Actual source code: mpiov.c
petsc-3.13.6 2020-09-29
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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;
     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,owner;
     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:   PetscMalloc2(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:   PetscMalloc1(nto+1,&toffsets);
    122:   toffsets[0] = 0;
    123:   for (i=0; i<nto; i++) {
    124:     toffsets[i+1]  = toffsets[i]+tosizes[2*i]; /* offsets */
    125:     tosizes[2*i+1] = toffsets[i]; /* offsets to send */
    126:   }
    127:   /* send information to other processors */
    128:   PetscCommBuildTwoSided(comm,2,MPIU_INT,nto,toranks,tosizes,&nfrom,&fromranks,&fromsizes);
    129:   nrecvrows = 0;
    130:   for (i=0; i<nfrom; i++) nrecvrows += fromsizes[2*i];
    131:   PetscMalloc1(nrecvrows,&remote);
    132:   nrecvrows = 0;
    133:   for (i=0; i<nfrom; i++) {
    134:     for (j=0; j<fromsizes[2*i]; j++) {
    135:       remote[nrecvrows].rank    = fromranks[i];
    136:       remote[nrecvrows++].index = fromsizes[2*i+1]+j;
    137:     }
    138:   }
    139:   PetscSFCreate(comm,&sf);
    140:   PetscSFSetGraph(sf,nrecvrows,nrecvrows,NULL,PETSC_OWN_POINTER,remote,PETSC_OWN_POINTER);
    141:   /* use two-sided communication by default since OPENMPI has some bugs for one-sided one */
    142:   PetscSFSetType(sf,PETSCSFBASIC);
    143:   PetscSFSetFromOptions(sf);
    144:   /* message pair <no of is, row>  */
    145:   PetscCalloc2(2*nrrows,&todata,nrecvrows,&fromdata);
    146:   for (i=0; i<nrrows; i++) {
    147:     owner = rrow_ranks[i]; /* processor */
    148:     j     = tosizes_temp[owner]; /* index */
    149:     todata[toffsets[j]++] = rrow_isids[i];
    150:     todata[toffsets[j]++] = remoterows[i];
    151:   }
    152:   PetscFree3(toranks,tosizes,tosizes_temp);
    153:   PetscFree3(remoterows,rrow_ranks,rrow_isids);
    154:   PetscFree(toffsets);
    155:   PetscSFBcastBegin(sf,MPIU_INT,todata,fromdata);
    156:   PetscSFBcastEnd(sf,MPIU_INT,todata,fromdata);
    157:   PetscSFDestroy(&sf);
    158:   /* send rows belonging to the remote so that then we could get the overlapping data back */
    159:   MatIncreaseOverlap_MPIAIJ_Send_Scalable(mat,nidx,nfrom,fromranks,fromsizes,fromdata,&sbsizes,&sbdata);
    160:   PetscFree2(todata,fromdata);
    161:   PetscFree(fromsizes);
    162:   PetscCommBuildTwoSided(comm,2,MPIU_INT,nfrom,fromranks,sbsizes,&nto,&toranks,&tosizes);
    163:   PetscFree(fromranks);
    164:   nrecvrows = 0;
    165:   for (i=0; i<nto; i++) nrecvrows += tosizes[2*i];
    166:   PetscCalloc1(nrecvrows,&todata);
    167:   PetscMalloc1(nrecvrows,&remote);
    168:   nrecvrows = 0;
    169:   for (i=0; i<nto; i++) {
    170:     for (j=0; j<tosizes[2*i]; j++) {
    171:       remote[nrecvrows].rank    = toranks[i];
    172:       remote[nrecvrows++].index = tosizes[2*i+1]+j;
    173:     }
    174:   }
    175:   PetscSFCreate(comm,&sf);
    176:   PetscSFSetGraph(sf,nrecvrows,nrecvrows,NULL,PETSC_OWN_POINTER,remote,PETSC_OWN_POINTER);
    177:   /* use two-sided communication by default since OPENMPI has some bugs for one-sided one */
    178:   PetscSFSetType(sf,PETSCSFBASIC);
    179:   PetscSFSetFromOptions(sf);
    180:   /* overlap communication and computation */
    181:   PetscSFBcastBegin(sf,MPIU_INT,sbdata,todata);
    182:   MatIncreaseOverlap_MPIAIJ_Local_Scalable(mat,nidx,is);
    183:   PetscSFBcastEnd(sf,MPIU_INT,sbdata,todata);
    184:   PetscSFDestroy(&sf);
    185:   PetscFree2(sbdata,sbsizes);
    186:   MatIncreaseOverlap_MPIAIJ_Receive_Scalable(mat,nidx,is,nrecvrows,todata);
    187:   PetscFree(toranks);
    188:   PetscFree(tosizes);
    189:   PetscFree(todata);
    190:   return(0);
    191: }

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

    202:   max_lsize = 0;
    203:   PetscMalloc1(nidx,&isz);
    204:   for (i=0; i<nidx; i++){
    205:     ISGetLocalSize(is[i],&lsize);
    206:     max_lsize = lsize>max_lsize ? lsize:max_lsize;
    207:     isz[i]    = lsize;
    208:   }
    209:   PetscMalloc2((max_lsize+nrecvs)*nidx,&indices_temp,nidx,&iscomms);
    210:   for (i=0; i<nidx; i++){
    211:     PetscCommDuplicate(PetscObjectComm((PetscObject)is[i]),&iscomms[i],NULL);
    212:     ISGetIndices(is[i],&indices_i_temp);
    213:     PetscArraycpy(indices_temp+i*(max_lsize+nrecvs),indices_i_temp, isz[i]);
    214:     ISRestoreIndices(is[i],&indices_i_temp);
    215:     ISDestroy(&is[i]);
    216:   }
    217:   /* retrieve information to get row id and its overlap */
    218:   for (i=0; i<nrecvs; ){
    219:     is_id     = recvdata[i++];
    220:     data_size = recvdata[i++];
    221:     indices_i = indices_temp+(max_lsize+nrecvs)*is_id;
    222:     isz_i     = isz[is_id];
    223:     for (j=0; j< data_size; j++){
    224:       col = recvdata[i++];
    225:       indices_i[isz_i++] = col;
    226:     }
    227:     isz[is_id] = isz_i;
    228:   }
    229:   /* remove duplicate entities */
    230:   for (i=0; i<nidx; i++){
    231:     indices_i = indices_temp+(max_lsize+nrecvs)*i;
    232:     isz_i     = isz[i];
    233:     PetscSortRemoveDupsInt(&isz_i,indices_i);
    234:     ISCreateGeneral(iscomms[i],isz_i,indices_i,PETSC_COPY_VALUES,&is[i]);
    235:     PetscCommDestroy(&iscomms[i]);
    236:   }
    237:   PetscFree(isz);
    238:   PetscFree2(indices_temp,iscomms);
    239:   return(0);
    240: }

