Date: 2022-03-04T17:37:46+00:00

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: {
     24:   PetscInt       i;

     27:   if (ov < 0) SETERRQ(PetscObjectComm((PetscObject)C),PETSC_ERR_ARG_OUTOFRANGE,"Negative overlap specified");
     28:   for (i=0; i<ov; ++i) {
     29:     MatIncreaseOverlap_MPIAIJ_Once(C,imax,is);
     30:   }
     31:   return(0);
     32: }

     34: PetscErrorCode MatIncreaseOverlap_MPIAIJ_Scalable(Mat C,PetscInt imax,IS is[],PetscInt ov)
     35: {
     37:   PetscInt       i;

     40:   if (ov < 0) SETERRQ(PetscObjectComm((PetscObject)C),PETSC_ERR_ARG_OUTOFRANGE,"Negative overlap specified");
     41:   for (i=0; i<ov; ++i) {
     42:     MatIncreaseOverlap_MPIAIJ_Once_Scalable(C,imax,is);
     43:   }
     44:   return(0);
     45: }

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

     61:   PetscObjectGetComm((PetscObject)mat,&comm);
     62:   MPI_Comm_rank(comm,&rank);
     63:   MPI_Comm_size(comm,&size);
     64:   /* get row map to determine where rows should be going */
     65:   MatGetLayouts(mat,&rmap,NULL);
     66:   /* retrieve IS data and put all together so that we
     67:    * can optimize communication
     68:    *  */
     69:   PetscMalloc2(nidx,(PetscInt ***)&indices,nidx,&length);
     70:   for (i=0,tlength=0; i<nidx; i++) {
     71:     ISGetLocalSize(is[i],&length[i]);
     72:     tlength += length[i];
     73:     ISGetIndices(is[i],&indices[i]);
     74:   }
     75:   /* find these rows on remote processors */
     76:   PetscCalloc3(tlength,&remoterows,tlength,&rrow_ranks,tlength,&rrow_isids);
     77:   PetscCalloc3(size,&toranks,2*size,&tosizes,size,&tosizes_temp);
     78:   nrrows = 0;
     79:   for (i=0; i<nidx; i++) {
     80:     length_i  = length[i];
     81:     indices_i = indices[i];
     82:     for (j=0; j<length_i; j++) {
     83:       owner = -1;
     84:       PetscLayoutFindOwner(rmap,indices_i[j],&owner);
     85:       /* remote processors */
     86:       if (owner != rank) {
     87:         tosizes_temp[owner]++; /* number of rows to owner */
     88:         rrow_ranks[nrrows]  = owner; /* processor */
     89:         rrow_isids[nrrows]   = i; /* is id */
     90:         remoterows[nrrows++] = indices_i[j]; /* row */
     91:       }
     92:     }
     93:     ISRestoreIndices(is[i],&indices[i]);
     94:   }
     95:   PetscFree2(*(PetscInt***)&indices,length);
     96:   /* test if we need to exchange messages
     97:    * generally speaking, we do not need to exchange
     98:    * data when overlap is 1
     99:    * */
    100:   MPIU_Allreduce(&nrrows,&reducednrrows,1,MPIU_INT,MPIU_MAX,comm);
    101:   /* we do not have any messages
    102:    * It usually corresponds to overlap 1
    103:    * */
    104:   if (!reducednrrows) {
    105:     PetscFree3(toranks,tosizes,tosizes_temp);
    106:     PetscFree3(remoterows,rrow_ranks,rrow_isids);
    107:     MatIncreaseOverlap_MPIAIJ_Local_Scalable(mat,nidx,is);
    108:     return(0);
    109:   }
    110:   nto = 0;
    111:   /* send sizes and ranks for building a two-sided communcation */
    112:   for (i=0; i<size; i++) {
    113:     if (tosizes_temp[i]) {
    114:       tosizes[nto*2]  = tosizes_temp[i]*2; /* size */
    115:       tosizes_temp[i] = nto; /* a map from processor to index */
    116:       toranks[nto++]  = i; /* processor */
    117:     }
    118:   }
    119:   PetscMalloc1(nto+1,&toffsets);
    120:   toffsets[0] = 0;
    121:   for (i=0; i<nto; i++) {
    122:     toffsets[i+1]  = toffsets[i]+tosizes[2*i]; /* offsets */
    123:     tosizes[2*i+1] = toffsets[i]; /* offsets to send */
    124:   }
    125:   /* send information to other processors */
    126:   PetscCommBuildTwoSided(comm,2,MPIU_INT,nto,toranks,tosizes,&nfrom,&fromranks,&fromsizes);
    127:   nrecvrows = 0;
    128:   for (i=0; i<nfrom; i++) nrecvrows += fromsizes[2*i];
    129:   PetscMalloc1(nrecvrows,&remote);
    130:   nrecvrows = 0;
    131:   for (i=0; i<nfrom; i++) {
    132:     for (j=0; j<fromsizes[2*i]; j++) {
    133:       remote[nrecvrows].rank    = fromranks[i];
    134:       remote[nrecvrows++].index = fromsizes[2*i+1]+j;
    135:     }
    136:   }
    137:   PetscSFCreate(comm,&sf);
    138:   PetscSFSetGraph(sf,nrecvrows,nrecvrows,NULL,PETSC_OWN_POINTER,remote,PETSC_OWN_POINTER);
    139:   /* use two-sided communication by default since OPENMPI has some bugs for one-sided one */
    140:   PetscSFSetType(sf,PETSCSFBASIC);
    141:   PetscSFSetFromOptions(sf);
    142:   /* message pair <no of is, row>  */
    143:   PetscCalloc2(2*nrrows,&todata,nrecvrows,&fromdata);
    144:   for (i=0; i<nrrows; i++) {
    145:     owner = rrow_ranks[i]; /* processor */
    146:     j     = tosizes_temp[owner]; /* index */
    147:     todata[toffsets[j]++] = rrow_isids[i];
    148:     todata[toffsets[j]++] = remoterows[i];
    149:   }
    150:   PetscFree3(toranks,tosizes,tosizes_temp);
    151:   PetscFree3(remoterows,rrow_ranks,rrow_isids);
    152:   PetscFree(toffsets);
    153:   PetscSFBcastBegin(sf,MPIU_INT,todata,fromdata,MPI_REPLACE);
    154:   PetscSFBcastEnd(sf,MPIU_INT,todata,fromdata,MPI_REPLACE);
    155:   PetscSFDestroy(&sf);
    156:   /* send rows belonging to the remote so that then we could get the overlapping data back */
    157:   MatIncreaseOverlap_MPIAIJ_Send_Scalable(mat,nidx,nfrom,fromranks,fromsizes,fromdata,&sbsizes,&sbdata);
    158:   PetscFree2(todata,fromdata);
    159:   PetscFree(fromsizes);
    160:   PetscCommBuildTwoSided(comm,2,MPIU_INT,nfrom,fromranks,sbsizes,&nto,&toranks,&tosizes);
    161:   PetscFree(fromranks);
    162:   nrecvrows = 0;
    163:   for (i=0; i<nto; i++) nrecvrows += tosizes[2*i];
    164:   PetscCalloc1(nrecvrows,&todata);
    165:   PetscMalloc1(nrecvrows,&remote);
    166:   nrecvrows = 0;
    167:   for (i=0; i<nto; i++) {
    168:     for (j=0; j<tosizes[2*i]; j++) {
    169:       remote[nrecvrows].rank    = toranks[i];
    170:       remote[nrecvrows++].index = tosizes[2*i+1]+j;
    171:     }
    172:   }
    173:   PetscSFCreate(comm,&sf);
    174:   PetscSFSetGraph(sf,nrecvrows,nrecvrows,NULL,PETSC_OWN_POINTER,remote,PETSC_OWN_POINTER);
    175:   /* use two-sided communication by default since OPENMPI has some bugs for one-sided one */
    176:   PetscSFSetType(sf,PETSCSFBASIC);
    177:   PetscSFSetFromOptions(sf);
    178:   /* overlap communication and computation */
    179:   PetscSFBcastBegin(sf,MPIU_INT,sbdata,todata,MPI_REPLACE);
    180:   MatIncreaseOverlap_MPIAIJ_Local_Scalable(mat,nidx,is);
    181:   PetscSFBcastEnd(sf,MPIU_INT,sbdata,todata,MPI_REPLACE);
    182:   PetscSFDestroy(&sf);
    183:   PetscFree2(sbdata,sbsizes);
    184:   MatIncreaseOverlap_MPIAIJ_Receive_Scalable(mat,nidx,is,nrecvrows,todata);
    185:   PetscFree(toranks);
    186:   PetscFree(tosizes);
    187:   PetscFree(todata);
    188:   return(0);
    189: }

    191: static PetscErrorCode MatIncreaseOverlap_MPIAIJ_Receive_Scalable(Mat mat,PetscInt nidx, IS is[], PetscInt nrecvs, PetscInt *recvdata)
    192: {
    193:   PetscInt         *isz,isz_i,i,j,is_id, data_size;
    194:   PetscInt          col,lsize,max_lsize,*indices_temp, *indices_i;
    195:   const PetscInt   *indices_i_temp;
    196:   MPI_Comm         *iscomms;
    197:   PetscErrorCode    ierr;

    200:   max_lsize = 0;
    201:   PetscMalloc1(nidx,&isz);
    202:   for (i=0; i<nidx; i++) {
    203:     ISGetLocalSize(is[i],&lsize);
    204:     max_lsize = lsize>max_lsize ? lsize:max_lsize;
    205:     isz[i]    = lsize;
    206:   }
    207:   PetscMalloc2((max_lsize+nrecvs)*nidx,&indices_temp,nidx,&iscomms);
    208:   for (i=0; i<nidx; i++) {
    209:     PetscCommDuplicate(PetscObjectComm((PetscObject)is[i]),&iscomms[i],NULL);
    210:     ISGetIndices(is[i],&indices_i_temp);
    211:     PetscArraycpy(indices_temp+i*(max_lsize+nrecvs),indices_i_temp, isz[i]);
    212:     ISRestoreIndices(is[i],&indices_i_temp);
    213:     ISDestroy(&is[i]);
    214:   }
    215:   /* retrieve information to get row id and its overlap */
    216:   for (i=0; i<nrecvs;) {
    217:     is_id     = recvdata[i++];
    218:     data_size = recvdata[i++];
    219:     indices_i = indices_temp+(max_lsize+nrecvs)*is_id;
    220:     isz_i     = isz[is_id];
    221:     for (j=0; j< data_size; j++) {
    222:       col = recvdata[i++];
    223:       indices_i[isz_i++] = col;
    224:     }
    225:     isz[is_id] = isz_i;
    226:   }
    227:   /* remove duplicate entities */
    228:   for (i=0; i<nidx; i++) {
    229:     indices_i = indices_temp+(max_lsize+nrecvs)*i;
    230:     isz_i     = isz[i];
    231:     PetscSortRemoveDupsInt(&isz_i,indices_i);
    232:     ISCreateGeneral(iscomms[i],isz_i,indices_i,PETSC_COPY_VALUES,&is[i]);
    233:     PetscCommDestroy(&iscomms[i]);
    234:   }
    235:   PetscFree(isz);
    236:   PetscFree2(indices_temp,iscomms);
    237:   return(0);
    238: }

    240: static PetscErrorCode MatIncreaseOverlap_MPIAIJ_Send_Scalable(Mat mat,PetscInt nidx, PetscMPIInt nfrom,PetscMPIInt *fromranks,PetscInt *fromsizes, PetscInt *fromrows, PetscInt **sbrowsizes, PetscInt **sbrows)
    241: {
    242:   PetscLayout       rmap,cmap;
    243:   PetscInt          i,j,k,l,*rows_i,*rows_data_ptr,**rows_data,max_fszs,rows_pos,*rows_pos_i;
    244:   PetscInt          is_id,tnz,an,bn,rstart,cstart,row,start,end,col,totalrows,*sbdata;
    245:   PetscInt         *indv_counts,indvc_ij,*sbsizes,*indices_tmp,*offsets;
    246:   const PetscInt   *gcols,*ai,*aj,*bi,*bj;
    247:   Mat               amat,bmat;
    248:   PetscMPIInt       rank;
    249:   PetscBool         done;
    250:   MPI_Comm          comm;
    251:   PetscErrorCode    ierr;

    254:   PetscObjectGetComm((PetscObject)mat,&comm);
    255:   MPI_Comm_rank(comm,&rank);
    256:   MatMPIAIJGetSeqAIJ(mat,&amat,&bmat,&gcols);
    257:   /* Even if the mat is symmetric, we still assume it is not symmetric */
    258:   MatGetRowIJ(amat,0,PETSC_FALSE,PETSC_FALSE,&an,&ai,&aj,&done);
    259:   if (!done) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONGSTATE,"can not get row IJ \n");
    260:   MatGetRowIJ(bmat,0,PETSC_FALSE,PETSC_FALSE,&bn,&bi,&bj,&done);
    261:   if (!done) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONGSTATE,"can not get row IJ \n");
    262:   /* total number of nonzero values is used to estimate the memory usage in the next step */
    263:   tnz  = ai[an]+bi[bn];
    264:   MatGetLayouts(mat,&rmap,&cmap);
    265:   PetscLayoutGetRange(rmap,&rstart,NULL);
    266:   PetscLayoutGetRange(cmap,&cstart,NULL);
    267:   /* to find the longest message */
    268:   max_fszs = 0;
    269:   for (i=0; i<nfrom; i++) max_fszs = fromsizes[2*i]>max_fszs ? fromsizes[2*i]:max_fszs;
    270:   /* better way to estimate number of nonzero in the mat??? */
    271:   PetscCalloc5(max_fszs*nidx,&rows_data_ptr,nidx,&rows_data,nidx,&rows_pos_i,nfrom*nidx,&indv_counts,tnz,&indices_tmp);
    272:   for (i=0; i<nidx; i++) rows_data[i] = rows_data_ptr+max_fszs*i;
    273:   rows_pos  = 0;
    274:   totalrows = 0;
    275:   for (i=0; i<nfrom; i++) {
    276:     PetscArrayzero(rows_pos_i,nidx);
    277:     /* group data together */
    278:     for (j=0; j<fromsizes[2*i]; j+=2) {
    279:       is_id                       = fromrows[rows_pos++];/* no of is */
    280:       rows_i                      = rows_data[is_id];
    281:       rows_i[rows_pos_i[is_id]++] = fromrows[rows_pos++];/* row */
    282:     }
    283:     /* estimate a space to avoid multiple allocations  */
    284:     for (j=0; j<nidx; j++) {
    285:       indvc_ij = 0;
    286:       rows_i   = rows_data[j];
    287:       for (l=0; l<rows_pos_i[j]; l++) {
    288:         row    = rows_i[l]-rstart;
    289:         start  = ai[row];
    290:         end    = ai[row+1];
    291:         for (k=start; k<end; k++) { /* Amat */
    292:           col = aj[k] + cstart;
    293:           indices_tmp[indvc_ij++] = col;/* do not count the rows from the original rank */
    294:         }
    295:         start = bi[row];
    296:         end   = bi[row+1];
    297:         for (k=start; k<end; k++) { /* Bmat */
    298:           col = gcols[bj[k]];
    299:           indices_tmp[indvc_ij++] = col;
    300:         }
    301:       }
    302:       PetscSortRemoveDupsInt(&indvc_ij,indices_tmp);
    303:       indv_counts[i*nidx+j] = indvc_ij;
    304:       totalrows            += indvc_ij;
    305:     }
    306:   }
    307:   /* message triple <no of is, number of rows, rows> */
    308:   PetscCalloc2(totalrows+nidx*nfrom*2,&sbdata,2*nfrom,&sbsizes);
    309:   totalrows = 0;
    310:   rows_pos  = 0;
    311:   /* use this code again */
    312:   for (i=0;i<nfrom;i++) {
    313:     PetscArrayzero(rows_pos_i,nidx);
    314:     for (j=0; j<fromsizes[2*i]; j+=2) {
    315:       is_id                       = fromrows[rows_pos++];
    316:       rows_i                      = rows_data[is_id];
    317:       rows_i[rows_pos_i[is_id]++] = fromrows[rows_pos++];
    318:     }
    319:     /* add data  */
    320:     for (j=0; j<nidx; j++) {
    321:       if (!indv_counts[i*nidx+j]) continue;
    322:       indvc_ij = 0;
    323:       sbdata[totalrows++] = j;
    324:       sbdata[totalrows++] = indv_counts[i*nidx+j];
    325:       sbsizes[2*i]       += 2;
    326:       rows_i              = rows_data[j];
    327:       for (l=0; l<rows_pos_i[j]; l++) {
    328:         row   = rows_i[l]-rstart;
    329:         start = ai[row];
    330:         end   = ai[row+1];
    331:         for (k=start; k<end; k++) { /* Amat */
    332:           col = aj[k] + cstart;
    333:           indices_tmp[indvc_ij++] = col;
    334:         }
    335:         start = bi[row];
    336:         end   = bi[row+1];
    337:         for (k=start; k<end; k++) { /* Bmat */
    338:           col = gcols[bj[k]];
    339:           indices_tmp[indvc_ij++] = col;
    340:         }
    341:       }
    342:       PetscSortRemoveDupsInt(&indvc_ij,indices_tmp);
    343:       sbsizes[2*i]  += indvc_ij;
    344:       PetscArraycpy(sbdata+totalrows,indices_tmp,indvc_ij);
    345:       totalrows += indvc_ij;
    346:     }
    347:   }
    348:   PetscMalloc1(nfrom+1,&offsets);
    349:   offsets[0] = 0;
    350:   for (i=0; i<nfrom; i++) {
    351:     offsets[i+1]   = offsets[i] + sbsizes[2*i];
    352:     sbsizes[2*i+1] = offsets[i];
    353:   }
    354:   PetscFree(offsets);
    355:   if (sbrowsizes) *sbrowsizes = sbsizes;
    356:   if (sbrows) *sbrows = sbdata;
    357:   PetscFree5(rows_data_ptr,rows_data,rows_pos_i,indv_counts,indices_tmp);
    358:   MatRestoreRowIJ(amat,0,PETSC_FALSE,PETSC_FALSE,&an,&ai,&aj,&done);
    359:   MatRestoreRowIJ(bmat,0,PETSC_FALSE,PETSC_FALSE,&bn,&bi,&bj,&done);
    360:   return(0);
    361: }

    363: static PetscErrorCode MatIncreaseOverlap_MPIAIJ_Local_Scalable(Mat mat,PetscInt nidx, IS is[])
    364: {
    365:   const PetscInt   *gcols,*ai,*aj,*bi,*bj, *indices;
    366:   PetscInt          tnz,an,bn,i,j,row,start,end,rstart,cstart,col,k,*indices_temp;
    367:   PetscInt          lsize,lsize_tmp;
    368:   PetscMPIInt       rank,owner;
    369:   Mat               amat,bmat;
    370:   PetscBool         done;
    371:   PetscLayout       cmap,rmap;
    372:   MPI_Comm          comm;
    373:   PetscErrorCode    ierr;

    376:   PetscObjectGetComm((PetscObject)mat,&comm);
    377:   MPI_Comm_rank(comm,&rank);
    378:   MatMPIAIJGetSeqAIJ(mat,&amat,&bmat,&gcols);
    379:   MatGetRowIJ(amat,0,PETSC_FALSE,PETSC_FALSE,&an,&ai,&aj,&done);
    380:   if (!done) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONGSTATE,"can not get row IJ \n");
    381:   MatGetRowIJ(bmat,0,PETSC_FALSE,PETSC_FALSE,&bn,&bi,&bj,&done);
    382:   if (!done) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONGSTATE,"can not get row IJ \n");
    383:   /* is it a safe way to compute number of nonzero values ? */
    384:   tnz  = ai[an]+bi[bn];
    385:   MatGetLayouts(mat,&rmap,&cmap);
    386:   PetscLayoutGetRange(rmap,&rstart,NULL);
    387:   PetscLayoutGetRange(cmap,&cstart,NULL);
    388:   /* it is a better way to estimate memory than the old implementation
    389:    * where global size of matrix is used
    390:    * */
    391:   PetscMalloc1(tnz,&indices_temp);
    392:   for (i=0; i<nidx; i++) {
    393:     MPI_Comm iscomm;

