Actual source code: mpiov.c
petsc-3.10.5 2019-03-28
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      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 *);

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

     28:   if (ov < 0) SETERRQ(PetscObjectComm((PetscObject)C),PETSC_ERR_ARG_OUTOFRANGE,"Negative overlap specified");
     29:   for (i=0; i<ov; ++i) {
     30:     MatIncreaseOverlap_MPIAIJ_Once(C,imax,is);
     31:   }
     32:   return(0);
     33: }

     35: PetscErrorCode MatIncreaseOverlap_MPIAIJ_Scalable(Mat C,PetscInt imax,IS is[],PetscInt ov)
     36: {
     38:   PetscInt       i;

     41:   if (ov < 0) SETERRQ(PetscObjectComm((PetscObject)C),PETSC_ERR_ARG_OUTOFRANGE,"Negative overlap specified");
     42:   for (i=0; i<ov; ++i) {
     43:     MatIncreaseOverlap_MPIAIJ_Once_Scalable(C,imax,is);
     44:   }
     45:   return(0);
     46: }

     49: static PetscErrorCode MatIncreaseOverlap_MPIAIJ_Once_Scalable(Mat mat,PetscInt nidx,IS is[])
     50: {
     52:   MPI_Comm       comm;
     53:   PetscInt       *length,length_i,tlength,*remoterows,nrrows,reducednrrows,*rrow_ranks,*rrow_isids,i,j,owner;
     54:   PetscInt       *tosizes,*tosizes_temp,*toffsets,*fromsizes,*todata,*fromdata;
     55:   PetscInt       nrecvrows,*sbsizes = 0,*sbdata = 0;
     56:   const PetscInt *indices_i,**indices;
     57:   PetscLayout    rmap;
     58:   PetscMPIInt    rank,size,*toranks,*fromranks,nto,nfrom;
     59:   PetscSF        sf;
     60:   PetscSFNode    *remote;

     63:   PetscObjectGetComm((PetscObject)mat,&comm);
     64:   MPI_Comm_rank(comm,&rank);
     65:   MPI_Comm_size(comm,&size);
     66:   /* get row map to determine where rows should be going */
     67:   MatGetLayouts(mat,&rmap,NULL);
     68:   /* retrieve IS data and put all together so that we
     69:    * can optimize communication
     70:    *  */
     71:   PetscCalloc2(nidx,(PetscInt ***)&indices,nidx,&length);
     72:   for (i=0,tlength=0; i<nidx; i++){
     73:     ISGetLocalSize(is[i],&length[i]);
     74:     tlength += length[i];
     75:     ISGetIndices(is[i],&indices[i]);
     76:   }
     77:   /* find these rows on remote processors */
     78:   PetscCalloc3(tlength,&remoterows,tlength,&rrow_ranks,tlength,&rrow_isids);
     79:   PetscCalloc3(size,&toranks,2*size,&tosizes,size,&tosizes_temp);
     80:   nrrows = 0;
     81:   for (i=0; i<nidx; i++) {
     82:     length_i  = length[i];
     83:     indices_i = indices[i];
     84:     for (j=0; j<length_i; j++) {
     85:       owner = -1;
     86:       PetscLayoutFindOwner(rmap,indices_i[j],&owner);
     87:       /* remote processors */
     88:       if (owner != rank) {
     89:         tosizes_temp[owner]++; /* number of rows to owner */
     90:         rrow_ranks[nrrows]  = owner; /* processor */
     91:         rrow_isids[nrrows]   = i; /* is id */
     92:         remoterows[nrrows++] = indices_i[j]; /* row */
     93:       }
     94:     }
     95:     ISRestoreIndices(is[i],&indices[i]);
     96:   }
     97:   PetscFree2(*(PetscInt***)&indices,length);
     98:   /* test if we need to exchange messages
     99:    * generally speaking, we do not need to exchange
    100:    * data when overlap is 1
    101:    * */
    102:   MPIU_Allreduce(&nrrows,&reducednrrows,1,MPIU_INT,MPIU_MAX,comm);
    103:   /* we do not have any messages
    104:    * It usually corresponds to overlap 1
    105:    * */
    106:   if (!reducednrrows) {
    107:     PetscFree3(toranks,tosizes,tosizes_temp);
    108:     PetscFree3(remoterows,rrow_ranks,rrow_isids);
    109:     MatIncreaseOverlap_MPIAIJ_Local_Scalable(mat,nidx,is);
    110:     return(0);
    111:   }
    112:   nto = 0;
    113:   /* send sizes and ranks for building a two-sided communcation */
    114:   for (i=0; i<size; i++) {
    115:     if (tosizes_temp[i]) {
    116:       tosizes[nto*2]  = tosizes_temp[i]*2; /* size */
    117:       tosizes_temp[i] = nto; /* a map from processor to index */
    118:       toranks[nto++]  = i; /* processor */
    119:     }
    120:   }
    121:   PetscCalloc1(nto+1,&toffsets);
    122:   for (i=0; i<nto; i++) {
    123:     toffsets[i+1]  = toffsets[i]+tosizes[2*i]; /* offsets */
    124:     tosizes[2*i+1] = toffsets[i]; /* offsets to send */
    125:   }
    126:   /* send information to other processors */
    127:   PetscCommBuildTwoSided(comm,2,MPIU_INT,nto,toranks,tosizes,&nfrom,&fromranks,&fromsizes);
    128:   nrecvrows = 0;
    129:   for (i=0; i<nfrom; i++) nrecvrows += fromsizes[2*i];
    130:   PetscMalloc1(nrecvrows,&remote);
    131:   nrecvrows = 0;
    132:   for (i=0; i<nfrom; i++) {
    133:     for (j=0; j<fromsizes[2*i]; j++) {
    134:       remote[nrecvrows].rank    = fromranks[i];
    135:       remote[nrecvrows++].index = fromsizes[2*i+1]+j;
    136:     }
    137:   }
    138:   PetscSFCreate(comm,&sf);
    139:   PetscSFSetGraph(sf,nrecvrows,nrecvrows,NULL,PETSC_OWN_POINTER,remote,PETSC_OWN_POINTER);
    140:   /* use two-sided communication by default since OPENMPI has some bugs for one-sided one */
    141:   PetscSFSetType(sf,PETSCSFBASIC);
    142:   PetscSFSetFromOptions(sf);
    143:   /* message pair <no of is, row>  */
    144:   PetscCalloc2(2*nrrows,&todata,nrecvrows,&fromdata);
    145:   for (i=0; i<nrrows; i++) {
    146:     owner = rrow_ranks[i]; /* processor */
    147:     j     = tosizes_temp[owner]; /* index */
    148:     todata[toffsets[j]++] = rrow_isids[i];
    149:     todata[toffsets[j]++] = remoterows[i];
    150:   }
    151:   PetscFree3(toranks,tosizes,tosizes_temp);
    152:   PetscFree3(remoterows,rrow_ranks,rrow_isids);
    153:   PetscFree(toffsets);
    154:   PetscSFBcastBegin(sf,MPIU_INT,todata,fromdata);
    155:   PetscSFBcastEnd(sf,MPIU_INT,todata,fromdata);
    156:   PetscSFDestroy(&sf);
    157:   /* send rows belonging to the remote so that then we could get the overlapping data back */
    158:   MatIncreaseOverlap_MPIAIJ_Send_Scalable(mat,nidx,nfrom,fromranks,fromsizes,fromdata,&sbsizes,&sbdata);
    159:   PetscFree2(todata,fromdata);
    160:   PetscFree(fromsizes);
    161:   PetscCommBuildTwoSided(comm,2,MPIU_INT,nfrom,fromranks,sbsizes,&nto,&toranks,&tosizes);
    162:   PetscFree(fromranks);
    163:   nrecvrows = 0;
    164:   for (i=0; i<nto; i++) nrecvrows += tosizes[2*i];
    165:   PetscCalloc1(nrecvrows,&todata);
    166:   PetscMalloc1(nrecvrows,&remote);
    167:   nrecvrows = 0;
    168:   for (i=0; i<nto; i++) {
    169:     for (j=0; j<tosizes[2*i]; j++) {
    170:       remote[nrecvrows].rank    = toranks[i];
    171:       remote[nrecvrows++].index = tosizes[2*i+1]+j;
    172:     }
    173:   }
    174:   PetscSFCreate(comm,&sf);
    175:   PetscSFSetGraph(sf,nrecvrows,nrecvrows,NULL,PETSC_OWN_POINTER,remote,PETSC_OWN_POINTER);
    176:   /* use two-sided communication by default since OPENMPI has some bugs for one-sided one */
    177:   PetscSFSetType(sf,PETSCSFBASIC);
    178:   PetscSFSetFromOptions(sf);
    179:   /* overlap communication and computation */
    180:   PetscSFBcastBegin(sf,MPIU_INT,sbdata,todata);
    181:   MatIncreaseOverlap_MPIAIJ_Local_Scalable(mat,nidx,is);
    182:   PetscSFBcastEnd(sf,MPIU_INT,sbdata,todata);
    183:   PetscSFDestroy(&sf);
    184:   PetscFree2(sbdata,sbsizes);
    185:   MatIncreaseOverlap_MPIAIJ_Receive_Scalable(mat,nidx,is,nrecvrows,todata);
    186:   PetscFree(toranks);
    187:   PetscFree(tosizes);
    188:   PetscFree(todata);
    189:   return(0);
    190: }

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

    201:   max_lsize = 0;
    202:   PetscMalloc1(nidx,&isz);
    203:   for (i=0; i<nidx; i++){
    204:     ISGetLocalSize(is[i],&lsize);
    205:     max_lsize = lsize>max_lsize ? lsize:max_lsize;
    206:     isz[i]    = lsize;
    207:   }
    208:   PetscMalloc2((max_lsize+nrecvs)*nidx,&indices_temp,nidx,&iscomms);
    209:   for (i=0; i<nidx; i++){
    210:     PetscCommDuplicate(PetscObjectComm((PetscObject)is[i]),&iscomms[i],NULL);
    211:     ISGetIndices(is[i],&indices_i_temp);
    212:     PetscMemcpy(indices_temp+i*(max_lsize+nrecvs),indices_i_temp, sizeof(PetscInt)*isz[i]);
    213:     ISRestoreIndices(is[i],&indices_i_temp);
    214:     ISDestroy(&is[i]);
    215:   }
    216:   /* retrieve information to get row id and its overlap */
    217:   for (i=0; i<nrecvs; ){
    218:     is_id     = recvdata[i++];
    219:     data_size = recvdata[i++];
    220:     indices_i = indices_temp+(max_lsize+nrecvs)*is_id;
    221:     isz_i     = isz[is_id];
    222:     for (j=0; j< data_size; j++){
    223:       col = recvdata[i++];
    224:       indices_i[isz_i++] = col;
    225:     }
    226:     isz[is_id] = isz_i;
    227:   }
    228:   /* remove duplicate entities */
    229:   for (i=0; i<nidx; i++){
    230:     indices_i = indices_temp+(max_lsize+nrecvs)*i;
    231:     isz_i     = isz[i];
    232:     PetscSortRemoveDupsInt(&isz_i,indices_i);
    233:     ISCreateGeneral(iscomms[i],isz_i,indices_i,PETSC_COPY_VALUES,&is[i]);
    234:     PetscCommDestroy(&iscomms[i]);
    235:   }
    236:   PetscFree(isz);
    237:   PetscFree2(indices_temp,iscomms);
    238:   return(0);
    239: }

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

    255:   PetscObjectGetComm((PetscObject)mat,&comm);
    256:   MPI_Comm_rank(comm,&rank);
    257:   MatMPIAIJGetSeqAIJ(mat,&amat,&bmat,&gcols);
    258:   /* Even if the mat is symmetric, we still assume it is not symmetric */
    259:   MatGetRowIJ(amat,0,PETSC_FALSE,PETSC_FALSE,&an,&ai,&aj,&done);
    260:   if (!done) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONGSTATE,"can not get row IJ \n");
    261:   MatGetRowIJ(bmat,0,PETSC_FALSE,PETSC_FALSE,&bn,&bi,&bj,&done);
    262:   if (!done) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONGSTATE,"can not get row IJ \n");
    263:   /* total number of nonzero values is used to estimate the memory usage in the next step */
    264:   tnz  = ai[an]+bi[bn];
    265:   MatGetLayouts(mat,&rmap,&cmap);
    266:   PetscLayoutGetRange(rmap,&rstart,NULL);
    267:   PetscLayoutGetRange(cmap,&cstart,NULL);
    268:   /* to find the longest message */
    269:   max_fszs = 0;
    270:   for (i=0; i<nfrom; i++) max_fszs = fromsizes[2*i]>max_fszs ? fromsizes[2*i]:max_fszs;
    271:   /* better way to estimate number of nonzero in the mat??? */
    272:   PetscCalloc5(max_fszs*nidx,&rows_data_ptr,nidx,&rows_data,nidx,&rows_pos_i,nfrom*nidx,&indv_counts,tnz,&indices_tmp);
    273:   for (i=0; i<nidx; i++) rows_data[i] = rows_data_ptr+max_fszs*i;
    274:   rows_pos  = 0;
    275:   totalrows = 0;
    276:   for (i=0; i<nfrom; i++){
    277:     PetscMemzero(rows_pos_i,sizeof(PetscInt)*nidx);
    278:     /* group data together */
    279:     for (j=0; j<fromsizes[2*i]; j+=2){
    280:       is_id                       = fromrows[rows_pos++];/* no of is */
    281:       rows_i                      = rows_data[is_id];
    282:       rows_i[rows_pos_i[is_id]++] = fromrows[rows_pos++];/* row */
    283:     }
    284:     /* estimate a space to avoid multiple allocations  */
    285:     for (j=0; j<nidx; j++){
    286:       indvc_ij = 0;
    287:       rows_i   = rows_data[j];
    288:       for (l=0; l<rows_pos_i[j]; l++){
    289:         row    = rows_i[l]-rstart;
    290:         start  = ai[row];
    291:         end    = ai[row+1];
    292:         for (k=start; k<end; k++){ /* Amat */
    293:           col = aj[k] + cstart;
    294:           indices_tmp[indvc_ij++] = col;/* do not count the rows from the original rank */
    295:         }
    296:         start = bi[row];
    297:         end   = bi[row+1];
    298:         for (k=start; k<end; k++) { /* Bmat */
    299:           col = gcols[bj[k]];
    300:           indices_tmp[indvc_ij++] = col;
    301:         }
    302:       }
    303:       PetscSortRemoveDupsInt(&indvc_ij,indices_tmp);
    304:       indv_counts[i*nidx+j] = indvc_ij;
    305:       totalrows            += indvc_ij;
    306:     }
    307:   }
    308:   /* message triple <no of is, number of rows, rows> */
    309:   PetscCalloc2(totalrows+nidx*nfrom*2,&sbdata,2*nfrom,&sbsizes);
    310:   totalrows = 0;
    311:   rows_pos  = 0;
    312:   /* use this code again */
    313:   for (i=0;i<nfrom;i++){
    314:     PetscMemzero(rows_pos_i,sizeof(PetscInt)*nidx);
    315:     for (j=0; j<fromsizes[2*i]; j+=2){
    316:       is_id                       = fromrows[rows_pos++];
    317:       rows_i                      = rows_data[is_id];
    318:       rows_i[rows_pos_i[is_id]++] = fromrows[rows_pos++];
    319:     }
    320:     /* add data  */
    321:     for (j=0; j<nidx; j++){
    322:       if (!indv_counts[i*nidx+j]) continue;
    323:       indvc_ij = 0;
    324:       sbdata[totalrows++] = j;
    325:       sbdata[totalrows++] = indv_counts[i*nidx+j];
    326:       sbsizes[2*i]       += 2;
    327:       rows_i              = rows_data[j];
    328:       for (l=0; l<rows_pos_i[j]; l++){
    329:         row   = rows_i[l]-rstart;
    330:         start = ai[row];
    331:         end   = ai[row+1];
    332:         for (k=start; k<end; k++){ /* Amat */
    333:           col = aj[k] + cstart;
    334:           indices_tmp[indvc_ij++] = col;
    335:         }
    336:         start = bi[row];
    337:         end   = bi[row+1];
    338:         for (k=start; k<end; k++) { /* Bmat */
    339:           col = gcols[bj[k]];
    340:           indices_tmp[indvc_ij++] = col;
    341:         }
    342:       }
    343:       PetscSortRemoveDupsInt(&indvc_ij,indices_tmp);
    344:       sbsizes[2*i]  += indvc_ij;
    345:       PetscMemcpy(sbdata+totalrows,indices_tmp,sizeof(PetscInt)*indvc_ij);
    346:       totalrows += indvc_ij;
    347:     }
    348:   }
    349:   PetscCalloc1(nfrom+1,&offsets);
    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,owner;
    368:   PetscMPIInt       rank;
    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: }

    432: /*
    433:   Sample message format:
    434:   If a processor A wants processor B to process some elements corresponding
    435:   to index sets is[1],is[5]
    436:   mesg [0] = 2   (no of index sets in the mesg)
    437:   -----------
    438:   mesg [1] = 1 => is[1]
    439:   mesg [2] = sizeof(is[1]);
    440:   -----------
    441:   mesg [3] = 5  => is[5]
    442:   mesg [4] = sizeof(is[5]);
    443:   -----------
    444:   mesg [5]
    445:   mesg [n]  datas[1]
    446:   -----------
    447:   mesg[n+1]
    448:   mesg[m]  data(is[5])
    449:   -----------

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

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

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

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

    489:   for (i=0; i<imax; i++) {
    490:     ISGetIndices(is[i],&idx[i]);
    491:     ISGetLocalSize(is[i],&n[i]);
    492:   }

    494:   /* evaluate communication - mesg to who,length of mesg, and buffer space
    495:      required. Based on this, buffers are allocated, and data copied into them  */
    496:   PetscMalloc4(size,&w1,size,&w2,size,&w3,size,&w4);
    497:   PetscMemzero(w1,size*sizeof(PetscMPIInt)); /* initialise work vector*/
    498:   PetscMemzero(w2,size*sizeof(PetscMPIInt)); /* initialise work vector*/
    499:   PetscMemzero(w3,size*sizeof(PetscMPIInt)); /* initialise work vector*/
    500:   for (i=0; i<imax; i++) {
    501:     PetscMemzero(w4,size*sizeof(PetscMPIInt)); /* initialise work vector*/
    502:     idx_i = idx[i];
    503:     len   = n[i];
    504:     for (j=0; j<len; j++) {
    505:       row = idx_i[j];
    506:       if (row < 0) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Index set cannot have negative entries");
    507:       PetscLayoutFindOwner(C->rmap,row,&proc);
    508:       w4[proc]++;
    509:     }
    510:     for (j=0; j<size; j++) {
    511:       if (w4[j]) { w1[j] += w4[j]; w3[j]++;}
    512:     }
    513:   }

    515:   nrqs     = 0;              /* no of outgoing messages */
    516:   msz      = 0;              /* total mesg length (for all proc */
    517:   w1[rank] = 0;              /* no mesg sent to intself */
    518:   w3[rank] = 0;
    519:   for (i=0; i<size; i++) {
    520:     if (w1[i])  {w2[i] = 1; nrqs++;} /* there exists a message to proc i */
    521:   }
    522:   /* pa - is list of processors to communicate with */
    523:   PetscMalloc1(nrqs+1,&pa);
    524:   for (i=0,j=0; i<size; i++) {
    525:     if (w1[i]) {pa[j] = i; j++;}
    526:   }