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

    256:   PetscObjectGetComm((PetscObject)mat,&comm);
    257:   MPI_Comm_rank(comm,&rank);
    258:   MatMPIAIJGetSeqAIJ(mat,&amat,&bmat,&gcols);
    259:   /* Even if the mat is symmetric, we still assume it is not symmetric */
    260:   MatGetRowIJ(amat,0,PETSC_FALSE,PETSC_FALSE,&an,&ai,&aj,&done);
    261:   if (!done) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONGSTATE,"can not get row IJ \n");
    262:   MatGetRowIJ(bmat,0,PETSC_FALSE,PETSC_FALSE,&bn,&bi,&bj,&done);
    263:   if (!done) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONGSTATE,"can not get row IJ \n");
    264:   /* total number of nonzero values is used to estimate the memory usage in the next step */
    265:   tnz  = ai[an]+bi[bn];
    266:   MatGetLayouts(mat,&rmap,&cmap);
    267:   PetscLayoutGetRange(rmap,&rstart,NULL);
    268:   PetscLayoutGetRange(cmap,&cstart,NULL);
    269:   /* to find the longest message */
    270:   max_fszs = 0;
    271:   for (i=0; i<nfrom; i++) max_fszs = fromsizes[2*i]>max_fszs ? fromsizes[2*i]:max_fszs;
    272:   /* better way to estimate number of nonzero in the mat??? */
    273:   PetscCalloc5(max_fszs*nidx,&rows_data_ptr,nidx,&rows_data,nidx,&rows_pos_i,nfrom*nidx,&indv_counts,tnz,&indices_tmp);
    274:   for (i=0; i<nidx; i++) rows_data[i] = rows_data_ptr+max_fszs*i;
    275:   rows_pos  = 0;
    276:   totalrows = 0;
    277:   for (i=0; i<nfrom; i++){
    278:     PetscArrayzero(rows_pos_i,nidx);
    279:     /* group data together */
    280:     for (j=0; j<fromsizes[2*i]; j+=2){
    281:       is_id                       = fromrows[rows_pos++];/* no of is */
    282:       rows_i                      = rows_data[is_id];
    283:       rows_i[rows_pos_i[is_id]++] = fromrows[rows_pos++];/* row */
    284:     }
    285:     /* estimate a space to avoid multiple allocations  */
    286:     for (j=0; j<nidx; j++){
    287:       indvc_ij = 0;
    288:       rows_i   = rows_data[j];
    289:       for (l=0; l<rows_pos_i[j]; l++){
    290:         row    = rows_i[l]-rstart;
    291:         start  = ai[row];
    292:         end    = ai[row+1];
    293:         for (k=start; k<end; k++){ /* Amat */
    294:           col = aj[k] + cstart;
    295:           indices_tmp[indvc_ij++] = col;/* do not count the rows from the original rank */
    296:         }
    297:         start = bi[row];
    298:         end   = bi[row+1];
    299:         for (k=start; k<end; k++) { /* Bmat */
    300:           col = gcols[bj[k]];
    301:           indices_tmp[indvc_ij++] = col;
    302:         }
    303:       }
    304:       PetscSortRemoveDupsInt(&indvc_ij,indices_tmp);
    305:       indv_counts[i*nidx+j] = indvc_ij;
    306:       totalrows            += indvc_ij;
    307:     }
    308:   }
    309:   /* message triple <no of is, number of rows, rows> */
    310:   PetscCalloc2(totalrows+nidx*nfrom*2,&sbdata,2*nfrom,&sbsizes);
    311:   totalrows = 0;
    312:   rows_pos  = 0;
    313:   /* use this code again */
    314:   for (i=0;i<nfrom;i++){
    315:     PetscArrayzero(rows_pos_i,nidx);
    316:     for (j=0; j<fromsizes[2*i]; j+=2){
    317:       is_id                       = fromrows[rows_pos++];
    318:       rows_i                      = rows_data[is_id];
    319:       rows_i[rows_pos_i[is_id]++] = fromrows[rows_pos++];
    320:     }
    321:     /* add data  */
    322:     for (j=0; j<nidx; j++){
    323:       if (!indv_counts[i*nidx+j]) continue;
    324:       indvc_ij = 0;
    325:       sbdata[totalrows++] = j;
    326:       sbdata[totalrows++] = indv_counts[i*nidx+j];
    327:       sbsizes[2*i]       += 2;
    328:       rows_i              = rows_data[j];
    329:       for (l=0; l<rows_pos_i[j]; l++){
    330:         row   = rows_i[l]-rstart;
    331:         start = ai[row];
    332:         end   = ai[row+1];
    333:         for (k=start; k<end; k++){ /* Amat */
    334:           col = aj[k] + cstart;
    335:           indices_tmp[indvc_ij++] = col;
    336:         }
    337:         start = bi[row];
    338:         end   = bi[row+1];
    339:         for (k=start; k<end; k++) { /* Bmat */
    340:           col = gcols[bj[k]];
    341:           indices_tmp[indvc_ij++] = col;
    342:         }
    343:       }
    344:       PetscSortRemoveDupsInt(&indvc_ij,indices_tmp);
    345:       sbsizes[2*i]  += indvc_ij;
    346:       PetscArraycpy(sbdata+totalrows,indices_tmp,indvc_ij);
    347:       totalrows += indvc_ij;
    348:     }
    349:   }
    350:   PetscMalloc1(nfrom+1,&offsets);
    351:   offsets[0] = 0;
    352:   for (i=0; i<nfrom; i++){
    353:     offsets[i+1]   = offsets[i] + sbsizes[2*i];
    354:     sbsizes[2*i+1] = offsets[i];
    355:   }
    356:   PetscFree(offsets);
    357:   if (sbrowsizes) *sbrowsizes = sbsizes;
    358:   if (sbrows) *sbrows = sbdata;
    359:   PetscFree5(rows_data_ptr,rows_data,rows_pos_i,indv_counts,indices_tmp);
    360:   MatRestoreRowIJ(amat,0,PETSC_FALSE,PETSC_FALSE,&an,&ai,&aj,&done);
    361:   MatRestoreRowIJ(bmat,0,PETSC_FALSE,PETSC_FALSE,&bn,&bi,&bj,&done);
    362:   return(0);
    363: }

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

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

    397:     ISGetLocalSize(is[i],&lsize);
    398:     ISGetIndices(is[i],&indices);
    399:     lsize_tmp = 0;
    400:     for (j=0; j<lsize; j++) {
    401:       owner = -1;
    402:       row   = indices[j];
    403:       PetscLayoutFindOwner(rmap,row,&owner);
    404:       if (owner != rank) continue;
    405:       /* local number */
    406:       row  -= rstart;
    407:       start = ai[row];
    408:       end   = ai[row+1];
    409:       for (k=start; k<end; k++) { /* Amat */
    410:         col = aj[k] + cstart;
    411:         indices_temp[lsize_tmp++] = col;
    412:       }
    413:       start = bi[row];
    414:       end   = bi[row+1];
    415:       for (k=start; k<end; k++) { /* Bmat */
    416:         col = gcols[bj[k]];
    417:         indices_temp[lsize_tmp++] = col;
    418:       }
    419:     }
    420:    ISRestoreIndices(is[i],&indices);
    421:    PetscCommDuplicate(PetscObjectComm((PetscObject)is[i]),&iscomm,NULL);
    422:    ISDestroy(&is[i]);
    423:    PetscSortRemoveDupsInt(&lsize_tmp,indices_temp);
    424:    ISCreateGeneral(iscomm,lsize_tmp,indices_temp,PETSC_COPY_VALUES,&is[i]);
    425:    PetscCommDestroy(&iscomm);
    426:   }
    427:   PetscFree(indices_temp);
    428:   MatRestoreRowIJ(amat,0,PETSC_FALSE,PETSC_FALSE,&an,&ai,&aj,&done);
    429:   MatRestoreRowIJ(bmat,0,PETSC_FALSE,PETSC_FALSE,&bn,&bi,&bj,&done);
    430:   return(0);
    431: }