    395:     ISGetLocalSize(is[i],&lsize);
    396:     ISGetIndices(is[i],&indices);
    397:     lsize_tmp = 0;
    398:     for (j=0; j<lsize; j++) {
    399:       owner = -1;
    400:       row   = indices[j];
    401:       PetscLayoutFindOwner(rmap,row,&owner);
    402:       if (owner != rank) continue;
    403:       /* local number */
    404:       row  -= rstart;
    405:       start = ai[row];
    406:       end   = ai[row+1];
    407:       for (k=start; k<end; k++) { /* Amat */
    408:         col = aj[k] + cstart;
    409:         indices_temp[lsize_tmp++] = col;
    410:       }
    411:       start = bi[row];
    412:       end   = bi[row+1];
    413:       for (k=start; k<end; k++) { /* Bmat */
    414:         col = gcols[bj[k]];
    415:         indices_temp[lsize_tmp++] = col;
    416:       }
    417:     }
    418:    ISRestoreIndices(is[i],&indices);
    419:    PetscCommDuplicate(PetscObjectComm((PetscObject)is[i]),&iscomm,NULL);
    420:    ISDestroy(&is[i]);
    421:    PetscSortRemoveDupsInt(&lsize_tmp,indices_temp);
    422:    ISCreateGeneral(iscomm,lsize_tmp,indices_temp,PETSC_COPY_VALUES,&is[i]);
    423:    PetscCommDestroy(&iscomm);
    424:   }
    425:   PetscFree(indices_temp);
    426:   MatRestoreRowIJ(amat,0,PETSC_FALSE,PETSC_FALSE,&an,&ai,&aj,&done);
    427:   MatRestoreRowIJ(bmat,0,PETSC_FALSE,PETSC_FALSE,&bn,&bi,&bj,&done);
    428:   return(0);
    429: }

    431: /*
    432:   Sample message format:
    433:   If a processor A wants processor B to process some elements corresponding
    434:   to index sets is[1],is[5]
    435:   mesg [0] = 2   (no of index sets in the mesg)
    436:   -----------
    437:   mesg [1] = 1 => is[1]
    438:   mesg [2] = sizeof(is[1]);
    439:   -----------
    440:   mesg [3] = 5  => is[5]
    441:   mesg [4] = sizeof(is[5]);
    442:   -----------
    443:   mesg [5]
    444:   mesg [n]  datas[1]
    445:   -----------
    446:   mesg[n+1]
    447:   mesg[m]  data(is[5])
    448:   -----------

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

    478:   PetscObjectGetComm((PetscObject)C,&comm);
    479:   size = c->size;
    480:   rank = c->rank;
    481:   M    = C->rmap->N;

    483:   PetscObjectGetNewTag((PetscObject)C,&tag1);
    484:   PetscObjectGetNewTag((PetscObject)C,&tag2);

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

    488:   for (i=0; i<imax; i++) {
    489:     ISGetIndices(is[i],&idx[i]);
    490:     ISGetLocalSize(is[i],&n[i]);
    491:   }

    493:   /* evaluate communication - mesg to who,length of mesg, and buffer space
    494:      required. Based on this, buffers are allocated, and data copied into them  */
    495:   PetscCalloc4(size,&w1,size,&w2,size,&w3,size,&w4);
    496:   for (i=0; i<imax; i++) {
    497:     PetscArrayzero(w4,size); /* initialise work vector*/
    498:     idx_i = idx[i];
    499:     len   = n[i];
    500:     for (j=0; j<len; j++) {
    501:       row = idx_i[j];
    502:       if (row < 0) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Index set cannot have negative entries");
    503:       PetscLayoutFindOwner(C->rmap,row,&proc);
    504:       w4[proc]++;
    505:     }
    506:     for (j=0; j<size; j++) {
    507:       if (w4[j]) { w1[j] += w4[j]; w3[j]++;}
    508:     }
    509:   }

    511:   nrqs     = 0;              /* no of outgoing messages */
    512:   msz      = 0;              /* total mesg length (for all proc */
    513:   w1[rank] = 0;              /* no mesg sent to intself */
    514:   w3[rank] = 0;
    515:   for (i=0; i<size; i++) {
    516:     if (w1[i])  {w2[i] = 1; nrqs++;} /* there exists a message to proc i */
    517:   }
    518:   /* pa - is list of processors to communicate with */
    519:   PetscMalloc1(nrqs,&pa);
    520:   for (i=0,j=0; i<size; i++) {
    521:     if (w1[i]) {pa[j] = i; j++;}
    522:   }

    524:   /* Each message would have a header = 1 + 2*(no of IS) + data */
    525:   for (i=0; i<nrqs; i++) {
    526:     j      = pa[i];
    527:     w1[j] += w2[j] + 2*w3[j];
    528:     msz   += w1[j];
    529:   }

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

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

    538:   /* Allocate Memory for outgoing messages */
    539:   PetscMalloc4(size,&outdat,size,&ptr,msz,&tmp,size,&ctr);
    540:   PetscArrayzero(outdat,size);
    541:   PetscArrayzero(ptr,size);

    543:   {
    544:     PetscInt *iptr = tmp,ict  = 0;
    545:     for (i=0; i<nrqs; i++) {
    546:       j         = pa[i];
    547:       iptr     +=  ict;
    548:       outdat[j] = iptr;
    549:       ict       = w1[j];
    550:     }
    551:   }

    553:   /* Form the outgoing messages */
    554:   /* plug in the headers */
    555:   for (i=0; i<nrqs; i++) {
    556:     j            = pa[i];
    557:     outdat[j][0] = 0;
    558:     PetscArrayzero(outdat[j]+1,2*w3[j]);
    559:     ptr[j]       = outdat[j] + 2*w3[j] + 1;
    560:   }

    562:   /* Memory for doing local proc's work */
    563:   {
    564:     PetscInt M_BPB_imax = 0;
    565: #if defined(PETSC_USE_CTABLE)
    566:     PetscIntMultError((M/PETSC_BITS_PER_BYTE+1),imax, &M_BPB_imax);
    567:     PetscMalloc1(imax,&table_data);
    568:     for (i=0; i<imax; i++) {
    569:       PetscTableCreate(n[i],M,&table_data[i]);
    570:     }
    571:     PetscCalloc4(imax,&table, imax,&data, imax,&isz, M_BPB_imax,&t_p);
    572:     for (i=0; i<imax; i++) {
    573:       table[i] = t_p + (M/PETSC_BITS_PER_BYTE+1)*i;
    574:     }
    575: #else
    576:     PetscInt Mimax = 0;
    577:     PetscIntMultError(M,imax, &Mimax);
    578:     PetscIntMultError((M/PETSC_BITS_PER_BYTE+1),imax, &M_BPB_imax);
    579:     PetscCalloc5(imax,&table, imax,&data, imax,&isz, Mimax,&d_p, M_BPB_imax,&t_p);
    580:     for (i=0; i<imax; i++) {
    581:       table[i] = t_p + (M/PETSC_BITS_PER_BYTE+1)*i;
    582:       data[i]  = d_p + M*i;
    583:     }
    584: #endif
    585:   }

    587:   /* Parse the IS and update local tables and the outgoing buf with the data */
    588:   {
    589:     PetscInt n_i,isz_i,*outdat_j,ctr_j;
    590:     PetscBT  table_i;

    592:     for (i=0; i<imax; i++) {
    593:       PetscArrayzero(ctr,size);
    594:       n_i     = n[i];
    595:       table_i = table[i];
    596:       idx_i   = idx[i];
    597: #if defined(PETSC_USE_CTABLE)
    598:       table_data_i = table_data[i];
    599: #else
    600:       data_i  = data[i];
    601: #endif
    602:       isz_i   = isz[i];
    603:       for (j=0; j<n_i; j++) {   /* parse the indices of each IS */
    604:         row  = idx_i[j];
    605:         PetscLayoutFindOwner(C->rmap,row,&proc);
    606:         if (proc != rank) { /* copy to the outgoing buffer */
    607:           ctr[proc]++;
    608:           *ptr[proc] = row;
    609:           ptr[proc]++;
    610:         } else if (!PetscBTLookupSet(table_i,row)) {
    611: #if defined(PETSC_USE_CTABLE)
    612:           PetscTableAdd(table_data_i,row+1,isz_i+1,INSERT_VALUES);
    613: #else
    614:           data_i[isz_i] = row; /* Update the local table */
    615: #endif
    616:           isz_i++;
    617:         }
    618:       }
    619:       /* Update the headers for the current IS */
    620:       for (j=0; j<size; j++) { /* Can Optimise this loop by using pa[] */
    621:         if ((ctr_j = ctr[j])) {
    622:           outdat_j        = outdat[j];
    623:           k               = ++outdat_j[0];
    624:           outdat_j[2*k]   = ctr_j;
    625:           outdat_j[2*k-1] = i;
    626:         }
    627:       }
    628:       isz[i] = isz_i;
    629:     }
    630:   }

    632:   /*  Now  post the sends */
    633:   PetscMalloc1(nrqs,&s_waits1);
    634:   for (i=0; i<nrqs; ++i) {
    635:     j    = pa[i];
    636:     MPI_Isend(outdat[j],w1[j],MPIU_INT,j,tag1,comm,s_waits1+i);
    637:   }

    639:   /* No longer need the original indices */
    640:   PetscMalloc1(imax,&iscomms);
    641:   for (i=0; i<imax; ++i) {
    642:     ISRestoreIndices(is[i],idx+i);
    643:     PetscCommDuplicate(PetscObjectComm((PetscObject)is[i]),&iscomms[i],NULL);
    644:   }
    645:   PetscFree2(*(PetscInt***)&idx,n);

    647:   for (i=0; i<imax; ++i) {
    648:     ISDestroy(&is[i]);
    649:   }

    651:   /* Do Local work */
    652: #if defined(PETSC_USE_CTABLE)
    653:   MatIncreaseOverlap_MPIAIJ_Local(C,imax,table,isz,NULL,table_data);
    654: #else
    655:   MatIncreaseOverlap_MPIAIJ_Local(C,imax,table,isz,data,NULL);
    656: #endif

    658:   /* Receive messages */
    659:   PetscMalloc1(nrqr,&recv_status);
    660:   MPI_Waitall(nrqr,r_waits1,recv_status);
    661:   MPI_Waitall(nrqs,s_waits1,MPI_STATUSES_IGNORE);

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

    667:   PetscMalloc1(nrqr,&xdata);
    668:   PetscMalloc1(nrqr,&isz1);
    669:   MatIncreaseOverlap_MPIAIJ_Receive(C,nrqr,rbuf,xdata,isz1);
    670:   PetscFree(rbuf[0]);
    671:   PetscFree(rbuf);

    673:   /* Send the data back */
    674:   /* Do a global reduction to know the buffer space req for incoming messages */
    675:   {
    676:     PetscMPIInt *rw1;

    678:     PetscCalloc1(size,&rw1);

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

    683:       if (proc != onodes1[i]) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_PLIB,"MPI_SOURCE mismatch");
    684:       rw1[proc] = isz1[i];
    685:     }
    686:     PetscFree(onodes1);
    687:     PetscFree(olengths1);

    689:     /* Determine the number of messages to expect, their lengths, from from-ids */
    690:     PetscGatherMessageLengths(comm,nrqr,nrqs,rw1,&onodes2,&olengths2);
    691:     PetscFree(rw1);
    692:   }
    693:   /* Now post the Irecvs corresponding to these messages */
    694:   PetscPostIrecvInt(comm,tag2,nrqs,onodes2,olengths2,&rbuf2,&r_waits2);

    696:   /* Now  post the sends */
    697:   PetscMalloc1(nrqr,&s_waits2);
    698:   for (i=0; i<nrqr; ++i) {
    699:     j    = recv_status[i].MPI_SOURCE;
    700:     MPI_Isend(xdata[i],isz1[i],MPIU_INT,j,tag2,comm,s_waits2+i);
    701:   }

    703:   /* receive work done on other processors */
    704:   {
    705:     PetscInt    is_no,ct1,max,*rbuf2_i,isz_i,jmax;
    706:     PetscMPIInt idex;
    707:     PetscBT     table_i;

    709:     for (i=0; i<nrqs; ++i) {
    710:       MPI_Waitany(nrqs,r_waits2,&idex,MPI_STATUS_IGNORE);
    711:       /* Process the message */
    712:       rbuf2_i = rbuf2[idex];
    713:       ct1     = 2*rbuf2_i[0]+1;
    714:       jmax    = rbuf2[idex][0];
    715:       for (j=1; j<=jmax; j++) {
    716:         max     = rbuf2_i[2*j];
    717:         is_no   = rbuf2_i[2*j-1];
    718:         isz_i   = isz[is_no];
    719:         table_i = table[is_no];
    720: #if defined(PETSC_USE_CTABLE)
    721:         table_data_i = table_data[is_no];
    722: #else
    723:         data_i  = data[is_no];
    724: #endif
    725:         for (k=0; k<max; k++,ct1++) {
    726:           row = rbuf2_i[ct1];
    727:           if (!PetscBTLookupSet(table_i,row)) {
    728: #if defined(PETSC_USE_CTABLE)
    729:             PetscTableAdd(table_data_i,row+1,isz_i+1,INSERT_VALUES);
    730: #else
    731:             data_i[isz_i] = row;
    732: #endif
    733:             isz_i++;
    734:           }
    735:         }
    736:         isz[is_no] = isz_i;
    737:       }
    738:     }

    740:     MPI_Waitall(nrqr,s_waits2,MPI_STATUSES_IGNORE);
    741:   }

    743: #if defined(PETSC_USE_CTABLE)
    744:   tcount_max = 0;
    745:   for (i=0; i<imax; ++i) {
    746:     table_data_i = table_data[i];
    747:     PetscTableGetCount(table_data_i,&tcount);
    748:     if (tcount_max < tcount) tcount_max = tcount;
    749:   }
    750:   PetscMalloc1(tcount_max+1,&tdata);
    751: #endif

    753:   for (i=0; i<imax; ++i) {
    754: #if defined(PETSC_USE_CTABLE)
    755:     PetscTablePosition tpos;
    756:     table_data_i = table_data[i];

    758:     PetscTableGetHeadPosition(table_data_i,&tpos);
    759:     while (tpos) {
    760:       PetscTableGetNext(table_data_i,&tpos,&k,&j);
    761:       tdata[--j] = --k;
    762:     }
    763:     ISCreateGeneral(iscomms[i],isz[i],tdata,PETSC_COPY_VALUES,is+i);
    764: #else
    765:     ISCreateGeneral(iscomms[i],isz[i],data[i],PETSC_COPY_VALUES,is+i);
    766: #endif
    767:     PetscCommDestroy(&iscomms[i]);
    768:   }

    770:   PetscFree(iscomms);
    771:   PetscFree(onodes2);
    772:   PetscFree(olengths2);

    774:   PetscFree(pa);
    775:   PetscFree(rbuf2[0]);
    776:   PetscFree(rbuf2);
    777:   PetscFree(s_waits1);
    778:   PetscFree(r_waits1);
    779:   PetscFree(s_waits2);
    780:   PetscFree(r_waits2);
    781:   PetscFree(recv_status);
    782:   if (xdata) {
    783:     PetscFree(xdata[0]);
    784:     PetscFree(xdata);
    785:   }
    786:   PetscFree(isz1);
    787: #if defined(PETSC_USE_CTABLE)
    788:   for (i=0; i<imax; i++) {
    789:     PetscTableDestroy((PetscTable*)&table_data[i]);
    790:   }
    791:   PetscFree(table_data);
    792:   PetscFree(tdata);
    793:   PetscFree4(table,data,isz,t_p);
    794: #else
    795:   PetscFree5(table,data,isz,d_p,t_p);
    796: #endif
    797:   return(0);
    798: }

    800: /*
    801:    MatIncreaseOverlap_MPIAIJ_Local - Called by MatincreaseOverlap, to do
    802:        the work on the local processor.

    804:      Inputs:
    805:       C      - MAT_MPIAIJ;
    806:       imax - total no of index sets processed at a time;
    807:       table  - an array of char - size = m bits.

    809:      Output:
    810:       isz    - array containing the count of the solution elements corresponding
    811:                to each index set;
    812:       data or table_data  - pointer to the solutions
    813: */
    814: static PetscErrorCode MatIncreaseOverlap_MPIAIJ_Local(Mat C,PetscInt imax,PetscBT *table,PetscInt *isz,PetscInt **data,PetscTable *table_data)
    815: {
    816:   Mat_MPIAIJ *c = (Mat_MPIAIJ*)C->data;
    817:   Mat        A  = c->A,B = c->B;
    818:   Mat_SeqAIJ *a = (Mat_SeqAIJ*)A->data,*b = (Mat_SeqAIJ*)B->data;
    819:   PetscInt   start,end,val,max,rstart,cstart,*ai,*aj;
    820:   PetscInt   *bi,*bj,*garray,i,j,k,row,isz_i;
    821:   PetscBT    table_i;
    822: #if defined(PETSC_USE_CTABLE)
    823:   PetscTable         table_data_i;
    824:   PetscErrorCode     ierr;
    825:   PetscTablePosition tpos;
    826:   PetscInt           tcount,*tdata;
    827: #else
    828:   PetscInt           *data_i;
    829: #endif

    832:   rstart = C->rmap->rstart;
    833:   cstart = C->cmap->rstart;
    834:   ai     = a->i;
    835:   aj     = a->j;
    836:   bi     = b->i;
    837:   bj     = b->j;
    838:   garray = c->garray;

    840:   for (i=0; i<imax; i++) {
    841: #if defined(PETSC_USE_CTABLE)
    842:     /* copy existing entries of table_data_i into tdata[] */
    843:     table_data_i = table_data[i];
    844:     PetscTableGetCount(table_data_i,&tcount);
    845:     if (tcount != isz[i]) SETERRQ3(PETSC_COMM_SELF,PETSC_ERR_PLIB," tcount %d != isz[%d] %d",tcount,i,isz[i]);

    847:     PetscMalloc1(tcount,&tdata);
    848:     PetscTableGetHeadPosition(table_data_i,&tpos);
    849:     while (tpos) {
    850:       PetscTableGetNext(table_data_i,&tpos,&row,&j);
    851:       tdata[--j] = --row;
    852:       if (j > tcount - 1) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_PLIB," j %d >= tcount %d",j,tcount);
    853:     }
    854: #else
    855:     data_i  = data[i];
    856: #endif
    857:     table_i = table[i];
    858:     isz_i   = isz[i];
    859:     max     = isz[i];

    861:     for (j=0; j<max; j++) {
    862: #if defined(PETSC_USE_CTABLE)
    863:       row   = tdata[j] - rstart;
    864: #else
    865:       row   = data_i[j] - rstart;
    866: #endif
    867:       start = ai[row];
    868:       end   = ai[row+1];
    869:       for (k=start; k<end; k++) { /* Amat */
    870:         val = aj[k] + cstart;
    871:         if (!PetscBTLookupSet(table_i,val)) {
    872: #if defined(PETSC_USE_CTABLE)
    873:           PetscTableAdd(table_data_i,val+1,isz_i+1,INSERT_VALUES);
    874: #else
    875:           data_i[isz_i] = val;
    876: #endif
    877:           isz_i++;
    878:         }
    879:       }
    880:       start = bi[row];
    881:       end   = bi[row+1];
    882:       for (k=start; k<end; k++) { /* Bmat */
    883:         val = garray[bj[k]];
    884:         if (!PetscBTLookupSet(table_i,val)) {
    885: #if defined(PETSC_USE_CTABLE)
    886:           PetscTableAdd(table_data_i,val+1,isz_i+1,INSERT_VALUES);
    887: #else
    888:           data_i[isz_i] = val;
    889: #endif
    890:           isz_i++;
    891:         }
    892:       }
    893:     }
    894:     isz[i] = isz_i;

    896: #if defined(PETSC_USE_CTABLE)
    897:     PetscFree(tdata);
    898: #endif
    899:   }
    900:   return(0);
    901: }

    903: /*
    904:       MatIncreaseOverlap_MPIAIJ_Receive - Process the received messages,
    905:          and return the output

    907:          Input:
    908:            C    - the matrix
    909:            nrqr - no of messages being processed.
    910:            rbuf - an array of pointers to the received requests

    912:          Output:
    913:            xdata - array of messages to be sent back
    914:            isz1  - size of each message