    528:   /* Each message would have a header = 1 + 2*(no of IS) + data */
    529:   for (i=0; i<nrqs; i++) {
    530:     j      = pa[i];
    531:     w1[j] += w2[j] + 2*w3[j];
    532:     msz   += w1[j];
    533:   }

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

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

    542:   /* Allocate Memory for outgoing messages */
    543:   PetscMalloc4(size,&outdat,size,&ptr,msz,&tmp,size,&ctr);
    544:   PetscMemzero(outdat,size*sizeof(PetscInt*));
    545:   PetscMemzero(ptr,size*sizeof(PetscInt*));

    547:   {
    548:     PetscInt *iptr = tmp,ict  = 0;
    549:     for (i=0; i<nrqs; i++) {
    550:       j         = pa[i];
    551:       iptr     +=  ict;
    552:       outdat[j] = iptr;
    553:       ict       = w1[j];
    554:     }
    555:   }

    557:   /* Form the outgoing messages */
    558:   /* plug in the headers */
    559:   for (i=0; i<nrqs; i++) {
    560:     j            = pa[i];
    561:     outdat[j][0] = 0;
    562:     PetscMemzero(outdat[j]+1,2*w3[j]*sizeof(PetscInt));
    563:     ptr[j]       = outdat[j] + 2*w3[j] + 1;
    564:   }

    566:   /* Memory for doing local proc's work */
    567:   {
    568:     PetscInt M_BPB_imax = 0;
    569: #if defined(PETSC_USE_CTABLE)
    570:     PetscIntMultError((M/PETSC_BITS_PER_BYTE+1),imax, &M_BPB_imax);
    571:     PetscMalloc1(imax,&table_data);
    572:     for (i=0; i<imax; i++) {
    573:       PetscTableCreate(n[i]+1,M+1,&table_data[i]);
    574:     }
    575:     PetscCalloc4(imax,&table, imax,&data, imax,&isz, M_BPB_imax,&t_p);
    576:     for (i=0; i<imax; i++) {
    577:       table[i] = t_p + (M/PETSC_BITS_PER_BYTE+1)*i;
    578:     }
    579: #else
    580:     PetscInt Mimax = 0;
    581:     PetscIntMultError(M,imax, &Mimax);
    582:     PetscIntMultError((M/PETSC_BITS_PER_BYTE+1),imax, &M_BPB_imax);
    583:     PetscCalloc5(imax,&table, imax,&data, imax,&isz, Mimax,&d_p, M_BPB_imax,&t_p);
    584:     for (i=0; i<imax; i++) {
    585:       table[i] = t_p + (M/PETSC_BITS_PER_BYTE+1)*i;
    586:       data[i]  = d_p + M*i;
    587:     }
    588: #endif
    589:   }

    591:   /* Parse the IS and update local tables and the outgoing buf with the data */
    592:   {
    593:     PetscInt n_i,isz_i,*outdat_j,ctr_j;
    594:     PetscBT  table_i;

    596:     for (i=0; i<imax; i++) {
    597:       PetscMemzero(ctr,size*sizeof(PetscInt));
    598:       n_i     = n[i];
    599:       table_i = table[i];
    600:       idx_i   = idx[i];
    601: #if defined(PETSC_USE_CTABLE)
    602:       table_data_i = table_data[i];
    603: #else
    604:       data_i  = data[i];
    605: #endif
    606:       isz_i   = isz[i];
    607:       for (j=0; j<n_i; j++) {   /* parse the indices of each IS */
    608:         row  = idx_i[j];
    609:         PetscLayoutFindOwner(C->rmap,row,&proc);
    610:         if (proc != rank) { /* copy to the outgoing buffer */
    611:           ctr[proc]++;
    612:           *ptr[proc] = row;
    613:           ptr[proc]++;
    614:         } else if (!PetscBTLookupSet(table_i,row)) {
    615: #if defined(PETSC_USE_CTABLE)
    616:           PetscTableAdd(table_data_i,row+1,isz_i+1,INSERT_VALUES);
    617: #else
    618:           data_i[isz_i] = row; /* Update the local table */
    619: #endif
    620:           isz_i++;
    621:         }
    622:       }
    623:       /* Update the headers for the current IS */
    624:       for (j=0; j<size; j++) { /* Can Optimise this loop by using pa[] */
    625:         if ((ctr_j = ctr[j])) {
    626:           outdat_j        = outdat[j];
    627:           k               = ++outdat_j[0];
    628:           outdat_j[2*k]   = ctr_j;
    629:           outdat_j[2*k-1] = i;
    630:         }
    631:       }
    632:       isz[i] = isz_i;
    633:     }
    634:   }

    636:   /*  Now  post the sends */
    637:   PetscMalloc1(nrqs+1,&s_waits1);
    638:   for (i=0; i<nrqs; ++i) {
    639:     j    = pa[i];
    640:     MPI_Isend(outdat[j],w1[j],MPIU_INT,j,tag1,comm,s_waits1+i);
    641:   }

    643:   /* No longer need the original indices */
    644:   PetscMalloc1(imax,&iscomms);
    645:   for (i=0; i<imax; ++i) {
    646:     ISRestoreIndices(is[i],idx+i);
    647:     PetscCommDuplicate(PetscObjectComm((PetscObject)is[i]),&iscomms[i],NULL);
    648:   }
    649:   PetscFree2(*(PetscInt***)&idx,n);

    651:   for (i=0; i<imax; ++i) {
    652:     ISDestroy(&is[i]);
    653:   }

    655:   /* Do Local work */
    656: #if defined(PETSC_USE_CTABLE)
    657:   MatIncreaseOverlap_MPIAIJ_Local(C,imax,table,isz,NULL,table_data);
    658: #else
    659:   MatIncreaseOverlap_MPIAIJ_Local(C,imax,table,isz,data,NULL);
    660: #endif

    662:   /* Receive messages */
    663:   PetscMalloc1(nrqr+1,&recv_status);
    664:   if (nrqr) {MPI_Waitall(nrqr,r_waits1,recv_status);}

    666:   PetscMalloc1(nrqs+1,&s_status);
    667:   if (nrqs) {MPI_Waitall(nrqs,s_waits1,s_status);}

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

    673:   PetscMalloc1(nrqr+1,&xdata);
    674:   PetscMalloc1(nrqr+1,&isz1);
    675:   MatIncreaseOverlap_MPIAIJ_Receive(C,nrqr,rbuf,xdata,isz1);
    676:   PetscFree(rbuf[0]);
    677:   PetscFree(rbuf);

    680:   /* Send the data back */
    681:   /* Do a global reduction to know the buffer space req for incoming messages */
    682:   {
    683:     PetscMPIInt *rw1;

    685:     PetscCalloc1(size,&rw1);

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

    690:       if (proc != onodes1[i]) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_PLIB,"MPI_SOURCE mismatch");
    691:       rw1[proc] = isz1[i];
    692:     }
    693:     PetscFree(onodes1);
    694:     PetscFree(olengths1);

    696:     /* Determine the number of messages to expect, their lengths, from from-ids */
    697:     PetscGatherMessageLengths(comm,nrqr,nrqs,rw1,&onodes2,&olengths2);
    698:     PetscFree(rw1);
    699:   }
    700:   /* Now post the Irecvs corresponding to these messages */
    701:   PetscPostIrecvInt(comm,tag2,nrqs,onodes2,olengths2,&rbuf2,&r_waits2);

    703:   /* Now  post the sends */
    704:   PetscMalloc1(nrqr+1,&s_waits2);
    705:   for (i=0; i<nrqr; ++i) {
    706:     j    = recv_status[i].MPI_SOURCE;
    707:     MPI_Isend(xdata[i],isz1[i],MPIU_INT,j,tag2,comm,s_waits2+i);
    708:   }

    710:   /* receive work done on other processors */
    711:   {
    712:     PetscInt    is_no,ct1,max,*rbuf2_i,isz_i,jmax;
    713:     PetscMPIInt idex;
    714:     PetscBT     table_i;
    715:     MPI_Status  *status2;

    717:     PetscMalloc1((PetscMax(nrqr,nrqs)+1),&status2);
    718:     for (i=0; i<nrqs; ++i) {
    719:       MPI_Waitany(nrqs,r_waits2,&idex,status2+i);
    720:       /* Process the message */
    721:       rbuf2_i = rbuf2[idex];
    722:       ct1     = 2*rbuf2_i[0]+1;
    723:       jmax    = rbuf2[idex][0];
    724:       for (j=1; j<=jmax; j++) {
    725:         max     = rbuf2_i[2*j];
    726:         is_no   = rbuf2_i[2*j-1];
    727:         isz_i   = isz[is_no];
    728:         table_i = table[is_no];
    729: #if defined(PETSC_USE_CTABLE)
    730:         table_data_i = table_data[is_no];
    731: #else
    732:         data_i  = data[is_no];
    733: #endif
    734:         for (k=0; k<max; k++,ct1++) {
    735:           row = rbuf2_i[ct1];
    736:           if (!PetscBTLookupSet(table_i,row)) {
    737: #if defined(PETSC_USE_CTABLE)
    738:             PetscTableAdd(table_data_i,row+1,isz_i+1,INSERT_VALUES);
    739: #else
    740:             data_i[isz_i] = row;
    741: #endif
    742:             isz_i++;
    743:           }
    744:         }
    745:         isz[is_no] = isz_i;
    746:       }
    747:     }

    749:     if (nrqr) {MPI_Waitall(nrqr,s_waits2,status2);}
    750:     PetscFree(status2);
    751:   }

    753: #if defined(PETSC_USE_CTABLE)
    754:   tcount_max = 0;
    755:   for (i=0; i<imax; ++i) {
    756:     table_data_i = table_data[i];
    757:     PetscTableGetCount(table_data_i,&tcount);
    758:     if (tcount_max < tcount) tcount_max = tcount;
    759:   }
    760:   PetscMalloc1(tcount_max+1,&tdata);
    761: #endif

    763:   for (i=0; i<imax; ++i) {
    764: #if defined(PETSC_USE_CTABLE)
    765:     PetscTablePosition tpos;
    766:     table_data_i = table_data[i];

    768:     PetscTableGetHeadPosition(table_data_i,&tpos);
    769:     while (tpos) {
    770:       PetscTableGetNext(table_data_i,&tpos,&k,&j);
    771:       tdata[--j] = --k;
    772:     }
    773:     ISCreateGeneral(iscomms[i],isz[i],tdata,PETSC_COPY_VALUES,is+i);
    774: #else
    775:     ISCreateGeneral(iscomms[i],isz[i],data[i],PETSC_COPY_VALUES,is+i);
    776: #endif
    777:     PetscCommDestroy(&iscomms[i]);
    778:   }

    780:   PetscFree(iscomms);
    781:   PetscFree(onodes2);
    782:   PetscFree(olengths2);

    784:   PetscFree(pa);
    785:   PetscFree(rbuf2[0]);
    786:   PetscFree(rbuf2);
    787:   PetscFree(s_waits1);
    788:   PetscFree(r_waits1);
    789:   PetscFree(s_waits2);
    790:   PetscFree(r_waits2);
    791:   PetscFree(s_status);
    792:   PetscFree(recv_status);
    793:   PetscFree(xdata[0]);
    794:   PetscFree(xdata);
    795:   PetscFree(isz1);
    796: #if defined(PETSC_USE_CTABLE)
    797:   for (i=0; i<imax; i++) {
    798:     PetscTableDestroy((PetscTable*)&table_data[i]);
    799:   }
    800:   PetscFree(table_data);
    801:   PetscFree(tdata);
    802:   PetscFree4(table,data,isz,t_p);
    803: #else
    804:   PetscFree5(table,data,isz,d_p,t_p);
    805: #endif
    806:   return(0);
    807: }

    809: /*
    810:    MatIncreaseOverlap_MPIAIJ_Local - Called by MatincreaseOverlap, to do
    811:        the work on the local processor.

    813:      Inputs:
    814:       C      - MAT_MPIAIJ;
    815:       imax - total no of index sets processed at a time;
    816:       table  - an array of char - size = m bits.

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

    841:   rstart = C->rmap->rstart;
    842:   cstart = C->cmap->rstart;
    843:   ai     = a->i;
    844:   aj     = a->j;
    845:   bi     = b->i;
    846:   bj     = b->j;
    847:   garray = c->garray;

    849:   for (i=0; i<imax; i++) {
    850: #if defined(PETSC_USE_CTABLE)
    851:     /* copy existing entries of table_data_i into tdata[] */
    852:     table_data_i = table_data[i];
    853:     PetscTableGetCount(table_data_i,&tcount);
    854:     if (tcount != isz[i]) SETERRQ3(PETSC_COMM_SELF,0," tcount %d != isz[%d] %d",tcount,i,isz[i]);

    856:     PetscMalloc1(tcount,&tdata);
    857:     PetscTableGetHeadPosition(table_data_i,&tpos);
    858:     while (tpos) {
    859:       PetscTableGetNext(table_data_i,&tpos,&row,&j);
    860:       tdata[--j] = --row;
    861:       if (j > tcount - 1) SETERRQ2(PETSC_COMM_SELF,0," j %d >= tcount %d",j,tcount);
    862:     }
    863: #else
    864:     data_i  = data[i];
    865: #endif
    866:     table_i = table[i];
    867:     isz_i   = isz[i];
    868:     max     = isz[i];

    870:     for (j=0; j<max; j++) {
    871: #if defined(PETSC_USE_CTABLE)
    872:       row   = tdata[j] - rstart;
    873: #else
    874:       row   = data_i[j] - rstart;
    875: #endif
    876:       start = ai[row];
    877:       end   = ai[row+1];
    878:       for (k=start; k<end; k++) { /* Amat */
    879:         val = aj[k] + cstart;
    880:         if (!PetscBTLookupSet(table_i,val)) {
    881: #if defined(PETSC_USE_CTABLE)
    882:           PetscTableAdd(table_data_i,val+1,isz_i+1,INSERT_VALUES);
    883: #else
    884:           data_i[isz_i] = val;
    885: #endif
    886:           isz_i++;
    887:         }
    888:       }
    889:       start = bi[row];
    890:       end   = bi[row+1];
    891:       for (k=start; k<end; k++) { /* Bmat */
    892:         val = garray[bj[k]];
    893:         if (!PetscBTLookupSet(table_i,val)) {
    894: #if defined(PETSC_USE_CTABLE)
    895:           PetscTableAdd(table_data_i,val+1,isz_i+1,INSERT_VALUES);
    896: #else
    897:           data_i[isz_i] = val;
    898: #endif
    899:           isz_i++;
    900:         }
    901:       }
    902:     }
    903:     isz[i] = isz_i;

    905: #if defined(PETSC_USE_CTABLE)
    906:     PetscFree(tdata);
    907: #endif
    908:   }
    909:   return(0);
    910: }

    912: /*
    913:       MatIncreaseOverlap_MPIAIJ_Receive - Process the recieved messages,
    914:          and return the output

    916:          Input:
    917:            C    - the matrix
    918:            nrqr - no of messages being processed.
    919:            rbuf - an array of pointers to the recieved requests

    921:          Output:
    922:            xdata - array of messages to be sent back
    923:            isz1  - size of each message

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

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

    944:   m      = C->rmap->N;
    945:   rstart = C->rmap->rstart;
    946:   cstart = C->cmap->rstart;
    947:   ai     = a->i;
    948:   aj     = a->j;
    949:   bi     = b->i;
    950:   bj     = b->j;
    951:   garray = c->garray;

    954:   for (i=0,ct=0,total_sz=0; i<nrqr; ++i) {
    955:     rbuf_i =  rbuf[i];
    956:     rbuf_0 =  rbuf_i[0];
    957:     ct    += rbuf_0;
    958:     for (j=1; j<=rbuf_0; j++) total_sz += rbuf_i[2*j];
    959:   }

    961:   if (C->rmap->n) max1 = ct*(a->nz + b->nz)/C->rmap->n;
    962:   else max1 = 1;
    963:   mem_estimate = 3*((total_sz > max1 ? total_sz : max1)+1);
    964:   PetscMalloc1(mem_estimate,&xdata[0]);
    965:   ++no_malloc;
    966:   PetscBTCreate(m,&xtable);
    967:   PetscMemzero(isz1,nrqr*sizeof(PetscInt));

    969:   ct3 = 0;
    970:   for (i=0; i<nrqr; i++) { /* for easch mesg from proc i */
    971:     rbuf_i =  rbuf[i];
    972:     rbuf_0 =  rbuf_i[0];
    973:     ct1    =  2*rbuf_0+1;
    974:     ct2    =  ct1;
    975:     ct3   += ct1;
    976:     for (j=1; j<=rbuf_0; j++) { /* for each IS from proc i*/
    977:       PetscBTMemzero(m,xtable);
    978:       oct2 = ct2;
    979:       kmax = rbuf_i[2*j];
    980:       for (k=0; k<kmax; k++,ct1++) {
    981:         row = rbuf_i[ct1];
    982:         if (!PetscBTLookupSet(xtable,row)) {
    983:           if (!(ct3 < mem_estimate)) {
    984:             new_estimate = (PetscInt)(1.5*mem_estimate)+1;
    985:             PetscMalloc1(new_estimate,&tmp);
    986:             PetscMemcpy(tmp,xdata[0],mem_estimate*sizeof(PetscInt));
    987:             PetscFree(xdata[0]);
    988:             xdata[0]     = tmp;
    989:             mem_estimate = new_estimate; ++no_malloc;
    990:             for (ctr=1; ctr<=i; ctr++) xdata[ctr] = xdata[ctr-1] + isz1[ctr-1];
    991:           }
    992:           xdata[i][ct2++] = row;
    993:           ct3++;
    994:         }
    995:       }
    996:       for (k=oct2,max2=ct2; k<max2; k++) {
    997:         row   = xdata[i][k] - rstart;
    998:         start = ai[row];
    999:         end   = ai[row+1];
    1000:         for (l=start; l<end; l++) {
    1001:           val = aj[l] + cstart;
    1002:           if (!PetscBTLookupSet(xtable,val)) {
    1003:             if (!(ct3 < mem_estimate)) {
    1004:               new_estimate = (PetscInt)(1.5*mem_estimate)+1;
    1005:               PetscMalloc1(new_estimate,&tmp);
    1006:               PetscMemcpy(tmp,xdata[0],mem_estimate*sizeof(PetscInt));
    1007:               PetscFree(xdata[0]);
    1008:               xdata[0]     = tmp;
    1009:               mem_estimate = new_estimate; ++no_malloc;
    1010:               for (ctr=1; ctr<=i; ctr++) xdata[ctr] = xdata[ctr-1] + isz1[ctr-1];
    1011:             }
    1012:             xdata[i][ct2++] = val;
    1013:             ct3++;
    1014:           }
    1015:         }
    1016:         start = bi[row];
    1017:         end   = bi[row+1];
    1018:         for (l=start; l<end; l++) {
    1019:           val = garray[bj[l]];
    1020:           if (!PetscBTLookupSet(xtable,val)) {
    1021:             if (!(ct3 < mem_estimate)) {
    1022:               new_estimate = (PetscInt)(1.5*mem_estimate)+1;
    1023:               PetscMalloc1(new_estimate,&tmp);
    1024:               PetscMemcpy(tmp,xdata[0],mem_estimate*sizeof(PetscInt));
    1025:               PetscFree(xdata[0]);
    1026:               xdata[0]     = tmp;
    1027:               mem_estimate = new_estimate; ++no_malloc;
    1028:               for (ctr =1; ctr <=i; ctr++) xdata[ctr] = xdata[ctr-1] + isz1[ctr-1];
    1029:             }
    1030:             xdata[i][ct2++] = val;
    1031:             ct3++;
    1032:           }
    1033:         }
    1034:       }
    1035:       /* Update the header*/
    1036:       xdata[i][2*j]   = ct2 - oct2; /* Undo the vector isz1 and use only a var*/
    1037:       xdata[i][2*j-1] = rbuf_i[2*j-1];
    1038:     }
    1039:     xdata[i][0] = rbuf_0;
    1040:     xdata[i+1]  = xdata[i] + ct2;
    1041:     isz1[i]     = ct2; /* size of each message */
    1042:   }
    1043:   PetscBTDestroy(&xtable);
    1044:   PetscInfo3(C,"Allocated %D bytes, required %D bytes, no of mallocs = %D\n",mem_estimate,ct3,no_malloc);
    1045:   return(0);
    1046: }
    1047: /* -------------------------------------------------------------------------*/
    1048: extern PetscErrorCode MatCreateSubMatrices_MPIAIJ_Local(Mat,PetscInt,const IS[],const IS[],MatReuse,Mat*);
    1049: /*
    1050:     Every processor gets the entire matrix
    1051: */
    1052: PetscErrorCode MatCreateSubMatrix_MPIAIJ_All(Mat A,MatCreateSubMatrixOption flag,MatReuse scall,Mat *Bin[])
    1053: {
    1054:   Mat            B;
    1055:   Mat_MPIAIJ     *a = (Mat_MPIAIJ*)A->data;
    1056:   Mat_SeqAIJ     *b,*ad = (Mat_SeqAIJ*)a->A->data,*bd = (Mat_SeqAIJ*)a->B->data;
    1058:   PetscMPIInt    size,rank,*recvcounts = 0,*displs = 0;
    1059:   PetscInt       sendcount,i,*rstarts = A->rmap->range,n,cnt,j;
    1060:   PetscInt       m,*b_sendj,*garray = a->garray,*lens,*jsendbuf,*a_jsendbuf,*b_jsendbuf;
    1061:   MatScalar      *sendbuf,*recvbuf,*a_sendbuf,*b_sendbuf;

