2991:         ++count;
    2992:       }
    2993:     }
    2994:     /* No assembly for aij->B is necessary. */
    2995:     /* FIXME: set aij->B's nonzerostate correctly. */
    2996:   } else {
    2997:     MatSetUp(aij->B);
    2998:   }
    2999:   C->preallocated  = PETSC_TRUE;
    3000:   C->was_assembled = PETSC_FALSE;
    3001:   C->assembled     = PETSC_FALSE;
    3002:    /*
    3003:       C will need to be assembled so that aij->B can be compressed into local form in MatSetUpMultiply_MPIAIJ().
    3004:       Furthermore, its nonzerostate will need to be based on that of aij->A's and aij->B's.
    3005:    */
    3006:   return 0;
    3007: }

    3009: /*
    3010:   B uses local indices with column indices ranging between 0 and N-n; they  must be interpreted using garray.
    3011:  */
    3012: PetscErrorCode MatGetSeqMats_MPIAIJ(Mat C,Mat *A,Mat *B)
    3013: {
    3014:   Mat_MPIAIJ *aij = (Mat_MPIAIJ*)C->data;

    3018:   /* FIXME: make sure C is assembled */
    3019:   *A = aij->A;
    3020:   *B = aij->B;
    3021:   /* Note that we don't incref *A and *B, so be careful! */
    3022:   return 0;
    3023: }

    3025: /*
    3026:   Extract MPI submatrices encoded by pairs of IS that may live on subcomms of C.
    3027:   NOT SCALABLE due to the use of ISGetNonlocalIS() (see below).
    3028: */
    3029: PetscErrorCode MatCreateSubMatricesMPI_MPIXAIJ(Mat C,PetscInt ismax,const IS isrow[],const IS iscol[],MatReuse scall,Mat *submat[],
    3030:                                                PetscErrorCode(*getsubmats_seq)(Mat,PetscInt,const IS[],const IS[],MatReuse,Mat**),
    3031:                                                PetscErrorCode(*getlocalmats)(Mat,Mat*,Mat*),
    3032:                                                PetscErrorCode(*setseqmat)(Mat,IS,IS,MatStructure,Mat),
    3033:                                                PetscErrorCode(*setseqmats)(Mat,IS,IS,IS,MatStructure,Mat,Mat))
    3034: {
    3035:   PetscMPIInt    size,flag;
    3036:   PetscInt       i,ii,cismax,ispar;
    3037:   Mat            *A,*B;
    3038:   IS             *isrow_p,*iscol_p,*cisrow,*ciscol,*ciscol_p;

    3040:   if (!ismax) return 0;

    3042:   for (i = 0, cismax = 0; i < ismax; ++i) {
    3043:     MPI_Comm_compare(((PetscObject)isrow[i])->comm,((PetscObject)iscol[i])->comm,&flag);
    3045:     MPI_Comm_size(((PetscObject)isrow[i])->comm, &size);
    3046:     if (size > 1) ++cismax;
    3047:   }

    3049:   /*
    3050:      If cismax is zero on all C's ranks, then and only then can we use purely sequential matrix extraction.
    3051:      ispar counts the number of parallel ISs across C's comm.
    3052:   */
    3053:   MPIU_Allreduce(&cismax,&ispar,1,MPIU_INT,MPI_MAX,PetscObjectComm((PetscObject)C));
    3054:   if (!ispar) { /* Sequential ISs only across C's comm, so can call the sequential matrix extraction subroutine. */
    3055:     (*getsubmats_seq)(C,ismax,isrow,iscol,scall,submat);
    3056:     return 0;
    3057:   }

    3059:   /* if (ispar) */
    3060:   /*
    3061:     Construct the "complements" -- the off-processor indices -- of the iscol ISs for parallel ISs only.
    3062:     These are used to extract the off-diag portion of the resulting parallel matrix.
    3063:     The row IS for the off-diag portion is the same as for the diag portion,
    3064:     so we merely alias (without increfing) the row IS, while skipping those that are sequential.
    3065:   */
    3066:   PetscMalloc2(cismax,&cisrow,cismax,&ciscol);
    3067:   PetscMalloc1(cismax,&ciscol_p);
    3068:   for (i = 0, ii = 0; i < ismax; ++i) {
    3069:     MPI_Comm_size(((PetscObject)isrow[i])->comm,&size);
    3070:     if (size > 1) {
    3071:       /*
    3072:          TODO: This is the part that's ***NOT SCALABLE***.
    3073:          To fix this we need to extract just the indices of C's nonzero columns
    3074:          that lie on the intersection of isrow[i] and ciscol[ii] -- the nonlocal
    3075:          part of iscol[i] -- without actually computing ciscol[ii]. This also has
    3076:          to be done without serializing on the IS list, so, most likely, it is best
    3077:          done by rewriting MatCreateSubMatrices_MPIAIJ() directly.
    3078:       */
    3079:       ISGetNonlocalIS(iscol[i],&(ciscol[ii]));
    3080:       /* Now we have to
    3081:          (a) make sure ciscol[ii] is sorted, since, even if the off-proc indices
    3082:              were sorted on each rank, concatenated they might no longer be sorted;
    3083:          (b) Use ISSortPermutation() to construct ciscol_p, the mapping from the
    3084:              indices in the nondecreasing order to the original index positions.
    3085:          If ciscol[ii] is strictly increasing, the permutation IS is NULL.
    3086:       */
    3087:       ISSortPermutation(ciscol[ii],PETSC_FALSE,ciscol_p+ii);
    3088:       ISSort(ciscol[ii]);
    3089:       ++ii;
    3090:     }
    3091:   }
    3092:   PetscMalloc2(ismax,&isrow_p,ismax,&iscol_p);
    3093:   for (i = 0, ii = 0; i < ismax; ++i) {
    3094:     PetscInt       j,issize;
    3095:     const PetscInt *indices;