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

    921: */
    922: static PetscErrorCode MatIncreaseOverlap_MPIAIJ_Receive(Mat C,PetscInt nrqr,PetscInt **rbuf,PetscInt **xdata,PetscInt * isz1)
    923: {
    924:   Mat_MPIAIJ     *c = (Mat_MPIAIJ*)C->data;
    925:   Mat            A  = c->A,B = c->B;
    926:   Mat_SeqAIJ     *a = (Mat_SeqAIJ*)A->data,*b = (Mat_SeqAIJ*)B->data;
    928:   PetscInt       rstart,cstart,*ai,*aj,*bi,*bj,*garray,i,j,k;
    929:   PetscInt       row,total_sz,ct,ct1,ct2,ct3,mem_estimate,oct2,l,start,end;
    930:   PetscInt       val,max1,max2,m,no_malloc =0,*tmp,new_estimate,ctr;
    931:   PetscInt       *rbuf_i,kmax,rbuf_0;
    932:   PetscBT        xtable;

    935:   m      = C->rmap->N;
    936:   rstart = C->rmap->rstart;
    937:   cstart = C->cmap->rstart;
    938:   ai     = a->i;
    939:   aj     = a->j;
    940:   bi     = b->i;
    941:   bj     = b->j;
    942:   garray = c->garray;

    944:   for (i=0,ct=0,total_sz=0; i<nrqr; ++i) {
    945:     rbuf_i =  rbuf[i];
    946:     rbuf_0 =  rbuf_i[0];
    947:     ct    += rbuf_0;
    948:     for (j=1; j<=rbuf_0; j++) total_sz += rbuf_i[2*j];
    949:   }

    951:   if (C->rmap->n) max1 = ct*(a->nz + b->nz)/C->rmap->n;
    952:   else max1 = 1;
    953:   mem_estimate = 3*((total_sz > max1 ? total_sz : max1)+1);
    954:   if (nrqr) {
    955:     PetscMalloc1(mem_estimate,&xdata[0]);
    956:     ++no_malloc;
    957:   }
    958:   PetscBTCreate(m,&xtable);
    959:   PetscArrayzero(isz1,nrqr);

    961:   ct3 = 0;
    962:   for (i=0; i<nrqr; i++) { /* for easch mesg from proc i */
    963:     rbuf_i =  rbuf[i];
    964:     rbuf_0 =  rbuf_i[0];
    965:     ct1    =  2*rbuf_0+1;
    966:     ct2    =  ct1;
    967:     ct3   += ct1;
    968:     for (j=1; j<=rbuf_0; j++) { /* for each IS from proc i*/
    969:       PetscBTMemzero(m,xtable);
    970:       oct2 = ct2;
    971:       kmax = rbuf_i[2*j];
    972:       for (k=0; k<kmax; k++,ct1++) {
    973:         row = rbuf_i[ct1];
    974:         if (!PetscBTLookupSet(xtable,row)) {
    975:           if (!(ct3 < mem_estimate)) {
    976:             new_estimate = (PetscInt)(1.5*mem_estimate)+1;
    977:             PetscMalloc1(new_estimate,&tmp);
    978:             PetscArraycpy(tmp,xdata[0],mem_estimate);
    979:             PetscFree(xdata[0]);
    980:             xdata[0]     = tmp;
    981:             mem_estimate = new_estimate; ++no_malloc;
    982:             for (ctr=1; ctr<=i; ctr++) xdata[ctr] = xdata[ctr-1] + isz1[ctr-1];
    983:           }
    984:           xdata[i][ct2++] = row;
    985:           ct3++;
    986:         }
    987:       }
    988:       for (k=oct2,max2=ct2; k<max2; k++) {
    989:         row   = xdata[i][k] - rstart;
    990:         start = ai[row];
    991:         end   = ai[row+1];
    992:         for (l=start; l<end; l++) {
    993:           val = aj[l] + cstart;
    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:         start = bi[row];
    1009:         end   = bi[row+1];
    1010:         for (l=start; l<end; l++) {
    1011:           val = garray[bj[l]];
    1012:           if (!PetscBTLookupSet(xtable,val)) {
    1013:             if (!(ct3 < mem_estimate)) {
    1014:               new_estimate = (PetscInt)(1.5*mem_estimate)+1;
    1015:               PetscMalloc1(new_estimate,&tmp);
    1016:               PetscArraycpy(tmp,xdata[0],mem_estimate);
    1017:               PetscFree(xdata[0]);
    1018:               xdata[0]     = tmp;
    1019:               mem_estimate = new_estimate; ++no_malloc;
    1020:               for (ctr =1; ctr <=i; ctr++) xdata[ctr] = xdata[ctr-1] + isz1[ctr-1];
    1021:             }
    1022:             xdata[i][ct2++] = val;
    1023:             ct3++;
    1024:           }
    1025:         }
    1026:       }
    1027:       /* Update the header*/
    1028:       xdata[i][2*j]   = ct2 - oct2; /* Undo the vector isz1 and use only a var*/
    1029:       xdata[i][2*j-1] = rbuf_i[2*j-1];
    1030:     }
    1031:     xdata[i][0] = rbuf_0;
    1032:     if (i+1<nrqr) xdata[i+1]  = xdata[i] + ct2;
    1033:     isz1[i]     = ct2; /* size of each message */
    1034:   }
    1035:   PetscBTDestroy(&xtable);
    1036:   PetscInfo3(C,"Allocated %D bytes, required %D bytes, no of mallocs = %D\n",mem_estimate,ct3,no_malloc);
    1037:   return(0);
    1038: }
    1039: /* -------------------------------------------------------------------------*/
    1040: extern PetscErrorCode MatCreateSubMatrices_MPIAIJ_Local(Mat,PetscInt,const IS[],const IS[],MatReuse,Mat*);
    1041: /*
    1042:     Every processor gets the entire matrix
    1043: */
    1044: PetscErrorCode MatCreateSubMatrix_MPIAIJ_All(Mat A,MatCreateSubMatrixOption flag,MatReuse scall,Mat *Bin[])
    1045: {
    1046:   Mat            B;
    1047:   Mat_MPIAIJ     *a = (Mat_MPIAIJ*)A->data;
    1048:   Mat_SeqAIJ     *b,*ad = (Mat_SeqAIJ*)a->A->data,*bd = (Mat_SeqAIJ*)a->B->data;
    1050:   PetscMPIInt    size,rank,*recvcounts = NULL,*displs = NULL;
    1051:   PetscInt       sendcount,i,*rstarts = A->rmap->range,n,cnt,j;
    1052:   PetscInt       m,*b_sendj,*garray = a->garray,*lens,*jsendbuf,*a_jsendbuf,*b_jsendbuf;

    1055:   MPI_Comm_size(PetscObjectComm((PetscObject)A),&size);
    1056:   MPI_Comm_rank(PetscObjectComm((PetscObject)A),&rank);
    1057:   if (scall == MAT_INITIAL_MATRIX) {
    1058:     /* ----------------------------------------------------------------
    1059:          Tell every processor the number of nonzeros per row
    1060:     */
    1061:     PetscMalloc1(A->rmap->N,&lens);
    1062:     for (i=A->rmap->rstart; i<A->rmap->rend; i++) {
    1063:       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];
    1064:     }
    1065:     PetscMalloc2(size,&recvcounts,size,&displs);
    1066:     for (i=0; i<size; i++) {
    1067:       recvcounts[i] = A->rmap->range[i+1] - A->rmap->range[i];
    1068:       displs[i]     = A->rmap->range[i];
    1069:     }
    1070: #if defined(PETSC_HAVE_MPI_IN_PLACE)
    1071:     MPI_Allgatherv(MPI_IN_PLACE,0,MPI_DATATYPE_NULL,lens,recvcounts,displs,MPIU_INT,PetscObjectComm((PetscObject)A));
    1072: #else
    1073:     sendcount = A->rmap->rend - A->rmap->rstart;
    1074:     MPI_Allgatherv(lens+A->rmap->rstart,sendcount,MPIU_INT,lens,recvcounts,displs,MPIU_INT,PetscObjectComm((PetscObject)A));
    1075: #endif
    1076:     /* ---------------------------------------------------------------
    1077:          Create the sequential matrix of the same type as the local block diagonal
    1078:     */
    1079:     MatCreate(PETSC_COMM_SELF,&B);
    1080:     MatSetSizes(B,A->rmap->N,A->cmap->N,PETSC_DETERMINE,PETSC_DETERMINE);
    1081:     MatSetBlockSizesFromMats(B,A,A);
    1082:     MatSetType(B,((PetscObject)a->A)->type_name);
    1083:     MatSeqAIJSetPreallocation(B,0,lens);
    1084:     PetscCalloc1(2,Bin);
    1085:     **Bin = B;
    1086:     b     = (Mat_SeqAIJ*)B->data;

    1088:     /*--------------------------------------------------------------------
    1089:        Copy my part of matrix column indices over
    1090:     */
    1091:     sendcount  = ad->nz + bd->nz;
    1092:     jsendbuf   = b->j + b->i[rstarts[rank]];
    1093:     a_jsendbuf = ad->j;
    1094:     b_jsendbuf = bd->j;
    1095:     n          = A->rmap->rend - A->rmap->rstart;
    1096:     cnt        = 0;
    1097:     for (i=0; i<n; i++) {
    1098:       /* put in lower diagonal portion */
    1099:       m = bd->i[i+1] - bd->i[i];
    1100:       while (m > 0) {
    1101:         /* is it above diagonal (in bd (compressed) numbering) */
    1102:         if (garray[*b_jsendbuf] > A->rmap->rstart + i) break;
    1103:         jsendbuf[cnt++] = garray[*b_jsendbuf++];
    1104:         m--;
    1105:       }

    1107:       /* put in diagonal portion */
    1108:       for (j=ad->i[i]; j<ad->i[i+1]; j++) {
    1109:         jsendbuf[cnt++] = A->rmap->rstart + *a_jsendbuf++;
    1110:       }

    1112:       /* put in upper diagonal portion */
    1113:       while (m-- > 0) {
    1114:         jsendbuf[cnt++] = garray[*b_jsendbuf++];
    1115:       }
    1116:     }
    1117:     if (cnt != sendcount) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_PLIB,"Corrupted PETSc matrix: nz given %D actual nz %D",sendcount,cnt);

    1119:     /*--------------------------------------------------------------------
    1120:        Gather all column indices to all processors
    1121:     */
    1122:     for (i=0; i<size; i++) {
    1123:       recvcounts[i] = 0;
    1124:       for (j=A->rmap->range[i]; j<A->rmap->range[i+1]; j++) {
    1125:         recvcounts[i] += lens[j];
    1126:       }
    1127:     }
    1128:     displs[0] = 0;
    1129:     for (i=1; i<size; i++) {
    1130:       displs[i] = displs[i-1] + recvcounts[i-1];
    1131:     }
    1132: #if defined(PETSC_HAVE_MPI_IN_PLACE)
    1133:     MPI_Allgatherv(MPI_IN_PLACE,0,MPI_DATATYPE_NULL,b->j,recvcounts,displs,MPIU_INT,PetscObjectComm((PetscObject)A));
    1134: #else
    1135:     MPI_Allgatherv(jsendbuf,sendcount,MPIU_INT,b->j,recvcounts,displs,MPIU_INT,PetscObjectComm((PetscObject)A));
    1136: #endif
    1137:     /*--------------------------------------------------------------------
    1138:         Assemble the matrix into useable form (note numerical values not yet set)
    1139:     */
    1140:     /* set the b->ilen (length of each row) values */
    1141:     PetscArraycpy(b->ilen,lens,A->rmap->N);
    1142:     /* set the b->i indices */
    1143:     b->i[0] = 0;
    1144:     for (i=1; i<=A->rmap->N; i++) {
    1145:       b->i[i] = b->i[i-1] + lens[i-1];
    1146:     }
    1147:     PetscFree(lens);
    1148:     MatAssemblyBegin(B,MAT_FINAL_ASSEMBLY);
    1149:     MatAssemblyEnd(B,MAT_FINAL_ASSEMBLY);

    1151:   } else {
    1152:     B = **Bin;
    1153:     b = (Mat_SeqAIJ*)B->data;
    1154:   }

    1156:   /*--------------------------------------------------------------------
    1157:        Copy my part of matrix numerical values into the values location
    1158:   */
    1159:   if (flag == MAT_GET_VALUES) {
    1160:     const PetscScalar *ada,*bda,*a_sendbuf,*b_sendbuf;
    1161:     MatScalar         *sendbuf,*recvbuf;

    1163:     MatSeqAIJGetArrayRead(a->A,&ada);
    1164:     MatSeqAIJGetArrayRead(a->B,&bda);
    1165:     sendcount = ad->nz + bd->nz;
    1166:     sendbuf   = b->a + b->i[rstarts[rank]];
    1167:     a_sendbuf = ada;
    1168:     b_sendbuf = bda;
    1169:     b_sendj   = bd->j;
    1170:     n         = A->rmap->rend - A->rmap->rstart;
    1171:     cnt       = 0;
    1172:     for (i=0; i<n; i++) {
    1173:       /* put in lower diagonal portion */
    1174:       m = bd->i[i+1] - bd->i[i];
    1175:       while (m > 0) {
    1176:         /* is it above diagonal (in bd (compressed) numbering) */
    1177:         if (garray[*b_sendj] > A->rmap->rstart + i) break;
    1178:         sendbuf[cnt++] = *b_sendbuf++;
    1179:         m--;
    1180:         b_sendj++;
    1181:       }

    1183:       /* put in diagonal portion */
    1184:       for (j=ad->i[i]; j<ad->i[i+1]; j++) {
    1185:         sendbuf[cnt++] = *a_sendbuf++;
    1186:       }

    1188:       /* put in upper diagonal portion */
    1189:       while (m-- > 0) {
    1190:         sendbuf[cnt++] = *b_sendbuf++;
    1191:         b_sendj++;
    1192:       }
    1193:     }
    1194:     if (cnt != sendcount) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_PLIB,"Corrupted PETSc matrix: nz given %D actual nz %D",sendcount,cnt);

    1196:     /* -----------------------------------------------------------------
    1197:        Gather all numerical values to all processors
    1198:     */
    1199:     if (!recvcounts) {
    1200:       PetscMalloc2(size,&recvcounts,size,&displs);
    1201:     }
    1202:     for (i=0; i<size; i++) {
    1203:       recvcounts[i] = b->i[rstarts[i+1]] - b->i[rstarts[i]];
    1204:     }
    1205:     displs[0] = 0;
    1206:     for (i=1; i<size; i++) {
    1207:       displs[i] = displs[i-1] + recvcounts[i-1];
    1208:     }
    1209:     recvbuf = b->a;
    1210: #if defined(PETSC_HAVE_MPI_IN_PLACE)
    1211:     MPI_Allgatherv(MPI_IN_PLACE,0,MPI_DATATYPE_NULL,recvbuf,recvcounts,displs,MPIU_SCALAR,PetscObjectComm((PetscObject)A));
    1212: #else
    1213:     MPI_Allgatherv(sendbuf,sendcount,MPIU_SCALAR,recvbuf,recvcounts,displs,MPIU_SCALAR,PetscObjectComm((PetscObject)A));
    1214: #endif
    1215:     MatSeqAIJRestoreArrayRead(a->A,&ada);
    1216:     MatSeqAIJRestoreArrayRead(a->B,&bda);
    1217:   }  /* endof (flag == MAT_GET_VALUES) */
    1218:   PetscFree2(recvcounts,displs);

    1220:   if (A->symmetric) {
    1221:     MatSetOption(B,MAT_SYMMETRIC,PETSC_TRUE);
    1222:   } else if (A->hermitian) {
    1223:     MatSetOption(B,MAT_HERMITIAN,PETSC_TRUE);
    1224:   } else if (A->structurally_symmetric) {
    1225:     MatSetOption(B,MAT_STRUCTURALLY_SYMMETRIC,PETSC_TRUE);
    1226:   }
    1227:   return(0);
    1228: }

    1230: PetscErrorCode MatCreateSubMatrices_MPIAIJ_SingleIS_Local(Mat C,PetscInt ismax,const IS isrow[],const IS iscol[],MatReuse scall,PetscBool allcolumns,Mat *submats)
    1231: {
    1232:   Mat_MPIAIJ     *c = (Mat_MPIAIJ*)C->data;
    1233:   Mat            submat,A = c->A,B = c->B;
    1234:   Mat_SeqAIJ     *a = (Mat_SeqAIJ*)A->data,*b = (Mat_SeqAIJ*)B->data,*subc;
    1235:   PetscInt       *ai=a->i,*aj=a->j,*bi=b->i,*bj=b->j,nzA,nzB;
    1236:   PetscInt       cstart = C->cmap->rstart,cend = C->cmap->rend,rstart = C->rmap->rstart,*bmap = c->garray;
    1237:   const PetscInt *icol,*irow;
    1238:   PetscInt       nrow,ncol,start;
    1240:   PetscMPIInt    rank,size,tag1,tag2,tag3,tag4,*w1,*w2,nrqr;
    1241:   PetscInt       **sbuf1,**sbuf2,i,j,k,l,ct1,ct2,ct3,**rbuf1,row,proc;
    1242:   PetscInt       nrqs=0,msz,**ptr,*req_size,*ctr,*pa,*tmp,tcol,*iptr;
    1243:   PetscInt       **rbuf3,*req_source1,*req_source2,**sbuf_aj,**rbuf2,max1,nnz;
    1244:   PetscInt       *lens,rmax,ncols,*cols,Crow;
    1245: #if defined(PETSC_USE_CTABLE)
    1246:   PetscTable     cmap,rmap;
    1247:   PetscInt       *cmap_loc,*rmap_loc;
    1248: #else
    1249:   PetscInt       *cmap,*rmap;
    1250: #endif
    1251:   PetscInt       ctr_j,*sbuf1_j,*sbuf_aj_i,*rbuf1_i,kmax,*sbuf1_i,*rbuf2_i,*rbuf3_i;
    1252:   PetscInt       *cworkB,lwrite,*subcols,*row2proc;
    1253:   PetscScalar    *vworkA,*vworkB,*a_a,*b_a,*subvals=NULL;
    1254:   MPI_Request    *s_waits1,*r_waits1,*s_waits2,*r_waits2,*r_waits3;
    1255:   MPI_Request    *r_waits4,*s_waits3 = NULL,*s_waits4;
    1256:   MPI_Status     *r_status1,*r_status2,*s_status1,*s_status3 = NULL,*s_status2;
    1257:   MPI_Status     *r_status3 = NULL,*r_status4,*s_status4;
    1258:   MPI_Comm       comm;
    1259:   PetscScalar    **rbuf4,**sbuf_aa,*vals,*sbuf_aa_i,*rbuf4_i;
    1260:   PetscMPIInt    *onodes1,*olengths1,idex,end;
    1261:   Mat_SubSppt    *smatis1;
    1262:   PetscBool      isrowsorted,iscolsorted;

    1267:   if (ismax != 1) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_SUP,"This routine only works when all processes have ismax=1");
    1268:   MatSeqAIJGetArrayRead(A,(const PetscScalar**)&a_a);
    1269:   MatSeqAIJGetArrayRead(B,(const PetscScalar**)&b_a);
    1270:   PetscObjectGetComm((PetscObject)C,&comm);
    1271:   size = c->size;
    1272:   rank = c->rank;

    1274:   ISSorted(iscol[0],&iscolsorted);
    1275:   ISSorted(isrow[0],&isrowsorted);
    1276:   ISGetIndices(isrow[0],&irow);
    1277:   ISGetLocalSize(isrow[0],&nrow);
    1278:   if (allcolumns) {
    1279:     icol = NULL;
    1280:     ncol = C->cmap->N;
    1281:   } else {
    1282:     ISGetIndices(iscol[0],&icol);
    1283:     ISGetLocalSize(iscol[0],&ncol);
    1284:   }

    1286:   if (scall == MAT_INITIAL_MATRIX) {
    1287:     PetscInt *sbuf2_i,*cworkA,lwrite,ctmp;

    1289:     /* Get some new tags to keep the communication clean */
    1290:     tag1 = ((PetscObject)C)->tag;
    1291:     PetscObjectGetNewTag((PetscObject)C,&tag2);
    1292:     PetscObjectGetNewTag((PetscObject)C,&tag3);

    1294:     /* evaluate communication - mesg to who, length of mesg, and buffer space
    1295:      required. Based on this, buffers are allocated, and data copied into them */
    1296:     PetscCalloc2(size,&w1,size,&w2);
    1297:     PetscMalloc1(nrow,&row2proc);