    1064:   MPI_Comm_size(PetscObjectComm((PetscObject)A),&size);
    1065:   MPI_Comm_rank(PetscObjectComm((PetscObject)A),&rank);

    1067:   if (scall == MAT_INITIAL_MATRIX) {
    1068:     /* ----------------------------------------------------------------
    1069:          Tell every processor the number of nonzeros per row
    1070:     */
    1071:     PetscMalloc1(A->rmap->N,&lens);
    1072:     for (i=A->rmap->rstart; i<A->rmap->rend; i++) {
    1073:       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];
    1074:     }
    1075:     PetscMalloc2(size,&recvcounts,size,&displs);
    1076:     for (i=0; i<size; i++) {
    1077:       recvcounts[i] = A->rmap->range[i+1] - A->rmap->range[i];
    1078:       displs[i]     = A->rmap->range[i];
    1079:     }
    1080: #if defined(PETSC_HAVE_MPI_IN_PLACE)
    1081:     MPI_Allgatherv(MPI_IN_PLACE,0,MPI_DATATYPE_NULL,lens,recvcounts,displs,MPIU_INT,PetscObjectComm((PetscObject)A));
    1082: #else
    1083:     sendcount = A->rmap->rend - A->rmap->rstart;
    1084:     MPI_Allgatherv(lens+A->rmap->rstart,sendcount,MPIU_INT,lens,recvcounts,displs,MPIU_INT,PetscObjectComm((PetscObject)A));
    1085: #endif
    1086:     /* ---------------------------------------------------------------
    1087:          Create the sequential matrix of the same type as the local block diagonal
    1088:     */
    1089:     MatCreate(PETSC_COMM_SELF,&B);
    1090:     MatSetSizes(B,A->rmap->N,A->cmap->N,PETSC_DETERMINE,PETSC_DETERMINE);
    1091:     MatSetBlockSizesFromMats(B,A,A);
    1092:     MatSetType(B,((PetscObject)a->A)->type_name);
    1093:     MatSeqAIJSetPreallocation(B,0,lens);
    1094:     PetscCalloc1(2,Bin);
    1095:     **Bin = B;
    1096:     b     = (Mat_SeqAIJ*)B->data;

    1098:     /*--------------------------------------------------------------------
    1099:        Copy my part of matrix column indices over
    1100:     */
    1101:     sendcount  = ad->nz + bd->nz;
    1102:     jsendbuf   = b->j + b->i[rstarts[rank]];
    1103:     a_jsendbuf = ad->j;
    1104:     b_jsendbuf = bd->j;
    1105:     n          = A->rmap->rend - A->rmap->rstart;
    1106:     cnt        = 0;
    1107:     for (i=0; i<n; i++) {

    1109:       /* put in lower diagonal portion */
    1110:       m = bd->i[i+1] - bd->i[i];
    1111:       while (m > 0) {
    1112:         /* is it above diagonal (in bd (compressed) numbering) */
    1113:         if (garray[*b_jsendbuf] > A->rmap->rstart + i) break;
    1114:         jsendbuf[cnt++] = garray[*b_jsendbuf++];
    1115:         m--;
    1116:       }

    1118:       /* put in diagonal portion */
    1119:       for (j=ad->i[i]; j<ad->i[i+1]; j++) {
    1120:         jsendbuf[cnt++] = A->rmap->rstart + *a_jsendbuf++;
    1121:       }

    1123:       /* put in upper diagonal portion */
    1124:       while (m-- > 0) {
    1125:         jsendbuf[cnt++] = garray[*b_jsendbuf++];
    1126:       }
    1127:     }
    1128:     if (cnt != sendcount) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_PLIB,"Corrupted PETSc matrix: nz given %D actual nz %D",sendcount,cnt);

    1130:     /*--------------------------------------------------------------------
    1131:        Gather all column indices to all processors
    1132:     */
    1133:     for (i=0; i<size; i++) {
    1134:       recvcounts[i] = 0;
    1135:       for (j=A->rmap->range[i]; j<A->rmap->range[i+1]; j++) {
    1136:         recvcounts[i] += lens[j];
    1137:       }
    1138:     }
    1139:     displs[0] = 0;
    1140:     for (i=1; i<size; i++) {
    1141:       displs[i] = displs[i-1] + recvcounts[i-1];
    1142:     }
    1143: #if defined(PETSC_HAVE_MPI_IN_PLACE)
    1144:     MPI_Allgatherv(MPI_IN_PLACE,0,MPI_DATATYPE_NULL,b->j,recvcounts,displs,MPIU_INT,PetscObjectComm((PetscObject)A));
    1145: #else
    1146:     MPI_Allgatherv(jsendbuf,sendcount,MPIU_INT,b->j,recvcounts,displs,MPIU_INT,PetscObjectComm((PetscObject)A));
    1147: #endif
    1148:     /*--------------------------------------------------------------------
    1149:         Assemble the matrix into useable form (note numerical values not yet set)
    1150:     */
    1151:     /* set the b->ilen (length of each row) values */
    1152:     PetscMemcpy(b->ilen,lens,A->rmap->N*sizeof(PetscInt));
    1153:     /* set the b->i indices */
    1154:     b->i[0] = 0;
    1155:     for (i=1; i<=A->rmap->N; i++) {
    1156:       b->i[i] = b->i[i-1] + lens[i-1];
    1157:     }
    1158:     PetscFree(lens);
    1159:     MatAssemblyBegin(B,MAT_FINAL_ASSEMBLY);
    1160:     MatAssemblyEnd(B,MAT_FINAL_ASSEMBLY);

    1162:   } else {
    1163:     B = **Bin;
    1164:     b = (Mat_SeqAIJ*)B->data;
    1165:   }

    1167:   /*--------------------------------------------------------------------
    1168:        Copy my part of matrix numerical values into the values location
    1169:   */
    1170:   if (flag == MAT_GET_VALUES) {
    1171:     sendcount = ad->nz + bd->nz;
    1172:     sendbuf   = b->a + b->i[rstarts[rank]];
    1173:     a_sendbuf = ad->a;
    1174:     b_sendbuf = bd->a;
    1175:     b_sendj   = bd->j;
    1176:     n         = A->rmap->rend - A->rmap->rstart;
    1177:     cnt       = 0;
    1178:     for (i=0; i<n; i++) {

    1180:       /* put in lower diagonal portion */
    1181:       m = bd->i[i+1] - bd->i[i];
    1182:       while (m > 0) {
    1183:         /* is it above diagonal (in bd (compressed) numbering) */
    1184:         if (garray[*b_sendj] > A->rmap->rstart + i) break;
    1185:         sendbuf[cnt++] = *b_sendbuf++;
    1186:         m--;
    1187:         b_sendj++;
    1188:       }

    1190:       /* put in diagonal portion */
    1191:       for (j=ad->i[i]; j<ad->i[i+1]; j++) {
    1192:         sendbuf[cnt++] = *a_sendbuf++;
    1193:       }

    1195:       /* put in upper diagonal portion */
    1196:       while (m-- > 0) {
    1197:         sendbuf[cnt++] = *b_sendbuf++;
    1198:         b_sendj++;
    1199:       }
    1200:     }
    1201:     if (cnt != sendcount) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_PLIB,"Corrupted PETSc matrix: nz given %D actual nz %D",sendcount,cnt);

    1203:     /* -----------------------------------------------------------------
    1204:        Gather all numerical values to all processors
    1205:     */
    1206:     if (!recvcounts) {
    1207:       PetscMalloc2(size,&recvcounts,size,&displs);
    1208:     }
    1209:     for (i=0; i<size; i++) {
    1210:       recvcounts[i] = b->i[rstarts[i+1]] - b->i[rstarts[i]];
    1211:     }
    1212:     displs[0] = 0;
    1213:     for (i=1; i<size; i++) {
    1214:       displs[i] = displs[i-1] + recvcounts[i-1];
    1215:     }
    1216:     recvbuf = b->a;
    1217: #if defined(PETSC_HAVE_MPI_IN_PLACE)
    1218:     MPI_Allgatherv(MPI_IN_PLACE,0,MPI_DATATYPE_NULL,recvbuf,recvcounts,displs,MPIU_SCALAR,PetscObjectComm((PetscObject)A));
    1219: #else
    1220:     MPI_Allgatherv(sendbuf,sendcount,MPIU_SCALAR,recvbuf,recvcounts,displs,MPIU_SCALAR,PetscObjectComm((PetscObject)A));
    1221: #endif
    1222:   }  /* endof (flag == MAT_GET_VALUES) */
    1223:   PetscFree2(recvcounts,displs);

    1225:   if (A->symmetric) {
    1226:     MatSetOption(B,MAT_SYMMETRIC,PETSC_TRUE);
    1227:   } else if (A->hermitian) {
    1228:     MatSetOption(B,MAT_HERMITIAN,PETSC_TRUE);
    1229:   } else if (A->structurally_symmetric) {
    1230:     MatSetOption(B,MAT_STRUCTURALLY_SYMMETRIC,PETSC_TRUE);
    1231:   }
    1232:   return(0);
    1233: }

    1235: PetscErrorCode MatCreateSubMatrices_MPIAIJ_SingleIS_Local(Mat C,PetscInt ismax,const IS isrow[],const IS iscol[],MatReuse scall,PetscBool allcolumns,Mat *submats)
    1236: {
    1237:   Mat_MPIAIJ     *c = (Mat_MPIAIJ*)C->data;
    1238:   Mat            submat,A = c->A,B = c->B;
    1239:   Mat_SeqAIJ     *a = (Mat_SeqAIJ*)A->data,*b = (Mat_SeqAIJ*)B->data,*subc;
    1240:   PetscInt       *ai=a->i,*aj=a->j,*bi=b->i,*bj=b->j,nzA,nzB;
    1241:   PetscInt       cstart = C->cmap->rstart,cend = C->cmap->rend,rstart = C->rmap->rstart,*bmap = c->garray;
    1242:   const PetscInt *icol,*irow;
    1243:   PetscInt       nrow,ncol,start;
    1245:   PetscMPIInt    rank,size,tag1,tag2,tag3,tag4,*w1,*w2,nrqr;
    1246:   PetscInt       **sbuf1,**sbuf2,i,j,k,l,ct1,ct2,ct3,**rbuf1,row,proc;
    1247:   PetscInt       nrqs=0,msz,**ptr,*req_size,*ctr,*pa,*tmp,tcol,*iptr;
    1248:   PetscInt       **rbuf3,*req_source1,*req_source2,**sbuf_aj,**rbuf2,max1,nnz;
    1249:   PetscInt       *lens,rmax,ncols,*cols,Crow;
    1250: #if defined(PETSC_USE_CTABLE)
    1251:   PetscTable     cmap,rmap;
    1252:   PetscInt       *cmap_loc,*rmap_loc;
    1253: #else
    1254:   PetscInt       *cmap,*rmap;
    1255: #endif
    1256:   PetscInt       ctr_j,*sbuf1_j,*sbuf_aj_i,*rbuf1_i,kmax,*sbuf1_i,*rbuf2_i,*rbuf3_i;
    1257:   PetscInt       *cworkB,lwrite,*subcols,*row2proc;
    1258:   PetscScalar    *vworkA,*vworkB,*a_a = a->a,*b_a = b->a,*subvals=NULL;
    1259:   MPI_Request    *s_waits1,*r_waits1,*s_waits2,*r_waits2,*r_waits3;
    1260:   MPI_Request    *r_waits4,*s_waits3 = NULL,*s_waits4;
    1261:   MPI_Status     *r_status1,*r_status2,*s_status1,*s_status3 = NULL,*s_status2;
    1262:   MPI_Status     *r_status3 = NULL,*r_status4,*s_status4;
    1263:   MPI_Comm       comm;
    1264:   PetscScalar    **rbuf4,**sbuf_aa,*vals,*sbuf_aa_i,*rbuf4_i;
    1265:   PetscMPIInt    *onodes1,*olengths1,idex,end;
    1266:   Mat_SubSppt    *smatis1;
    1267:   PetscBool      isrowsorted,iscolsorted;

    1270:   if (ismax != 1) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_SUP,"This routine only works when all processes have ismax=1");

    1272:   PetscObjectGetComm((PetscObject)C,&comm);
    1273:   size = c->size;
    1274:   rank = c->rank;

    1276:   ISSorted(iscol[0],&iscolsorted);
    1277:   ISSorted(isrow[0],&isrowsorted);
    1278:   ISGetIndices(isrow[0],&irow);
    1279:   ISGetLocalSize(isrow[0],&nrow);
    1280:   if (allcolumns) {
    1281:     icol = NULL;
    1282:     ncol = C->cmap->N;
    1283:   } else {
    1284:     ISGetIndices(iscol[0],&icol);
    1285:     ISGetLocalSize(iscol[0],&ncol);
    1286:   }

    1288:   if (scall == MAT_INITIAL_MATRIX) {
    1289:     PetscInt *sbuf2_i,*cworkA,lwrite,ctmp;

    1291:     /* Get some new tags to keep the communication clean */
    1292:     tag1 = ((PetscObject)C)->tag;
    1293:     PetscObjectGetNewTag((PetscObject)C,&tag2);
    1294:     PetscObjectGetNewTag((PetscObject)C,&tag3);

    1296:     /* evaluate communication - mesg to who, length of mesg, and buffer space
    1297:      required. Based on this, buffers are allocated, and data copied into them */
    1298:     PetscCalloc2(size,&w1,size,&w2);
    1299:     PetscMalloc1(nrow,&row2proc);

    1301:     /* w1[proc] = num of rows owned by proc -- to be requested */
    1302:     proc = 0;
    1303:     nrqs = 0; /* num of outgoing messages */
    1304:     for (j=0; j<nrow; j++) {
    1305:       row  = irow[j];
    1306:       if (!isrowsorted) proc = 0;
    1307:       while (row >= C->rmap->range[proc+1]) proc++;
    1308:       w1[proc]++;
    1309:       row2proc[j] = proc; /* map row index to proc */

    1311:       if (proc != rank && !w2[proc]) {
    1312:         w2[proc] = 1; nrqs++;
    1313:       }
    1314:     }
    1315:     w1[rank] = 0;  /* rows owned by self will not be requested */

    1317:     PetscMalloc1(nrqs+1,&pa); /*(proc -array)*/
    1318:     for (proc=0,j=0; proc<size; proc++) {
    1319:       if (w1[proc]) { pa[j++] = proc;}
    1320:     }

    1322:     /* Each message would have a header = 1 + 2*(num of IS) + data (here,num of IS = 1) */
    1323:     msz = 0;              /* total mesg length (for all procs) */
    1324:     for (i=0; i<nrqs; i++) {
    1325:       proc      = pa[i];
    1326:       w1[proc] += 3;
    1327:       msz      += w1[proc];
    1328:     }
    1329:     PetscInfo2(0,"Number of outgoing messages %D Total message length %D\n",nrqs,msz);

    1331:     /* Determine nrqr, the number of messages to expect, their lengths, from from-ids */
    1332:     /* if w2[proc]=1, a message of length w1[proc] will be sent to proc; */
    1333:     PetscGatherNumberOfMessages(comm,w2,w1,&nrqr);

    1335:     /* Input: nrqs: nsend; nrqr: nrecv; w1: msg length to be sent;
    1336:        Output: onodes1: recv node-ids; olengths1: corresponding recv message length */
    1337:     PetscGatherMessageLengths(comm,nrqs,nrqr,w1,&onodes1,&olengths1);

    1339:     /* Now post the Irecvs corresponding to these messages */
    1340:     PetscPostIrecvInt(comm,tag1,nrqr,onodes1,olengths1,&rbuf1,&r_waits1);

    1342:     PetscFree(onodes1);
    1343:     PetscFree(olengths1);

    1345:     /* Allocate Memory for outgoing messages */
    1346:     PetscMalloc4(size,&sbuf1,size,&ptr,2*msz,&tmp,size,&ctr);
    1347:     PetscMemzero(sbuf1,size*sizeof(PetscInt*));
    1348:     PetscMemzero(ptr,size*sizeof(PetscInt*));

    1350:     /* subf1[pa[0]] = tmp, subf1[pa[i]] = subf1[pa[i-1]] + w1[pa[i-1]] */
    1351:     iptr = tmp;
    1352:     for (i=0; i<nrqs; i++) {
    1353:       proc        = pa[i];
    1354:       sbuf1[proc] = iptr;
    1355:       iptr       += w1[proc];
    1356:     }

    1358:     /* Form the outgoing messages */
    1359:     /* Initialize the header space */
    1360:     for (i=0; i<nrqs; i++) {
    1361:       proc      = pa[i];
    1362:       PetscMemzero(sbuf1[proc],3*sizeof(PetscInt));
    1363:       ptr[proc] = sbuf1[proc] + 3;
    1364:     }