    434: /*
    435:   Sample message format:
    436:   If a processor A wants processor B to process some elements corresponding
    437:   to index sets is[1],is[5]
    438:   mesg [0] = 2   (no of index sets in the mesg)
    439:   -----------
    440:   mesg [1] = 1 => is[1]
    441:   mesg [2] = sizeof(is[1]);
    442:   -----------
    443:   mesg [3] = 5  => is[5]
    444:   mesg [4] = sizeof(is[5]);
    445:   -----------
    446:   mesg [5]
    447:   mesg [n]  datas[1]
    448:   -----------
    449:   mesg[n+1]
    450:   mesg[m]  data(is[5])
    451:   -----------

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

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

    486:   PetscObjectGetNewTag((PetscObject)C,&tag1);
    487:   PetscObjectGetNewTag((PetscObject)C,&tag2);

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

    491:   for (i=0; i<imax; i++) {
    492:     ISGetIndices(is[i],&idx[i]);
    493:     ISGetLocalSize(is[i],&n[i]);
    494:   }

    496:   /* evaluate communication - mesg to who,length of mesg, and buffer space
    497:      required. Based on this, buffers are allocated, and data copied into them  */
    498:   PetscCalloc4(size,&w1,size,&w2,size,&w3,size,&w4);
    499:   for (i=0; i<imax; i++) {
    500:     PetscArrayzero(w4,size); /* initialise work vector*/
    501:     idx_i = idx[i];
    502:     len   = n[i];
    503:     for (j=0; j<len; j++) {
    504:       row = idx_i[j];
    505:       if (row < 0) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Index set cannot have negative entries");
    506:       PetscLayoutFindOwner(C->rmap,row,&proc);
    507:       w4[proc]++;
    508:     }
    509:     for (j=0; j<size; j++) {
    510:       if (w4[j]) { w1[j] += w4[j]; w3[j]++;}
    511:     }
    512:   }

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

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

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

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

    541:   /* Allocate Memory for outgoing messages */
    542:   PetscMalloc4(size,&outdat,size,&ptr,msz,&tmp,size,&ctr);
    543:   PetscArrayzero(outdat,size);
    544:   PetscArrayzero(ptr,size);

    546:   {
    547:     PetscInt *iptr = tmp,ict  = 0;
    548:     for (i=0; i<nrqs; i++) {
    549:       j         = pa[i];
    550:       iptr     +=  ict;
    551:       outdat[j] = iptr;
    552:       ict       = w1[j];
    553:     }
    554:   }

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

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

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

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

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

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

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

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

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

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

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

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

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

    684:     PetscCalloc1(size,&rw1);

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

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

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

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

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

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

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

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

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

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

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

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

    808: /*
    809:    MatIncreaseOverlap_MPIAIJ_Local - Called by MatincreaseOverlap, to do
    810:        the work on the local processor.

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

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

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

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

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

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

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

    911: /*
    912:       MatIncreaseOverlap_MPIAIJ_Receive - Process the received messages,
    913:          and return the output

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

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

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

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

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

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

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

    968:   ct3 = 0;
    969:   for (i=0; i<nrqr; i++) { /* for easch mesg from proc i */
    970:     rbuf_i =  rbuf[i];
    971:     rbuf_0 =  rbuf_i[0];
    972:     ct1    =  2*rbuf_0+1;
    973:     ct2    =  ct1;
    974:     ct3   += ct1;
    975:     for (j=1; j<=rbuf_0; j++) { /* for each IS from proc i*/
    976:       PetscBTMemzero(m,xtable);
    977:       oct2 = ct2;
    978:       kmax = rbuf_i[2*j];
    979:       for (k=0; k<kmax; k++,ct1++) {
    980:         row = rbuf_i[ct1];
    981:         if (!PetscBTLookupSet(xtable,row)) {
    982:           if (!(ct3 < mem_estimate)) {
    983:             new_estimate = (PetscInt)(1.5*mem_estimate)+1;
    984:             PetscMalloc1(new_estimate,&tmp);
    985:             PetscArraycpy(tmp,xdata[0],mem_estimate);
    986:             PetscFree(xdata[0]);
    987:             xdata[0]     = tmp;
    988:             mem_estimate = new_estimate; ++no_malloc;
    989:             for (ctr=1; ctr<=i; ctr++) xdata[ctr] = xdata[ctr-1] + isz1[ctr-1];
    990:           }
    991:           xdata[i][ct2++] = row;
    992:           ct3++;
    993:         }
    994:       }
    995:       for (k=oct2,max2=ct2; k<max2; k++) {
    996:         row   = xdata[i][k] - rstart;
    997:         start = ai[row];
    998:         end   = ai[row+1];
    999:         for (l=start; l<end; l++) {
    1000:           val = aj[l] + cstart;
    1001:           if (!PetscBTLookupSet(xtable,val)) {
    1002:             if (!(ct3 < mem_estimate)) {
    1003:               new_estimate = (PetscInt)(1.5*mem_estimate)+1;
    1004:               PetscMalloc1(new_estimate,&tmp);
    1005:               PetscArraycpy(tmp,xdata[0],mem_estimate);
    1006:               PetscFree(xdata[0]);
    1007:               xdata[0]     = tmp;
    1008:               mem_estimate = new_estimate; ++no_malloc;
    1009:               for (ctr=1; ctr<=i; ctr++) xdata[ctr] = xdata[ctr-1] + isz1[ctr-1];
    1010:             }
    1011:             xdata[i][ct2++] = val;
    1012:             ct3++;
    1013:           }
    1014:         }
    1015:         start = bi[row];
    1016:         end   = bi[row+1];
    1017:         for (l=start; l<end; l++) {
    1018:           val = garray[bj[l]];
    1019:           if (!PetscBTLookupSet(xtable,val)) {
    1020:             if (!(ct3 < mem_estimate)) {
    1021:               new_estimate = (PetscInt)(1.5*mem_estimate)+1;
    1022:               PetscMalloc1(new_estimate,&tmp);
    1023:               PetscArraycpy(tmp,xdata[0],mem_estimate);
    1024:               PetscFree(xdata[0]);
    1025:               xdata[0]     = tmp;
    1026:               mem_estimate = new_estimate; ++no_malloc;
    1027:               for (ctr =1; ctr <=i; ctr++) xdata[ctr] = xdata[ctr-1] + isz1[ctr-1];
    1028:             }
    1029:             xdata[i][ct2++] = val;
    1030:             ct3++;
    1031:           }
    1032:         }
    1033:       }
    1034:       /* Update the header*/
    1035:       xdata[i][2*j]   = ct2 - oct2; /* Undo the vector isz1 and use only a var*/
    1036:       xdata[i][2*j-1] = rbuf_i[2*j-1];
    1037:     }
    1038:     xdata[i][0] = rbuf_0;
    1039:     xdata[i+1]  = xdata[i] + ct2;
    1040:     isz1[i]     = ct2; /* size of each message */
    1041:   }
    1042:   PetscBTDestroy(&xtable);
    1043:   PetscInfo3(C,"Allocated %D bytes, required %D bytes, no of mallocs = %D\n",mem_estimate,ct3,no_malloc);
    1044:   return(0);
    1045: }
    1046: /* -------------------------------------------------------------------------*/
    1047: extern PetscErrorCode MatCreateSubMatrices_MPIAIJ_Local(Mat,PetscInt,const IS[],const IS[],MatReuse,Mat*);
    1048: /*
    1049:     Every processor gets the entire matrix
    1050: */
    1051: PetscErrorCode MatCreateSubMatrix_MPIAIJ_All(Mat A,MatCreateSubMatrixOption flag,MatReuse scall,Mat *Bin[])
    1052: {
    1053:   Mat            B;
    1054:   Mat_MPIAIJ     *a = (Mat_MPIAIJ*)A->data;
    1055:   Mat_SeqAIJ     *b,*ad = (Mat_SeqAIJ*)a->A->data,*bd = (Mat_SeqAIJ*)a->B->data;
    1057:   PetscMPIInt    size,rank,*recvcounts = 0,*displs = 0;
    1058:   PetscInt       sendcount,i,*rstarts = A->rmap->range,n,cnt,j;
    1059:   PetscInt       m,*b_sendj,*garray = a->garray,*lens,*jsendbuf,*a_jsendbuf,*b_jsendbuf;
    1060:   MatScalar      *sendbuf,*recvbuf,*a_sendbuf,*b_sendbuf;