    1299:     /* w1[proc] = num of rows owned by proc -- to be requested */
    1300:     proc = 0;
    1301:     nrqs = 0; /* num of outgoing messages */
    1302:     for (j=0; j<nrow; j++) {
    1303:       row  = irow[j];
    1304:       if (!isrowsorted) proc = 0;
    1305:       while (row >= C->rmap->range[proc+1]) proc++;
    1306:       w1[proc]++;
    1307:       row2proc[j] = proc; /* map row index to proc */

    1309:       if (proc != rank && !w2[proc]) {
    1310:         w2[proc] = 1; nrqs++;
    1311:       }
    1312:     }
    1313:     w1[rank] = 0;  /* rows owned by self will not be requested */

    1315:     PetscMalloc1(nrqs,&pa); /*(proc -array)*/
    1316:     for (proc=0,j=0; proc<size; proc++) {
    1317:       if (w1[proc]) { pa[j++] = proc;}
    1318:     }

    1320:     /* Each message would have a header = 1 + 2*(num of IS) + data (here,num of IS = 1) */
    1321:     msz = 0;              /* total mesg length (for all procs) */
    1322:     for (i=0; i<nrqs; i++) {
    1323:       proc      = pa[i];
    1324:       w1[proc] += 3;
    1325:       msz      += w1[proc];
    1326:     }
    1327:     PetscInfo2(0,"Number of outgoing messages %D Total message length %D\n",nrqs,msz);

    1329:     /* Determine nrqr, the number of messages to expect, their lengths, from from-ids */
    1330:     /* if w2[proc]=1, a message of length w1[proc] will be sent to proc; */
    1331:     PetscGatherNumberOfMessages(comm,w2,w1,&nrqr);

    1333:     /* Input: nrqs: nsend; nrqr: nrecv; w1: msg length to be sent;
    1334:        Output: onodes1: recv node-ids; olengths1: corresponding recv message length */
    1335:     PetscGatherMessageLengths(comm,nrqs,nrqr,w1,&onodes1,&olengths1);

    1337:     /* Now post the Irecvs corresponding to these messages */
    1338:     PetscPostIrecvInt(comm,tag1,nrqr,onodes1,olengths1,&rbuf1,&r_waits1);

    1340:     PetscFree(onodes1);
    1341:     PetscFree(olengths1);

    1343:     /* Allocate Memory for outgoing messages */
    1344:     PetscMalloc4(size,&sbuf1,size,&ptr,2*msz,&tmp,size,&ctr);
    1345:     PetscArrayzero(sbuf1,size);
    1346:     PetscArrayzero(ptr,size);

    1348:     /* subf1[pa[0]] = tmp, subf1[pa[i]] = subf1[pa[i-1]] + w1[pa[i-1]] */
    1349:     iptr = tmp;
    1350:     for (i=0; i<nrqs; i++) {
    1351:       proc        = pa[i];
    1352:       sbuf1[proc] = iptr;
    1353:       iptr       += w1[proc];
    1354:     }

    1356:     /* Form the outgoing messages */
    1357:     /* Initialize the header space */
    1358:     for (i=0; i<nrqs; i++) {
    1359:       proc      = pa[i];
    1360:       PetscArrayzero(sbuf1[proc],3);
    1361:       ptr[proc] = sbuf1[proc] + 3;
    1362:     }

    1364:     /* Parse the isrow and copy data into outbuf */
    1365:     PetscArrayzero(ctr,size);
    1366:     for (j=0; j<nrow; j++) {  /* parse the indices of each IS */
    1367:       proc = row2proc[j];
    1368:       if (proc != rank) { /* copy to the outgoing buf*/
    1369:         *ptr[proc] = irow[j];
    1370:         ctr[proc]++; ptr[proc]++;
    1371:       }
    1372:     }

    1374:     /* Update the headers for the current IS */
    1375:     for (j=0; j<size; j++) { /* Can Optimise this loop too */
    1376:       if ((ctr_j = ctr[j])) {
    1377:         sbuf1_j        = sbuf1[j];
    1378:         k              = ++sbuf1_j[0];
    1379:         sbuf1_j[2*k]   = ctr_j;
    1380:         sbuf1_j[2*k-1] = 0;
    1381:       }
    1382:     }

    1384:     /* Now post the sends */
    1385:     PetscMalloc1(nrqs,&s_waits1);
    1386:     for (i=0; i<nrqs; ++i) {
    1387:       proc = pa[i];
    1388:       MPI_Isend(sbuf1[proc],w1[proc],MPIU_INT,proc,tag1,comm,s_waits1+i);
    1389:     }

    1391:     /* Post Receives to capture the buffer size */
    1392:     PetscMalloc4(nrqs,&r_status2,nrqr,&s_waits2,nrqs,&r_waits2,nrqr,&s_status2);
    1393:     PetscMalloc3(nrqs,&req_source2,nrqs,&rbuf2,nrqs,&rbuf3);

    1395:     if (nrqs) rbuf2[0] = tmp + msz;
    1396:     for (i=1; i<nrqs; ++i) rbuf2[i] = rbuf2[i-1] + w1[pa[i-1]];

    1398:     for (i=0; i<nrqs; ++i) {
    1399:       proc = pa[i];
    1400:       MPI_Irecv(rbuf2[i],w1[proc],MPIU_INT,proc,tag2,comm,r_waits2+i);
    1401:     }

    1403:     PetscFree2(w1,w2);

    1405:     /* Send to other procs the buf size they should allocate */
    1406:     /* Receive messages*/
    1407:     PetscMalloc1(nrqr,&r_status1);
    1408:     PetscMalloc3(nrqr,&sbuf2,nrqr,&req_size,nrqr,&req_source1);

    1410:     MPI_Waitall(nrqr,r_waits1,r_status1);
    1411:     for (i=0; i<nrqr; ++i) {
    1412:       req_size[i] = 0;
    1413:       rbuf1_i        = rbuf1[i];
    1414:       start          = 2*rbuf1_i[0] + 1;
    1415:       MPI_Get_count(r_status1+i,MPIU_INT,&end);
    1416:       PetscMalloc1(end,&sbuf2[i]);
    1417:       sbuf2_i        = sbuf2[i];
    1418:       for (j=start; j<end; j++) {
    1419:         k            = rbuf1_i[j] - rstart;
    1420:         ncols        = ai[k+1] - ai[k] + bi[k+1] - bi[k];
    1421:         sbuf2_i[j]   = ncols;
    1422:         req_size[i] += ncols;
    1423:       }
    1424:       req_source1[i] = r_status1[i].MPI_SOURCE;

    1426:       /* form the header */
    1427:       sbuf2_i[0] = req_size[i];
    1428:       for (j=1; j<start; j++) sbuf2_i[j] = rbuf1_i[j];

    1430:       MPI_Isend(sbuf2_i,end,MPIU_INT,req_source1[i],tag2,comm,s_waits2+i);
    1431:     }

    1433:     PetscFree(r_status1);
    1434:     PetscFree(r_waits1);

    1436:     /* rbuf2 is received, Post recv column indices a->j */
    1437:     MPI_Waitall(nrqs,r_waits2,r_status2);

    1439:     PetscMalloc4(nrqs,&r_waits3,nrqr,&s_waits3,nrqs,&r_status3,nrqr,&s_status3);
    1440:     for (i=0; i<nrqs; ++i) {
    1441:       PetscMalloc1(rbuf2[i][0],&rbuf3[i]);
    1442:       req_source2[i] = r_status2[i].MPI_SOURCE;
    1443:       MPI_Irecv(rbuf3[i],rbuf2[i][0],MPIU_INT,req_source2[i],tag3,comm,r_waits3+i);
    1444:     }

    1446:     /* Wait on sends1 and sends2 */
    1447:     PetscMalloc1(nrqs,&s_status1);
    1448:     MPI_Waitall(nrqs,s_waits1,s_status1);
    1449:     PetscFree(s_waits1);
    1450:     PetscFree(s_status1);

    1452:     MPI_Waitall(nrqr,s_waits2,s_status2);
    1453:     PetscFree4(r_status2,s_waits2,r_waits2,s_status2);

    1455:     /* Now allocate sending buffers for a->j, and send them off */
    1456:     PetscMalloc1(nrqr,&sbuf_aj);
    1457:     for (i=0,j=0; i<nrqr; i++) j += req_size[i];
    1458:     if (nrqr) {PetscMalloc1(j,&sbuf_aj[0]);}
    1459:     for (i=1; i<nrqr; i++) sbuf_aj[i] = sbuf_aj[i-1] + req_size[i-1];

    1461:     for (i=0; i<nrqr; i++) { /* for each requested message */
    1462:       rbuf1_i   = rbuf1[i];
    1463:       sbuf_aj_i = sbuf_aj[i];
    1464:       ct1       = 2*rbuf1_i[0] + 1;
    1465:       ct2       = 0;
    1466:       /* max1=rbuf1_i[0]; if (max1 != 1) SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_PLIB,"max1 %d != 1",max1); */

    1468:       kmax = rbuf1[i][2];
    1469:       for (k=0; k<kmax; k++,ct1++) { /* for each row */
    1470:         row    = rbuf1_i[ct1] - rstart;
    1471:         nzA    = ai[row+1] - ai[row];
    1472:         nzB    = bi[row+1] - bi[row];
    1473:         ncols  = nzA + nzB;
    1474:         cworkA = aj + ai[row]; cworkB = bj + bi[row];

    1476:         /* load the column indices for this row into cols*/
    1477:         cols = sbuf_aj_i + ct2;

    1479:         lwrite = 0;
    1480:         for (l=0; l<nzB; l++) {
    1481:           if ((ctmp = bmap[cworkB[l]]) < cstart) cols[lwrite++] = ctmp;
    1482:         }
    1483:         for (l=0; l<nzA; l++) cols[lwrite++] = cstart + cworkA[l];
    1484:         for (l=0; l<nzB; l++) {
    1485:           if ((ctmp = bmap[cworkB[l]]) >= cend) cols[lwrite++] = ctmp;
    1486:         }

    1488:         ct2 += ncols;
    1489:       }
    1490:       MPI_Isend(sbuf_aj_i,req_size[i],MPIU_INT,req_source1[i],tag3,comm,s_waits3+i);
    1491:     }

    1493:     /* create column map (cmap): global col of C -> local col of submat */
    1494: #if defined(PETSC_USE_CTABLE)
    1495:     if (!allcolumns) {
    1496:       PetscTableCreate(ncol,C->cmap->N,&cmap);
    1497:       PetscCalloc1(C->cmap->n,&cmap_loc);
    1498:       for (j=0; j<ncol; j++) { /* use array cmap_loc[] for local col indices */
    1499:         if (icol[j] >= cstart && icol[j] <cend) {
    1500:           cmap_loc[icol[j] - cstart] = j+1;
    1501:         } else { /* use PetscTable for non-local col indices */
    1502:           PetscTableAdd(cmap,icol[j]+1,j+1,INSERT_VALUES);
    1503:         }
    1504:       }
    1505:     } else {
    1506:       cmap     = NULL;
    1507:       cmap_loc = NULL;
    1508:     }
    1509:     PetscCalloc1(C->rmap->n,&rmap_loc);
    1510: #else
    1511:     if (!allcolumns) {
    1512:       PetscCalloc1(C->cmap->N,&cmap);
    1513:       for (j=0; j<ncol; j++) cmap[icol[j]] = j+1;
    1514:     } else {
    1515:       cmap = NULL;
    1516:     }
    1517: #endif

    1519:     /* Create lens for MatSeqAIJSetPreallocation() */
    1520:     PetscCalloc1(nrow,&lens);

    1522:     /* Compute lens from local part of C */
    1523:     for (j=0; j<nrow; j++) {
    1524:       row  = irow[j];
    1525:       proc = row2proc[j];
    1526:       if (proc == rank) {
    1527:         /* diagonal part A = c->A */
    1528:         ncols = ai[row-rstart+1] - ai[row-rstart];
    1529:         cols  = aj + ai[row-rstart];
    1530:         if (!allcolumns) {
    1531:           for (k=0; k<ncols; k++) {
    1532: #if defined(PETSC_USE_CTABLE)
    1533:             tcol = cmap_loc[cols[k]];
    1534: #else
    1535:             tcol = cmap[cols[k]+cstart];
    1536: #endif
    1537:             if (tcol) lens[j]++;
    1538:           }
    1539:         } else { /* allcolumns */
    1540:           lens[j] = ncols;
    1541:         }

    1543:         /* off-diagonal part B = c->B */
    1544:         ncols = bi[row-rstart+1] - bi[row-rstart];
    1545:         cols  = bj + bi[row-rstart];
    1546:         if (!allcolumns) {
    1547:           for (k=0; k<ncols; k++) {
    1548: #if defined(PETSC_USE_CTABLE)
    1549:             PetscTableFind(cmap,bmap[cols[k]]+1,&tcol);
    1550: #else
    1551:             tcol = cmap[bmap[cols[k]]];
    1552: #endif
    1553:             if (tcol) lens[j]++;
    1554:           }
    1555:         } else { /* allcolumns */
    1556:           lens[j] += ncols;
    1557:         }
    1558:       }
    1559:     }

    1561:     /* Create row map (rmap): global row of C -> local row of submat */
    1562: #if defined(PETSC_USE_CTABLE)
    1563:     PetscTableCreate(nrow,C->rmap->N,&rmap);
    1564:     for (j=0; j<nrow; j++) {
    1565:       row  = irow[j];
    1566:       proc = row2proc[j];
    1567:       if (proc == rank) { /* a local row */
    1568:         rmap_loc[row - rstart] = j;
    1569:       } else {
    1570:         PetscTableAdd(rmap,irow[j]+1,j+1,INSERT_VALUES);
    1571:       }
    1572:     }
    1573: #else
    1574:     PetscCalloc1(C->rmap->N,&rmap);
    1575:     for (j=0; j<nrow; j++) {
    1576:       rmap[irow[j]] = j;
    1577:     }
    1578: #endif

    1580:     /* Update lens from offproc data */
    1581:     /* recv a->j is done */
    1582:     MPI_Waitall(nrqs,r_waits3,r_status3);
    1583:     for (i=0; i<nrqs; i++) {
    1584:       proc    = pa[i];
    1585:       sbuf1_i = sbuf1[proc];
    1586:       /* jmax    = sbuf1_i[0]; if (jmax != 1) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_PLIB,"jmax !=1"); */
    1587:       ct1     = 2 + 1;
    1588:       ct2     = 0;
    1589:       rbuf2_i = rbuf2[i]; /* received length of C->j */
    1590:       rbuf3_i = rbuf3[i]; /* received C->j */

    1592:       /* is_no  = sbuf1_i[2*j-1]; if (is_no != 0) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_PLIB,"is_no !=0"); */
    1593:       max1   = sbuf1_i[2];
    1594:       for (k=0; k<max1; k++,ct1++) {
    1595: #if defined(PETSC_USE_CTABLE)
    1596:         PetscTableFind(rmap,sbuf1_i[ct1]+1,&row);
    1597:         row--;
    1598:         if (row < 0) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_PLIB,"row not found in table");
    1599: #else
    1600:         row = rmap[sbuf1_i[ct1]]; /* the row index in submat */
    1601: #endif
    1602:         /* Now, store row index of submat in sbuf1_i[ct1] */
    1603:         sbuf1_i[ct1] = row;

    1605:         nnz = rbuf2_i[ct1];
    1606:         if (!allcolumns) {
    1607:           for (l=0; l<nnz; l++,ct2++) {
    1608: #if defined(PETSC_USE_CTABLE)
    1609:             if (rbuf3_i[ct2] >= cstart && rbuf3_i[ct2] <cend) {
    1610:               tcol = cmap_loc[rbuf3_i[ct2] - cstart];
    1611:             } else {
    1612:               PetscTableFind(cmap,rbuf3_i[ct2]+1,&tcol);
    1613:             }
    1614: #else
    1615:             tcol = cmap[rbuf3_i[ct2]]; /* column index in submat */
    1616: #endif
    1617:             if (tcol) lens[row]++;
    1618:           }
    1619:         } else { /* allcolumns */
    1620:           lens[row] += nnz;
    1621:         }
    1622:       }
    1623:     }
    1624:     MPI_Waitall(nrqr,s_waits3,s_status3);
    1625:     PetscFree4(r_waits3,s_waits3,r_status3,s_status3);

    1627:     /* Create the submatrices */
    1628:     MatCreate(PETSC_COMM_SELF,&submat);
    1629:     MatSetSizes(submat,nrow,ncol,PETSC_DETERMINE,PETSC_DETERMINE);

    1631:     ISGetBlockSize(isrow[0],&i);
    1632:     ISGetBlockSize(iscol[0],&j);
    1633:     MatSetBlockSizes(submat,i,j);
    1634:     MatSetType(submat,((PetscObject)A)->type_name);
    1635:     MatSeqAIJSetPreallocation(submat,0,lens);

    1637:     /* create struct Mat_SubSppt and attached it to submat */
    1638:     PetscNew(&smatis1);
    1639:     subc = (Mat_SeqAIJ*)submat->data;
    1640:     subc->submatis1 = smatis1;

    1642:     smatis1->id          = 0;
    1643:     smatis1->nrqs        = nrqs;
    1644:     smatis1->nrqr        = nrqr;
    1645:     smatis1->rbuf1       = rbuf1;
    1646:     smatis1->rbuf2       = rbuf2;
    1647:     smatis1->rbuf3       = rbuf3;
    1648:     smatis1->sbuf2       = sbuf2;
    1649:     smatis1->req_source2 = req_source2;

    1651:     smatis1->sbuf1       = sbuf1;
    1652:     smatis1->ptr         = ptr;
    1653:     smatis1->tmp         = tmp;
    1654:     smatis1->ctr         = ctr;

    1656:     smatis1->pa           = pa;
    1657:     smatis1->req_size     = req_size;
    1658:     smatis1->req_source1  = req_source1;

    1660:     smatis1->allcolumns  = allcolumns;
    1661:     smatis1->singleis    = PETSC_TRUE;
    1662:     smatis1->row2proc    = row2proc;
    1663:     smatis1->rmap        = rmap;
    1664:     smatis1->cmap        = cmap;
    1665: #if defined(PETSC_USE_CTABLE)
    1666:     smatis1->rmap_loc    = rmap_loc;
    1667:     smatis1->cmap_loc    = cmap_loc;
    1668: #endif

    1670:     smatis1->destroy     = submat->ops->destroy;
    1671:     submat->ops->destroy = MatDestroySubMatrix_SeqAIJ;
    1672:     submat->factortype   = C->factortype;

    1674:     /* compute rmax */
    1675:     rmax = 0;
    1676:     for (i=0; i<nrow; i++) rmax = PetscMax(rmax,lens[i]);

    1678:   } else { /* scall == MAT_REUSE_MATRIX */
    1679:     submat = submats[0];
    1680:     if (submat->rmap->n != nrow || submat->cmap->n != ncol) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_SIZ,"Cannot reuse matrix. wrong size");

    1682:     subc    = (Mat_SeqAIJ*)submat->data;
    1683:     rmax    = subc->rmax;
    1684:     smatis1 = subc->submatis1;
    1685:     nrqs        = smatis1->nrqs;
    1686:     nrqr        = smatis1->nrqr;
    1687:     rbuf1       = smatis1->rbuf1;
    1688:     rbuf2       = smatis1->rbuf2;
    1689:     rbuf3       = smatis1->rbuf3;
    1690:     req_source2 = smatis1->req_source2;

    1692:     sbuf1     = smatis1->sbuf1;
    1693:     sbuf2     = smatis1->sbuf2;
    1694:     ptr       = smatis1->ptr;
    1695:     tmp       = smatis1->tmp;
    1696:     ctr       = smatis1->ctr;

    1698:     pa         = smatis1->pa;
    1699:     req_size   = smatis1->req_size;
    1700:     req_source1 = smatis1->req_source1;

    1702:     allcolumns = smatis1->allcolumns;
    1703:     row2proc   = smatis1->row2proc;
    1704:     rmap       = smatis1->rmap;
    1705:     cmap       = smatis1->cmap;
    1706: #if defined(PETSC_USE_CTABLE)
    1707:     rmap_loc   = smatis1->rmap_loc;
    1708:     cmap_loc   = smatis1->cmap_loc;
    1709: #endif
    1710:   }