    1366:     /* Parse the isrow and copy data into outbuf */
    1367:     PetscMemzero(ctr,size*sizeof(PetscInt));
    1368:     for (j=0; j<nrow; j++) {  /* parse the indices of each IS */
    1369:       proc = row2proc[j];
    1370:       if (proc != rank) { /* copy to the outgoing buf*/
    1371:         *ptr[proc] = irow[j];
    1372:         ctr[proc]++; ptr[proc]++;
    1373:       }
    1374:     }

    1376:     /* Update the headers for the current IS */
    1377:     for (j=0; j<size; j++) { /* Can Optimise this loop too */
    1378:       if ((ctr_j = ctr[j])) {
    1379:         sbuf1_j        = sbuf1[j];
    1380:         k              = ++sbuf1_j[0];
    1381:         sbuf1_j[2*k]   = ctr_j;
    1382:         sbuf1_j[2*k-1] = 0;
    1383:       }
    1384:     }

    1386:     /* Now post the sends */
    1387:     PetscMalloc1(nrqs+1,&s_waits1);
    1388:     for (i=0; i<nrqs; ++i) {
    1389:       proc = pa[i];
    1390:       MPI_Isend(sbuf1[proc],w1[proc],MPIU_INT,proc,tag1,comm,s_waits1+i);
    1391:     }

    1393:     /* Post Receives to capture the buffer size */
    1394:     PetscMalloc4(nrqs+1,&r_status2,nrqr+1,&s_waits2,nrqs+1,&r_waits2,nrqr+1,&s_status2);
    1395:     PetscMalloc3(nrqs+1,&req_source2,nrqs+1,&rbuf2,nrqs+1,&rbuf3);

    1397:     rbuf2[0] = tmp + msz;
    1398:     for (i=1; i<nrqs; ++i) rbuf2[i] = rbuf2[i-1] + w1[pa[i-1]];

    1400:     for (i=0; i<nrqs; ++i) {
    1401:       proc = pa[i];
    1402:       MPI_Irecv(rbuf2[i],w1[proc],MPIU_INT,proc,tag2,comm,r_waits2+i);
    1403:     }

    1405:     PetscFree2(w1,w2);

    1407:     /* Send to other procs the buf size they should allocate */
    1408:     /* Receive messages*/
    1409:     PetscMalloc1(nrqr+1,&r_status1);
    1410:     PetscMalloc3(nrqr,&sbuf2,nrqr,&req_size,nrqr,&req_source1);

    1412:     MPI_Waitall(nrqr,r_waits1,r_status1);
    1413:     for (i=0; i<nrqr; ++i) {
    1414:       req_size[i] = 0;
    1415:       rbuf1_i        = rbuf1[i];
    1416:       start          = 2*rbuf1_i[0] + 1;
    1417:       MPI_Get_count(r_status1+i,MPIU_INT,&end);
    1418:       PetscMalloc1(end+1,&sbuf2[i]);
    1419:       sbuf2_i        = sbuf2[i];
    1420:       for (j=start; j<end; j++) {
    1421:         k            = rbuf1_i[j] - rstart;
    1422:         ncols        = ai[k+1] - ai[k] + bi[k+1] - bi[k];
    1423:         sbuf2_i[j]   = ncols;
    1424:         req_size[i] += ncols;
    1425:       }
    1426:       req_source1[i] = r_status1[i].MPI_SOURCE;

    1428:       /* form the header */
    1429:       sbuf2_i[0] = req_size[i];
    1430:       for (j=1; j<start; j++) sbuf2_i[j] = rbuf1_i[j];

    1432:       MPI_Isend(sbuf2_i,end,MPIU_INT,req_source1[i],tag2,comm,s_waits2+i);
    1433:     }

    1435:     PetscFree(r_status1);
    1436:     PetscFree(r_waits1);

    1438:     /* rbuf2 is received, Post recv column indices a->j */
    1439:     MPI_Waitall(nrqs,r_waits2,r_status2);

    1441:     PetscMalloc4(nrqs+1,&r_waits3,nrqr+1,&s_waits3,nrqs+1,&r_status3,nrqr+1,&s_status3);
    1442:     for (i=0; i<nrqs; ++i) {
    1443:       PetscMalloc1(rbuf2[i][0]+1,&rbuf3[i]);
    1444:       req_source2[i] = r_status2[i].MPI_SOURCE;
    1445:       MPI_Irecv(rbuf3[i],rbuf2[i][0],MPIU_INT,req_source2[i],tag3,comm,r_waits3+i);
    1446:     }

    1448:     /* Wait on sends1 and sends2 */
    1449:     PetscMalloc1(nrqs+1,&s_status1);
    1450:     MPI_Waitall(nrqs,s_waits1,s_status1);
    1451:     PetscFree(s_waits1);
    1452:     PetscFree(s_status1);

    1454:     MPI_Waitall(nrqr,s_waits2,s_status2);
    1455:     PetscFree4(r_status2,s_waits2,r_waits2,s_status2);

    1457:     /* Now allocate sending buffers for a->j, and send them off */
    1458:     PetscMalloc1(nrqr+1,&sbuf_aj);
    1459:     for (i=0,j=0; i<nrqr; i++) j += req_size[i];
    1460:     PetscMalloc1(j+1,&sbuf_aj[0]);
    1461:     for (i=1; i<nrqr; i++) sbuf_aj[i] = sbuf_aj[i-1] + req_size[i-1];

    1463:     for (i=0; i<nrqr; i++) { /* for each requested message */
    1464:       rbuf1_i   = rbuf1[i];
    1465:       sbuf_aj_i = sbuf_aj[i];
    1466:       ct1       = 2*rbuf1_i[0] + 1;
    1467:       ct2       = 0;
    1468:       /* max1=rbuf1_i[0]; if (max1 != 1) SETERRQ1(PETSC_COMM_SELF,0,"max1 %d != 1",max1); */

    1470:       kmax = rbuf1[i][2];
    1471:       for (k=0; k<kmax; k++,ct1++) { /* for each row */
    1472:         row    = rbuf1_i[ct1] - rstart;
    1473:         nzA    = ai[row+1] - ai[row];
    1474:         nzB    = bi[row+1] - bi[row];
    1475:         ncols  = nzA + nzB;
    1476:         cworkA = aj + ai[row]; cworkB = bj + bi[row];

    1478:         /* load the column indices for this row into cols*/
    1479:         cols = sbuf_aj_i + ct2;

    1481:         lwrite = 0;
    1482:         for (l=0; l<nzB; l++) {
    1483:           if ((ctmp = bmap[cworkB[l]]) < cstart) cols[lwrite++] = ctmp;
    1484:         }
    1485:         for (l=0; l<nzA; l++) cols[lwrite++] = cstart + cworkA[l];
    1486:         for (l=0; l<nzB; l++) {
    1487:           if ((ctmp = bmap[cworkB[l]]) >= cend) cols[lwrite++] = ctmp;
    1488:         }

    1490:         ct2 += ncols;
    1491:       }
    1492:       MPI_Isend(sbuf_aj_i,req_size[i],MPIU_INT,req_source1[i],tag3,comm,s_waits3+i);
    1493:     }

    1495:     /* create column map (cmap): global col of C -> local col of submat */
    1496: #if defined(PETSC_USE_CTABLE)
    1497:     if (!allcolumns) {
    1498:       PetscTableCreate(ncol+1,C->cmap->N+1,&cmap);
    1499:       PetscCalloc1(C->cmap->n,&cmap_loc);
    1500:       for (j=0; j<ncol; j++) { /* use array cmap_loc[] for local col indices */
    1501:         if (icol[j] >= cstart && icol[j] <cend) {
    1502:           cmap_loc[icol[j] - cstart] = j+1;
    1503:         } else { /* use PetscTable for non-local col indices */
    1504:           PetscTableAdd(cmap,icol[j]+1,j+1,INSERT_VALUES);
    1505:         }
    1506:       }
    1507:     } else {
    1508:       cmap     = NULL;
    1509:       cmap_loc = NULL;
    1510:     }
    1511:     PetscCalloc1(C->rmap->n,&rmap_loc);
    1512: #else
    1513:     if (!allcolumns) {
    1514:       PetscCalloc1(C->cmap->N,&cmap);
    1515:       for (j=0; j<ncol; j++) cmap[icol[j]] = j+1;
    1516:     } else {
    1517:       cmap = NULL;
    1518:     }
    1519: #endif

    1521:     /* Create lens for MatSeqAIJSetPreallocation() */
    1522:     PetscCalloc1(nrow,&lens);

    1524:     /* Compute lens from local part of C */
    1525:     for (j=0; j<nrow; j++) {
    1526:       row  = irow[j];
    1527:       proc = row2proc[j];
    1528:       if (proc == rank) {
    1529:         /* diagonal part A = c->A */
    1530:         ncols = ai[row-rstart+1] - ai[row-rstart];
    1531:         cols  = aj + ai[row-rstart];
    1532:         if (!allcolumns) {
    1533:           for (k=0; k<ncols; k++) {
    1534: #if defined(PETSC_USE_CTABLE)
    1535:             tcol = cmap_loc[cols[k]];
    1536: #else
    1537:             tcol = cmap[cols[k]+cstart];
    1538: #endif
    1539:             if (tcol) lens[j]++;
    1540:           }
    1541:         } else { /* allcolumns */
    1542:           lens[j] = ncols;
    1543:         }

    1545:         /* off-diagonal part B = c->B */
    1546:         ncols = bi[row-rstart+1] - bi[row-rstart];
    1547:         cols  = bj + bi[row-rstart];
    1548:         if (!allcolumns) {
    1549:           for (k=0; k<ncols; k++) {
    1550: #if defined(PETSC_USE_CTABLE)
    1551:             PetscTableFind(cmap,bmap[cols[k]]+1,&tcol);
    1552: #else
    1553:             tcol = cmap[bmap[cols[k]]];
    1554: #endif
    1555:             if (tcol) lens[j]++;
    1556:           }
    1557:         } else { /* allcolumns */
    1558:           lens[j] += ncols;
    1559:         }
    1560:       }
    1561:     }

    1563:     /* Create row map (rmap): global row of C -> local row of submat */
    1564: #if defined(PETSC_USE_CTABLE)
    1565:     PetscTableCreate(nrow+1,C->rmap->N+1,&rmap);
    1566:     for (j=0; j<nrow; j++) {
    1567:       row  = irow[j];
    1568:       proc = row2proc[j];
    1569:       if (proc == rank) { /* a local row */
    1570:         rmap_loc[row - rstart] = j;
    1571:       } else {
    1572:         PetscTableAdd(rmap,irow[j]+1,j+1,INSERT_VALUES);
    1573:       }
    1574:     }
    1575: #else
    1576:     PetscCalloc1(C->rmap->N,&rmap);
    1577:     for (j=0; j<nrow; j++) {
    1578:       rmap[irow[j]] = j;
    1579:     }
    1580: #endif

    1582:     /* Update lens from offproc data */
    1583:     /* recv a->j is done */
    1584:     MPI_Waitall(nrqs,r_waits3,r_status3);
    1585:     for (i=0; i<nrqs; i++) {
    1586:       proc    = pa[i];
    1587:       sbuf1_i = sbuf1[proc];
    1588:       /* jmax    = sbuf1_i[0]; if (jmax != 1) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_PLIB,"jmax !=1"); */
    1589:       ct1     = 2 + 1;
    1590:       ct2     = 0;
    1591:       rbuf2_i = rbuf2[i]; /* received length of C->j */
    1592:       rbuf3_i = rbuf3[i]; /* received C->j */

    1594:       /* is_no  = sbuf1_i[2*j-1]; if (is_no != 0) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_PLIB,"is_no !=0"); */
    1595:       max1   = sbuf1_i[2];
    1596:       for (k=0; k<max1; k++,ct1++) {
    1597: #if defined(PETSC_USE_CTABLE)
    1598:         PetscTableFind(rmap,sbuf1_i[ct1]+1,&row);
    1599:         row--;
    1600:         if (row < 0) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_PLIB,"row not found in table");
    1601: #else
    1602:         row = rmap[sbuf1_i[ct1]]; /* the row index in submat */
    1603: #endif
    1604:         /* Now, store row index of submat in sbuf1_i[ct1] */
    1605:         sbuf1_i[ct1] = row;

    1607:         nnz = rbuf2_i[ct1];
    1608:         if (!allcolumns) {
    1609:           for (l=0; l<nnz; l++,ct2++) {
    1610: #if defined(PETSC_USE_CTABLE)
    1611:             if (rbuf3_i[ct2] >= cstart && rbuf3_i[ct2] <cend) {
    1612:               tcol = cmap_loc[rbuf3_i[ct2] - cstart];
    1613:             } else {
    1614:               PetscTableFind(cmap,rbuf3_i[ct2]+1,&tcol);
    1615:             }
    1616: #else
    1617:             tcol = cmap[rbuf3_i[ct2]]; /* column index in submat */
    1618: #endif
    1619:             if (tcol) lens[row]++;
    1620:           }
    1621:         } else { /* allcolumns */
    1622:           lens[row] += nnz;
    1623:         }
    1624:       }
    1625:     }
    1626:     MPI_Waitall(nrqr,s_waits3,s_status3);
    1627:     PetscFree4(r_waits3,s_waits3,r_status3,s_status3);

    1629:     /* Create the submatrices */
    1630:     MatCreate(PETSC_COMM_SELF,&submat);
    1631:     MatSetSizes(submat,nrow,ncol,PETSC_DETERMINE,PETSC_DETERMINE);

    1633:     ISGetBlockSize(isrow[0],&i);
    1634:     ISGetBlockSize(iscol[0],&j);
    1635:     MatSetBlockSizes(submat,i,j);
    1636:     MatSetType(submat,((PetscObject)A)->type_name);
    1637:     MatSeqAIJSetPreallocation(submat,0,lens);

    1639:     /* create struct Mat_SubSppt and attached it to submat */
    1640:     PetscNew(&smatis1);
    1641:     subc = (Mat_SeqAIJ*)submat->data;
    1642:     subc->submatis1 = smatis1;

    1644:     smatis1->id          = 0;
    1645:     smatis1->nrqs        = nrqs;
    1646:     smatis1->nrqr        = nrqr;
    1647:     smatis1->rbuf1       = rbuf1;
    1648:     smatis1->rbuf2       = rbuf2;
    1649:     smatis1->rbuf3       = rbuf3;
    1650:     smatis1->sbuf2       = sbuf2;
    1651:     smatis1->req_source2 = req_source2;

    1653:     smatis1->sbuf1       = sbuf1;
    1654:     smatis1->ptr         = ptr;
    1655:     smatis1->tmp         = tmp;
    1656:     smatis1->ctr         = ctr;

    1658:     smatis1->pa           = pa;
    1659:     smatis1->req_size     = req_size;
    1660:     smatis1->req_source1  = req_source1;

    1662:     smatis1->allcolumns  = allcolumns;
    1663:     smatis1->singleis    = PETSC_TRUE;
    1664:     smatis1->row2proc    = row2proc;
    1665:     smatis1->rmap        = rmap;
    1666:     smatis1->cmap        = cmap;
    1667: #if defined(PETSC_USE_CTABLE)
    1668:     smatis1->rmap_loc    = rmap_loc;
    1669:     smatis1->cmap_loc    = cmap_loc;
    1670: #endif

    1672:     smatis1->destroy     = submat->ops->destroy;
    1673:     submat->ops->destroy = MatDestroySubMatrix_SeqAIJ;
    1674:     submat->factortype   = C->factortype;

    1676:     /* compute rmax */
    1677:     rmax = 0;
    1678:     for (i=0; i<nrow; i++) rmax = PetscMax(rmax,lens[i]);

    1680:   } else { /* scall == MAT_REUSE_MATRIX */
    1681:     submat = submats[0];
    1682:     if (submat->rmap->n != nrow || submat->cmap->n != ncol) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_SIZ,"Cannot reuse matrix. wrong size");

    1684:     subc    = (Mat_SeqAIJ*)submat->data;
    1685:     rmax    = subc->rmax;
    1686:     smatis1 = subc->submatis1;
    1687:     nrqs        = smatis1->nrqs;
    1688:     nrqr        = smatis1->nrqr;
    1689:     rbuf1       = smatis1->rbuf1;
    1690:     rbuf2       = smatis1->rbuf2;
    1691:     rbuf3       = smatis1->rbuf3;
    1692:     req_source2 = smatis1->req_source2;

    1694:     sbuf1     = smatis1->sbuf1;
    1695:     sbuf2     = smatis1->sbuf2;
    1696:     ptr       = smatis1->ptr;
    1697:     tmp       = smatis1->tmp;
    1698:     ctr       = smatis1->ctr;

    1700:     pa         = smatis1->pa;
    1701:     req_size   = smatis1->req_size;
    1702:     req_source1 = smatis1->req_source1;

    1704:     allcolumns = smatis1->allcolumns;
    1705:     row2proc   = smatis1->row2proc;
    1706:     rmap       = smatis1->rmap;
    1707:     cmap       = smatis1->cmap;
    1708: #if defined(PETSC_USE_CTABLE)
    1709:     rmap_loc   = smatis1->rmap_loc;
    1710:     cmap_loc   = smatis1->cmap_loc;
    1711: #endif
    1712:   }

    1714:   /* Post recv matrix values */
    1715:   PetscMalloc3(nrqs+1,&rbuf4, rmax,&subcols, rmax,&subvals);
    1716:   PetscMalloc4(nrqs+1,&r_waits4,nrqr+1,&s_waits4,nrqs+1,&r_status4,nrqr+1,&s_status4);
    1717:   PetscObjectGetNewTag((PetscObject)C,&tag4);
    1718:   for (i=0; i<nrqs; ++i) {
    1719:     PetscMalloc1(rbuf2[i][0]+1,&rbuf4[i]);
    1720:     MPI_Irecv(rbuf4[i],rbuf2[i][0],MPIU_SCALAR,req_source2[i],tag4,comm,r_waits4+i);
    1721:   }

    1723:   /* Allocate sending buffers for a->a, and send them off */
    1724:   PetscMalloc1(nrqr+1,&sbuf_aa);
    1725:   for (i=0,j=0; i<nrqr; i++) j += req_size[i];
    1726:   PetscMalloc1(j+1,&sbuf_aa[0]);
    1727:   for (i=1; i<nrqr; i++) sbuf_aa[i] = sbuf_aa[i-1] + req_size[i-1];

    1729:   for (i=0; i<nrqr; i++) {
    1730:     rbuf1_i   = rbuf1[i];
    1731:     sbuf_aa_i = sbuf_aa[i];
    1732:     ct1       = 2*rbuf1_i[0]+1;
    1733:     ct2       = 0;
    1734:     /* max1=rbuf1_i[0]; if (max1 != 1) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_PLIB,"max1 !=1"); */

    1736:     kmax = rbuf1_i[2];
    1737:     for (k=0; k<kmax; k++,ct1++) {
    1738:       row = rbuf1_i[ct1] - rstart;
    1739:       nzA = ai[row+1] - ai[row];
    1740:       nzB = bi[row+1] - bi[row];
    1741:       ncols  = nzA + nzB;
    1742:       cworkB = bj + bi[row];
    1743:       vworkA = a_a + ai[row];
    1744:       vworkB = b_a + bi[row];

    1746:       /* load the column values for this row into vals*/
    1747:       vals = sbuf_aa_i + ct2;