    3097:     /*
    3098:        Permute the indices into a nondecreasing order. Reject row and col indices with duplicates.
    3099:      */
    3100:     ISSortPermutation(isrow[i],PETSC_FALSE,isrow_p+i);
    3101:     ISSort(isrow[i]);
    3102:     ISGetLocalSize(isrow[i],&issize);
    3103:     ISGetIndices(isrow[i],&indices);
    3104:     for (j = 1; j < issize; ++j) {
    3106:     }
    3107:     ISRestoreIndices(isrow[i],&indices);
    3108:     ISSortPermutation(iscol[i],PETSC_FALSE,iscol_p+i);
    3109:     ISSort(iscol[i]);
    3110:     ISGetLocalSize(iscol[i],&issize);
    3111:     ISGetIndices(iscol[i],&indices);
    3112:     for (j = 1; j < issize; ++j) {
    3114:     }
    3115:     ISRestoreIndices(iscol[i],&indices);
    3116:     MPI_Comm_size(((PetscObject)isrow[i])->comm,&size);
    3117:     if (size > 1) {
    3118:       cisrow[ii] = isrow[i];
    3119:       ++ii;
    3120:     }
    3121:   }
    3122:   /*
    3123:     Allocate the necessary arrays to hold the resulting parallel matrices as well as the intermediate
    3124:     array of sequential matrices underlying the resulting parallel matrices.
    3125:     Which arrays to allocate is based on the value of MatReuse scall and whether ISs are sorted and/or
    3126:     contain duplicates.

    3128:     There are as many diag matrices as there are original index sets. There are only as many parallel
    3129:     and off-diag matrices, as there are parallel (comm size > 1) index sets.

    3131:     ARRAYS that can hold Seq matrices get allocated in any event -- either here or by getsubmats_seq():
    3132:     - If the array of MPI matrices already exists and is being reused, we need to allocate the array
    3133:       and extract the underlying seq matrices into it to serve as placeholders, into which getsubmats_seq
    3134:       will deposite the extracted diag and off-diag parts. Thus, we allocate the A&B arrays and fill them
    3135:       with A[i] and B[ii] extracted from the corresponding MPI submat.
    3136:     - However, if the rows, A's column indices or B's column indices are not sorted, the extracted A[i] & B[ii]
    3137:       will have a different order from what getsubmats_seq expects.  To handle this case -- indicated
    3138:       by a nonzero isrow_p[i], iscol_p[i], or ciscol_p[ii] -- we duplicate A[i] --> AA[i], B[ii] --> BB[ii]
    3139:       (retrieve composed AA[i] or BB[ii]) and reuse them here. AA[i] and BB[ii] are then used to permute its
    3140:       values into A[i] and B[ii] sitting inside the corresponding submat.
    3141:     - If no reuse is taking place then getsubmats_seq will allocate the A&B arrays and create the corresponding
    3142:       A[i], B[ii], AA[i] or BB[ii] matrices.
    3143:   */
    3144:   /* Parallel matrix array is allocated here only if no reuse is taking place. If reused, it is passed in by the caller. */
    3145:   if (scall == MAT_INITIAL_MATRIX) {
    3146:     PetscMalloc1(ismax,submat);
    3147:   }

    3149:   /* Now obtain the sequential A and B submatrices separately. */
    3150:   /* scall=MAT_REUSE_MATRIX is not handled yet, because getsubmats_seq() requires reuse of A and B */
    3151:   (*getsubmats_seq)(C,ismax,isrow,iscol,MAT_INITIAL_MATRIX,&A);
    3152:   (*getsubmats_seq)(C,cismax,cisrow,ciscol,MAT_INITIAL_MATRIX,&B);