    1712:   /* Post recv matrix values */
    1713:   PetscMalloc3(nrqs,&rbuf4, rmax,&subcols, rmax,&subvals);
    1714:   PetscMalloc4(nrqs,&r_waits4,nrqr,&s_waits4,nrqs,&r_status4,nrqr,&s_status4);
    1715:   PetscObjectGetNewTag((PetscObject)C,&tag4);
    1716:   for (i=0; i<nrqs; ++i) {
    1717:     PetscMalloc1(rbuf2[i][0],&rbuf4[i]);
    1718:     MPI_Irecv(rbuf4[i],rbuf2[i][0],MPIU_SCALAR,req_source2[i],tag4,comm,r_waits4+i);
    1719:   }

    1721:   /* Allocate sending buffers for a->a, and send them off */
    1722:   PetscMalloc1(nrqr,&sbuf_aa);
    1723:   for (i=0,j=0; i<nrqr; i++) j += req_size[i];
    1724:   if (nrqr) {PetscMalloc1(j,&sbuf_aa[0]);}
    1725:   for (i=1; i<nrqr; i++) sbuf_aa[i] = sbuf_aa[i-1] + req_size[i-1];

    1727:   for (i=0; i<nrqr; i++) {
    1728:     rbuf1_i   = rbuf1[i];
    1729:     sbuf_aa_i = sbuf_aa[i];
    1730:     ct1       = 2*rbuf1_i[0]+1;
    1731:     ct2       = 0;
    1732:     /* max1=rbuf1_i[0]; if (max1 != 1) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_PLIB,"max1 !=1"); */

    1734:     kmax = rbuf1_i[2];
    1735:     for (k=0; k<kmax; k++,ct1++) {
    1736:       row = rbuf1_i[ct1] - rstart;
    1737:       nzA = ai[row+1] - ai[row];
    1738:       nzB = bi[row+1] - bi[row];
    1739:       ncols  = nzA + nzB;
    1740:       cworkB = bj + bi[row];
    1741:       vworkA = a_a + ai[row];
    1742:       vworkB = b_a + bi[row];

    1744:       /* load the column values for this row into vals*/
    1745:       vals = sbuf_aa_i + ct2;

    1747:       lwrite = 0;
    1748:       for (l=0; l<nzB; l++) {
    1749:         if ((bmap[cworkB[l]]) < cstart) vals[lwrite++] = vworkB[l];
    1750:       }
    1751:       for (l=0; l<nzA; l++) vals[lwrite++] = vworkA[l];
    1752:       for (l=0; l<nzB; l++) {
    1753:         if ((bmap[cworkB[l]]) >= cend) vals[lwrite++] = vworkB[l];
    1754:       }

    1756:       ct2 += ncols;
    1757:     }
    1758:     MPI_Isend(sbuf_aa_i,req_size[i],MPIU_SCALAR,req_source1[i],tag4,comm,s_waits4+i);
    1759:   }

    1761:   /* Assemble submat */
    1762:   /* First assemble the local rows */
    1763:   for (j=0; j<nrow; j++) {
    1764:     row  = irow[j];
    1765:     proc = row2proc[j];
    1766:     if (proc == rank) {
    1767:       Crow = row - rstart;  /* local row index of C */
    1768: #if defined(PETSC_USE_CTABLE)
    1769:       row = rmap_loc[Crow]; /* row index of submat */
    1770: #else
    1771:       row = rmap[row];
    1772: #endif

    1774:       if (allcolumns) {
    1775:         /* diagonal part A = c->A */
    1776:         ncols = ai[Crow+1] - ai[Crow];
    1777:         cols  = aj + ai[Crow];
    1778:         vals  = a_a + ai[Crow];
    1779:         i     = 0;
    1780:         for (k=0; k<ncols; k++) {
    1781:           subcols[i]   = cols[k] + cstart;
    1782:           subvals[i++] = vals[k];
    1783:         }

    1785:         /* off-diagonal part B = c->B */
    1786:         ncols = bi[Crow+1] - bi[Crow];
    1787:         cols  = bj + bi[Crow];
    1788:         vals  = b_a + bi[Crow];
    1789:         for (k=0; k<ncols; k++) {
    1790:           subcols[i]   = bmap[cols[k]];
    1791:           subvals[i++] = vals[k];
    1792:         }

    1794:         MatSetValues_SeqAIJ(submat,1,&row,i,subcols,subvals,INSERT_VALUES);

    1796:       } else { /* !allcolumns */
    1797: #if defined(PETSC_USE_CTABLE)
    1798:         /* diagonal part A = c->A */
    1799:         ncols = ai[Crow+1] - ai[Crow];
    1800:         cols  = aj + ai[Crow];
    1801:         vals  = a_a + ai[Crow];
    1802:         i     = 0;
    1803:         for (k=0; k<ncols; k++) {
    1804:           tcol = cmap_loc[cols[k]];
    1805:           if (tcol) {
    1806:             subcols[i]   = --tcol;
    1807:             subvals[i++] = vals[k];
    1808:           }
    1809:         }

    1811:         /* off-diagonal part B = c->B */
    1812:         ncols = bi[Crow+1] - bi[Crow];
    1813:         cols  = bj + bi[Crow];
    1814:         vals  = b_a + bi[Crow];
    1815:         for (k=0; k<ncols; k++) {
    1816:           PetscTableFind(cmap,bmap[cols[k]]+1,&tcol);
    1817:           if (tcol) {
    1818:             subcols[i]   = --tcol;
    1819:             subvals[i++] = vals[k];
    1820:           }
    1821:         }
    1822: #else
    1823:         /* diagonal part A = c->A */
    1824:         ncols = ai[Crow+1] - ai[Crow];
    1825:         cols  = aj + ai[Crow];
    1826:         vals  = a_a + ai[Crow];
    1827:         i     = 0;
    1828:         for (k=0; k<ncols; k++) {
    1829:           tcol = cmap[cols[k]+cstart];
    1830:           if (tcol) {
    1831:             subcols[i]   = --tcol;
    1832:             subvals[i++] = vals[k];
    1833:           }
    1834:         }

    1836:         /* off-diagonal part B = c->B */
    1837:         ncols = bi[Crow+1] - bi[Crow];
    1838:         cols  = bj + bi[Crow];
    1839:         vals  = b_a + bi[Crow];
    1840:         for (k=0; k<ncols; k++) {
    1841:           tcol = cmap[bmap[cols[k]]];
    1842:           if (tcol) {
    1843:             subcols[i]   = --tcol;
    1844:             subvals[i++] = vals[k];
    1845:           }
    1846:         }
    1847: #endif
    1848:         MatSetValues_SeqAIJ(submat,1,&row,i,subcols,subvals,INSERT_VALUES);
    1849:       }
    1850:     }
    1851:   }

    1853:   /* Now assemble the off-proc rows */
    1854:   for (i=0; i<nrqs; i++) { /* for each requested message */
    1855:     /* recv values from other processes */
    1856:     MPI_Waitany(nrqs,r_waits4,&idex,r_status4+i);
    1857:     proc    = pa[idex];
    1858:     sbuf1_i = sbuf1[proc];
    1859:     /* jmax    = sbuf1_i[0]; if (jmax != 1)SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_PLIB,"jmax %d != 1",jmax); */
    1860:     ct1     = 2 + 1;
    1861:     ct2     = 0; /* count of received C->j */
    1862:     ct3     = 0; /* count of received C->j that will be inserted into submat */
    1863:     rbuf2_i = rbuf2[idex]; /* int** received length of C->j from other processes */
    1864:     rbuf3_i = rbuf3[idex]; /* int** received C->j from other processes */
    1865:     rbuf4_i = rbuf4[idex]; /* scalar** received C->a from other processes */

    1867:     /* is_no = sbuf1_i[2*j-1]; if (is_no != 0) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_PLIB,"is_no !=0"); */
    1868:     max1 = sbuf1_i[2];             /* num of rows */
    1869:     for (k=0; k<max1; k++,ct1++) { /* for each recved row */
    1870:       row = sbuf1_i[ct1]; /* row index of submat */
    1871:       if (!allcolumns) {
    1872:         idex = 0;
    1873:         if (scall == MAT_INITIAL_MATRIX || !iscolsorted) {
    1874:           nnz  = rbuf2_i[ct1]; /* num of C entries in this row */
    1875:           for (l=0; l<nnz; l++,ct2++) { /* for each recved column */
    1876: #if defined(PETSC_USE_CTABLE)
    1877:             if (rbuf3_i[ct2] >= cstart && rbuf3_i[ct2] <cend) {
    1878:               tcol = cmap_loc[rbuf3_i[ct2] - cstart];
    1879:             } else {
    1880:               PetscTableFind(cmap,rbuf3_i[ct2]+1,&tcol);
    1881:             }
    1882: #else
    1883:             tcol = cmap[rbuf3_i[ct2]];
    1884: #endif
    1885:             if (tcol) {
    1886:               subcols[idex]   = --tcol; /* may not be sorted */
    1887:               subvals[idex++] = rbuf4_i[ct2];

    1889:               /* We receive an entire column of C, but a subset of it needs to be inserted into submat.
    1890:                For reuse, we replace received C->j with index that should be inserted to submat */
    1891:               if (iscolsorted) rbuf3_i[ct3++] = ct2;
    1892:             }
    1893:           }
    1894:           MatSetValues_SeqAIJ(submat,1,&row,idex,subcols,subvals,INSERT_VALUES);
    1895:         } else { /* scall == MAT_REUSE_MATRIX */
    1896:           submat = submats[0];
    1897:           subc   = (Mat_SeqAIJ*)submat->data;

    1899:           nnz = subc->i[row+1] - subc->i[row]; /* num of submat entries in this row */
    1900:           for (l=0; l<nnz; l++) {
    1901:             ct2 = rbuf3_i[ct3++]; /* index of rbuf4_i[] which needs to be inserted into submat */
    1902:             subvals[idex++] = rbuf4_i[ct2];
    1903:           }

    1905:           bj = subc->j + subc->i[row]; /* sorted column indices */
    1906:           MatSetValues_SeqAIJ(submat,1,&row,nnz,bj,subvals,INSERT_VALUES);
    1907:         }
    1908:       } else { /* allcolumns */
    1909:         nnz  = rbuf2_i[ct1]; /* num of C entries in this row */
    1910:         MatSetValues_SeqAIJ(submat,1,&row,nnz,rbuf3_i+ct2,rbuf4_i+ct2,INSERT_VALUES);
    1911:         ct2 += nnz;
    1912:       }
    1913:     }
    1914:   }

    1916:   /* sending a->a are done */
    1917:   MPI_Waitall(nrqr,s_waits4,s_status4);
    1918:   PetscFree4(r_waits4,s_waits4,r_status4,s_status4);

    1920:   MatAssemblyBegin(submat,MAT_FINAL_ASSEMBLY);
    1921:   MatAssemblyEnd(submat,MAT_FINAL_ASSEMBLY);
    1922:   submats[0] = submat;

    1924:   /* Restore the indices */
    1925:   ISRestoreIndices(isrow[0],&irow);
    1926:   if (!allcolumns) {
    1927:     ISRestoreIndices(iscol[0],&icol);
    1928:   }

    1930:   /* Destroy allocated memory */
    1931:   for (i=0; i<nrqs; ++i) {
    1932:     PetscFree(rbuf4[i]);
    1933:   }
    1934:   PetscFree3(rbuf4,subcols,subvals);
    1935:   if (sbuf_aa) {
    1936:     PetscFree(sbuf_aa[0]);
    1937:     PetscFree(sbuf_aa);
    1938:   }

    1940:   if (scall == MAT_INITIAL_MATRIX) {
    1941:     PetscFree(lens);
    1942:     if (sbuf_aj) {
    1943:       PetscFree(sbuf_aj[0]);
    1944:       PetscFree(sbuf_aj);
    1945:     }
    1946:   }
    1947:   MatSeqAIJRestoreArrayRead(A,(const PetscScalar**)&a_a);
    1948:   MatSeqAIJRestoreArrayRead(B,(const PetscScalar**)&b_a);
    1949:   return(0);
    1950: }

    1952: PetscErrorCode MatCreateSubMatrices_MPIAIJ_SingleIS(Mat C,PetscInt ismax,const IS isrow[],const IS iscol[],MatReuse scall,Mat *submat[])
    1953: {
    1955:   PetscInt       ncol;
    1956:   PetscBool      colflag,allcolumns=PETSC_FALSE;

    1959:   /* Allocate memory to hold all the submatrices */
    1960:   if (scall == MAT_INITIAL_MATRIX) {
    1961:     PetscCalloc1(2,submat);
    1962:   }

    1964:   /* Check for special case: each processor gets entire matrix columns */
    1965:   ISIdentity(iscol[0],&colflag);
    1966:   ISGetLocalSize(iscol[0],&ncol);
    1967:   if (colflag && ncol == C->cmap->N) allcolumns = PETSC_TRUE;

    1969:   MatCreateSubMatrices_MPIAIJ_SingleIS_Local(C,ismax,isrow,iscol,scall,allcolumns,*submat);
    1970:   return(0);
    1971: }

    1973: PetscErrorCode MatCreateSubMatrices_MPIAIJ(Mat C,PetscInt ismax,const IS isrow[],const IS iscol[],MatReuse scall,Mat *submat[])
    1974: {
    1976:   PetscInt       nmax,nstages=0,i,pos,max_no,nrow,ncol,in[2],out[2];
    1977:   PetscBool      rowflag,colflag,wantallmatrix=PETSC_FALSE;
    1978:   Mat_SeqAIJ     *subc;
    1979:   Mat_SubSppt    *smat;

    1982:   /* Check for special case: each processor has a single IS */
    1983:   if (C->submat_singleis) { /* flag is set in PCSetUp_ASM() to skip MPI_Allreduce() */
    1984:     MatCreateSubMatrices_MPIAIJ_SingleIS(C,ismax,isrow,iscol,scall,submat);
    1985:     C->submat_singleis = PETSC_FALSE; /* resume its default value in case C will be used for non-single IS */
    1986:     return(0);
    1987:   }

    1989:   /* Collect global wantallmatrix and nstages */
    1990:   if (!C->cmap->N) nmax=20*1000000/sizeof(PetscInt);
    1991:   else nmax = 20*1000000 / (C->cmap->N * sizeof(PetscInt));
    1992:   if (!nmax) nmax = 1;

    1994:   if (scall == MAT_INITIAL_MATRIX) {
    1995:     /* Collect global wantallmatrix and nstages */
    1996:     if (ismax == 1 && C->rmap->N == C->cmap->N) {
    1997:       ISIdentity(*isrow,&rowflag);
    1998:       ISIdentity(*iscol,&colflag);
    1999:       ISGetLocalSize(*isrow,&nrow);
    2000:       ISGetLocalSize(*iscol,&ncol);
    2001:       if (rowflag && colflag && nrow == C->rmap->N && ncol == C->cmap->N) {
    2002:         wantallmatrix = PETSC_TRUE;

    2004:         PetscOptionsGetBool(((PetscObject)C)->options,((PetscObject)C)->prefix,"-use_fast_submatrix",&wantallmatrix,NULL);
    2005:       }
    2006:     }

    2008:     /* Determine the number of stages through which submatrices are done
    2009:        Each stage will extract nmax submatrices.
    2010:        nmax is determined by the matrix column dimension.
    2011:        If the original matrix has 20M columns, only one submatrix per stage is allowed, etc.
    2012:     */
    2013:     nstages = ismax/nmax + ((ismax % nmax) ? 1 : 0); /* local nstages */

    2015:     in[0] = -1*(PetscInt)wantallmatrix;
    2016:     in[1] = nstages;
    2017:     MPIU_Allreduce(in,out,2,MPIU_INT,MPI_MAX,PetscObjectComm((PetscObject)C));
    2018:     wantallmatrix = (PetscBool)(-out[0]);
    2019:     nstages       = out[1]; /* Make sure every processor loops through the global nstages */

    2021:   } else { /* MAT_REUSE_MATRIX */
    2022:     if (ismax) {
    2023:       subc = (Mat_SeqAIJ*)(*submat)[0]->data;
    2024:       smat = subc->submatis1;
    2025:     } else { /* (*submat)[0] is a dummy matrix */
    2026:       smat = (Mat_SubSppt*)(*submat)[0]->data;
    2027:     }
    2028:     if (!smat) {
    2029:       /* smat is not generated by MatCreateSubMatrix_MPIAIJ_All(...,MAT_INITIAL_MATRIX,...) */
    2030:       wantallmatrix = PETSC_TRUE;
    2031:     } else if (smat->singleis) {
    2032:       MatCreateSubMatrices_MPIAIJ_SingleIS(C,ismax,isrow,iscol,scall,submat);
    2033:       return(0);
    2034:     } else {
    2035:       nstages = smat->nstages;
    2036:     }
    2037:   }

    2039:   if (wantallmatrix) {
    2040:     MatCreateSubMatrix_MPIAIJ_All(C,MAT_GET_VALUES,scall,submat);
    2041:     return(0);
    2042:   }

    2044:   /* Allocate memory to hold all the submatrices and dummy submatrices */
    2045:   if (scall == MAT_INITIAL_MATRIX) {
    2046:     PetscCalloc1(ismax+nstages,submat);
    2047:   }

    2049:   for (i=0,pos=0; i<nstages; i++) {
    2050:     if (pos+nmax <= ismax) max_no = nmax;
    2051:     else if (pos >= ismax) max_no = 0;
    2052:     else                   max_no = ismax-pos;

    2054:     MatCreateSubMatrices_MPIAIJ_Local(C,max_no,isrow+pos,iscol+pos,scall,*submat+pos);
    2055:     if (!max_no) {
    2056:       if (scall == MAT_INITIAL_MATRIX) { /* submat[pos] is a dummy matrix */
    2057:         smat = (Mat_SubSppt*)(*submat)[pos]->data;
    2058:         smat->nstages = nstages;
    2059:       }
    2060:       pos++; /* advance to next dummy matrix if any */
    2061:     } else pos += max_no;
    2062:   }

    2064:   if (ismax && scall == MAT_INITIAL_MATRIX) {
    2065:     /* save nstages for reuse */
    2066:     subc = (Mat_SeqAIJ*)(*submat)[0]->data;
    2067:     smat = subc->submatis1;
    2068:     smat->nstages = nstages;
    2069:   }
    2070:   return(0);
    2071: }

    2073: /* -------------------------------------------------------------------------*/
    2074: PetscErrorCode MatCreateSubMatrices_MPIAIJ_Local(Mat C,PetscInt ismax,const IS isrow[],const IS iscol[],MatReuse scall,Mat *submats)
    2075: {
    2076:   Mat_MPIAIJ     *c = (Mat_MPIAIJ*)C->data;
    2077:   Mat            A  = c->A;
    2078:   Mat_SeqAIJ     *a = (Mat_SeqAIJ*)A->data,*b = (Mat_SeqAIJ*)c->B->data,*subc;
    2079:   const PetscInt **icol,**irow;
    2080:   PetscInt       *nrow,*ncol,start;
    2082:   PetscMPIInt    rank,size,tag0,tag2,tag3,tag4,*w1,*w2,*w3,*w4,nrqr;
    2083:   PetscInt       **sbuf1,**sbuf2,i,j,k,l,ct1,ct2,**rbuf1,row,proc=-1;
    2084:   PetscInt       nrqs=0,msz,**ptr=NULL,*req_size=NULL,*ctr=NULL,*pa,*tmp=NULL,tcol;
    2085:   PetscInt       **rbuf3=NULL,*req_source1=NULL,*req_source2,**sbuf_aj,**rbuf2=NULL,max1,max2;
    2086:   PetscInt       **lens,is_no,ncols,*cols,mat_i,*mat_j,tmp2,jmax;
    2087: #if defined(PETSC_USE_CTABLE)
    2088:   PetscTable     *cmap,cmap_i=NULL,*rmap,rmap_i;
    2089: #else
    2090:   PetscInt       **cmap,*cmap_i=NULL,**rmap,*rmap_i;
    2091: #endif
    2092:   const PetscInt *irow_i;
    2093:   PetscInt       ctr_j,*sbuf1_j,*sbuf_aj_i,*rbuf1_i,kmax,*lens_i;
    2094:   MPI_Request    *s_waits1,*r_waits1,*s_waits2,*r_waits2,*r_waits3;
    2095:   MPI_Request    *r_waits4,*s_waits3,*s_waits4;
    2096:   MPI_Comm       comm;
    2097:   PetscScalar    **rbuf4,*rbuf4_i,**sbuf_aa,*vals,*mat_a,*imat_a,*sbuf_aa_i;
    2098:   PetscMPIInt    *onodes1,*olengths1,end;
    2099:   PetscInt       **row2proc,*row2proc_i,ilen_row,*imat_ilen,*imat_j,*imat_i,old_row;
    2100:   Mat_SubSppt    *smat_i;
    2101:   PetscBool      *issorted,*allcolumns,colflag,iscsorted=PETSC_TRUE;
    2102:   PetscInt       *sbuf1_i,*rbuf2_i,*rbuf3_i,ilen;