    1749:       lwrite = 0;
    1750:       for (l=0; l<nzB; l++) {
    1751:         if ((bmap[cworkB[l]]) < cstart) vals[lwrite++] = vworkB[l];
    1752:       }
    1753:       for (l=0; l<nzA; l++) vals[lwrite++] = vworkA[l];
    1754:       for (l=0; l<nzB; l++) {
    1755:         if ((bmap[cworkB[l]]) >= cend) vals[lwrite++] = vworkB[l];
    1756:       }

    1758:       ct2 += ncols;
    1759:     }
    1760:     MPI_Isend(sbuf_aa_i,req_size[i],MPIU_SCALAR,req_source1[i],tag4,comm,s_waits4+i);
    1761:   }

    1763:   /* Assemble submat */
    1764:   /* First assemble the local rows */
    1765:   for (j=0; j<nrow; j++) {
    1766:     row  = irow[j];
    1767:     proc = row2proc[j];
    1768:     if (proc == rank) {
    1769:       Crow = row - rstart;  /* local row index of C */
    1770: #if defined(PETSC_USE_CTABLE)
    1771:       row = rmap_loc[Crow]; /* row index of submat */
    1772: #else
    1773:       row = rmap[row];
    1774: #endif

    1776:       if (allcolumns) {
    1777:         /* diagonal part A = c->A */
    1778:         ncols = ai[Crow+1] - ai[Crow];
    1779:         cols  = aj + ai[Crow];
    1780:         vals  = a->a + ai[Crow];
    1781:         i     = 0;
    1782:         for (k=0; k<ncols; k++) {
    1783:           subcols[i]   = cols[k] + cstart;
    1784:           subvals[i++] = vals[k];
    1785:         }

    1787:         /* off-diagonal part B = c->B */
    1788:         ncols = bi[Crow+1] - bi[Crow];
    1789:         cols  = bj + bi[Crow];
    1790:         vals  = b->a + bi[Crow];
    1791:         for (k=0; k<ncols; k++) {
    1792:           subcols[i]   = bmap[cols[k]];
    1793:           subvals[i++] = vals[k];
    1794:         }

    1796:         MatSetValues_SeqAIJ(submat,1,&row,i,subcols,subvals,INSERT_VALUES);

    1798:       } else { /* !allcolumns */
    1799: #if defined(PETSC_USE_CTABLE)
    1800:         /* diagonal part A = c->A */
    1801:         ncols = ai[Crow+1] - ai[Crow];
    1802:         cols  = aj + ai[Crow];
    1803:         vals  = a->a + ai[Crow];
    1804:         i     = 0;
    1805:         for (k=0; k<ncols; k++) {
    1806:           tcol = cmap_loc[cols[k]];
    1807:           if (tcol) {
    1808:             subcols[i]   = --tcol;
    1809:             subvals[i++] = vals[k];
    1810:           }
    1811:         }

    1813:         /* off-diagonal part B = c->B */
    1814:         ncols = bi[Crow+1] - bi[Crow];
    1815:         cols  = bj + bi[Crow];
    1816:         vals  = b->a + bi[Crow];
    1817:         for (k=0; k<ncols; k++) {
    1818:           PetscTableFind(cmap,bmap[cols[k]]+1,&tcol);
    1819:           if (tcol) {
    1820:             subcols[i]   = --tcol;
    1821:             subvals[i++] = vals[k];
    1822:           }
    1823:         }
    1824: #else
    1825:         /* diagonal part A = c->A */
    1826:         ncols = ai[Crow+1] - ai[Crow];
    1827:         cols  = aj + ai[Crow];
    1828:         vals  = a->a + ai[Crow];
    1829:         i     = 0;
    1830:         for (k=0; k<ncols; k++) {
    1831:           tcol = cmap[cols[k]+cstart];
    1832:           if (tcol) {
    1833:             subcols[i]   = --tcol;
    1834:             subvals[i++] = vals[k];
    1835:           }
    1836:         }

    1838:         /* off-diagonal part B = c->B */
    1839:         ncols = bi[Crow+1] - bi[Crow];
    1840:         cols  = bj + bi[Crow];
    1841:         vals  = b->a + bi[Crow];
    1842:         for (k=0; k<ncols; k++) {
    1843:           tcol = cmap[bmap[cols[k]]];
    1844:           if (tcol) {
    1845:             subcols[i]   = --tcol;
    1846:             subvals[i++] = vals[k];
    1847:           }
    1848:         }
    1849: #endif
    1850:         MatSetValues_SeqAIJ(submat,1,&row,i,subcols,subvals,INSERT_VALUES);
    1851:       }
    1852:     }
    1853:   }

    1855:   /* Now assemble the off-proc rows */
    1856:   for (i=0; i<nrqs; i++) { /* for each requested message */
    1857:     /* recv values from other processes */
    1858:     MPI_Waitany(nrqs,r_waits4,&idex,r_status4+i);
    1859:     proc    = pa[idex];
    1860:     sbuf1_i = sbuf1[proc];
    1861:     /* jmax    = sbuf1_i[0]; if (jmax != 1)SETERRQ1(PETSC_COMM_SELF,0,"jmax %d != 1",jmax); */
    1862:     ct1     = 2 + 1;
    1863:     ct2     = 0; /* count of received C->j */
    1864:     ct3     = 0; /* count of received C->j that will be inserted into submat */
    1865:     rbuf2_i = rbuf2[idex]; /* int** received length of C->j from other processes */
    1866:     rbuf3_i = rbuf3[idex]; /* int** received C->j from other processes */
    1867:     rbuf4_i = rbuf4[idex]; /* scalar** received C->a from other processes */

    1869:     /* is_no = sbuf1_i[2*j-1]; if (is_no != 0) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_PLIB,"is_no !=0"); */
    1870:     max1 = sbuf1_i[2];             /* num of rows */
    1871:     for (k=0; k<max1; k++,ct1++) { /* for each recved row */
    1872:       row = sbuf1_i[ct1]; /* row index of submat */
    1873:       if (!allcolumns) {
    1874:         idex = 0;
    1875:         if (scall == MAT_INITIAL_MATRIX || !iscolsorted) {
    1876:           nnz  = rbuf2_i[ct1]; /* num of C entries in this row */
    1877:           for (l=0; l<nnz; l++,ct2++) { /* for each recved column */
    1878: #if defined(PETSC_USE_CTABLE)
    1879:             if (rbuf3_i[ct2] >= cstart && rbuf3_i[ct2] <cend) {
    1880:               tcol = cmap_loc[rbuf3_i[ct2] - cstart];
    1881:             } else {
    1882:               PetscTableFind(cmap,rbuf3_i[ct2]+1,&tcol);
    1883:             }
    1884: #else
    1885:             tcol = cmap[rbuf3_i[ct2]];
    1886: #endif
    1887:             if (tcol) {
    1888:               subcols[idex]   = --tcol; /* may not be sorted */
    1889:               subvals[idex++] = rbuf4_i[ct2];

    1891:               /* We receive an entire column of C, but a subset of it needs to be inserted into submat.
    1892:                For reuse, we replace received C->j with index that should be inserted to submat */
    1893:               if (iscolsorted) rbuf3_i[ct3++] = ct2;
    1894:             }
    1895:           }
    1896:           MatSetValues_SeqAIJ(submat,1,&row,idex,subcols,subvals,INSERT_VALUES);
    1897:         } else { /* scall == MAT_REUSE_MATRIX */
    1898:           submat = submats[0];
    1899:           subc   = (Mat_SeqAIJ*)submat->data;

    1901:           nnz = subc->i[row+1] - subc->i[row]; /* num of submat entries in this row */
    1902:           for (l=0; l<nnz; l++) {
    1903:             ct2 = rbuf3_i[ct3++]; /* index of rbuf4_i[] which needs to be inserted into submat */
    1904:             subvals[idex++] = rbuf4_i[ct2];
    1905:           }

    1907:           bj = subc->j + subc->i[row]; /* sorted column indices */
    1908:           MatSetValues_SeqAIJ(submat,1,&row,nnz,bj,subvals,INSERT_VALUES);
    1909:         }
    1910:       } else { /* allcolumns */
    1911:         nnz  = rbuf2_i[ct1]; /* num of C entries in this row */
    1912:         MatSetValues_SeqAIJ(submat,1,&row,nnz,rbuf3_i+ct2,rbuf4_i+ct2,INSERT_VALUES);
    1913:         ct2 += nnz;
    1914:       }
    1915:     }
    1916:   }

    1918:   /* sending a->a are done */
    1919:   MPI_Waitall(nrqr,s_waits4,s_status4);
    1920:   PetscFree4(r_waits4,s_waits4,r_status4,s_status4);

    1922:   MatAssemblyBegin(submat,MAT_FINAL_ASSEMBLY);
    1923:   MatAssemblyEnd(submat,MAT_FINAL_ASSEMBLY);
    1924:   submats[0] = submat;

    1926:   /* Restore the indices */
    1927:   ISRestoreIndices(isrow[0],&irow);
    1928:   if (!allcolumns) {
    1929:     ISRestoreIndices(iscol[0],&icol);
    1930:   }

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

    1940:   if (scall == MAT_INITIAL_MATRIX) {
    1941:     PetscFree(lens);
    1942:     PetscFree(sbuf_aj[0]);
    1943:     PetscFree(sbuf_aj);
    1944:   }
    1945:   return(0);
    1946: }

    1948: PetscErrorCode MatCreateSubMatrices_MPIAIJ_SingleIS(Mat C,PetscInt ismax,const IS isrow[],const IS iscol[],MatReuse scall,Mat *submat[])
    1949: {
    1951:   PetscInt       ncol;
    1952:   PetscBool      colflag,allcolumns=PETSC_FALSE;

    1955:   /* Allocate memory to hold all the submatrices */
    1956:   if (scall == MAT_INITIAL_MATRIX) {
    1957:     PetscCalloc1(2,submat);
    1958:   }

    1960:   /* Check for special case: each processor gets entire matrix columns */
    1961:   ISIdentity(iscol[0],&colflag);
    1962:   ISGetLocalSize(iscol[0],&ncol);
    1963:   if (colflag && ncol == C->cmap->N) allcolumns = PETSC_TRUE;

    1965:   MatCreateSubMatrices_MPIAIJ_SingleIS_Local(C,ismax,isrow,iscol,scall,allcolumns,*submat);
    1966:   return(0);
    1967: }

    1969: PetscErrorCode MatCreateSubMatrices_MPIAIJ(Mat C,PetscInt ismax,const IS isrow[],const IS iscol[],MatReuse scall,Mat *submat[])
    1970: {
    1972:   PetscInt       nmax,nstages=0,i,pos,max_no,nrow,ncol,in[2],out[2];
    1973:   PetscBool      rowflag,colflag,wantallmatrix=PETSC_FALSE;
    1974:   Mat_SeqAIJ     *subc;
    1975:   Mat_SubSppt    *smat;

    1978:   /* Check for special case: each processor has a single IS */
    1979:   if (C->submat_singleis) { /* flag is set in PCSetUp_ASM() to skip MPIU_Allreduce() */
    1980:     MatCreateSubMatrices_MPIAIJ_SingleIS(C,ismax,isrow,iscol,scall,submat);
    1981:     C->submat_singleis = PETSC_FALSE; /* resume its default value in case C will be used for non-singlis */
    1982:     return(0);
    1983:   }

    1985:   /* Collect global wantallmatrix and nstages */
    1986:   if (!C->cmap->N) nmax=20*1000000/sizeof(PetscInt);
    1987:   else nmax = 20*1000000 / (C->cmap->N * sizeof(PetscInt));
    1988:   if (!nmax) nmax = 1;

    1990:   if (scall == MAT_INITIAL_MATRIX) {
    1991:     /* Collect global wantallmatrix and nstages */
    1992:     if (ismax == 1 && C->rmap->N == C->cmap->N) {
    1993:       ISIdentity(*isrow,&rowflag);
    1994:       ISIdentity(*iscol,&colflag);
    1995:       ISGetLocalSize(*isrow,&nrow);
    1996:       ISGetLocalSize(*iscol,&ncol);
    1997:       if (rowflag && colflag && nrow == C->rmap->N && ncol == C->cmap->N) {
    1998:         wantallmatrix = PETSC_TRUE;

    2000:         PetscOptionsGetBool(((PetscObject)C)->options,((PetscObject)C)->prefix,"-use_fast_submatrix",&wantallmatrix,NULL);
    2001:       }
    2002:     }

    2004:     /* Determine the number of stages through which submatrices are done
    2005:        Each stage will extract nmax submatrices.
    2006:        nmax is determined by the matrix column dimension.
    2007:        If the original matrix has 20M columns, only one submatrix per stage is allowed, etc.
    2008:     */
    2009:     nstages = ismax/nmax + ((ismax % nmax) ? 1 : 0); /* local nstages */

    2011:     in[0] = -1*(PetscInt)wantallmatrix;
    2012:     in[1] = nstages;
    2013:     MPIU_Allreduce(in,out,2,MPIU_INT,MPI_MAX,PetscObjectComm((PetscObject)C));
    2014:     wantallmatrix = (PetscBool)(-out[0]);
    2015:     nstages       = out[1]; /* Make sure every processor loops through the global nstages */

    2017:   } else { /* MAT_REUSE_MATRIX */
    2018:     if (ismax) {
    2019:       subc = (Mat_SeqAIJ*)(*submat)[0]->data;
    2020:       smat = subc->submatis1;
    2021:     } else { /* (*submat)[0] is a dummy matrix */
    2022:       smat = (Mat_SubSppt*)(*submat)[0]->data;
    2023:     }
    2024:     if (!smat) {
    2025:       /* smat is not generated by MatCreateSubMatrix_MPIAIJ_All(...,MAT_INITIAL_MATRIX,...) */
    2026:       wantallmatrix = PETSC_TRUE;
    2027:     } else if (smat->singleis) {
    2028:       MatCreateSubMatrices_MPIAIJ_SingleIS(C,ismax,isrow,iscol,scall,submat);
    2029:       return(0);
    2030:     } else {
    2031:       nstages = smat->nstages;
    2032:     }
    2033:   }

    2035:   if (wantallmatrix) {
    2036:     MatCreateSubMatrix_MPIAIJ_All(C,MAT_GET_VALUES,scall,submat);
    2037:     return(0);
    2038:   }

    2040:   /* Allocate memory to hold all the submatrices and dummy submatrices */
    2041:   if (scall == MAT_INITIAL_MATRIX) {
    2042:     PetscCalloc1(ismax+nstages,submat);
    2043:   }

    2045:   for (i=0,pos=0; i<nstages; i++) {
    2046:     if (pos+nmax <= ismax) max_no = nmax;
    2047:     else if (pos >= ismax) max_no = 0;
    2048:     else                   max_no = ismax-pos;

    2050:     MatCreateSubMatrices_MPIAIJ_Local(C,max_no,isrow+pos,iscol+pos,scall,*submat+pos);
    2051:     if (!max_no && scall == MAT_INITIAL_MATRIX) { /* submat[pos] is a dummy matrix */
    2052:       smat = (Mat_SubSppt*)(*submat)[pos]->data; pos++;
    2053:       smat->nstages = nstages;
    2054:     }
    2055:     pos += max_no;
    2056:   }

    2058:   if (ismax && scall == MAT_INITIAL_MATRIX) {
    2059:     /* save nstages for reuse */
    2060:     subc = (Mat_SeqAIJ*)(*submat)[0]->data;
    2061:     smat = subc->submatis1;
    2062:     smat->nstages = nstages;
    2063:   }
    2064:   return(0);
    2065: }

    2067: /* -------------------------------------------------------------------------*/
    2068: PetscErrorCode MatCreateSubMatrices_MPIAIJ_Local(Mat C,PetscInt ismax,const IS isrow[],const IS iscol[],MatReuse scall,Mat *submats)
    2069: {
    2070:   Mat_MPIAIJ     *c = (Mat_MPIAIJ*)C->data;
    2071:   Mat            A  = c->A;
    2072:   Mat_SeqAIJ     *a = (Mat_SeqAIJ*)A->data,*b = (Mat_SeqAIJ*)c->B->data,*subc;
    2073:   const PetscInt **icol,**irow;
    2074:   PetscInt       *nrow,*ncol,start;
    2076:   PetscMPIInt    rank,size,tag0,tag2,tag3,tag4,*w1,*w2,*w3,*w4,nrqr;
    2077:   PetscInt       **sbuf1,**sbuf2,i,j,k,l,ct1,ct2,**rbuf1,row,proc=-1;
    2078:   PetscInt       nrqs=0,msz,**ptr=NULL,*req_size=NULL,*ctr=NULL,*pa,*tmp=NULL,tcol;
    2079:   PetscInt       **rbuf3=NULL,*req_source1=NULL,*req_source2,**sbuf_aj,**rbuf2=NULL,max1,max2;
    2080:   PetscInt       **lens,is_no,ncols,*cols,mat_i,*mat_j,tmp2,jmax;
    2081: #if defined(PETSC_USE_CTABLE)
    2082:   PetscTable     *cmap,cmap_i=NULL,*rmap,rmap_i;
    2083: #else
    2084:   PetscInt       **cmap,*cmap_i=NULL,**rmap,*rmap_i;
    2085: #endif
    2086:   const PetscInt *irow_i;
    2087:   PetscInt       ctr_j,*sbuf1_j,*sbuf_aj_i,*rbuf1_i,kmax,*lens_i;
    2088:   MPI_Request    *s_waits1,*r_waits1,*s_waits2,*r_waits2,*r_waits3;
    2089:   MPI_Request    *r_waits4,*s_waits3,*s_waits4;
    2090:   MPI_Status     *r_status1,*r_status2,*s_status1,*s_status3,*s_status2;
    2091:   MPI_Status     *r_status3,*r_status4,*s_status4;
    2092:   MPI_Comm       comm;
    2093:   PetscScalar    **rbuf4,*rbuf4_i,**sbuf_aa,*vals,*mat_a,*imat_a,*sbuf_aa_i;
    2094:   PetscMPIInt    *onodes1,*olengths1,end;
    2095:   PetscInt       **row2proc,*row2proc_i,ilen_row,*imat_ilen,*imat_j,*imat_i,old_row;
    2096:   Mat_SubSppt    *smat_i;
    2097:   PetscBool      *issorted,*allcolumns,colflag,iscsorted=PETSC_TRUE;
    2098:   PetscInt       *sbuf1_i,*rbuf2_i,*rbuf3_i,ilen;

    2101:   PetscObjectGetComm((PetscObject)C,&comm);
    2102:   size = c->size;
    2103:   rank = c->rank;

    2105:   PetscMalloc4(ismax,&row2proc,ismax,&cmap,ismax,&rmap,ismax+1,&allcolumns);
    2106:   PetscMalloc5(ismax,(PetscInt***)&irow,ismax,(PetscInt***)&icol,ismax,&nrow,ismax,&ncol,ismax,&issorted);

    2108:   for (i=0; i<ismax; i++) {
    2109:     ISSorted(iscol[i],&issorted[i]);
    2110:     if (!issorted[i]) iscsorted = issorted[i];

    2112:     ISSorted(isrow[i],&issorted[i]);

    2114:     ISGetIndices(isrow[i],&irow[i]);
    2115:     ISGetLocalSize(isrow[i],&nrow[i]);