    1063:   MPI_Comm_size(PetscObjectComm((PetscObject)A),&size);
    1064:   MPI_Comm_rank(PetscObjectComm((PetscObject)A),&rank);

    1066:   if (scall == MAT_INITIAL_MATRIX) {
    1067:     /* ----------------------------------------------------------------
    1068:          Tell every processor the number of nonzeros per row
    1069:     */
    1070:     PetscMalloc1(A->rmap->N,&lens);
    1071:     for (i=A->rmap->rstart; i<A->rmap->rend; i++) {
    1072:       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];
    1073:     }
    1074:     PetscMalloc2(size,&recvcounts,size,&displs);
    1075:     for (i=0; i<size; i++) {
    1076:       recvcounts[i] = A->rmap->range[i+1] - A->rmap->range[i];
    1077:       displs[i]     = A->rmap->range[i];
    1078:     }
    1079: #if defined(PETSC_HAVE_MPI_IN_PLACE)
    1080:     MPI_Allgatherv(MPI_IN_PLACE,0,MPI_DATATYPE_NULL,lens,recvcounts,displs,MPIU_INT,PetscObjectComm((PetscObject)A));
    1081: #else
    1082:     sendcount = A->rmap->rend - A->rmap->rstart;
    1083:     MPI_Allgatherv(lens+A->rmap->rstart,sendcount,MPIU_INT,lens,recvcounts,displs,MPIU_INT,PetscObjectComm((PetscObject)A));
    1084: #endif
    1085:     /* ---------------------------------------------------------------
    1086:          Create the sequential matrix of the same type as the local block diagonal
    1087:     */
    1088:     MatCreate(PETSC_COMM_SELF,&B);
    1089:     MatSetSizes(B,A->rmap->N,A->cmap->N,PETSC_DETERMINE,PETSC_DETERMINE);
    1090:     MatSetBlockSizesFromMats(B,A,A);
    1091:     MatSetType(B,((PetscObject)a->A)->type_name);
    1092:     MatSeqAIJSetPreallocation(B,0,lens);
    1093:     PetscCalloc1(2,Bin);
    1094:     **Bin = B;
    1095:     b     = (Mat_SeqAIJ*)B->data;

    1097:     /*--------------------------------------------------------------------
    1098:        Copy my part of matrix column indices over
    1099:     */
    1100:     sendcount  = ad->nz + bd->nz;
    1101:     jsendbuf   = b->j + b->i[rstarts[rank]];
    1102:     a_jsendbuf = ad->j;
    1103:     b_jsendbuf = bd->j;
    1104:     n          = A->rmap->rend - A->rmap->rstart;
    1105:     cnt        = 0;
    1106:     for (i=0; i<n; i++) {

    1108:       /* put in lower diagonal portion */
    1109:       m = bd->i[i+1] - bd->i[i];
    1110:       while (m > 0) {
    1111:         /* is it above diagonal (in bd (compressed) numbering) */
    1112:         if (garray[*b_jsendbuf] > A->rmap->rstart + i) break;
    1113:         jsendbuf[cnt++] = garray[*b_jsendbuf++];
    1114:         m--;
    1115:       }

    1117:       /* put in diagonal portion */
    1118:       for (j=ad->i[i]; j<ad->i[i+1]; j++) {
    1119:         jsendbuf[cnt++] = A->rmap->rstart + *a_jsendbuf++;
    1120:       }

    1122:       /* put in upper diagonal portion */
    1123:       while (m-- > 0) {
    1124:         jsendbuf[cnt++] = garray[*b_jsendbuf++];
    1125:       }
    1126:     }
    1127:     if (cnt != sendcount) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_PLIB,"Corrupted PETSc matrix: nz given %D actual nz %D",sendcount,cnt);

    1129:     /*--------------------------------------------------------------------
    1130:        Gather all column indices to all processors
    1131:     */
    1132:     for (i=0; i<size; i++) {
    1133:       recvcounts[i] = 0;
    1134:       for (j=A->rmap->range[i]; j<A->rmap->range[i+1]; j++) {
    1135:         recvcounts[i] += lens[j];
    1136:       }
    1137:     }
    1138:     displs[0] = 0;
    1139:     for (i=1; i<size; i++) {
    1140:       displs[i] = displs[i-1] + recvcounts[i-1];
    1141:     }
    1142: #if defined(PETSC_HAVE_MPI_IN_PLACE)
    1143:     MPI_Allgatherv(MPI_IN_PLACE,0,MPI_DATATYPE_NULL,b->j,recvcounts,displs,MPIU_INT,PetscObjectComm((PetscObject)A));
    1144: #else
    1145:     MPI_Allgatherv(jsendbuf,sendcount,MPIU_INT,b->j,recvcounts,displs,MPIU_INT,PetscObjectComm((PetscObject)A));
    1146: #endif
    1147:     /*--------------------------------------------------------------------
    1148:         Assemble the matrix into useable form (note numerical values not yet set)
    1149:     */
    1150:     /* set the b->ilen (length of each row) values */
    1151:     PetscArraycpy(b->ilen,lens,A->rmap->N);
    1152:     /* set the b->i indices */
    1153:     b->i[0] = 0;
    1154:     for (i=1; i<=A->rmap->N; i++) {
    1155:       b->i[i] = b->i[i-1] + lens[i-1];
    1156:     }
    1157:     PetscFree(lens);
    1158:     MatAssemblyBegin(B,MAT_FINAL_ASSEMBLY);
    1159:     MatAssemblyEnd(B,MAT_FINAL_ASSEMBLY);