    2105:   PetscObjectGetComm((PetscObject)C,&comm);
    2106:   size = c->size;
    2107:   rank = c->rank;

    2109:   PetscMalloc4(ismax,&row2proc,ismax,&cmap,ismax,&rmap,ismax+1,&allcolumns);
    2110:   PetscMalloc5(ismax,(PetscInt***)&irow,ismax,(PetscInt***)&icol,ismax,&nrow,ismax,&ncol,ismax,&issorted);

    2112:   for (i=0; i<ismax; i++) {
    2113:     ISSorted(iscol[i],&issorted[i]);
    2114:     if (!issorted[i]) iscsorted = issorted[i];

    2116:     ISSorted(isrow[i],&issorted[i]);

    2118:     ISGetIndices(isrow[i],&irow[i]);
    2119:     ISGetLocalSize(isrow[i],&nrow[i]);

    2121:     /* Check for special case: allcolumn */
    2122:     ISIdentity(iscol[i],&colflag);
    2123:     ISGetLocalSize(iscol[i],&ncol[i]);
    2124:     if (colflag && ncol[i] == C->cmap->N) {
    2125:       allcolumns[i] = PETSC_TRUE;
    2126:       icol[i] = NULL;
    2127:     } else {
    2128:       allcolumns[i] = PETSC_FALSE;
    2129:       ISGetIndices(iscol[i],&icol[i]);
    2130:     }
    2131:   }

    2133:   if (scall == MAT_REUSE_MATRIX) {
    2134:     /* Assumes new rows are same length as the old rows */
    2135:     for (i=0; i<ismax; i++) {
    2136:       if (!submats[i]) SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_ARG_NULL,"submats[%D] is null, cannot reuse",i);
    2137:       subc = (Mat_SeqAIJ*)submats[i]->data;
    2138:       if ((submats[i]->rmap->n != nrow[i]) || (submats[i]->cmap->n != ncol[i])) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_SIZ,"Cannot reuse matrix. wrong size");

    2140:       /* Initial matrix as if empty */
    2141:       PetscArrayzero(subc->ilen,submats[i]->rmap->n);

    2143:       smat_i   = subc->submatis1;

    2145:       nrqs        = smat_i->nrqs;
    2146:       nrqr        = smat_i->nrqr;
    2147:       rbuf1       = smat_i->rbuf1;
    2148:       rbuf2       = smat_i->rbuf2;
    2149:       rbuf3       = smat_i->rbuf3;
    2150:       req_source2 = smat_i->req_source2;

    2152:       sbuf1     = smat_i->sbuf1;
    2153:       sbuf2     = smat_i->sbuf2;
    2154:       ptr       = smat_i->ptr;
    2155:       tmp       = smat_i->tmp;
    2156:       ctr       = smat_i->ctr;

    2158:       pa          = smat_i->pa;
    2159:       req_size    = smat_i->req_size;
    2160:       req_source1 = smat_i->req_source1;

    2162:       allcolumns[i] = smat_i->allcolumns;
    2163:       row2proc[i]   = smat_i->row2proc;
    2164:       rmap[i]       = smat_i->rmap;
    2165:       cmap[i]       = smat_i->cmap;
    2166:     }

    2168:     if (!ismax) { /* Get dummy submatrices and retrieve struct submatis1 */
    2169:       if (!submats[0]) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_NULL,"submats are null, cannot reuse");
    2170:       smat_i = (Mat_SubSppt*)submats[0]->data;

    2172:       nrqs        = smat_i->nrqs;
    2173:       nrqr        = smat_i->nrqr;
    2174:       rbuf1       = smat_i->rbuf1;
    2175:       rbuf2       = smat_i->rbuf2;
    2176:       rbuf3       = smat_i->rbuf3;
    2177:       req_source2 = smat_i->req_source2;

    2179:       sbuf1       = smat_i->sbuf1;
    2180:       sbuf2       = smat_i->sbuf2;
    2181:       ptr         = smat_i->ptr;
    2182:       tmp         = smat_i->tmp;
    2183:       ctr         = smat_i->ctr;

    2185:       pa          = smat_i->pa;
    2186:       req_size    = smat_i->req_size;
    2187:       req_source1 = smat_i->req_source1;

    2189:       allcolumns[0] = PETSC_FALSE;
    2190:     }
    2191:   } else { /* scall == MAT_INITIAL_MATRIX */
    2192:     /* Get some new tags to keep the communication clean */
    2193:     PetscObjectGetNewTag((PetscObject)C,&tag2);
    2194:     PetscObjectGetNewTag((PetscObject)C,&tag3);

    2196:     /* evaluate communication - mesg to who, length of mesg, and buffer space
    2197:      required. Based on this, buffers are allocated, and data copied into them*/
    2198:     PetscCalloc4(size,&w1,size,&w2,size,&w3,size,&w4);   /* mesg size, initialize work vectors */

    2200:     for (i=0; i<ismax; i++) {
    2201:       jmax   = nrow[i];
    2202:       irow_i = irow[i];

    2204:       PetscMalloc1(jmax,&row2proc_i);
    2205:       row2proc[i] = row2proc_i;

    2207:       if (issorted[i]) proc = 0;
    2208:       for (j=0; j<jmax; j++) {
    2209:         if (!issorted[i]) proc = 0;
    2210:         row = irow_i[j];
    2211:         while (row >= C->rmap->range[proc+1]) proc++;
    2212:         w4[proc]++;
    2213:         row2proc_i[j] = proc; /* map row index to proc */
    2214:       }
    2215:       for (j=0; j<size; j++) {
    2216:         if (w4[j]) { w1[j] += w4[j];  w3[j]++; w4[j] = 0;}
    2217:       }
    2218:     }

    2220:     nrqs     = 0;              /* no of outgoing messages */
    2221:     msz      = 0;              /* total mesg length (for all procs) */
    2222:     w1[rank] = 0;              /* no mesg sent to self */
    2223:     w3[rank] = 0;
    2224:     for (i=0; i<size; i++) {
    2225:       if (w1[i])  { w2[i] = 1; nrqs++;} /* there exists a message to proc i */
    2226:     }
    2227:     PetscMalloc1(nrqs,&pa); /*(proc -array)*/
    2228:     for (i=0,j=0; i<size; i++) {
    2229:       if (w1[i]) { pa[j] = i; j++; }
    2230:     }

    2232:     /* Each message would have a header = 1 + 2*(no of IS) + data */
    2233:     for (i=0; i<nrqs; i++) {
    2234:       j      = pa[i];
    2235:       w1[j] += w2[j] + 2* w3[j];
    2236:       msz   += w1[j];
    2237:     }
    2238:     PetscInfo2(0,"Number of outgoing messages %D Total message length %D\n",nrqs,msz);

    2240:     /* Determine the number of messages to expect, their lengths, from from-ids */
    2241:     PetscGatherNumberOfMessages(comm,w2,w1,&nrqr);
    2242:     PetscGatherMessageLengths(comm,nrqs,nrqr,w1,&onodes1,&olengths1);

    2244:     /* Now post the Irecvs corresponding to these messages */
    2245:     PetscObjectGetNewTag((PetscObject)C,&tag0);
    2246:     PetscPostIrecvInt(comm,tag0,nrqr,onodes1,olengths1,&rbuf1,&r_waits1);

    2248:     /* Allocate Memory for outgoing messages */
    2249:     PetscMalloc4(size,&sbuf1,size,&ptr,2*msz,&tmp,size,&ctr);
    2250:     PetscArrayzero(sbuf1,size);
    2251:     PetscArrayzero(ptr,size);

    2253:     {
    2254:       PetscInt *iptr = tmp;
    2255:       k    = 0;
    2256:       for (i=0; i<nrqs; i++) {
    2257:         j        = pa[i];
    2258:         iptr    += k;
    2259:         sbuf1[j] = iptr;
    2260:         k        = w1[j];
    2261:       }
    2262:     }

    2264:     /* Form the outgoing messages. Initialize the header space */
    2265:     for (i=0; i<nrqs; i++) {
    2266:       j           = pa[i];
    2267:       sbuf1[j][0] = 0;
    2268:       PetscArrayzero(sbuf1[j]+1,2*w3[j]);
    2269:       ptr[j]      = sbuf1[j] + 2*w3[j] + 1;
    2270:     }

    2272:     /* Parse the isrow and copy data into outbuf */
    2273:     for (i=0; i<ismax; i++) {
    2274:       row2proc_i = row2proc[i];
    2275:       PetscArrayzero(ctr,size);
    2276:       irow_i = irow[i];
    2277:       jmax   = nrow[i];
    2278:       for (j=0; j<jmax; j++) {  /* parse the indices of each IS */
    2279:         proc = row2proc_i[j];
    2280:         if (proc != rank) { /* copy to the outgoing buf*/
    2281:           ctr[proc]++;
    2282:           *ptr[proc] = irow_i[j];
    2283:           ptr[proc]++;
    2284:         }
    2285:       }
    2286:       /* Update the headers for the current IS */
    2287:       for (j=0; j<size; j++) { /* Can Optimise this loop too */
    2288:         if ((ctr_j = ctr[j])) {
    2289:           sbuf1_j        = sbuf1[j];
    2290:           k              = ++sbuf1_j[0];
    2291:           sbuf1_j[2*k]   = ctr_j;
    2292:           sbuf1_j[2*k-1] = i;
    2293:         }
    2294:       }
    2295:     }

    2297:     /*  Now  post the sends */
    2298:     PetscMalloc1(nrqs,&s_waits1);
    2299:     for (i=0; i<nrqs; ++i) {
    2300:       j    = pa[i];
    2301:       MPI_Isend(sbuf1[j],w1[j],MPIU_INT,j,tag0,comm,s_waits1+i);
    2302:     }

    2304:     /* Post Receives to capture the buffer size */
    2305:     PetscMalloc1(nrqs,&r_waits2);
    2306:     PetscMalloc3(nrqs,&req_source2,nrqs,&rbuf2,nrqs,&rbuf3);
    2307:     if (nrqs) rbuf2[0] = tmp + msz;
    2308:     for (i=1; i<nrqs; ++i) {
    2309:       rbuf2[i] = rbuf2[i-1]+w1[pa[i-1]];
    2310:     }
    2311:     for (i=0; i<nrqs; ++i) {
    2312:       j    = pa[i];
    2313:       MPI_Irecv(rbuf2[i],w1[j],MPIU_INT,j,tag2,comm,r_waits2+i);
    2314:     }

    2316:     /* Send to other procs the buf size they should allocate */
    2317:     /* Receive messages*/
    2318:     PetscMalloc1(nrqr,&s_waits2);
    2319:     PetscMalloc3(nrqr,&sbuf2,nrqr,&req_size,nrqr,&req_source1);
    2320:     {
    2321:       PetscInt   *sAi = a->i,*sBi = b->i,id,rstart = C->rmap->rstart;
    2322:       PetscInt   *sbuf2_i;

    2324:       MPI_Waitall(nrqr,r_waits1,MPI_STATUSES_IGNORE);
    2325:       for (i=0; i<nrqr; ++i) {
    2326:         req_size[i] = 0;
    2327:         rbuf1_i        = rbuf1[i];
    2328:         start          = 2*rbuf1_i[0] + 1;
    2329:         end            = olengths1[i];
    2330:         PetscMalloc1(end,&sbuf2[i]);
    2331:         sbuf2_i        = sbuf2[i];
    2332:         for (j=start; j<end; j++) {
    2333:           id              = rbuf1_i[j] - rstart;
    2334:           ncols           = sAi[id+1] - sAi[id] + sBi[id+1] - sBi[id];
    2335:           sbuf2_i[j]      = ncols;
    2336:           req_size[i] += ncols;
    2337:         }
    2338:         req_source1[i] = onodes1[i];
    2339:         /* form the header */
    2340:         sbuf2_i[0] = req_size[i];
    2341:         for (j=1; j<start; j++) sbuf2_i[j] = rbuf1_i[j];

    2343:         MPI_Isend(sbuf2_i,end,MPIU_INT,req_source1[i],tag2,comm,s_waits2+i);
    2344:       }
    2345:     }

    2347:     PetscFree(onodes1);
    2348:     PetscFree(olengths1);
    2349:     PetscFree(r_waits1);
    2350:     PetscFree4(w1,w2,w3,w4);

    2352:     /* Receive messages*/
    2353:     PetscMalloc1(nrqs,&r_waits3);
    2354:     MPI_Waitall(nrqs,r_waits2,MPI_STATUSES_IGNORE);
    2355:     for (i=0; i<nrqs; ++i) {
    2356:       PetscMalloc1(rbuf2[i][0],&rbuf3[i]);
    2357:       req_source2[i] = pa[i];
    2358:       MPI_Irecv(rbuf3[i],rbuf2[i][0],MPIU_INT,req_source2[i],tag3,comm,r_waits3+i);
    2359:     }
    2360:     PetscFree(r_waits2);

    2362:     /* Wait on sends1 and sends2 */
    2363:     MPI_Waitall(nrqs,s_waits1,MPI_STATUSES_IGNORE);
    2364:     MPI_Waitall(nrqr,s_waits2,MPI_STATUSES_IGNORE);
    2365:     PetscFree(s_waits1);
    2366:     PetscFree(s_waits2);

    2368:     /* Now allocate sending buffers for a->j, and send them off */
    2369:     PetscMalloc1(nrqr,&sbuf_aj);
    2370:     for (i=0,j=0; i<nrqr; i++) j += req_size[i];
    2371:     if (nrqr) {PetscMalloc1(j,&sbuf_aj[0]);}
    2372:     for (i=1; i<nrqr; i++) sbuf_aj[i] = sbuf_aj[i-1] + req_size[i-1];

    2374:     PetscMalloc1(nrqr,&s_waits3);
    2375:     {
    2376:       PetscInt nzA,nzB,*a_i = a->i,*b_i = b->i,lwrite;
    2377:       PetscInt *cworkA,*cworkB,cstart = C->cmap->rstart,rstart = C->rmap->rstart,*bmap = c->garray;
    2378:       PetscInt cend = C->cmap->rend;
    2379:       PetscInt *a_j = a->j,*b_j = b->j,ctmp;

    2381:       for (i=0; i<nrqr; i++) {
    2382:         rbuf1_i   = rbuf1[i];
    2383:         sbuf_aj_i = sbuf_aj[i];
    2384:         ct1       = 2*rbuf1_i[0] + 1;
    2385:         ct2       = 0;
    2386:         for (j=1,max1=rbuf1_i[0]; j<=max1; j++) {
    2387:           kmax = rbuf1[i][2*j];
    2388:           for (k=0; k<kmax; k++,ct1++) {
    2389:             row    = rbuf1_i[ct1] - rstart;
    2390:             nzA    = a_i[row+1] - a_i[row];
    2391:             nzB    = b_i[row+1] - b_i[row];
    2392:             ncols  = nzA + nzB;
    2393:             cworkA = a_j + a_i[row];
    2394:             cworkB = b_j + b_i[row];

    2396:             /* load the column indices for this row into cols */
    2397:             cols = sbuf_aj_i + ct2;

    2399:             lwrite = 0;
    2400:             for (l=0; l<nzB; l++) {
    2401:               if ((ctmp = bmap[cworkB[l]]) < cstart) cols[lwrite++] = ctmp;
    2402:             }
    2403:             for (l=0; l<nzA; l++) cols[lwrite++] = cstart + cworkA[l];
    2404:             for (l=0; l<nzB; l++) {
    2405:               if ((ctmp = bmap[cworkB[l]]) >= cend) cols[lwrite++] = ctmp;
    2406:             }

    2408:             ct2 += ncols;
    2409:           }
    2410:         }
    2411:         MPI_Isend(sbuf_aj_i,req_size[i],MPIU_INT,req_source1[i],tag3,comm,s_waits3+i);
    2412:       }
    2413:     }

    2415:     /* create col map: global col of C -> local col of submatrices */
    2416:     {
    2417:       const PetscInt *icol_i;
    2418: #if defined(PETSC_USE_CTABLE)
    2419:       for (i=0; i<ismax; i++) {
    2420:         if (!allcolumns[i]) {
    2421:           PetscTableCreate(ncol[i],C->cmap->N,&cmap[i]);

    2423:           jmax   = ncol[i];
    2424:           icol_i = icol[i];
    2425:           cmap_i = cmap[i];
    2426:           for (j=0; j<jmax; j++) {
    2427:             PetscTableAdd(cmap[i],icol_i[j]+1,j+1,INSERT_VALUES);
    2428:           }
    2429:         } else cmap[i] = NULL;
    2430:       }
    2431: #else
    2432:       for (i=0; i<ismax; i++) {
    2433:         if (!allcolumns[i]) {
    2434:           PetscCalloc1(C->cmap->N,&cmap[i]);
    2435:           jmax   = ncol[i];
    2436:           icol_i = icol[i];
    2437:           cmap_i = cmap[i];
    2438:           for (j=0; j<jmax; j++) {
    2439:             cmap_i[icol_i[j]] = j+1;
    2440:           }
    2441:         } else cmap[i] = NULL;
    2442:       }
    2443: #endif
    2444:     }

    2446:     /* Create lens which is required for MatCreate... */
    2447:     for (i=0,j=0; i<ismax; i++) j += nrow[i];
    2448:     PetscMalloc1(ismax,&lens);

    2450:     if (ismax) {
    2451:       PetscCalloc1(j,&lens[0]);
    2452:     }
    2453:     for (i=1; i<ismax; i++) lens[i] = lens[i-1] + nrow[i-1];

    2455:     /* Update lens from local data */
    2456:     for (i=0; i<ismax; i++) {
    2457:       row2proc_i = row2proc[i];
    2458:       jmax = nrow[i];
    2459:       if (!allcolumns[i]) cmap_i = cmap[i];
    2460:       irow_i = irow[i];
    2461:       lens_i = lens[i];
    2462:       for (j=0; j<jmax; j++) {
    2463:         row = irow_i[j];
    2464:         proc = row2proc_i[j];
    2465:         if (proc == rank) {
    2466:           MatGetRow_MPIAIJ(C,row,&ncols,&cols,NULL);
    2467:           if (!allcolumns[i]) {
    2468:             for (k=0; k<ncols; k++) {
    2469: #if defined(PETSC_USE_CTABLE)
    2470:               PetscTableFind(cmap_i,cols[k]+1,&tcol);
    2471: #else
    2472:               tcol = cmap_i[cols[k]];
    2473: #endif
    2474:               if (tcol) lens_i[j]++;
    2475:             }
    2476:           } else { /* allcolumns */
    2477:             lens_i[j] = ncols;
    2478:           }
    2479:           MatRestoreRow_MPIAIJ(C,row,&ncols,&cols,NULL);
    2480:         }
    2481:       }
    2482:     }

    2484:     /* Create row map: global row of C -> local row of submatrices */
    2485: #if defined(PETSC_USE_CTABLE)
    2486:     for (i=0; i<ismax; i++) {
    2487:       PetscTableCreate(nrow[i],C->rmap->N,&rmap[i]);
    2488:       irow_i = irow[i];
    2489:       jmax   = nrow[i];
    2490:       for (j=0; j<jmax; j++) {
    2491:       PetscTableAdd(rmap[i],irow_i[j]+1,j+1,INSERT_VALUES);
    2492:       }
    2493:     }
    2494: #else
    2495:     for (i=0; i<ismax; i++) {
    2496:       PetscCalloc1(C->rmap->N,&rmap[i]);
    2497:       rmap_i = rmap[i];
    2498:       irow_i = irow[i];
    2499:       jmax   = nrow[i];
    2500:       for (j=0; j<jmax; j++) {
    2501:         rmap_i[irow_i[j]] = j;
    2502:       }
    2503:     }
    2504: #endif

    2506:     /* Update lens from offproc data */
    2507:     {
    2508:       PetscInt *rbuf2_i,*rbuf3_i,*sbuf1_i;