    2117:     /* Check for special case: allcolumn */
    2118:     ISIdentity(iscol[i],&colflag);
    2119:     ISGetLocalSize(iscol[i],&ncol[i]);
    2120:     if (colflag && ncol[i] == C->cmap->N) {
    2121:       allcolumns[i] = PETSC_TRUE;
    2122:       icol[i] = NULL;
    2123:     } else {
    2124:       allcolumns[i] = PETSC_FALSE;
    2125:       ISGetIndices(iscol[i],&icol[i]);
    2126:     }
    2127:   }

    2129:   if (scall == MAT_REUSE_MATRIX) {
    2130:     /* Assumes new rows are same length as the old rows */
    2131:     for (i=0; i<ismax; i++) {
    2132:       if (!submats[i]) SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_ARG_NULL,"submats[%D] is null, cannot reuse",i);
    2133:       subc = (Mat_SeqAIJ*)submats[i]->data;
    2134:       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");

    2136:       /* Initial matrix as if empty */
    2137:       PetscMemzero(subc->ilen,submats[i]->rmap->n*sizeof(PetscInt));

    2139:       smat_i   = subc->submatis1;

    2141:       nrqs        = smat_i->nrqs;
    2142:       nrqr        = smat_i->nrqr;
    2143:       rbuf1       = smat_i->rbuf1;
    2144:       rbuf2       = smat_i->rbuf2;
    2145:       rbuf3       = smat_i->rbuf3;
    2146:       req_source2 = smat_i->req_source2;

    2148:       sbuf1     = smat_i->sbuf1;
    2149:       sbuf2     = smat_i->sbuf2;
    2150:       ptr       = smat_i->ptr;
    2151:       tmp       = smat_i->tmp;
    2152:       ctr       = smat_i->ctr;

    2154:       pa          = smat_i->pa;
    2155:       req_size    = smat_i->req_size;
    2156:       req_source1 = smat_i->req_source1;

    2158:       allcolumns[i] = smat_i->allcolumns;
    2159:       row2proc[i]   = smat_i->row2proc;
    2160:       rmap[i]       = smat_i->rmap;
    2161:       cmap[i]       = smat_i->cmap;
    2162:     }

    2164:     if (!ismax){ /* Get dummy submatrices and retrieve struct submatis1 */
    2165:       if (!submats[0]) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_NULL,"submats are null, cannot reuse");
    2166:       smat_i = (Mat_SubSppt*)submats[0]->data;

    2168:       nrqs        = smat_i->nrqs;
    2169:       nrqr        = smat_i->nrqr;
    2170:       rbuf1       = smat_i->rbuf1;
    2171:       rbuf2       = smat_i->rbuf2;
    2172:       rbuf3       = smat_i->rbuf3;
    2173:       req_source2 = smat_i->req_source2;

    2175:       sbuf1       = smat_i->sbuf1;
    2176:       sbuf2       = smat_i->sbuf2;
    2177:       ptr         = smat_i->ptr;
    2178:       tmp         = smat_i->tmp;
    2179:       ctr         = smat_i->ctr;

    2181:       pa          = smat_i->pa;
    2182:       req_size    = smat_i->req_size;
    2183:       req_source1 = smat_i->req_source1;

    2185:       allcolumns[0] = PETSC_FALSE;
    2186:     }
    2187:   } else { /* scall == MAT_INITIAL_MATRIX */
    2188:     /* Get some new tags to keep the communication clean */
    2189:     PetscObjectGetNewTag((PetscObject)C,&tag2);
    2190:     PetscObjectGetNewTag((PetscObject)C,&tag3);

    2192:     /* evaluate communication - mesg to who, length of mesg, and buffer space
    2193:      required. Based on this, buffers are allocated, and data copied into them*/
    2194:     PetscCalloc4(size,&w1,size,&w2,size,&w3,size,&w4);   /* mesg size, initialize work vectors */

    2196:     for (i=0; i<ismax; i++) {
    2197:       jmax   = nrow[i];
    2198:       irow_i = irow[i];

    2200:       PetscMalloc1(jmax,&row2proc_i);
    2201:       row2proc[i] = row2proc_i;

    2203:       if (issorted[i]) proc = 0;
    2204:       for (j=0; j<jmax; j++) {
    2205:         if (!issorted[i]) proc = 0;
    2206:         row = irow_i[j];
    2207:         while (row >= C->rmap->range[proc+1]) proc++;
    2208:         w4[proc]++;
    2209:         row2proc_i[j] = proc; /* map row index to proc */
    2210:       }
    2211:       for (j=0; j<size; j++) {
    2212:         if (w4[j]) { w1[j] += w4[j];  w3[j]++; w4[j] = 0;}
    2213:       }
    2214:     }

    2216:     nrqs     = 0;              /* no of outgoing messages */
    2217:     msz      = 0;              /* total mesg length (for all procs) */
    2218:     w1[rank] = 0;              /* no mesg sent to self */
    2219:     w3[rank] = 0;
    2220:     for (i=0; i<size; i++) {
    2221:       if (w1[i])  { w2[i] = 1; nrqs++;} /* there exists a message to proc i */
    2222:     }
    2223:     PetscMalloc1(nrqs+1,&pa); /*(proc -array)*/
    2224:     for (i=0,j=0; i<size; i++) {
    2225:       if (w1[i]) { pa[j] = i; j++; }
    2226:     }

    2228:     /* Each message would have a header = 1 + 2*(no of IS) + data */
    2229:     for (i=0; i<nrqs; i++) {
    2230:       j      = pa[i];
    2231:       w1[j] += w2[j] + 2* w3[j];
    2232:       msz   += w1[j];
    2233:     }
    2234:     PetscInfo2(0,"Number of outgoing messages %D Total message length %D\n",nrqs,msz);

    2236:     /* Determine the number of messages to expect, their lengths, from from-ids */
    2237:     PetscGatherNumberOfMessages(comm,w2,w1,&nrqr);
    2238:     PetscGatherMessageLengths(comm,nrqs,nrqr,w1,&onodes1,&olengths1);

    2240:     /* Now post the Irecvs corresponding to these messages */
    2241:     tag0 = ((PetscObject)C)->tag;
    2242:     PetscPostIrecvInt(comm,tag0,nrqr,onodes1,olengths1,&rbuf1,&r_waits1);

    2244:     PetscFree(onodes1);
    2245:     PetscFree(olengths1);

    2247:     /* Allocate Memory for outgoing messages */
    2248:     PetscMalloc4(size,&sbuf1,size,&ptr,2*msz,&tmp,size,&ctr);
    2249:     PetscMemzero(sbuf1,size*sizeof(PetscInt*));
    2250:     PetscMemzero(ptr,size*sizeof(PetscInt*));

    2252:     {
    2253:       PetscInt *iptr = tmp;
    2254:       k    = 0;
    2255:       for (i=0; i<nrqs; i++) {
    2256:         j        = pa[i];
    2257:         iptr    += k;
    2258:         sbuf1[j] = iptr;
    2259:         k        = w1[j];
    2260:       }
    2261:     }

    2263:     /* Form the outgoing messages. Initialize the header space */
    2264:     for (i=0; i<nrqs; i++) {
    2265:       j           = pa[i];
    2266:       sbuf1[j][0] = 0;
    2267:       PetscMemzero(sbuf1[j]+1,2*w3[j]*sizeof(PetscInt));
    2268:       ptr[j]      = sbuf1[j] + 2*w3[j] + 1;
    2269:     }

    2271:     /* Parse the isrow and copy data into outbuf */
    2272:     for (i=0; i<ismax; i++) {
    2273:       row2proc_i = row2proc[i];
    2274:       PetscMemzero(ctr,size*sizeof(PetscInt));
    2275:       irow_i = irow[i];
    2276:       jmax   = nrow[i];
    2277:       for (j=0; j<jmax; j++) {  /* parse the indices of each IS */
    2278:         proc = row2proc_i[j];
    2279:         if (proc != rank) { /* copy to the outgoing buf*/
    2280:           ctr[proc]++;
    2281:           *ptr[proc] = irow_i[j];
    2282:           ptr[proc]++;
    2283:         }
    2284:       }
    2285:       /* Update the headers for the current IS */
    2286:       for (j=0; j<size; j++) { /* Can Optimise this loop too */
    2287:         if ((ctr_j = ctr[j])) {
    2288:           sbuf1_j        = sbuf1[j];
    2289:           k              = ++sbuf1_j[0];
    2290:           sbuf1_j[2*k]   = ctr_j;
    2291:           sbuf1_j[2*k-1] = i;
    2292:         }
    2293:       }
    2294:     }

    2296:     /*  Now  post the sends */
    2297:     PetscMalloc1(nrqs+1,&s_waits1);
    2298:     for (i=0; i<nrqs; ++i) {
    2299:       j    = pa[i];
    2300:       MPI_Isend(sbuf1[j],w1[j],MPIU_INT,j,tag0,comm,s_waits1+i);
    2301:     }

    2303:     /* Post Receives to capture the buffer size */
    2304:     PetscMalloc1(nrqs+1,&r_waits2);
    2305:     PetscMalloc3(nrqs+1,&req_source2,nrqs+1,&rbuf2,nrqs+1,&rbuf3);
    2306:     rbuf2[0] = tmp + msz;
    2307:     for (i=1; i<nrqs; ++i) {
    2308:       rbuf2[i] = rbuf2[i-1]+w1[pa[i-1]];
    2309:     }
    2310:     for (i=0; i<nrqs; ++i) {
    2311:       j    = pa[i];
    2312:       MPI_Irecv(rbuf2[i],w1[j],MPIU_INT,j,tag2,comm,r_waits2+i);
    2313:     }

    2315:     /* Send to other procs the buf size they should allocate */
    2316:     /* Receive messages*/
    2317:     PetscMalloc1(nrqr+1,&s_waits2);
    2318:     PetscMalloc1(nrqr+1,&r_status1);
    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,r_status1);
    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:         MPI_Get_count(r_status1+i,MPIU_INT,&end);
    2330:         PetscMalloc1(end+1,&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] = r_status1[i].MPI_SOURCE;
    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:     }
    2346:     PetscFree(r_status1);
    2347:     PetscFree(r_waits1);
    2348:     PetscFree4(w1,w2,w3,w4);

    2350:     /* Receive messages*/
    2351:     PetscMalloc1(nrqs+1,&r_waits3);
    2352:     PetscMalloc1(nrqs+1,&r_status2);

    2354:     MPI_Waitall(nrqs,r_waits2,r_status2);
    2355:     for (i=0; i<nrqs; ++i) {
    2356:       PetscMalloc1(rbuf2[i][0]+1,&rbuf3[i]);
    2357:       req_source2[i] = r_status2[i].MPI_SOURCE;
    2358:       MPI_Irecv(rbuf3[i],rbuf2[i][0],MPIU_INT,req_source2[i],tag3,comm,r_waits3+i);
    2359:     }
    2360:     PetscFree(r_status2);
    2361:     PetscFree(r_waits2);

    2363:     /* Wait on sends1 and sends2 */
    2364:     PetscMalloc1(nrqs+1,&s_status1);
    2365:     PetscMalloc1(nrqr+1,&s_status2);

    2367:     if (nrqs) {MPI_Waitall(nrqs,s_waits1,s_status1);}
    2368:     if (nrqr) {MPI_Waitall(nrqr,s_waits2,s_status2);}
    2369:     PetscFree(s_status1);
    2370:     PetscFree(s_status2);
    2371:     PetscFree(s_waits1);
    2372:     PetscFree(s_waits2);

    2374:     /* Now allocate sending buffers for a->j, and send them off */
    2375:     PetscMalloc1(nrqr+1,&sbuf_aj);
    2376:     for (i=0,j=0; i<nrqr; i++) j += req_size[i];
    2377:     PetscMalloc1(j+1,&sbuf_aj[0]);
    2378:     for (i=1; i<nrqr; i++) sbuf_aj[i] = sbuf_aj[i-1] + req_size[i-1];

    2380:     PetscMalloc1(nrqr+1,&s_waits3);
    2381:     {
    2382:       PetscInt nzA,nzB,*a_i = a->i,*b_i = b->i,lwrite;
    2383:       PetscInt *cworkA,*cworkB,cstart = C->cmap->rstart,rstart = C->rmap->rstart,*bmap = c->garray;
    2384:       PetscInt cend = C->cmap->rend;
    2385:       PetscInt *a_j = a->j,*b_j = b->j,ctmp;

    2387:       for (i=0; i<nrqr; i++) {
    2388:         rbuf1_i   = rbuf1[i];
    2389:         sbuf_aj_i = sbuf_aj[i];
    2390:         ct1       = 2*rbuf1_i[0] + 1;
    2391:         ct2       = 0;
    2392:         for (j=1,max1=rbuf1_i[0]; j<=max1; j++) {
    2393:           kmax = rbuf1[i][2*j];
    2394:           for (k=0; k<kmax; k++,ct1++) {
    2395:             row    = rbuf1_i[ct1] - rstart;
    2396:             nzA    = a_i[row+1] - a_i[row]; nzB = b_i[row+1] - b_i[row];
    2397:             ncols  = nzA + nzB;
    2398:             cworkA = a_j + a_i[row]; cworkB = b_j + b_i[row];

    2400:             /* load the column indices for this row into cols */
    2401:             cols = sbuf_aj_i + ct2;

    2403:             lwrite = 0;
    2404:             for (l=0; l<nzB; l++) {
    2405:               if ((ctmp = bmap[cworkB[l]]) < cstart) cols[lwrite++] = ctmp;
    2406:             }
    2407:             for (l=0; l<nzA; l++) cols[lwrite++] = cstart + cworkA[l];
    2408:             for (l=0; l<nzB; l++) {
    2409:               if ((ctmp = bmap[cworkB[l]]) >= cend) cols[lwrite++] = ctmp;
    2410:             }

    2412:             ct2 += ncols;
    2413:           }
    2414:         }
    2415:         MPI_Isend(sbuf_aj_i,req_size[i],MPIU_INT,req_source1[i],tag3,comm,s_waits3+i);
    2416:       }
    2417:     }
    2418:     PetscMalloc2(nrqs+1,&r_status3,nrqr+1,&s_status3);

    2420:     /* create col map: global col of C -> local col of submatrices */
    2421:     {
    2422:       const PetscInt *icol_i;
    2423: #if defined(PETSC_USE_CTABLE)
    2424:       for (i=0; i<ismax; i++) {
    2425:         if (!allcolumns[i]) {
    2426:           PetscTableCreate(ncol[i]+1,C->cmap->N+1,&cmap[i]);

    2428:           jmax   = ncol[i];
    2429:           icol_i = icol[i];
    2430:           cmap_i = cmap[i];
    2431:           for (j=0; j<jmax; j++) {
    2432:             PetscTableAdd(cmap[i],icol_i[j]+1,j+1,INSERT_VALUES);
    2433:           }
    2434:         } else cmap[i] = NULL;
    2435:       }
    2436: #else
    2437:       for (i=0; i<ismax; i++) {
    2438:         if (!allcolumns[i]) {
    2439:           PetscCalloc1(C->cmap->N,&cmap[i]);
    2440:           jmax   = ncol[i];
    2441:           icol_i = icol[i];
    2442:           cmap_i = cmap[i];
    2443:           for (j=0; j<jmax; j++) {
    2444:             cmap_i[icol_i[j]] = j+1;
    2445:           }
    2446:         } else cmap[i] = NULL;
    2447:       }
    2448: #endif
    2449:     }

    2451:     /* Create lens which is required for MatCreate... */
    2452:     for (i=0,j=0; i<ismax; i++) j += nrow[i];
    2453:     PetscMalloc1(ismax,&lens);

    2455:     if (ismax) {
    2456:       PetscCalloc1(j,&lens[0]);
    2457:     }
    2458:     for (i=1; i<ismax; i++) lens[i] = lens[i-1] + nrow[i-1];

    2460:     /* Update lens from local data */
    2461:     for (i=0; i<ismax; i++) {
    2462:       row2proc_i = row2proc[i];
    2463:       jmax = nrow[i];
    2464:       if (!allcolumns[i]) cmap_i = cmap[i];
    2465:       irow_i = irow[i];
    2466:       lens_i = lens[i];
    2467:       for (j=0; j<jmax; j++) {
    2468:         row = irow_i[j];
    2469:         proc = row2proc_i[j];
    2470:         if (proc == rank) {
    2471:           MatGetRow_MPIAIJ(C,row,&ncols,&cols,0);
    2472:           if (!allcolumns[i]) {
    2473:             for (k=0; k<ncols; k++) {
    2474: #if defined(PETSC_USE_CTABLE)
    2475:               PetscTableFind(cmap_i,cols[k]+1,&tcol);
    2476: #else
    2477:               tcol = cmap_i[cols[k]];
    2478: #endif
    2479:               if (tcol) lens_i[j]++;
    2480:             }
    2481:           } else { /* allcolumns */
    2482:             lens_i[j] = ncols;
    2483:           }
    2484:           MatRestoreRow_MPIAIJ(C,row,&ncols,&cols,0);
    2485:         }
    2486:       }
    2487:     }

    2489:     /* Create row map: global row of C -> local row of submatrices */
    2490: #if defined(PETSC_USE_CTABLE)
    2491:     for (i=0; i<ismax; i++) {
    2492:       PetscTableCreate(nrow[i]+1,C->rmap->N+1,&rmap[i]);
    2493:       irow_i = irow[i];
    2494:       jmax   = nrow[i];
    2495:       for (j=0; j<jmax; j++) {
    2496:       PetscTableAdd(rmap[i],irow_i[j]+1,j+1,INSERT_VALUES);
    2497:       }
    2498:     }
    2499: #else
    2500:     for (i=0; i<ismax; i++) {
    2501:       PetscCalloc1(C->rmap->N,&rmap[i]);
    2502:       rmap_i = rmap[i];
    2503:       irow_i = irow[i];
    2504:       jmax   = nrow[i];
    2505:       for (j=0; j<jmax; j++) {
    2506:         rmap_i[irow_i[j]] = j;
    2507:       }
    2508:     }
    2509: #endif

    2511:     /* Update lens from offproc data */
    2512:     {
    2513:       PetscInt *rbuf2_i,*rbuf3_i,*sbuf1_i;

    2515:       MPI_Waitall(nrqs,r_waits3,r_status3);
    2516:       for (tmp2=0; tmp2<nrqs; tmp2++) {
    2517:         sbuf1_i = sbuf1[pa[tmp2]];
    2518:         jmax    = sbuf1_i[0];
    2519:         ct1     = 2*jmax+1;
    2520:         ct2     = 0;
    2521:         rbuf2_i = rbuf2[tmp2];
    2522:         rbuf3_i = rbuf3[tmp2];
    2523:         for (j=1; j<=jmax; j++) {
    2524:           is_no  = sbuf1_i[2*j-1];
    2525:           max1   = sbuf1_i[2*j];
    2526:           lens_i = lens[is_no];
    2527:           if (!allcolumns[is_no]) cmap_i = cmap[is_no];
    2528:           rmap_i = rmap[is_no];
    2529:           for (k=0; k<max1; k++,ct1++) {
    2530: #if defined(PETSC_USE_CTABLE)
    2531:             PetscTableFind(rmap_i,sbuf1_i[ct1]+1,&row);
    2532:             row--;
    2533:             if (row < 0) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_PLIB,"row not found in table");
    2534: #else
    2535:             row = rmap_i[sbuf1_i[ct1]]; /* the val in the new matrix to be */
    2536: #endif
    2537:             max2 = rbuf2_i[ct1];
    2538:             for (l=0; l<max2; l++,ct2++) {
    2539:               if (!allcolumns[is_no]) {
    2540: #if defined(PETSC_USE_CTABLE)
    2541:                 PetscTableFind(cmap_i,rbuf3_i[ct2]+1,&tcol);
    2542: #else
    2543:                 tcol = cmap_i[rbuf3_i[ct2]];
    2544: #endif
    2545:                 if (tcol) lens_i[row]++;
    2546:               } else { /* allcolumns */
    2547:                 lens_i[row]++; /* lens_i[row] += max2 ? */
    2548:               }
    2549:             }
    2550:           }
    2551:         }
    2552:       }
    2553:     }
    2554:     PetscFree(r_waits3);
    2555:     if (nrqr) {MPI_Waitall(nrqr,s_waits3,s_status3);}
    2556:     PetscFree2(r_status3,s_status3);
    2557:     PetscFree(s_waits3);