    3154:   /*
    3155:     If scall == MAT_REUSE_MATRIX AND the permutations are NULL, we are done, since the sequential
    3156:     matrices A & B have been extracted directly into the parallel matrices containing them, or
    3157:     simply into the sequential matrix identical with the corresponding A (if size == 1).
    3158:     Note that in that case colmap doesn't need to be rebuilt, since the matrices are expected
    3159:     to have the same sparsity pattern.
    3160:     Otherwise, A and/or B have to be properly embedded into C's index spaces and the correct colmap
    3161:     must be constructed for C. This is done by setseqmat(s).
    3162:   */
    3163:   for (i = 0, ii = 0; i < ismax; ++i) {
    3164:     /*
    3165:        TODO: cache ciscol, permutation ISs and maybe cisrow? What about isrow & iscol?
    3166:        That way we can avoid sorting and computing permutations when reusing.
    3167:        To this end:
    3168:         - remove the old cache, if it exists, when extracting submatrices with MAT_INITIAL_MATRIX
    3169:         - if caching arrays to hold the ISs, make and compose a container for them so that it can
    3170:           be destroyed upon destruction of C (use PetscContainerUserDestroy() to clear out the contents).
    3171:     */
    3172:     MatStructure pattern = DIFFERENT_NONZERO_PATTERN;

    3174:     MPI_Comm_size(((PetscObject)isrow[i])->comm,&size);
    3175:     /* Construct submat[i] from the Seq pieces A (and B, if necessary). */
    3176:     if (size > 1) {
    3177:       if (scall == MAT_INITIAL_MATRIX) {
    3178:         MatCreate(((PetscObject)isrow[i])->comm,(*submat)+i);
    3179:         MatSetSizes((*submat)[i],A[i]->rmap->n,A[i]->cmap->n,PETSC_DETERMINE,PETSC_DETERMINE);
    3180:         MatSetType((*submat)[i],MATMPIAIJ);
    3181:         PetscLayoutSetUp((*submat)[i]->rmap);
    3182:         PetscLayoutSetUp((*submat)[i]->cmap);
    3183:       }
    3184:       /*
    3185:         For each parallel isrow[i], insert the extracted sequential matrices into the parallel matrix.
    3186:       */
    3187:       {
    3188:         Mat AA = A[i],BB = B[ii];

    3190:         if (AA || BB) {
    3191:           setseqmats((*submat)[i],isrow_p[i],iscol_p[i],ciscol_p[ii],pattern,AA,BB);
    3192:           MatAssemblyBegin((*submat)[i],MAT_FINAL_ASSEMBLY);
    3193:           MatAssemblyEnd((*submat)[i],MAT_FINAL_ASSEMBLY);
    3194:         }
    3195:         MatDestroy(&AA);
    3196:       }
    3197:       ISDestroy(ciscol+ii);
    3198:       ISDestroy(ciscol_p+ii);
    3199:       ++ii;
    3200:     } else { /* if (size == 1) */
    3201:       if (scall == MAT_REUSE_MATRIX) {
    3202:         MatDestroy(&(*submat)[i]);
    3203:       }
    3204:       if (isrow_p[i] || iscol_p[i]) {
    3205:         MatDuplicate(A[i],MAT_DO_NOT_COPY_VALUES,(*submat)+i);
    3206:         setseqmat((*submat)[i],isrow_p[i],iscol_p[i],pattern,A[i]);
    3207:         /* Otherwise A is extracted straight into (*submats)[i]. */
    3208:         /* TODO: Compose A[i] on (*submat([i] for future use, if ((isrow_p[i] || iscol_p[i]) && MAT_INITIAL_MATRIX). */
    3209:         MatDestroy(A+i);
    3210:       } else (*submat)[i] = A[i];
    3211:     }
    3212:     ISDestroy(&isrow_p[i]);
    3213:     ISDestroy(&iscol_p[i]);
    3214:   }
    3215:   PetscFree2(cisrow,ciscol);
    3216:   PetscFree2(isrow_p,iscol_p);
    3217:   PetscFree(ciscol_p);
    3218:   PetscFree(A);
    3219:   MatDestroySubMatrices(cismax,&B);
    3220:   return 0;
    3221: }

    3223: PetscErrorCode MatCreateSubMatricesMPI_MPIAIJ(Mat C,PetscInt ismax,const IS isrow[],const IS iscol[],MatReuse scall,Mat *submat[])
    3224: {
    3225:   MatCreateSubMatricesMPI_MPIXAIJ(C,ismax,isrow,iscol,scall,submat,MatCreateSubMatrices_MPIAIJ,MatGetSeqMats_MPIAIJ,MatSetSeqMat_SeqAIJ,MatSetSeqMats_MPIAIJ);
    3226:   return 0;
    3227: }