    2510:       MPI_Waitall(nrqs,r_waits3,MPI_STATUSES_IGNORE);
    2511:       for (tmp2=0; tmp2<nrqs; tmp2++) {
    2512:         sbuf1_i = sbuf1[pa[tmp2]];
    2513:         jmax    = sbuf1_i[0];
    2514:         ct1     = 2*jmax+1;
    2515:         ct2     = 0;
    2516:         rbuf2_i = rbuf2[tmp2];
    2517:         rbuf3_i = rbuf3[tmp2];
    2518:         for (j=1; j<=jmax; j++) {
    2519:           is_no  = sbuf1_i[2*j-1];
    2520:           max1   = sbuf1_i[2*j];
    2521:           lens_i = lens[is_no];
    2522:           if (!allcolumns[is_no]) cmap_i = cmap[is_no];
    2523:           rmap_i = rmap[is_no];
    2524:           for (k=0; k<max1; k++,ct1++) {
    2525: #if defined(PETSC_USE_CTABLE)
    2526:             PetscTableFind(rmap_i,sbuf1_i[ct1]+1,&row);
    2527:             row--;
    2528:             if (row < 0) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_PLIB,"row not found in table");
    2529: #else
    2530:             row = rmap_i[sbuf1_i[ct1]]; /* the val in the new matrix to be */
    2531: #endif
    2532:             max2 = rbuf2_i[ct1];
    2533:             for (l=0; l<max2; l++,ct2++) {
    2534:               if (!allcolumns[is_no]) {
    2535: #if defined(PETSC_USE_CTABLE)
    2536:                 PetscTableFind(cmap_i,rbuf3_i[ct2]+1,&tcol);
    2537: #else
    2538:                 tcol = cmap_i[rbuf3_i[ct2]];
    2539: #endif
    2540:                 if (tcol) lens_i[row]++;
    2541:               } else { /* allcolumns */
    2542:                 lens_i[row]++; /* lens_i[row] += max2 ? */
    2543:               }
    2544:             }
    2545:           }
    2546:         }
    2547:       }
    2548:     }
    2549:     PetscFree(r_waits3);
    2550:     MPI_Waitall(nrqr,s_waits3,MPI_STATUSES_IGNORE);
    2551:     PetscFree(s_waits3);

    2553:     /* Create the submatrices */
    2554:     for (i=0; i<ismax; i++) {
    2555:       PetscInt    rbs,cbs;

    2557:       ISGetBlockSize(isrow[i],&rbs);
    2558:       ISGetBlockSize(iscol[i],&cbs);

    2560:       MatCreate(PETSC_COMM_SELF,submats+i);
    2561:       MatSetSizes(submats[i],nrow[i],ncol[i],PETSC_DETERMINE,PETSC_DETERMINE);

    2563:       MatSetBlockSizes(submats[i],rbs,cbs);
    2564:       MatSetType(submats[i],((PetscObject)A)->type_name);
    2565:       MatSeqAIJSetPreallocation(submats[i],0,lens[i]);

    2567:       /* create struct Mat_SubSppt and attached it to submat */
    2568:       PetscNew(&smat_i);
    2569:       subc = (Mat_SeqAIJ*)submats[i]->data;
    2570:       subc->submatis1 = smat_i;

    2572:       smat_i->destroy          = submats[i]->ops->destroy;
    2573:       submats[i]->ops->destroy = MatDestroySubMatrix_SeqAIJ;
    2574:       submats[i]->factortype   = C->factortype;

    2576:       smat_i->id          = i;
    2577:       smat_i->nrqs        = nrqs;
    2578:       smat_i->nrqr        = nrqr;
    2579:       smat_i->rbuf1       = rbuf1;
    2580:       smat_i->rbuf2       = rbuf2;
    2581:       smat_i->rbuf3       = rbuf3;
    2582:       smat_i->sbuf2       = sbuf2;
    2583:       smat_i->req_source2 = req_source2;

    2585:       smat_i->sbuf1       = sbuf1;
    2586:       smat_i->ptr         = ptr;
    2587:       smat_i->tmp         = tmp;
    2588:       smat_i->ctr         = ctr;

    2590:       smat_i->pa           = pa;
    2591:       smat_i->req_size     = req_size;
    2592:       smat_i->req_source1  = req_source1;

    2594:       smat_i->allcolumns  = allcolumns[i];
    2595:       smat_i->singleis    = PETSC_FALSE;
    2596:       smat_i->row2proc    = row2proc[i];
    2597:       smat_i->rmap        = rmap[i];
    2598:       smat_i->cmap        = cmap[i];
    2599:     }

    2601:     if (!ismax) { /* Create dummy submats[0] for reuse struct subc */
    2602:       MatCreate(PETSC_COMM_SELF,&submats[0]);
    2603:       MatSetSizes(submats[0],0,0,PETSC_DETERMINE,PETSC_DETERMINE);
    2604:       MatSetType(submats[0],MATDUMMY);

    2606:       /* create struct Mat_SubSppt and attached it to submat */
    2607:       PetscNewLog(submats[0],&smat_i);
    2608:       submats[0]->data = (void*)smat_i;

    2610:       smat_i->destroy          = submats[0]->ops->destroy;
    2611:       submats[0]->ops->destroy = MatDestroySubMatrix_Dummy;
    2612:       submats[0]->factortype   = C->factortype;

    2614:       smat_i->id          = 0;
    2615:       smat_i->nrqs        = nrqs;
    2616:       smat_i->nrqr        = nrqr;
    2617:       smat_i->rbuf1       = rbuf1;
    2618:       smat_i->rbuf2       = rbuf2;
    2619:       smat_i->rbuf3       = rbuf3;
    2620:       smat_i->sbuf2       = sbuf2;
    2621:       smat_i->req_source2 = req_source2;

    2623:       smat_i->sbuf1       = sbuf1;
    2624:       smat_i->ptr         = ptr;
    2625:       smat_i->tmp         = tmp;
    2626:       smat_i->ctr         = ctr;

    2628:       smat_i->pa           = pa;
    2629:       smat_i->req_size     = req_size;
    2630:       smat_i->req_source1  = req_source1;

    2632:       smat_i->allcolumns  = PETSC_FALSE;
    2633:       smat_i->singleis    = PETSC_FALSE;
    2634:       smat_i->row2proc    = NULL;
    2635:       smat_i->rmap        = NULL;
    2636:       smat_i->cmap        = NULL;
    2637:     }

    2639:     if (ismax) {PetscFree(lens[0]);}
    2640:     PetscFree(lens);
    2641:     if (sbuf_aj) {
    2642:       PetscFree(sbuf_aj[0]);
    2643:       PetscFree(sbuf_aj);
    2644:     }

    2646:   } /* endof scall == MAT_INITIAL_MATRIX */

    2648:   /* Post recv matrix values */
    2649:   PetscObjectGetNewTag((PetscObject)C,&tag4);
    2650:   PetscMalloc1(nrqs,&rbuf4);
    2651:   PetscMalloc1(nrqs,&r_waits4);
    2652:   for (i=0; i<nrqs; ++i) {
    2653:     PetscMalloc1(rbuf2[i][0],&rbuf4[i]);
    2654:     MPI_Irecv(rbuf4[i],rbuf2[i][0],MPIU_SCALAR,req_source2[i],tag4,comm,r_waits4+i);
    2655:   }

    2657:   /* Allocate sending buffers for a->a, and send them off */
    2658:   PetscMalloc1(nrqr,&sbuf_aa);
    2659:   for (i=0,j=0; i<nrqr; i++) j += req_size[i];
    2660:   if (nrqr) {PetscMalloc1(j,&sbuf_aa[0]);}
    2661:   for (i=1; i<nrqr; i++) sbuf_aa[i] = sbuf_aa[i-1] + req_size[i-1];

    2663:   PetscMalloc1(nrqr,&s_waits4);
    2664:   {
    2665:     PetscInt    nzA,nzB,*a_i = a->i,*b_i = b->i, *cworkB,lwrite;
    2666:     PetscInt    cstart = C->cmap->rstart,rstart = C->rmap->rstart,*bmap = c->garray;
    2667:     PetscInt    cend   = C->cmap->rend;
    2668:     PetscInt    *b_j   = b->j;
    2669:     PetscScalar *vworkA,*vworkB,*a_a,*b_a;

    2671:     MatSeqAIJGetArrayRead(A,(const PetscScalar**)&a_a);
    2672:     MatSeqAIJGetArrayRead(c->B,(const PetscScalar**)&b_a);
    2673:     for (i=0; i<nrqr; i++) {
    2674:       rbuf1_i   = rbuf1[i];
    2675:       sbuf_aa_i = sbuf_aa[i];
    2676:       ct1       = 2*rbuf1_i[0]+1;
    2677:       ct2       = 0;
    2678:       for (j=1,max1=rbuf1_i[0]; j<=max1; j++) {
    2679:         kmax = rbuf1_i[2*j];
    2680:         for (k=0; k<kmax; k++,ct1++) {
    2681:           row    = rbuf1_i[ct1] - rstart;
    2682:           nzA    = a_i[row+1] - a_i[row];
    2683:           nzB    = b_i[row+1] - b_i[row];
    2684:           ncols  = nzA + nzB;
    2685:           cworkB = b_j + b_i[row];
    2686:           vworkA = a_a + a_i[row];
    2687:           vworkB = b_a + b_i[row];

    2689:           /* load the column values for this row into vals*/
    2690:           vals = sbuf_aa_i+ct2;

    2692:           lwrite = 0;
    2693:           for (l=0; l<nzB; l++) {
    2694:             if ((bmap[cworkB[l]]) < cstart) vals[lwrite++] = vworkB[l];
    2695:           }
    2696:           for (l=0; l<nzA; l++) vals[lwrite++] = vworkA[l];
    2697:           for (l=0; l<nzB; l++) {
    2698:             if ((bmap[cworkB[l]]) >= cend) vals[lwrite++] = vworkB[l];
    2699:           }

    2701:           ct2 += ncols;
    2702:         }
    2703:       }
    2704:       MPI_Isend(sbuf_aa_i,req_size[i],MPIU_SCALAR,req_source1[i],tag4,comm,s_waits4+i);
    2705:     }
    2706:     MatSeqAIJRestoreArrayRead(A,(const PetscScalar**)&a_a);
    2707:     MatSeqAIJRestoreArrayRead(c->B,(const PetscScalar**)&b_a);
    2708:   }

    2710:   /* Assemble the matrices */
    2711:   /* First assemble the local rows */
    2712:   for (i=0; i<ismax; i++) {
    2713:     row2proc_i = row2proc[i];
    2714:     subc      = (Mat_SeqAIJ*)submats[i]->data;
    2715:     imat_ilen = subc->ilen;
    2716:     imat_j    = subc->j;
    2717:     imat_i    = subc->i;
    2718:     imat_a    = subc->a;

    2720:     if (!allcolumns[i]) cmap_i = cmap[i];
    2721:     rmap_i = rmap[i];
    2722:     irow_i = irow[i];
    2723:     jmax   = nrow[i];
    2724:     for (j=0; j<jmax; j++) {
    2725:       row  = irow_i[j];
    2726:       proc = row2proc_i[j];
    2727:       if (proc == rank) {
    2728:         old_row = row;
    2729: #if defined(PETSC_USE_CTABLE)
    2730:         PetscTableFind(rmap_i,row+1,&row);
    2731:         row--;
    2732: #else
    2733:         row = rmap_i[row];
    2734: #endif
    2735:         ilen_row = imat_ilen[row];
    2736:         MatGetRow_MPIAIJ(C,old_row,&ncols,&cols,&vals);
    2737:         mat_i    = imat_i[row];
    2738:         mat_a    = imat_a + mat_i;
    2739:         mat_j    = imat_j + mat_i;
    2740:         if (!allcolumns[i]) {
    2741:           for (k=0; k<ncols; k++) {
    2742: #if defined(PETSC_USE_CTABLE)
    2743:             PetscTableFind(cmap_i,cols[k]+1,&tcol);
    2744: #else
    2745:             tcol = cmap_i[cols[k]];
    2746: #endif
    2747:             if (tcol) {
    2748:               *mat_j++ = tcol - 1;
    2749:               *mat_a++ = vals[k];
    2750:               ilen_row++;
    2751:             }
    2752:           }
    2753:         } else { /* allcolumns */
    2754:           for (k=0; k<ncols; k++) {
    2755:             *mat_j++ = cols[k];  /* global col index! */
    2756:             *mat_a++ = vals[k];
    2757:             ilen_row++;
    2758:           }
    2759:         }
    2760:         MatRestoreRow_MPIAIJ(C,old_row,&ncols,&cols,&vals);

    2762:         imat_ilen[row] = ilen_row;
    2763:       }
    2764:     }
    2765:   }

    2767:   /* Now assemble the off proc rows */
    2768:   MPI_Waitall(nrqs,r_waits4,MPI_STATUSES_IGNORE);
    2769:   for (tmp2=0; tmp2<nrqs; tmp2++) {
    2770:     sbuf1_i = sbuf1[pa[tmp2]];
    2771:     jmax    = sbuf1_i[0];
    2772:     ct1     = 2*jmax + 1;
    2773:     ct2     = 0;
    2774:     rbuf2_i = rbuf2[tmp2];
    2775:     rbuf3_i = rbuf3[tmp2];
    2776:     rbuf4_i = rbuf4[tmp2];
    2777:     for (j=1; j<=jmax; j++) {
    2778:       is_no     = sbuf1_i[2*j-1];
    2779:       rmap_i    = rmap[is_no];
    2780:       if (!allcolumns[is_no]) cmap_i = cmap[is_no];
    2781:       subc      = (Mat_SeqAIJ*)submats[is_no]->data;
    2782:       imat_ilen = subc->ilen;
    2783:       imat_j    = subc->j;
    2784:       imat_i    = subc->i;
    2785:       imat_a    = subc->a;
    2786:       max1      = sbuf1_i[2*j];
    2787:       for (k=0; k<max1; k++,ct1++) {
    2788:         row = sbuf1_i[ct1];
    2789: #if defined(PETSC_USE_CTABLE)
    2790:         PetscTableFind(rmap_i,row+1,&row);
    2791:         row--;
    2792: #else
    2793:         row = rmap_i[row];
    2794: #endif
    2795:         ilen  = imat_ilen[row];
    2796:         mat_i = imat_i[row];
    2797:         mat_a = imat_a + mat_i;
    2798:         mat_j = imat_j + mat_i;
    2799:         max2  = rbuf2_i[ct1];
    2800:         if (!allcolumns[is_no]) {
    2801:           for (l=0; l<max2; l++,ct2++) {
    2802: #if defined(PETSC_USE_CTABLE)
    2803:             PetscTableFind(cmap_i,rbuf3_i[ct2]+1,&tcol);
    2804: #else
    2805:             tcol = cmap_i[rbuf3_i[ct2]];
    2806: #endif
    2807:             if (tcol) {
    2808:               *mat_j++ = tcol - 1;
    2809:               *mat_a++ = rbuf4_i[ct2];
    2810:               ilen++;
    2811:             }
    2812:           }
    2813:         } else { /* allcolumns */
    2814:           for (l=0; l<max2; l++,ct2++) {
    2815:             *mat_j++ = rbuf3_i[ct2]; /* same global column index of C */
    2816:             *mat_a++ = rbuf4_i[ct2];
    2817:             ilen++;
    2818:           }
    2819:         }
    2820:         imat_ilen[row] = ilen;
    2821:       }
    2822:     }
    2823:   }

    2825:   if (!iscsorted) { /* sort column indices of the rows */
    2826:     for (i=0; i<ismax; i++) {
    2827:       subc      = (Mat_SeqAIJ*)submats[i]->data;
    2828:       imat_j    = subc->j;
    2829:       imat_i    = subc->i;
    2830:       imat_a    = subc->a;
    2831:       imat_ilen = subc->ilen;

    2833:       if (allcolumns[i]) continue;
    2834:       jmax = nrow[i];
    2835:       for (j=0; j<jmax; j++) {
    2836:         mat_i = imat_i[j];
    2837:         mat_a = imat_a + mat_i;
    2838:         mat_j = imat_j + mat_i;
    2839:         PetscSortIntWithScalarArray(imat_ilen[j],mat_j,mat_a);
    2840:       }
    2841:     }
    2842:   }

    2844:   PetscFree(r_waits4);
    2845:   MPI_Waitall(nrqr,s_waits4,MPI_STATUSES_IGNORE);
    2846:   PetscFree(s_waits4);

    2848:   /* Restore the indices */
    2849:   for (i=0; i<ismax; i++) {
    2850:     ISRestoreIndices(isrow[i],irow+i);
    2851:     if (!allcolumns[i]) {
    2852:       ISRestoreIndices(iscol[i],icol+i);
    2853:     }
    2854:   }

    2856:   for (i=0; i<ismax; i++) {
    2857:     MatAssemblyBegin(submats[i],MAT_FINAL_ASSEMBLY);
    2858:     MatAssemblyEnd(submats[i],MAT_FINAL_ASSEMBLY);
    2859:   }

    2861:   /* Destroy allocated memory */
    2862:   if (sbuf_aa) {
    2863:     PetscFree(sbuf_aa[0]);
    2864:     PetscFree(sbuf_aa);
    2865:   }
    2866:   PetscFree5(*(PetscInt***)&irow,*(PetscInt***)&icol,nrow,ncol,issorted);

    2868:   for (i=0; i<nrqs; ++i) {
    2869:     PetscFree(rbuf4[i]);
    2870:   }
    2871:   PetscFree(rbuf4);

    2873:   PetscFree4(row2proc,cmap,rmap,allcolumns);
    2874:   return(0);
    2875: }

    2877: /*
    2878:  Permute A & B into C's *local* index space using rowemb,dcolemb for A and rowemb,ocolemb for B.
    2879:  Embeddings are supposed to be injections and the above implies that the range of rowemb is a subset
    2880:  of [0,m), dcolemb is in [0,n) and ocolemb is in [N-n).
    2881:  If pattern == DIFFERENT_NONZERO_PATTERN, C is preallocated according to A&B.
    2882:  After that B's columns are mapped into C's global column space, so that C is in the "disassembled"
    2883:  state, and needs to be "assembled" later by compressing B's column space.

    2885:  This function may be called in lieu of preallocation, so C should not be expected to be preallocated.
    2886:  Following this call, C->A & C->B have been created, even if empty.
    2887:  */
    2888: PetscErrorCode MatSetSeqMats_MPIAIJ(Mat C,IS rowemb,IS dcolemb,IS ocolemb,MatStructure pattern,Mat A,Mat B)
    2889: {
    2890:   /* If making this function public, change the error returned in this function away from _PLIB. */
    2892:   Mat_MPIAIJ     *aij;
    2893:   Mat_SeqAIJ     *Baij;
    2894:   PetscBool      seqaij,Bdisassembled;
    2895:   PetscInt       m,n,*nz,i,j,ngcol,col,rstart,rend,shift,count;
    2896:   PetscScalar    v;
    2897:   const PetscInt *rowindices,*colindices;

    2900:   /* Check to make sure the component matrices (and embeddings) are compatible with C. */
    2901:   if (A) {
    2902:     PetscObjectBaseTypeCompare((PetscObject)A,MATSEQAIJ,&seqaij);
    2903:     if (!seqaij) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_PLIB,"Diagonal matrix is of wrong type");
    2904:     if (rowemb) {
    2905:       ISGetLocalSize(rowemb,&m);
    2906:       if (m != A->rmap->n) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_PLIB,"Row IS of size %D is incompatible with diag matrix row size %D",m,A->rmap->n);
    2907:     } else {
    2908:       if (C->rmap->n != A->rmap->n) {
    2909:         SETERRQ(PETSC_COMM_SELF,PETSC_ERR_PLIB,"Diag seq matrix is row-incompatible with the MPIAIJ matrix");
    2910:       }
    2911:     }
    2912:     if (dcolemb) {
    2913:       ISGetLocalSize(dcolemb,&n);
    2914:       if (n != A->cmap->n) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_PLIB,"Diag col IS of size %D is incompatible with diag matrix col size %D",n,A->cmap->n);
    2915:     } else {
    2916:       if (C->cmap->n != A->cmap->n) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_PLIB,"Diag seq matrix is col-incompatible with the MPIAIJ matrix");
    2917:     }
    2918:   }
    2919:   if (B) {
    2920:     PetscObjectBaseTypeCompare((PetscObject)B,MATSEQAIJ,&seqaij);
    2921:     if (!seqaij) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_PLIB,"Off-diagonal matrix is of wrong type");
    2922:     if (rowemb) {
    2923:       ISGetLocalSize(rowemb,&m);
    2924:       if (m != B->rmap->n) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_PLIB,"Row IS of size %D is incompatible with off-diag matrix row size %D",m,A->rmap->n);
    2925:     } else {
    2926:       if (C->rmap->n != B->rmap->n) {
    2927:         SETERRQ(PETSC_COMM_SELF,PETSC_ERR_PLIB,"Off-diag seq matrix is row-incompatible with the MPIAIJ matrix");
    2928:       }
    2929:     }
    2930:     if (ocolemb) {
    2931:       ISGetLocalSize(ocolemb,&n);
    2932:       if (n != B->cmap->n) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_PLIB,"Off-diag col IS of size %D is incompatible with off-diag matrix col size %D",n,B->cmap->n);
    2933:     } else {
    2934:       if (C->cmap->N - C->cmap->n != B->cmap->n) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_PLIB,"Off-diag seq matrix is col-incompatible with the MPIAIJ matrix");
    2935:     }
    2936:   }

    2938:   aij = (Mat_MPIAIJ*)C->data;
    2939:   if (!aij->A) {
    2940:     /* Mimic parts of MatMPIAIJSetPreallocation() */
    2941:     MatCreate(PETSC_COMM_SELF,&aij->A);
    2942:     MatSetSizes(aij->A,C->rmap->n,C->cmap->n,C->rmap->n,C->cmap->n);
    2943:     MatSetBlockSizesFromMats(aij->A,C,C);
    2944:     MatSetType(aij->A,MATSEQAIJ);
    2945:     PetscLogObjectParent((PetscObject)C,(PetscObject)aij->A);
    2946:   }
    2947:   if (A) {
    2948:     MatSetSeqMat_SeqAIJ(aij->A,rowemb,dcolemb,pattern,A);
    2949:   } else {
    2950:     MatSetUp(aij->A);
    2951:   }
    2952:   if (B) { /* Destroy the old matrix or the column map, depending on the sparsity pattern. */
    2953:     /*
    2954:       If pattern == DIFFERENT_NONZERO_PATTERN, we reallocate B and
    2955:       need to "disassemble" B -- convert it to using C's global indices.
    2956:       To insert the values we take the safer, albeit more expensive, route of MatSetValues().