    1161:   } else {
    1162:     B = **Bin;
    1163:     b = (Mat_SeqAIJ*)B->data;
    1164:   }

    1166:   /*--------------------------------------------------------------------
    1167:        Copy my part of matrix numerical values into the values location
    1168:   */
    1169:   if (flag == MAT_GET_VALUES) {
    1170:     sendcount = ad->nz + bd->nz;
    1171:     sendbuf   = b->a + b->i[rstarts[rank]];
    1172:     a_sendbuf = ad->a;
    1173:     b_sendbuf = bd->a;
    1174:     b_sendj   = bd->j;
    1175:     n         = A->rmap->rend - A->rmap->rstart;
    1176:     cnt       = 0;
    1177:     for (i=0; i<n; i++) {

    1179:       /* put in lower diagonal portion */
    1180:       m = bd->i[i+1] - bd->i[i];
    1181:       while (m > 0) {
    1182:         /* is it above diagonal (in bd (compressed) numbering) */
    1183:         if (garray[*b_sendj] > A->rmap->rstart + i) break;
    1184:         sendbuf[cnt++] = *b_sendbuf++;
    1185:         m--;
    1186:         b_sendj++;
    1187:       }

    1189:       /* put in diagonal portion */
    1190:       for (j=ad->i[i]; j<ad->i[i+1]; j++) {
    1191:         sendbuf[cnt++] = *a_sendbuf++;
    1192:       }

    1194:       /* put in upper diagonal portion */
    1195:       while (m-- > 0) {
    1196:         sendbuf[cnt++] = *b_sendbuf++;
    1197:         b_sendj++;
    1198:       }
    1199:     }
    1200:     if (cnt != sendcount) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_PLIB,"Corrupted PETSc matrix: nz given %D actual nz %D",sendcount,cnt);

    1202:     /* -----------------------------------------------------------------
    1203:        Gather all numerical values to all processors
    1204:     */
    1205:     if (!recvcounts) {
    1206:       PetscMalloc2(size,&recvcounts,size,&displs);
    1207:     }
    1208:     for (i=0; i<size; i++) {
    1209:       recvcounts[i] = b->i[rstarts[i+1]] - b->i[rstarts[i]];
    1210:     }
    1211:     displs[0] = 0;
    1212:     for (i=1; i<size; i++) {
    1213:       displs[i] = displs[i-1] + recvcounts[i-1];
    1214:     }
    1215:     recvbuf = b->a;
    1216: #if defined(PETSC_HAVE_MPI_IN_PLACE)
    1217:     MPI_Allgatherv(MPI_IN_PLACE,0,MPI_DATATYPE_NULL,recvbuf,recvcounts,displs,MPIU_SCALAR,PetscObjectComm((PetscObject)A));
    1218: #else
    1219:     MPI_Allgatherv(sendbuf,sendcount,MPIU_SCALAR,recvbuf,recvcounts,displs,MPIU_SCALAR,PetscObjectComm((PetscObject)A));
    1220: #endif
    1221:   }  /* endof (flag == MAT_GET_VALUES) */
    1222:   PetscFree2(recvcounts,displs);

    1224:   if (A->symmetric) {
    1225:     MatSetOption(B,MAT_SYMMETRIC,PETSC_TRUE);
    1226:   } else if (A->hermitian) {
    1227:     MatSetOption(B,MAT_HERMITIAN,PETSC_TRUE);
    1228:   } else if (A->structurally_symmetric) {
    1229:     MatSetOption(B,MAT_STRUCTURALLY_SYMMETRIC,PETSC_TRUE);
    1230:   }
    1231:   return(0);
    1232: }

    1234: PetscErrorCode MatCreateSubMatrices_MPIAIJ_SingleIS_Local(Mat C,PetscInt ismax,const IS isrow[],const IS iscol[],MatReuse scall,PetscBool allcolumns,Mat *submats)
    1235: {
    1236:   Mat_MPIAIJ     *c = (Mat_MPIAIJ*)C->data;
    1237:   Mat            submat,A = c->A,B = c->B;
    1238:   Mat_SeqAIJ     *a = (Mat_SeqAIJ*)A->data,*b = (Mat_SeqAIJ*)B->data,*subc;
    1239:   PetscInt       *ai=a->i,*aj=a->j,*bi=b->i,*bj=b->j,nzA,nzB;
    1240:   PetscInt       cstart = C->cmap->rstart,cend = C->cmap->rend,rstart = C->rmap->rstart,*bmap = c->garray;
    1241:   const PetscInt *icol,*irow;
    1242:   PetscInt       nrow,ncol,start;
    1244:   PetscMPIInt    rank,size,tag1,tag2,tag3,tag4,*w1,*w2,nrqr;
    1245:   PetscInt       **sbuf1,**sbuf2,i,j,k,l,ct1,ct2,ct3,**rbuf1,row,proc;
    1246:   PetscInt       nrqs=0,msz,**ptr,*req_size,*ctr,*pa,*tmp,tcol,*iptr;
    1247:   PetscInt       **rbuf3,*req_source1,*req_source2,**sbuf_aj,**rbuf2,max1,nnz;
    1248:   PetscInt       *lens,rmax,ncols,*cols,Crow;
    1249: #if defined(PETSC_USE_CTABLE)
    1250:   PetscTable     cmap,rmap;
    1251:   PetscInt       *cmap_loc,*rmap_loc;
    1252: #else
    1253:   PetscInt       *cmap,*rmap;
    1254: #endif
    1255:   PetscInt       ctr_j,*sbuf1_j,*sbuf_aj_i,*rbuf1_i,kmax,*sbuf1_i,*rbuf2_i,*rbuf3_i;
    1256:   PetscInt       *cworkB,lwrite,*subcols,*row2proc;
    1257:   PetscScalar    *vworkA,*vworkB,*a_a = a->a,*b_a = b->a,*subvals=NULL;
    1258:   MPI_Request    *s_waits1,*r_waits1,*s_waits2,*r_waits2,*r_waits3;
    1259:   MPI_Request    *r_waits4,*s_waits3 = NULL,*s_waits4;
    1260:   MPI_Status     *r_status1,*r_status2,*s_status1,*s_status3 = NULL,*s_status2;
    1261:   MPI_Status     *r_status3 = NULL,*r_status4,*s_status4;
    1262:   MPI_Comm       comm;
    1263:   PetscScalar    **rbuf4,**sbuf_aa,*vals,*sbuf_aa_i,*rbuf4_i;
    1264:   PetscMPIInt    *onodes1,*olengths1,idex,end;
    1265:   Mat_SubSppt    *smatis1;
    1266:   PetscBool      isrowsorted,iscolsorted;