    2559:     /* Create the submatrices */
    2560:     for (i=0; i<ismax; i++) {
    2561:       PetscInt    rbs,cbs;

    2563:       ISGetBlockSize(isrow[i],&rbs);
    2564:       ISGetBlockSize(iscol[i],&cbs);

    2566:       MatCreate(PETSC_COMM_SELF,submats+i);
    2567:       MatSetSizes(submats[i],nrow[i],ncol[i],PETSC_DETERMINE,PETSC_DETERMINE);

    2569:       MatSetBlockSizes(submats[i],rbs,cbs);
    2570:       MatSetType(submats[i],((PetscObject)A)->type_name);
    2571:       MatSeqAIJSetPreallocation(submats[i],0,lens[i]);

    2573:       /* create struct Mat_SubSppt and attached it to submat */
    2574:       PetscNew(&smat_i);
    2575:       subc = (Mat_SeqAIJ*)submats[i]->data;
    2576:       subc->submatis1 = smat_i;

    2578:       smat_i->destroy          = submats[i]->ops->destroy;
    2579:       submats[i]->ops->destroy = MatDestroySubMatrix_SeqAIJ;
    2580:       submats[i]->factortype   = C->factortype;

    2582:       smat_i->id          = i;
    2583:       smat_i->nrqs        = nrqs;
    2584:       smat_i->nrqr        = nrqr;
    2585:       smat_i->rbuf1       = rbuf1;
    2586:       smat_i->rbuf2       = rbuf2;
    2587:       smat_i->rbuf3       = rbuf3;
    2588:       smat_i->sbuf2       = sbuf2;
    2589:       smat_i->req_source2 = req_source2;

    2591:       smat_i->sbuf1       = sbuf1;
    2592:       smat_i->ptr         = ptr;
    2593:       smat_i->tmp         = tmp;
    2594:       smat_i->ctr         = ctr;

    2596:       smat_i->pa           = pa;
    2597:       smat_i->req_size     = req_size;
    2598:       smat_i->req_source1  = req_source1;

    2600:       smat_i->allcolumns  = allcolumns[i];
    2601:       smat_i->singleis    = PETSC_FALSE;
    2602:       smat_i->row2proc    = row2proc[i];
    2603:       smat_i->rmap        = rmap[i];
    2604:       smat_i->cmap        = cmap[i];
    2605:     }

    2607:     if (!ismax) { /* Create dummy submats[0] for reuse struct subc */
    2608:       MatCreate(PETSC_COMM_SELF,&submats[0]);
    2609:       MatSetSizes(submats[0],0,0,PETSC_DETERMINE,PETSC_DETERMINE);
    2610:       MatSetType(submats[0],MATDUMMY);

    2612:       /* create struct Mat_SubSppt and attached it to submat */
    2613:       PetscNewLog(submats[0],&smat_i);
    2614:       submats[0]->data = (void*)smat_i;

    2616:       smat_i->destroy          = submats[0]->ops->destroy;
    2617:       submats[0]->ops->destroy = MatDestroySubMatrix_Dummy;
    2618:       submats[0]->factortype   = C->factortype;

    2620:       smat_i->id          = 0;
    2621:       smat_i->nrqs        = nrqs;
    2622:       smat_i->nrqr        = nrqr;
    2623:       smat_i->rbuf1       = rbuf1;
    2624:       smat_i->rbuf2       = rbuf2;
    2625:       smat_i->rbuf3       = rbuf3;
    2626:       smat_i->sbuf2       = sbuf2;
    2627:       smat_i->req_source2 = req_source2;

    2629:       smat_i->sbuf1       = sbuf1;
    2630:       smat_i->ptr         = ptr;
    2631:       smat_i->tmp         = tmp;
    2632:       smat_i->ctr         = ctr;

    2634:       smat_i->pa           = pa;
    2635:       smat_i->req_size     = req_size;
    2636:       smat_i->req_source1  = req_source1;

    2638:       smat_i->allcolumns  = PETSC_FALSE;
    2639:       smat_i->singleis    = PETSC_FALSE;
    2640:       smat_i->row2proc    = NULL;
    2641:       smat_i->rmap        = NULL;
    2642:       smat_i->cmap        = NULL;
    2643:     }

    2645:     if (ismax) {PetscFree(lens[0]);}
    2646:     PetscFree(lens);
    2647:     PetscFree(sbuf_aj[0]);
    2648:     PetscFree(sbuf_aj);

    2650:   } /* endof scall == MAT_INITIAL_MATRIX */

    2652:   /* Post recv matrix values */
    2653:   PetscObjectGetNewTag((PetscObject)C,&tag4);
    2654:   PetscMalloc1(nrqs+1,&rbuf4);
    2655:   PetscMalloc1(nrqs+1,&r_waits4);
    2656:   PetscMalloc1(nrqs+1,&r_status4);
    2657:   PetscMalloc1(nrqr+1,&s_status4);
    2658:   for (i=0; i<nrqs; ++i) {
    2659:     PetscMalloc1(rbuf2[i][0]+1,&rbuf4[i]);
    2660:     MPI_Irecv(rbuf4[i],rbuf2[i][0],MPIU_SCALAR,req_source2[i],tag4,comm,r_waits4+i);
    2661:   }

    2663:   /* Allocate sending buffers for a->a, and send them off */
    2664:   PetscMalloc1(nrqr+1,&sbuf_aa);
    2665:   for (i=0,j=0; i<nrqr; i++) j += req_size[i];
    2666:   PetscMalloc1(j+1,&sbuf_aa[0]);
    2667:   for (i=1; i<nrqr; i++) sbuf_aa[i] = sbuf_aa[i-1] + req_size[i-1];

    2669:   PetscMalloc1(nrqr+1,&s_waits4);
    2670:   {
    2671:     PetscInt    nzA,nzB,*a_i = a->i,*b_i = b->i, *cworkB,lwrite;
    2672:     PetscInt    cstart = C->cmap->rstart,rstart = C->rmap->rstart,*bmap = c->garray;
    2673:     PetscInt    cend   = C->cmap->rend;
    2674:     PetscInt    *b_j   = b->j;
    2675:     PetscScalar *vworkA,*vworkB,*a_a = a->a,*b_a = b->a;

    2677:     for (i=0; i<nrqr; i++) {
    2678:       rbuf1_i   = rbuf1[i];
    2679:       sbuf_aa_i = sbuf_aa[i];
    2680:       ct1       = 2*rbuf1_i[0]+1;
    2681:       ct2       = 0;
    2682:       for (j=1,max1=rbuf1_i[0]; j<=max1; j++) {
    2683:         kmax = rbuf1_i[2*j];
    2684:         for (k=0; k<kmax; k++,ct1++) {
    2685:           row    = rbuf1_i[ct1] - rstart;
    2686:           nzA    = a_i[row+1] - a_i[row];     nzB = b_i[row+1] - b_i[row];
    2687:           ncols  = nzA + nzB;
    2688:           cworkB = b_j + b_i[row];
    2689:           vworkA = a_a + a_i[row];
    2690:           vworkB = b_a + b_i[row];

    2692:           /* load the column values for this row into vals*/
    2693:           vals = sbuf_aa_i+ct2;

    2695:           lwrite = 0;
    2696:           for (l=0; l<nzB; l++) {
    2697:             if ((bmap[cworkB[l]]) < cstart) vals[lwrite++] = vworkB[l];
    2698:           }
    2699:           for (l=0; l<nzA; l++) vals[lwrite++] = vworkA[l];
    2700:           for (l=0; l<nzB; l++) {
    2701:             if ((bmap[cworkB[l]]) >= cend) vals[lwrite++] = vworkB[l];
    2702:           }

    2704:           ct2 += ncols;
    2705:         }
    2706:       }
    2707:       MPI_Isend(sbuf_aa_i,req_size[i],MPIU_SCALAR,req_source1[i],tag4,comm,s_waits4+i);
    2708:     }
    2709:   }

    2711:   /* Assemble the matrices */
    2712:   /* First assemble the local rows */
    2713:   for (i=0; i<ismax; i++) {
    2714:     row2proc_i = row2proc[i];
    2715:     subc      = (Mat_SeqAIJ*)submats[i]->data;
    2716:     imat_ilen = subc->ilen;
    2717:     imat_j    = subc->j;
    2718:     imat_i    = subc->i;
    2719:     imat_a    = subc->a;

    2721:     if (!allcolumns[i]) cmap_i = cmap[i];
    2722:     rmap_i = rmap[i];
    2723:     irow_i = irow[i];
    2724:     jmax   = nrow[i];
    2725:     for (j=0; j<jmax; j++) {
    2726:       row  = irow_i[j];
    2727:       proc = row2proc_i[j];
    2728:       if (proc == rank) {
    2729:         old_row = row;
    2730: #if defined(PETSC_USE_CTABLE)
    2731:         PetscTableFind(rmap_i,row+1,&row);
    2732:         row--;
    2733: #else
    2734:         row = rmap_i[row];
    2735: #endif
    2736:         ilen_row = imat_ilen[row];
    2737:         MatGetRow_MPIAIJ(C,old_row,&ncols,&cols,&vals);
    2738:         mat_i    = imat_i[row];
    2739:         mat_a    = imat_a + mat_i;
    2740:         mat_j    = imat_j + mat_i;
    2741:         if (!allcolumns[i]) {
    2742:           for (k=0; k<ncols; k++) {
    2743: #if defined(PETSC_USE_CTABLE)
    2744:             PetscTableFind(cmap_i,cols[k]+1,&tcol);
    2745: #else
    2746:             tcol = cmap_i[cols[k]];
    2747: #endif
    2748:             if (tcol) {
    2749:               *mat_j++ = tcol - 1;
    2750:               *mat_a++ = vals[k];
    2751:               ilen_row++;
    2752:             }
    2753:           }
    2754:         } else { /* allcolumns */
    2755:           for (k=0; k<ncols; k++) {
    2756:             *mat_j++ = cols[k];  /* global col index! */
    2757:             *mat_a++ = vals[k];
    2758:             ilen_row++;
    2759:           }
    2760:         }
    2761:         MatRestoreRow_MPIAIJ(C,old_row,&ncols,&cols,&vals);

    2763:         imat_ilen[row] = ilen_row;
    2764:       }
    2765:     }
    2766:   }

    2768:   /* Now assemble the off proc rows */
    2769:   MPI_Waitall(nrqs,r_waits4,r_status4);
    2770:   for (tmp2=0; tmp2<nrqs; tmp2++) {
    2771:     sbuf1_i = sbuf1[pa[tmp2]];
    2772:     jmax    = sbuf1_i[0];
    2773:     ct1     = 2*jmax + 1;
    2774:     ct2     = 0;
    2775:     rbuf2_i = rbuf2[tmp2];
    2776:     rbuf3_i = rbuf3[tmp2];
    2777:     rbuf4_i = rbuf4[tmp2];
    2778:     for (j=1; j<=jmax; j++) {
    2779:       is_no     = sbuf1_i[2*j-1];
    2780:       rmap_i    = rmap[is_no];
    2781:       if (!allcolumns[is_no]) cmap_i = cmap[is_no];
    2782:       subc      = (Mat_SeqAIJ*)submats[is_no]->data;
    2783:       imat_ilen = subc->ilen;
    2784:       imat_j    = subc->j;
    2785:       imat_i    = subc->i;
    2786:       imat_a    = subc->a;
    2787:       max1      = sbuf1_i[2*j];
    2788:       for (k=0; k<max1; k++,ct1++) {
    2789:         row = sbuf1_i[ct1];
    2790: #if defined(PETSC_USE_CTABLE)
    2791:         PetscTableFind(rmap_i,row+1,&row);
    2792:         row--;
    2793: #else
    2794:         row = rmap_i[row];
    2795: #endif
    2796:         ilen  = imat_ilen[row];
    2797:         mat_i = imat_i[row];
    2798:         mat_a = imat_a + mat_i;
    2799:         mat_j = imat_j + mat_i;
    2800:         max2  = rbuf2_i[ct1];
    2801:         if (!allcolumns[is_no]) {
    2802:           for (l=0; l<max2; l++,ct2++) {
    2803: #if defined(PETSC_USE_CTABLE)
    2804:             PetscTableFind(cmap_i,rbuf3_i[ct2]+1,&tcol);
    2805: #else
    2806:             tcol = cmap_i[rbuf3_i[ct2]];
    2807: #endif
    2808:             if (tcol) {
    2809:               *mat_j++ = tcol - 1;
    2810:               *mat_a++ = rbuf4_i[ct2];
    2811:               ilen++;
    2812:             }
    2813:           }
    2814:         } else { /* allcolumns */
    2815:           for (l=0; l<max2; l++,ct2++) {
    2816:             *mat_j++ = rbuf3_i[ct2]; /* same global column index of C */
    2817:             *mat_a++ = rbuf4_i[ct2];
    2818:             ilen++;
    2819:           }
    2820:         }
    2821:         imat_ilen[row] = ilen;
    2822:       }
    2823:     }
    2824:   }

    2826:   if (!iscsorted) { /* sort column indices of the rows */
    2827:     for (i=0; i<ismax; i++) {
    2828:       subc      = (Mat_SeqAIJ*)submats[i]->data;
    2829:       imat_j    = subc->j;
    2830:       imat_i    = subc->i;
    2831:       imat_a    = subc->a;
    2832:       imat_ilen = subc->ilen;

    2834:       if (allcolumns[i]) continue;
    2835:       jmax = nrow[i];
    2836:       for (j=0; j<jmax; j++) {
    2837:         mat_i = imat_i[j];
    2838:         mat_a = imat_a + mat_i;
    2839:         mat_j = imat_j + mat_i;
    2840:         PetscSortIntWithScalarArray(imat_ilen[j],mat_j,mat_a);
    2841:       }
    2842:     }
    2843:   }

    2845:   PetscFree(r_status4);
    2846:   PetscFree(r_waits4);
    2847:   if (nrqr) {MPI_Waitall(nrqr,s_waits4,s_status4);}
    2848:   PetscFree(s_waits4);
    2849:   PetscFree(s_status4);

    2851:   /* Restore the indices */
    2852:   for (i=0; i<ismax; i++) {
    2853:     ISRestoreIndices(isrow[i],irow+i);
    2854:     if (!allcolumns[i]) {
    2855:       ISRestoreIndices(iscol[i],icol+i);
    2856:     }
    2857:   }

    2859:   for (i=0; i<ismax; i++) {
    2860:     MatAssemblyBegin(submats[i],MAT_FINAL_ASSEMBLY);
    2861:     MatAssemblyEnd(submats[i],MAT_FINAL_ASSEMBLY);
    2862:   }

    2864:   /* Destroy allocated memory */
    2865:   PetscFree(sbuf_aa[0]);
    2866:   PetscFree(sbuf_aa);
    2867:   PetscFree5(*(PetscInt***)&irow,*(PetscInt***)&icol,nrow,ncol,issorted);

    2869:   for (i=0; i<nrqs; ++i) {
    2870:     PetscFree(rbuf4[i]);
    2871:   }
    2872:   PetscFree(rbuf4);

    2874:   PetscFree4(row2proc,cmap,rmap,allcolumns);
    2875:   return(0);
    2876: }

    2878: /*
    2879:  Permute A & B into C's *local* index space using rowemb,dcolemb for A and rowemb,ocolemb for B.
    2880:  Embeddings are supposed to be injections and the above implies that the range of rowemb is a subset
    2881:  of [0,m), dcolemb is in [0,n) and ocolemb is in [N-n).
    2882:  If pattern == DIFFERENT_NONZERO_PATTERN, C is preallocated according to A&B.
    2883:  After that B's columns are mapped into C's global column space, so that C is in the "disassembled"
    2884:  state, and needs to be "assembled" later by compressing B's column space.

    2886:  This function may be called in lieu of preallocation, so C should not be expected to be preallocated.
    2887:  Following this call, C->A & C->B have been created, even if empty.
    2888:  */
    2889: PetscErrorCode MatSetSeqMats_MPIAIJ(Mat C,IS rowemb,IS dcolemb,IS ocolemb,MatStructure pattern,Mat A,Mat B)
    2890: {
    2891:   /* If making this function public, change the error returned in this function away from _PLIB. */
    2893:   Mat_MPIAIJ     *aij;
    2894:   Mat_SeqAIJ     *Baij;
    2895:   PetscBool      seqaij,Bdisassembled;
    2896:   PetscInt       m,n,*nz,i,j,ngcol,col,rstart,rend,shift,count;
    2897:   PetscScalar    v;
    2898:   const PetscInt *rowindices,*colindices;

    2901:   /* Check to make sure the component matrices (and embeddings) are compatible with C. */
    2902:   if (A) {
    2903:     PetscObjectBaseTypeCompare((PetscObject)A,MATSEQAIJ,&seqaij);
    2904:     if (!seqaij) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_PLIB,"Diagonal matrix is of wrong type");
    2905:     if (rowemb) {
    2906:       ISGetLocalSize(rowemb,&m);
    2907:       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);
    2908:     } else {
    2909:       if (C->rmap->n != A->rmap->n) {
    2910:         SETERRQ(PETSC_COMM_SELF,PETSC_ERR_PLIB,"Diag seq matrix is row-incompatible with the MPIAIJ matrix");
    2911:       }
    2912:     }
    2913:     if (dcolemb) {
    2914:       ISGetLocalSize(dcolemb,&n);
    2915:       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);
    2916:     } else {
    2917:       if (C->cmap->n != A->cmap->n) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_PLIB,"Diag seq matrix is col-incompatible with the MPIAIJ matrix");
    2918:     }
    2919:   }
    2920:   if (B) {
    2921:     PetscObjectBaseTypeCompare((PetscObject)B,MATSEQAIJ,&seqaij);
    2922:     if (!seqaij) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_PLIB,"Off-diagonal matrix is of wrong type");
    2923:     if (rowemb) {
    2924:       ISGetLocalSize(rowemb,&m);
    2925:       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);
    2926:     } else {
    2927:       if (C->rmap->n != B->rmap->n) {
    2928:         SETERRQ(PETSC_COMM_SELF,PETSC_ERR_PLIB,"Off-diag seq matrix is row-incompatible with the MPIAIJ matrix");
    2929:       }
    2930:     }
    2931:     if (ocolemb) {
    2932:       ISGetLocalSize(ocolemb,&n);
    2933:       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);
    2934:     } else {
    2935:       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");
    2936:     }
    2937:   }

    2939:   aij = (Mat_MPIAIJ*)C->data;
    2940:   if (!aij->A) {
    2941:     /* Mimic parts of MatMPIAIJSetPreallocation() */
    2942:     MatCreate(PETSC_COMM_SELF,&aij->A);
    2943:     MatSetSizes(aij->A,C->rmap->n,C->cmap->n,C->rmap->n,C->cmap->n);
    2944:     MatSetBlockSizesFromMats(aij->A,C,C);
    2945:     MatSetType(aij->A,MATSEQAIJ);
    2946:     PetscLogObjectParent((PetscObject)C,(PetscObject)aij->A);
    2947:   }
    2948:   if (A) {
    2949:     MatSetSeqMat_SeqAIJ(aij->A,rowemb,dcolemb,pattern,A);
    2950:   } else {
    2951:     MatSetUp(aij->A);
    2952:   }
    2953:   if (B) { /* Destroy the old matrix or the column map, depending on the sparsity pattern. */
    2954:     /*
    2955:       If pattern == DIFFERENT_NONZERO_PATTERN, we reallocate B and
    2956:       need to "disassemble" B -- convert it to using C's global indices.
    2957:       To insert the values we take the safer, albeit more expensive, route of MatSetValues().