    2958:       If pattern == SUBSET_NONZERO_PATTERN, we do not "disassemble" B and do not reallocate;
    2959:       we MatZeroValues(B) first, so there may be a bunch of zeros that, perhaps, could be compacted out.

    2961:       TODO: Put B's values into aij->B's aij structure in place using the embedding ISs?
    2962:       At least avoid calling MatSetValues() and the implied searches?
    2963:     */

    2965:     if (B && pattern == DIFFERENT_NONZERO_PATTERN) {
    2966: #if defined(PETSC_USE_CTABLE)
    2967:       PetscTableDestroy(&aij->colmap);
    2968: #else
    2969:       PetscFree(aij->colmap);
    2970:       /* A bit of a HACK: ideally we should deal with case aij->B all in one code block below. */
    2971:       if (aij->B) {
    2972:         PetscLogObjectMemory((PetscObject)C,-aij->B->cmap->n*sizeof(PetscInt));
    2973:       }
    2974: #endif
    2975:       ngcol = 0;
    2976:       if (aij->lvec) {
    2977:         VecGetSize(aij->lvec,&ngcol);
    2978:       }
    2979:       if (aij->garray) {
    2980:         PetscFree(aij->garray);
    2981:         PetscLogObjectMemory((PetscObject)C,-ngcol*sizeof(PetscInt));
    2982:       }
    2983:       VecDestroy(&aij->lvec);
    2984:       VecScatterDestroy(&aij->Mvctx);
    2985:     }
    2986:     if (aij->B && B && pattern == DIFFERENT_NONZERO_PATTERN) {
    2987:       MatDestroy(&aij->B);
    2988:     }
    2989:     if (aij->B && B && pattern == SUBSET_NONZERO_PATTERN) {
    2990:       MatZeroEntries(aij->B);
    2991:     }
    2992:   }
    2993:   Bdisassembled = PETSC_FALSE;
    2994:   if (!aij->B) {
    2995:     MatCreate(PETSC_COMM_SELF,&aij->B);
    2996:     PetscLogObjectParent((PetscObject)C,(PetscObject)aij->B);
    2997:     MatSetSizes(aij->B,C->rmap->n,C->cmap->N,C->rmap->n,C->cmap->N);
    2998:     MatSetBlockSizesFromMats(aij->B,B,B);
    2999:     MatSetType(aij->B,MATSEQAIJ);
    3000:     Bdisassembled = PETSC_TRUE;
    3001:   }
    3002:   if (B) {
    3003:     Baij = (Mat_SeqAIJ*)B->data;
    3004:     if (pattern == DIFFERENT_NONZERO_PATTERN) {
    3005:       PetscMalloc1(B->rmap->n,&nz);
    3006:       for (i=0; i<B->rmap->n; i++) {
    3007:         nz[i] = Baij->i[i+1] - Baij->i[i];
    3008:       }
    3009:       MatSeqAIJSetPreallocation(aij->B,0,nz);
    3010:       PetscFree(nz);
    3011:     }

    3013:     PetscLayoutGetRange(C->rmap,&rstart,&rend);
    3014:     shift = rend-rstart;
    3015:     count = 0;
    3016:     rowindices = NULL;
    3017:     colindices = NULL;
    3018:     if (rowemb) {
    3019:       ISGetIndices(rowemb,&rowindices);
    3020:     }
    3021:     if (ocolemb) {
    3022:       ISGetIndices(ocolemb,&colindices);
    3023:     }
    3024:     for (i=0; i<B->rmap->n; i++) {
    3025:       PetscInt row;
    3026:       row = i;
    3027:       if (rowindices) row = rowindices[i];
    3028:       for (j=Baij->i[i]; j<Baij->i[i+1]; j++) {
    3029:         col  = Baij->j[count];
    3030:         if (colindices) col = colindices[col];
    3031:         if (Bdisassembled && col>=rstart) col += shift;
    3032:         v    = Baij->a[count];
    3033:         MatSetValues(aij->B,1,&row,1,&col,&v,INSERT_VALUES);
    3034:         ++count;
    3035:       }
    3036:     }
    3037:     /* No assembly for aij->B is necessary. */
    3038:     /* FIXME: set aij->B's nonzerostate correctly. */
    3039:   } else {
    3040:     MatSetUp(aij->B);
    3041:   }
    3042:   C->preallocated  = PETSC_TRUE;
    3043:   C->was_assembled = PETSC_FALSE;
    3044:   C->assembled     = PETSC_FALSE;
    3045:    /*
    3046:       C will need to be assembled so that aij->B can be compressed into local form in MatSetUpMultiply_MPIAIJ().
    3047:       Furthermore, its nonzerostate will need to be based on that of aij->A's and aij->B's.
    3048:    */
    3049:   return(0);
    3050: }

    3052: /*
    3053:   B uses local indices with column indices ranging between 0 and N-n; they  must be interpreted using garray.
    3054:  */
    3055: PetscErrorCode MatGetSeqMats_MPIAIJ(Mat C,Mat *A,Mat *B)
    3056: {
    3057:   Mat_MPIAIJ *aij = (Mat_MPIAIJ*)C->data;

    3062:   /* FIXME: make sure C is assembled */
    3063:   *A = aij->A;
    3064:   *B = aij->B;
    3065:   /* Note that we don't incref *A and *B, so be careful! */
    3066:   return(0);
    3067: }

    3069: /*
    3070:   Extract MPI submatrices encoded by pairs of IS that may live on subcomms of C.
    3071:   NOT SCALABLE due to the use of ISGetNonlocalIS() (see below).
    3072: */
    3073: PetscErrorCode MatCreateSubMatricesMPI_MPIXAIJ(Mat C,PetscInt ismax,const IS isrow[],const IS iscol[],MatReuse scall,Mat *submat[],
    3074:                                                PetscErrorCode(*getsubmats_seq)(Mat,PetscInt,const IS[],const IS[],MatReuse,Mat**),
    3075:                                                PetscErrorCode(*getlocalmats)(Mat,Mat*,Mat*),
    3076:                                                PetscErrorCode(*setseqmat)(Mat,IS,IS,MatStructure,Mat),
    3077:                                                PetscErrorCode(*setseqmats)(Mat,IS,IS,IS,MatStructure,Mat,Mat))
    3078: {
    3080:   PetscMPIInt    size,flag;
    3081:   PetscInt       i,ii,cismax,ispar;
    3082:   Mat            *A,*B;
    3083:   IS             *isrow_p,*iscol_p,*cisrow,*ciscol,*ciscol_p;

    3086:   if (!ismax) return(0);

    3088:   for (i = 0, cismax = 0; i < ismax; ++i) {
    3089:     MPI_Comm_compare(((PetscObject)isrow[i])->comm,((PetscObject)iscol[i])->comm,&flag);
    3090:     if (flag != MPI_IDENT) SETERRQ(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Row and column index sets must have the same communicator");
    3091:     MPI_Comm_size(((PetscObject)isrow[i])->comm, &size);
    3092:     if (size > 1) ++cismax;
    3093:   }

    3095:   /*
    3096:      If cismax is zero on all C's ranks, then and only then can we use purely sequential matrix extraction.
    3097:      ispar counts the number of parallel ISs across C's comm.
    3098:   */
    3099:   MPIU_Allreduce(&cismax,&ispar,1,MPIU_INT,MPI_MAX,PetscObjectComm((PetscObject)C));
    3100:   if (!ispar) { /* Sequential ISs only across C's comm, so can call the sequential matrix extraction subroutine. */
    3101:     (*getsubmats_seq)(C,ismax,isrow,iscol,scall,submat);
    3102:     return(0);
    3103:   }

    3105:   /* if (ispar) */
    3106:   /*
    3107:     Construct the "complements" -- the off-processor indices -- of the iscol ISs for parallel ISs only.
    3108:     These are used to extract the off-diag portion of the resulting parallel matrix.
    3109:     The row IS for the off-diag portion is the same as for the diag portion,
    3110:     so we merely alias (without increfing) the row IS, while skipping those that are sequential.
    3111:   */
    3112:   PetscMalloc2(cismax,&cisrow,cismax,&ciscol);
    3113:   PetscMalloc1(cismax,&ciscol_p);
    3114:   for (i = 0, ii = 0; i < ismax; ++i) {
    3115:     MPI_Comm_size(((PetscObject)isrow[i])->comm,&size);
    3116:     if (size > 1) {
    3117:       /*
    3118:          TODO: This is the part that's ***NOT SCALABLE***.
    3119:          To fix this we need to extract just the indices of C's nonzero columns
    3120:          that lie on the intersection of isrow[i] and ciscol[ii] -- the nonlocal
    3121:          part of iscol[i] -- without actually computing ciscol[ii]. This also has
    3122:          to be done without serializing on the IS list, so, most likely, it is best
    3123:          done by rewriting MatCreateSubMatrices_MPIAIJ() directly.
    3124:       */
    3125:       ISGetNonlocalIS(iscol[i],&(ciscol[ii]));
    3126:       /* Now we have to
    3127:          (a) make sure ciscol[ii] is sorted, since, even if the off-proc indices
    3128:              were sorted on each rank, concatenated they might no longer be sorted;
    3129:          (b) Use ISSortPermutation() to construct ciscol_p, the mapping from the
    3130:              indices in the nondecreasing order to the original index positions.
    3131:          If ciscol[ii] is strictly increasing, the permutation IS is NULL.
    3132:       */
    3133:       ISSortPermutation(ciscol[ii],PETSC_FALSE,ciscol_p+ii);
    3134:       ISSort(ciscol[ii]);
    3135:       ++ii;
    3136:     }
    3137:   }
    3138:   PetscMalloc2(ismax,&isrow_p,ismax,&iscol_p);
    3139:   for (i = 0, ii = 0; i < ismax; ++i) {
    3140:     PetscInt       j,issize;
    3141:     const PetscInt *indices;

    3143:     /*
    3144:        Permute the indices into a nondecreasing order. Reject row and col indices with duplicates.
    3145:      */
    3146:     ISSortPermutation(isrow[i],PETSC_FALSE,isrow_p+i);
    3147:     ISSort(isrow[i]);
    3148:     ISGetLocalSize(isrow[i],&issize);
    3149:     ISGetIndices(isrow[i],&indices);
    3150:     for (j = 1; j < issize; ++j) {
    3151:       if (indices[j] == indices[j-1]) SETERRQ4(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONG,"Repeated indices in row IS %D: indices at %D and %D are both %D",i,j-1,j,indices[j]);
    3152:     }
    3153:     ISRestoreIndices(isrow[i],&indices);
    3154:     ISSortPermutation(iscol[i],PETSC_FALSE,iscol_p+i);
    3155:     ISSort(iscol[i]);
    3156:     ISGetLocalSize(iscol[i],&issize);
    3157:     ISGetIndices(iscol[i],&indices);
    3158:     for (j = 1; j < issize; ++j) {
    3159:       if (indices[j-1] == indices[j]) SETERRQ4(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONG,"Repeated indices in col IS %D: indices at %D and %D are both %D",i,j-1,j,indices[j]);
    3160:     }
    3161:     ISRestoreIndices(iscol[i],&indices);
    3162:     MPI_Comm_size(((PetscObject)isrow[i])->comm,&size);
    3163:     if (size > 1) {
    3164:       cisrow[ii] = isrow[i];
    3165:       ++ii;
    3166:     }
    3167:   }
    3168:   /*
    3169:     Allocate the necessary arrays to hold the resulting parallel matrices as well as the intermediate
    3170:     array of sequential matrices underlying the resulting parallel matrices.
    3171:     Which arrays to allocate is based on the value of MatReuse scall and whether ISs are sorted and/or
    3172:     contain duplicates.

    3174:     There are as many diag matrices as there are original index sets. There are only as many parallel
    3175:     and off-diag matrices, as there are parallel (comm size > 1) index sets.

    3177:     ARRAYS that can hold Seq matrices get allocated in any event -- either here or by getsubmats_seq():
    3178:     - If the array of MPI matrices already exists and is being reused, we need to allocate the array
    3179:       and extract the underlying seq matrices into it to serve as placeholders, into which getsubmats_seq
    3180:       will deposite the extracted diag and off-diag parts. Thus, we allocate the A&B arrays and fill them
    3181:       with A[i] and B[ii] extracted from the corresponding MPI submat.
    3182:     - However, if the rows, A's column indices or B's column indices are not sorted, the extracted A[i] & B[ii]
    3183:       will have a different order from what getsubmats_seq expects.  To handle this case -- indicated
    3184:       by a nonzero isrow_p[i], iscol_p[i], or ciscol_p[ii] -- we duplicate A[i] --> AA[i], B[ii] --> BB[ii]
    3185:       (retrieve composed AA[i] or BB[ii]) and reuse them here. AA[i] and BB[ii] are then used to permute its
    3186:       values into A[i] and B[ii] sitting inside the corresponding submat.
    3187:     - If no reuse is taking place then getsubmats_seq will allocate the A&B arrays and create the corresponding
    3188:       A[i], B[ii], AA[i] or BB[ii] matrices.
    3189:   */
    3190:   /* Parallel matrix array is allocated here only if no reuse is taking place. If reused, it is passed in by the caller. */
    3191:   if (scall == MAT_INITIAL_MATRIX) {
    3192:     PetscMalloc1(ismax,submat);
    3193:   }

    3195:   /* Now obtain the sequential A and B submatrices separately. */
    3196:   /* scall=MAT_REUSE_MATRIX is not handled yet, because getsubmats_seq() requires reuse of A and B */
    3197:   (*getsubmats_seq)(C,ismax,isrow,iscol,MAT_INITIAL_MATRIX,&A);
    3198:   (*getsubmats_seq)(C,cismax,cisrow,ciscol,MAT_INITIAL_MATRIX,&B);

    3200:   /*
    3201:     If scall == MAT_REUSE_MATRIX AND the permutations are NULL, we are done, since the sequential
    3202:     matrices A & B have been extracted directly into the parallel matrices containing them, or
    3203:     simply into the sequential matrix identical with the corresponding A (if size == 1).
    3204:     Note that in that case colmap doesn't need to be rebuilt, since the matrices are expected
    3205:     to have the same sparsity pattern.
    3206:     Otherwise, A and/or B have to be properly embedded into C's index spaces and the correct colmap
    3207:     must be constructed for C. This is done by setseqmat(s).
    3208:   */
    3209:   for (i = 0, ii = 0; i < ismax; ++i) {
    3210:     /*
    3211:        TODO: cache ciscol, permutation ISs and maybe cisrow? What about isrow & iscol?
    3212:        That way we can avoid sorting and computing permutations when reusing.
    3213:        To this end:
    3214:         - remove the old cache, if it exists, when extracting submatrices with MAT_INITIAL_MATRIX
    3215:         - if caching arrays to hold the ISs, make and compose a container for them so that it can
    3216:           be destroyed upon destruction of C (use PetscContainerUserDestroy() to clear out the contents).
    3217:     */
    3218:     MatStructure pattern = DIFFERENT_NONZERO_PATTERN;

    3220:     MPI_Comm_size(((PetscObject)isrow[i])->comm,&size);
    3221:     /* Construct submat[i] from the Seq pieces A (and B, if necessary). */
    3222:     if (size > 1) {
    3223:       if (scall == MAT_INITIAL_MATRIX) {
    3224:         MatCreate(((PetscObject)isrow[i])->comm,(*submat)+i);
    3225:         MatSetSizes((*submat)[i],A[i]->rmap->n,A[i]->cmap->n,PETSC_DETERMINE,PETSC_DETERMINE);
    3226:         MatSetType((*submat)[i],MATMPIAIJ);
    3227:         PetscLayoutSetUp((*submat)[i]->rmap);
    3228:         PetscLayoutSetUp((*submat)[i]->cmap);
    3229:       }
    3230:       /*
    3231:         For each parallel isrow[i], insert the extracted sequential matrices into the parallel matrix.
    3232:       */
    3233:       {
    3234:         Mat AA = A[i],BB = B[ii];

    3236:         if (AA || BB) {
    3237:           setseqmats((*submat)[i],isrow_p[i],iscol_p[i],ciscol_p[ii],pattern,AA,BB);
    3238:           MatAssemblyBegin((*submat)[i],MAT_FINAL_ASSEMBLY);
    3239:           MatAssemblyEnd((*submat)[i],MAT_FINAL_ASSEMBLY);
    3240:         }
    3241:         MatDestroy(&AA);
    3242:       }
    3243:       ISDestroy(ciscol+ii);
    3244:       ISDestroy(ciscol_p+ii);
    3245:       ++ii;
    3246:     } else { /* if (size == 1) */
    3247:       if (scall == MAT_REUSE_MATRIX) {
    3248:         MatDestroy(&(*submat)[i]);
    3249:       }
    3250:       if (isrow_p[i] || iscol_p[i]) {
    3251:         MatDuplicate(A[i],MAT_DO_NOT_COPY_VALUES,(*submat)+i);
    3252:         setseqmat((*submat)[i],isrow_p[i],iscol_p[i],pattern,A[i]);
    3253:         /* Otherwise A is extracted straight into (*submats)[i]. */
    3254:         /* TODO: Compose A[i] on (*submat([i] for future use, if ((isrow_p[i] || iscol_p[i]) && MAT_INITIAL_MATRIX). */
    3255:         MatDestroy(A+i);
    3256:       } else (*submat)[i] = A[i];
    3257:     }
    3258:     ISDestroy(&isrow_p[i]);
    3259:     ISDestroy(&iscol_p[i]);
    3260:   }
    3261:   PetscFree2(cisrow,ciscol);
    3262:   PetscFree2(isrow_p,iscol_p);
    3263:   PetscFree(ciscol_p);
    3264:   PetscFree(A);
    3265:   MatDestroySubMatrices(cismax,&B);
    3266:   return(0);
    3267: }

    3269: PetscErrorCode MatCreateSubMatricesMPI_MPIAIJ(Mat C,PetscInt ismax,const IS isrow[],const IS iscol[],MatReuse scall,Mat *submat[])
    3270: {

    3274:   MatCreateSubMatricesMPI_MPIXAIJ(C,ismax,isrow,iscol,scall,submat,MatCreateSubMatrices_MPIAIJ,MatGetSeqMats_MPIAIJ,MatSetSeqMat_SeqAIJ,MatSetSeqMats_MPIAIJ);
    3275:   return(0);
    3276: }