    1271:   if (ismax != 1) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_SUP,"This routine only works when all processes have ismax=1");

    1273:   PetscObjectGetComm((PetscObject)C,&comm);
    1274:   size = c->size;
    1275:   rank = c->rank;

    1277:   ISSorted(iscol[0],&iscolsorted);
    1278:   ISSorted(isrow[0],&isrowsorted);
    1279:   ISGetIndices(isrow[0],&irow);
    1280:   ISGetLocalSize(isrow[0],&nrow);
    1281:   if (allcolumns) {
    1282:     icol = NULL;
    1283:     ncol = C->cmap->N;
    1284:   } else {
    1285:     ISGetIndices(iscol[0],&icol);
    1286:     ISGetLocalSize(iscol[0],&ncol);
    1287:   }

    1289:   if (scall == MAT_INITIAL_MATRIX) {
    1290:     PetscInt *sbuf2_i,*cworkA,lwrite,ctmp;

    1292:     /* Get some new tags to keep the communication clean */
    1293:     tag1 = ((PetscObject)C)->tag;
    1294:     PetscObjectGetNewTag((PetscObject)C,&tag2);
    1295:     PetscObjectGetNewTag((PetscObject)C,&tag3);

    1297:     /* evaluate communication - mesg to who, length of mesg, and buffer space
    1298:      required. Based on this, buffers are allocated, and data copied into them */
    1299:     PetscCalloc2(size,&w1,size,&w2);
    1300:     PetscMalloc1(nrow,&row2proc);

    1302:     /* w1[proc] = num of rows owned by proc -- to be requested */
    1303:     proc = 0;
    1304:     nrqs = 0; /* num of outgoing messages */
    1305:     for (j=0; j<nrow; j++) {
    1306:       row  = irow[j];
    1307:       if (!isrowsorted) proc = 0;
    1308:       while (row >= C->rmap->range[proc+1]) proc++;
    1309:       w1[proc]++;
    1310:       row2proc[j] = proc; /* map row index to proc */

    1312:       if (proc != rank && !w2[proc]) {
    1313:         w2[proc] = 1; nrqs++;
    1314:       }
    1315:     }
    1316:     w1[rank] = 0;  /* rows owned by self will not be requested */

    1318:     PetscMalloc1(nrqs+1,&pa); /*(proc -array)*/
    1319:     for (proc=0,j=0; proc<size; proc++) {
    1320:       if (w1[proc]) { pa[j++] = proc;}
    1321:     }

    1323:     /* Each message would have a header = 1 + 2*(num of IS) + data (here,num of IS = 1) */
    1324:     msz = 0;              /* total mesg length (for all procs) */
    1325:     for (i=0; i<nrqs; i++) {
    1326:       proc      = pa[i];
    1327:       w1[proc] += 3;
    1328:       msz      += w1[proc];
    1329:     }
    1330:     PetscInfo2(0,"Number of outgoing messages %D Total message length %D\n",nrqs,msz);

    1332:     /* Determine nrqr, the number of messages to expect, their lengths, from from-ids */
    1333:     /* if w2[proc]=1, a message of length w1[proc] will be sent to proc; */
    1334:     PetscGatherNumberOfMessages(comm,w2,w1,&nrqr);

    1336:     /* Input: nrqs: nsend; nrqr: nrecv; w1: msg length to be sent;
    1337:        Output: onodes1: recv node-ids; olengths1: corresponding recv message length */
    1338:     PetscGatherMessageLengths(comm,nrqs,nrqr,w1,&onodes1,&olengths1);

    1340:     /* Now post the Irecvs corresponding to these messages */
    1341:     PetscPostIrecvInt(comm,tag1,nrqr,onodes1,olengths1,&rbuf1,&r_waits1);

    1343:     PetscFree(onodes1);
    1344:     PetscFree(olengths1);

    1346:     /* Allocate Memory for outgoing messages */
    1347:     PetscMalloc4(size,&sbuf1,size,&ptr,2*msz,&tmp,size,&ctr);
    1348:     PetscArrayzero(sbuf1,size);
    1349:     PetscArrayzero(ptr,size);

    1351:     /* subf1[pa[0]] = tmp, subf1[pa[i]] = subf1[pa[i-1]] + w1[pa[i-1]] */
    1352:     iptr = tmp;
    1353:     for (i=0; i<nrqs; i++) {
    1354:       proc        = pa[i];
    1355:       sbuf1[proc] = iptr;
    1356:       iptr       += w1[proc];
    1357:     }

    1359:     /* Form the outgoing messages */
    1360:     /* Initialize the header space */
    1361:     for (i=0; i<nrqs; i++) {
    1362:       proc      = pa[i];
    1363:       PetscArrayzero(sbuf1[proc],3);
    1364:       ptr[proc] = sbuf1[proc] + 3;
    1365:     }

    1367:     /* Parse the isrow and copy data into outbuf */
    1368:     PetscArrayzero(ctr,size);
    1369:     for (j=0; j<nrow; j++) {  /* parse the indices of each IS */
    1370:       proc = row2proc[j];
    1371:       if (proc != rank) { /* copy to the outgoing buf*/
    1372:         *ptr[proc] = irow[j];
    1373:         ctr[proc]++; ptr[proc]++;
    1374:       }
    1375:     }

    1377:     /* Update the headers for the current IS */
    1378:     for (j=0; j<size; j++) { /* Can Optimise this loop too */
    1379:       if ((ctr_j = ctr[j])) {
    1380:         sbuf1_j        = sbuf1[j];
    1381:         k              = ++sbuf1_j[0];
    1382:         sbuf1_j[2*k]   = ctr_j;
    1383:         sbuf1_j[2*k-1] = 0;
    1384:       }
    1385:     }

    1387:     /* Now post the sends */
    1388:     PetscMalloc1(nrqs+1,&s_waits1);
    1389:     for (i=0; i<nrqs; ++i) {
    1390:       proc = pa[i];
    1391:       MPI_Isend(sbuf1[proc],w1[proc],MPIU_INT,proc,tag1,comm,s_waits1+i);
    1392:     }

    1394:     /* Post Receives to capture the buffer size */
    1395:     PetscMalloc4(nrqs+1,&r_status2,nrqr+1,&s_waits2,nrqs+1,&r_waits2,nrqr+1,&s_status2);
    1396:     PetscMalloc3(nrqs+1,&req_source2,nrqs+1,&rbuf2,nrqs+1,&rbuf3);

    1398:     rbuf2[0] = tmp + msz;
    1399:     for (i=1; i<nrqs; ++i) rbuf2[i] = rbuf2[i-1] + w1[pa[i-1]];

    1401:     for (i=0; i<nrqs; ++i) {
    1402:       proc = pa[i];
    1403:       MPI_Irecv(rbuf2[i],w1[proc],MPIU_INT,proc,tag2,comm,r_waits2+i);
    1404:     }