    2959:       If pattern == SUBSET_NONZERO_PATTERN, we do not "disassemble" B and do not reallocate;
    2960:       we MatZeroValues(B) first, so there may be a bunch of zeros that, perhaps, could be compacted out.

    2962:       TODO: Put B's values into aij->B's aij structure in place using the embedding ISs?
    2963:       At least avoid calling MatSetValues() and the implied searches?
    2964:     */

    2966:     if (B && pattern == DIFFERENT_NONZERO_PATTERN) {
    2967: #if defined(PETSC_USE_CTABLE)
    2968:       PetscTableDestroy(&aij->colmap);
    2969: #else
    2970:       PetscFree(aij->colmap);
    2971:       /* A bit of a HACK: ideally we should deal with case aij->B all in one code block below. */
    2972:       if (aij->B) {
    2973:         PetscLogObjectMemory((PetscObject)C,-aij->B->cmap->n*sizeof(PetscInt));
    2974:       }
    2975: #endif
    2976:       ngcol = 0;
    2977:       if (aij->lvec) {
    2978:         VecGetSize(aij->lvec,&ngcol);
    2979:       }
    2980:       if (aij->garray) {
    2981:         PetscFree(aij->garray);
    2982:         PetscLogObjectMemory((PetscObject)C,-ngcol*sizeof(PetscInt));
    2983:       }
    2984:       VecDestroy(&aij->lvec);
    2985:       VecScatterDestroy(&aij->Mvctx);
    2986:     }
    2987:     if (aij->B && B && pattern == DIFFERENT_NONZERO_PATTERN) {
    2988:       MatDestroy(&aij->B);
    2989:     }
    2990:     if (aij->B && B && pattern == SUBSET_NONZERO_PATTERN) {
    2991:       MatZeroEntries(aij->B);
    2992:     }
    2993:   }
    2994:   Bdisassembled = PETSC_FALSE;
    2995:   if (!aij->B) {
    2996:     MatCreate(PETSC_COMM_SELF,&aij->B);
    2997:     PetscLogObjectParent((PetscObject)C,(PetscObject)aij->B);
    2998:     MatSetSizes(aij->B,C->rmap->n,C->cmap->N,C->rmap->n,C->cmap->N);
    2999:     MatSetBlockSizesFromMats(aij->B,B,B);
    3000:     MatSetType(aij->B,MATSEQAIJ);
    3001:     Bdisassembled = PETSC_TRUE;
    3002:   }
    3003:   if (B) {
    3004:     Baij = (Mat_SeqAIJ*)B->data;
    3005:     if (pattern == DIFFERENT_NONZERO_PATTERN) {
    3006:       PetscMalloc1(B->rmap->n,&nz);
    3007:       for (i=0; i<B->rmap->n; i++) {
    3008:         nz[i] = Baij->i[i+1] - Baij->i[i];
    3009:       }
    3010:       MatSeqAIJSetPreallocation(aij->B,0,nz);
    3011:       PetscFree(nz);
    3012:     }

    3014:     PetscLayoutGetRange(C->rmap,&rstart,&rend);
    3015:     shift = rend-rstart;
    3016:     count = 0;
    3017:     rowindices = NULL;
    3018:     colindices = NULL;
    3019:     if (rowemb) {
    3020:       ISGetIndices(rowemb,&rowindices);
    3021:     }
    3022:     if (ocolemb) {
    3023:       ISGetIndices(ocolemb,&colindices);
    3024:     }
    3025:     for (i=0; i<B->rmap->n; i++) {
    3026:       PetscInt row;
    3027:       row = i;
    3028:       if (rowindices) row = rowindices[i];
    3029:       for (j=Baij->i[i]; j<Baij->i[i+1]; j++) {
    3030:         col  = Baij->j[count];
    3031:         if (colindices) col = colindices[col];
    3032:         if (Bdisassembled && col>=rstart) col += shift;
    3033:         v    = Baij->a[count];
    3034:         MatSetValues(aij->B,1,&row,1,&col,&v,INSERT_VALUES);
    3035:         ++count;
    3036:       }
    3037:     }
    3038:     /* No assembly for aij->B is necessary. */
    3039:     /* FIXME: set aij->B's nonzerostate correctly. */
    3040:   } else {
    3041:     MatSetUp(aij->B);
    3042:   }
    3043:   C->preallocated  = PETSC_TRUE;
    3044:   C->was_assembled = PETSC_FALSE;
    3045:   C->assembled     = PETSC_FALSE;
    3046:    /*
    3047:       C will need to be assembled so that aij->B can be compressed into local form in MatSetUpMultiply_MPIAIJ().
    3048:       Furthermore, its nonzerostate will need to be based on that of aij->A's and aij->B's.
    3049:    */
    3050:   return(0);
    3051: }

    3053: /*
    3054:   B uses local indices with column indices ranging between 0 and N-n; they  must be interpreted using garray.
    3055:  */
    3056: PetscErrorCode MatGetSeqMats_MPIAIJ(Mat C,Mat *A,Mat *B)
    3057: {
    3058:   Mat_MPIAIJ *aij = (Mat_MPIAIJ*)C->data;

    3063:   /* FIXME: make sure C is assembled */
    3064:   *A = aij->A;
    3065:   *B = aij->B;
    3066:   /* Note that we don't incref *A and *B, so be careful! */
    3067:   return(0);
    3068: }

    3070: /*
    3071:   Extract MPI submatrices encoded by pairs of IS that may live on subcomms of C.
    3072:   NOT SCALABLE due to the use of ISGetNonlocalIS() (see below).
    3073: */
    3074: PetscErrorCode MatCreateSubMatricesMPI_MPIXAIJ(Mat C,PetscInt ismax,const IS isrow[],const IS iscol[],MatReuse scall,Mat *submat[],
    3075:                                                  PetscErrorCode(*getsubmats_seq)(Mat,PetscInt,const IS[],const IS[],MatReuse,Mat**),
    3076:                                                  PetscErrorCode(*getlocalmats)(Mat,Mat*,Mat*),
    3077:                                                  PetscErrorCode(*setseqmat)(Mat,IS,IS,MatStructure,Mat),
    3078:                                                  PetscErrorCode(*setseqmats)(Mat,IS,IS,IS,MatStructure,Mat,Mat))
    3079: {
    3081:   PetscMPIInt    isize,flag;
    3082:   PetscInt       i,ii,cismax,ispar;
    3083:   Mat            *A,*B;
    3084:   IS             *isrow_p,*iscol_p,*cisrow,*ciscol,*ciscol_p;

    3087:   if (!ismax) return(0);

    3089:   for (i = 0, cismax = 0; i < ismax; ++i) {
    3090:     PetscMPIInt isize;
    3091:     MPI_Comm_compare(((PetscObject)isrow[i])->comm,((PetscObject)iscol[i])->comm,&flag);
    3092:     if (flag != MPI_IDENT) SETERRQ(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Row and column index sets must have the same communicator");
    3093:     MPI_Comm_size(((PetscObject)isrow[i])->comm, &isize);
    3094:     if (isize > 1) ++cismax;
    3095:   }

    3097:   /*
    3098:      If cismax is zero on all C's ranks, then and only then can we use purely sequential matrix extraction.
    3099:      ispar counts the number of parallel ISs across C's comm.
    3100:   */
    3101:   MPIU_Allreduce(&cismax,&ispar,1,MPIU_INT,MPI_MAX,PetscObjectComm((PetscObject)C));
    3102:   if (!ispar) { /* Sequential ISs only across C's comm, so can call the sequential matrix extraction subroutine. */
    3103:     (*getsubmats_seq)(C,ismax,isrow,iscol,scall,submat);
    3104:     return(0);
    3105:   }

    3107:   /* if (ispar) */
    3108:   /*
    3109:     Construct the "complements" -- the off-processor indices -- of the iscol ISs for parallel ISs only.
    3110:     These are used to extract the off-diag portion of the resulting parallel matrix.
    3111:     The row IS for the off-diag portion is the same as for the diag portion,
    3112:     so we merely alias (without increfing) the row IS, while skipping those that are sequential.
    3113:   */
    3114:   PetscMalloc2(cismax,&cisrow,cismax,&ciscol);
    3115:   PetscMalloc1(cismax,&ciscol_p);
    3116:   for (i = 0, ii = 0; i < ismax; ++i) {
    3117:     MPI_Comm_size(((PetscObject)isrow[i])->comm,&isize);
    3118:     if (isize > 1) {
    3119:       /*
    3120:          TODO: This is the part that's ***NOT SCALABLE***.
    3121:          To fix this we need to extract just the indices of C's nonzero columns
    3122:          that lie on the intersection of isrow[i] and ciscol[ii] -- the nonlocal
    3123:          part of iscol[i] -- without actually computing ciscol[ii]. This also has
    3124:          to be done without serializing on the IS list, so, most likely, it is best
    3125:          done by rewriting MatCreateSubMatrices_MPIAIJ() directly.
    3126:       */
    3127:       ISGetNonlocalIS(iscol[i],&(ciscol[ii]));
    3128:       /* Now we have to
    3129:          (a) make sure ciscol[ii] is sorted, since, even if the off-proc indices
    3130:              were sorted on each rank, concatenated they might no longer be sorted;
    3131:          (b) Use ISSortPermutation() to construct ciscol_p, the mapping from the
    3132:              indices in the nondecreasing order to the original index positions.
    3133:          If ciscol[ii] is strictly increasing, the permutation IS is NULL.
    3134:       */
    3135:       ISSortPermutation(ciscol[ii],PETSC_FALSE,ciscol_p+ii);
    3136:       ISSort(ciscol[ii]);
    3137:       ++ii;
    3138:     }
    3139:   }
    3140:   PetscMalloc2(ismax,&isrow_p,ismax,&iscol_p);
    3141:   for (i = 0, ii = 0; i < ismax; ++i) {
    3142:     PetscInt       j,issize;
    3143:     const PetscInt *indices;

    3145:     /*
    3146:        Permute the indices into a nondecreasing order. Reject row and col indices with duplicates.
    3147:      */
    3148:     ISSortPermutation(isrow[i],PETSC_FALSE,isrow_p+i);
    3149:     ISSort(isrow[i]);
    3150:     ISGetLocalSize(isrow[i],&issize);
    3151:     ISGetIndices(isrow[i],&indices);
    3152:     for (j = 1; j < issize; ++j) {
    3153:       if (indices[j] == indices[j-1]) {
    3154:         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]);
    3155:       }
    3156:     }
    3157:     ISRestoreIndices(isrow[i],&indices);

    3160:     ISSortPermutation(iscol[i],PETSC_FALSE,iscol_p+i);
    3161:     ISSort(iscol[i]);
    3162:     ISGetLocalSize(iscol[i],&issize);
    3163:     ISGetIndices(iscol[i],&indices);
    3164:     for (j = 1; j < issize; ++j) {
    3165:       if (indices[j-1] == indices[j]) {
    3166:         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]);
    3167:       }
    3168:     }
    3169:     ISRestoreIndices(iscol[i],&indices);
    3170:     MPI_Comm_size(((PetscObject)isrow[i])->comm,&isize);
    3171:     if (isize > 1) {
    3172:       cisrow[ii] = isrow[i];
    3173:       ++ii;
    3174:     }
    3175:   }
    3176:   /*
    3177:     Allocate the necessary arrays to hold the resulting parallel matrices as well as the intermediate
    3178:     array of sequential matrices underlying the resulting parallel matrices.
    3179:     Which arrays to allocate is based on the value of MatReuse scall and whether ISs are sorted and/or
    3180:     contain duplicates.

    3182:     There are as many diag matrices as there are original index sets. There are only as many parallel
    3183:     and off-diag matrices, as there are parallel (comm size > 1) index sets.

    3185:     ARRAYS that can hold Seq matrices get allocated in any event -- either here or by getsubmats_seq():
    3186:     - If the array of MPI matrices already exists and is being reused, we need to allocate the array
    3187:       and extract the underlying seq matrices into it to serve as placeholders, into which getsubmats_seq
    3188:       will deposite the extracted diag and off-diag parts. Thus, we allocate the A&B arrays and fill them
    3189:       with A[i] and B[ii] extracted from the corresponding MPI submat.
    3190:     - However, if the rows, A's column indices or B's column indices are not sorted, the extracted A[i] & B[ii]
    3191:       will have a different order from what getsubmats_seq expects.  To handle this case -- indicated
    3192:       by a nonzero isrow_p[i], iscol_p[i], or ciscol_p[ii] -- we duplicate A[i] --> AA[i], B[ii] --> BB[ii]
    3193:       (retrieve composed AA[i] or BB[ii]) and reuse them here. AA[i] and BB[ii] are then used to permute its
    3194:       values into A[i] and B[ii] sitting inside the corresponding submat.
    3195:     - If no reuse is taking place then getsubmats_seq will allocate the A&B arrays and create the corresponding
    3196:       A[i], B[ii], AA[i] or BB[ii] matrices.
    3197:   */
    3198:   /* Parallel matrix array is allocated here only if no reuse is taking place. If reused, it is passed in by the caller. */
    3199:   if (scall == MAT_INITIAL_MATRIX) {
    3200:     PetscMalloc1(ismax,submat);
    3201:   }

    3203:   /* Now obtain the sequential A and B submatrices separately. */
    3204:   /* scall=MAT_REUSE_MATRIX is not handled yet, because getsubmats_seq() requires reuse of A and B */
    3205:   (*getsubmats_seq)(C,ismax,isrow,iscol,MAT_INITIAL_MATRIX,&A);
    3206:   (*getsubmats_seq)(C,cismax,cisrow,ciscol,MAT_INITIAL_MATRIX,&B);

    3208:   /*
    3209:     If scall == MAT_REUSE_MATRIX AND the permutations are NULL, we are done, since the sequential
    3210:     matrices A & B have been extracted directly into the parallel matrices containing them, or
    3211:     simply into the sequential matrix identical with the corresponding A (if isize == 1).
    3212:     Note that in that case colmap doesn't need to be rebuilt, since the matrices are expected
    3213:     to have the same sparsity pattern.
    3214:     Otherwise, A and/or B have to be properly embedded into C's index spaces and the correct colmap
    3215:     must be constructed for C. This is done by setseqmat(s).
    3216:   */
    3217:   for (i = 0, ii = 0; i < ismax; ++i) {
    3218:     /*
    3219:        TODO: cache ciscol, permutation ISs and maybe cisrow? What about isrow & iscol?
    3220:        That way we can avoid sorting and computing permutations when reusing.
    3221:        To this end:
    3222:         - remove the old cache, if it exists, when extracting submatrices with MAT_INITIAL_MATRIX
    3223:         - if caching arrays to hold the ISs, make and compose a container for them so that it can
    3224:           be destroyed upon destruction of C (use PetscContainerUserDestroy() to clear out the contents).
    3225:     */
    3226:     MatStructure pattern;
    3227:     pattern = DIFFERENT_NONZERO_PATTERN;

    3229:     MPI_Comm_size(((PetscObject)isrow[i])->comm,&isize);
    3230:     /* Construct submat[i] from the Seq pieces A (and B, if necessary). */
    3231:     if (isize > 1) {
    3232:       if (scall == MAT_INITIAL_MATRIX) {
    3233:         MatCreate(((PetscObject)isrow[i])->comm,(*submat)+i);
    3234:         MatSetSizes((*submat)[i],A[i]->rmap->n,A[i]->cmap->n,PETSC_DETERMINE,PETSC_DETERMINE);
    3235:         MatSetType((*submat)[i],MATMPIAIJ);
    3236:         PetscLayoutSetUp((*submat)[i]->rmap);
    3237:         PetscLayoutSetUp((*submat)[i]->cmap);
    3238:       }
    3239:       /*
    3240:         For each parallel isrow[i], insert the extracted sequential matrices into the parallel matrix.
    3241:       */
    3242:       {
    3243:         Mat AA,BB;
    3244:         AA = A[i];
    3245:         BB = B[ii];
    3246:         if (AA || BB) {
    3247:           setseqmats((*submat)[i],isrow_p[i],iscol_p[i],ciscol_p[ii],pattern,AA,BB);
    3248:           MatAssemblyBegin((*submat)[i],MAT_FINAL_ASSEMBLY);
    3249:           MatAssemblyEnd((*submat)[i],MAT_FINAL_ASSEMBLY);
    3250:         }

    3252:         MatDestroy(&AA);
    3253:       }
    3254:       ISDestroy(ciscol+ii);
    3255:       ISDestroy(ciscol_p+ii);
    3256:       ++ii;
    3257:     } else { /* if (isize == 1) */
    3258:       if (scall == MAT_REUSE_MATRIX) {
    3259:         MatDestroy(&(*submat)[i]);
    3260:       }
    3261:       if (isrow_p[i] || iscol_p[i]) {
    3262:         MatDuplicate(A[i],MAT_DO_NOT_COPY_VALUES,(*submat)+i);
    3263:         setseqmat((*submat)[i],isrow_p[i],iscol_p[i],pattern,A[i]);
    3264:         /* Otherwise A is extracted straight into (*submats)[i]. */
    3265:         /* TODO: Compose A[i] on (*submat([i] for future use, if ((isrow_p[i] || iscol_p[i]) && MAT_INITIAL_MATRIX). */
    3266:         MatDestroy(A+i);
    3267:       } else (*submat)[i] = A[i];
    3268:     }
    3269:     ISDestroy(&isrow_p[i]);
    3270:     ISDestroy(&iscol_p[i]);
    3271:   }
    3272:   PetscFree2(cisrow,ciscol);
    3273:   PetscFree2(isrow_p,iscol_p);
    3274:   PetscFree(ciscol_p);
    3275:   PetscFree(A);
    3276:   MatDestroySubMatrices(cismax,&B);
    3277:   return(0);
    3278: }

    3280: PetscErrorCode MatCreateSubMatricesMPI_MPIAIJ(Mat C,PetscInt ismax,const IS isrow[],const IS iscol[],MatReuse scall,Mat *submat[])
    3281: {

    3285:   MatCreateSubMatricesMPI_MPIXAIJ(C,ismax,isrow,iscol,scall,submat,MatCreateSubMatrices_MPIAIJ,MatGetSeqMats_MPIAIJ,MatSetSeqMat_SeqAIJ,MatSetSeqMats_MPIAIJ);
    3286:   return(0);
    3287: }