    1406:     PetscFree2(w1,w2);

    1408:     /* Send to other procs the buf size they should allocate */
    1409:     /* Receive messages*/
    1410:     PetscMalloc1(nrqr+1,&r_status1);
    1411:     PetscMalloc3(nrqr,&sbuf2,nrqr,&req_size,nrqr,&req_source1);

    1413:     MPI_Waitall(nrqr,r_waits1,r_status1);
    1414:     for (i=0; i<nrqr; ++i) {
    1415:       req_size[i] = 0;
    1416:       rbuf1_i        = rbuf1[i];
    1417:       start          = 2*rbuf1_i[0] + 1;
    1418:       MPI_Get_count(r_status1+i,MPIU_INT,&end);
    1419:       PetscMalloc1(end+1,&sbuf2[i]);
    1420:       sbuf2_i        = sbuf2[i];
    1421:       for (j=start; j<end; j++) {
    1422:         k            = rbuf1_i[j] - rstart;
    1423:         ncols        = ai[k+1] - ai[k] + bi[k+1] - bi[k];
    1424:         sbuf2_i[j]   = ncols;
    1425:         req_size[i] += ncols;
    1426:       }
    1427:       req_source1[i] = r_status1[i].MPI_SOURCE;

    1429:       /* form the header */
    1430:       sbuf2_i[0] = req_size[i];
    1431:       for (j=1; j<start; j++) sbuf2_i[j] = rbuf1_i[j];

    1433:       MPI_Isend(sbuf2_i,end,MPIU_INT,req_source1[i],tag2,comm,s_waits2+i);
    1434:     }

    1436:     PetscFree(r_status1);
    1437:     PetscFree(r_waits1);

    1439:     /* rbuf2 is received, Post recv column indices a->j */
    1440:     MPI_Waitall(nrqs,r_waits2,r_status2);

    1442:     PetscMalloc4(nrqs+1,&r_waits3,nrqr+1,&s_waits3,nrqs+1,&r_status3,nrqr+1,&s_status3);
    1443:     for (i=0; i<nrqs; ++i) {
    1444:       PetscMalloc1(rbuf2[i][0]+1,&rbuf3[i]);
    1445:       req_source2[i] = r_status2[i].MPI_SOURCE;
    1446:       MPI_Irecv(rbuf3[i],rbuf2[i][0],MPIU_INT,req_source2[i],tag3,comm,r_waits3+i);
    1447:     }

    1449:     /* Wait on sends1 and sends2 */
    1450:     PetscMalloc1(nrqs+1,&s_status1);
    1451:     MPI_Waitall(nrqs,s_waits1,s_status1);
    1452:     PetscFree(s_waits1);
    1453:     PetscFree(s_status1);

    1455:     MPI_Waitall(nrqr,s_waits2,s_status2);
    1456:     PetscFree4(r_status2,s_waits2,r_waits2,s_status2);

    1458:     /* Now allocate sending buffers for a->j, and send them off */
    1459:     PetscMalloc1(nrqr+1,&sbuf_aj);
    1460:     for (i=0,j=0; i<nrqr; i++) j += req_size[i];
    1461:     PetscMalloc1(j+1,&sbuf_aj[0]);
    1462:     for (i=1; i<nrqr; i++) sbuf_aj[i] = sbuf_aj[i-1] + req_size[i-1];

    1464:     for (i=0; i<nrqr; i++) { /* for each requested message */
    1465:       rbuf1_i   = rbuf1[i];
    1466:       sbuf_aj_i = sbuf_aj[i];
    1467:       ct1       = 2*rbuf1_i[0] + 1;
    1468:       ct2       = 0;
    1469:       /* max1=rbuf1_i[0]; if (max1 != 1) SETERRQ1(PETSC_COMM_SELF,0,"max1 %d != 1",max1); */

    1471:       kmax = rbuf1[i][2];
    1472:       for (k=0; k<kmax; k++,ct1++) { /* for each row */
    1473:         row    = rbuf1_i[ct1] - rstart;
    1474:         nzA    = ai[row+1] - ai[row];
    1475:         nzB    = bi[row+1] - bi[row];
    1476:         ncols  = nzA + nzB;
    1477:         cworkA = aj + ai[row]; cworkB = bj + bi[row];

    1479:         /* load the column indices for this row into cols*/
    1480:         cols = sbuf_aj_i + ct2;

    1482:         lwrite = 0;
    1483:         for (l=0; l<nzB; l++) {
    1484:           if ((ctmp = bmap[cworkB[l]]) < cstart) cols[lwrite++] = ctmp;
    1485:         }
    1486:         for (l=0; l<nzA; l++) cols[lwrite++] = cstart + cworkA[l];
    1487:         for (l=0; l<nzB; l++) {
    1488:           if ((ctmp = bmap[cworkB[l]]) >= cend) cols[lwrite++] = ctmp;
    1489:         }

    1491:         ct2 += ncols;
    1492:       }
    1493:       MPI_Isend(sbuf_aj_i,req_size[i],MPIU_INT,req_source1[i],tag3,comm,s_waits3+i);
    1494:     }

    1496:     /* create column map (cmap): global col of C -> local col of submat */
    1497: #if defined(PETSC_USE_CTABLE)
    1498:     if (!allcolumns) {
    1499:       PetscTableCreate(ncol+1,C->cmap->N+1,&cmap);
    1500:       PetscCalloc1(C->cmap->n,&cmap_loc);
    1501:       for (j=0; j<ncol; j++) { /* use array cmap_loc[] for local col indices */
    1502:         if (icol[j] >= cstart && icol[j] <cend) {
    1503:           cmap_loc[icol[j] - cstart] = j+1;
    1504:         } else { /* use PetscTable for non-local col indices */
    1505:           PetscTableAdd(cmap,icol[j]+1,j+1,INSERT_VALUES);
    1506:         }
    1507:       }
    1508:     } else {
    1509:       cmap     = NULL;
    1510:       cmap_loc = NULL;
    1511:     }
    1512:     PetscCalloc1(C->rmap->n,&rmap_loc);
    1513: #else
    1514:     if (!allcolumns) {
    1515:       PetscCalloc1(C->cmap->N,&cmap);
    1516:       for (j=0; j<ncol; j++) cmap[icol[j]] = j+1;
    1517:     } else {
    1518:       cmap = NULL;
    1519:     }
    1520: #endif

    1522:     /* Create lens for MatSeqAIJSetPreallocation() */
    1523:     PetscCalloc1(nrow,&lens);

    1525:     /* Compute lens from local part of C */
    1526:     for (j=0; j<nrow; j++) {
    1527:       row  = irow[j];
    1528:       proc = row2proc[j];
    1529:       if (proc == rank) {
    1530:         /* diagonal part A = c->A */
    1531:         ncols = ai[row-rstart+1] - ai[row-rstart];
    1532:         cols  = aj + ai[row-rstart];
    1533:         if (!allcolumns) {
    1534:           for (k=0; k<ncols; k++) {
    1535: #if defined(PETSC_USE_CTABLE)
    1536:             tcol = cmap_loc[cols[k]];
    1537: #else
    1538:             tcol = cmap[cols[k]+cstart];
    1539: #endif
    1540:             if (tcol) lens[j]++;
    1541:           }
    1542:         } else { /* allcolumns */
    1543:           lens[j] = ncols;
    1544:         }

    1546:         /* off-diagonal part B = c->B */
    1547:         ncols = bi[row-rstart+1] - bi[row-rstart];
    1548:         cols  = bj + bi[row-rstart];
    1549:         if (!allcolumns) {
    1550:           for (k=0; k<ncols; k++) {
    1551: #if defined(PETSC_USE_CTABLE)
    1552:             PetscTableFind(cmap,bmap[cols[k]]+1,&tcol);
    1553: #else
    1554:             tcol = cmap[bmap[cols[k]]];
    1555: #endif
    1556:             if (tcol) lens[j]++;
    1557:           }
    1558:         } else { /* allcolumns */
    1559:           lens[j] += ncols;
    1560:         }
    1561:       }
    1562:     }

    1564:     /* Create row map (rmap): global row of C -> local row of submat */
    1565: #if defined(PETSC_USE_CTABLE)
    1566:     PetscTableCreate(nrow+1,C->rmap->N+1,&rmap);
    1567:     for (j=0; j<nrow; j++) {
    1568:       row  = irow[j];
    1569:       proc = row2proc[j];
    1570:       if (proc == rank) { /* a local row */
    1571:         rmap_loc[row - rstart] = j;
    1572:       } else {
    1573:         PetscTableAdd(rmap,irow[j]+1,j+1,INSERT_VALUES);
    1574:       }
    1575:     }
    1576: #else
    1577:     PetscCalloc1(C->rmap->N,&rmap);
    1578:     for (j=0; j<nrow; j++) {
    1579:       rmap[irow[j]] = j;
    1580:     }
    1581: #endif

    1583:     /* Update lens from offproc data */
    1584:     /* recv a->j is done */
    1585:     MPI_Waitall(nrqs,r_waits3,r_status3);
    1586:     for (i=0; i<nrqs; i++) {
    1587:       proc    = pa[i];
    1588:       sbuf1_i = sbuf1[proc];
    1589:       /* jmax    = sbuf1_i[0]; if (jmax != 1) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_PLIB,"jmax !=1"); */
    1590:       ct1     = 2 + 1;
    1591:       ct2     = 0;
    1592:       rbuf2_i = rbuf2[i]; /* received length of C->j */
    1593:       rbuf3_i = rbuf3[i]; /* received C->j */

    1595:       /* is_no  = sbuf1_i[2*j-1]; if (is_no != 0) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_PLIB,"is_no !=0"); */
    1596:       max1   = sbuf1_i[2];
    1597:       for (k=0; k<max1; k++,ct1++) {
    1598: #if defined(PETSC_USE_CTABLE)
    1599:         PetscTableFind(rmap,sbuf1_i[ct1]+1,&row);
    1600:         row--;
    1601:         if (row < 0) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_PLIB,"row not found in table");
    1602: #else
    1603:         row = rmap[sbuf1_i[ct1]]; /* the row index in submat */
    1604: #endif
    1605:         /* Now, store row index of submat in sbuf1_i[ct1] */
    1606:         sbuf1_i[ct1] = row;

    1608:         nnz = rbuf2_i[ct1];
    1609:         if (!allcolumns) {
    1610:           for (l=0; l<nnz; l++,ct2++) {
    1611: #if defined(PETSC_USE_CTABLE)
    1612:             if (rbuf3_i[ct2] >= cstart && rbuf3_i[ct2] <cend) {
    1613:               tcol = cmap_loc[rbuf3_i[ct2] - cstart];
    1614:             } else {
    1615:               PetscTableFind(cmap,rbuf3_i[ct2]+1,&tcol);
    1616:             }
    1617: #else
    1618:             tcol = cmap[rbuf3_i[ct2]]; /* column index in submat */
    1619: #endif
    1620:             if (tcol) lens[row]++;
    1621:           }
    1622:         } else { /* allcolumns */
    1623:           lens[row] += nnz;
    1624:         }
    1625:       }
    1626:     }
    1627:     MPI_Waitall(nrqr,s_waits3,s_status3);
    1628:     PetscFree4(r_waits3,s_waits3,r_status3,s_status3);

    1630:     /* Create the submatrices */
    1631:     MatCreate(PETSC_COMM_SELF,&submat);
    1632:     MatSetSizes(submat,nrow,ncol,PETSC_DETERMINE,PETSC_DETERMINE);

    1634:     ISGetBlockSize(isrow[0],&i);
    1635:     ISGetBlockSize(iscol[0],&j);
    1636:     MatSetBlockSizes(submat,i,j);
    1637:     MatSetType(submat,((PetscObject)A)->type_name);
    1638:     MatSeqAIJSetPreallocation(submat,0,lens);

    1640:     /* create struct Mat_SubSppt and attached it to submat */
    1641:     PetscNew(&smatis1);
    1642:     subc = (Mat_SeqAIJ*)submat->data;
    1643:     subc->submatis1 = smatis1;

    1645:     smatis1->id          = 0;
    1646:     smatis1->nrqs        = nrqs;
    1647:     smatis1->nrqr        = nrqr;
    1648:     smatis1->rbuf1       = rbuf1;
    1649:     smatis1->rbuf2       = rbuf2;
    1650:     smatis1->rbuf3       = rbuf3;
    1651:     smatis1->sbuf2       = sbuf2;
    1652:     smatis1->req_source2 = req_source2;

    1654:     smatis1->sbuf1       = sbuf1;
    1655:     smatis1->ptr         = ptr;
    1656:     smatis1->tmp         = tmp;
    1657:     smatis1->ctr         = ctr;

    1659:     smatis1->pa           = pa;
    1660:     smatis1->req_size     = req_size;
    1661:     smatis1->req_source1  = req_source1;

    1663:     smatis1->allcolumns  = allcolumns;
    1664:     smatis1->singleis    = PETSC_TRUE;
    1665:     smatis1->row2proc    = row2proc;
    1666:     smatis1->rmap        = rmap;
    1667:     smatis1->cmap        = cmap;
    1668: #if defined(PETSC_USE_CTABLE)
    1669:     smatis1->rmap_loc    = rmap_loc;
    1670:     smatis1->cmap_loc    = cmap_loc;
    1671: #endif

    1673:     smatis1->destroy     = submat->ops->destroy;
    1674:     submat->ops->destroy = MatDestroySubMatrix_SeqAIJ;
    1675:     submat->factortype   = C->factortype;

    1677:     /* compute rmax */
    1678:     rmax = 0;
    1679:     for (i=0; i<nrow; i++) rmax = PetscMax(rmax,lens[i]);

    1681:   } else { /* scall == MAT_REUSE_MATRIX */
    1682:     submat = submats[0];
    1683:     if (submat->rmap->n != nrow || submat->cmap->n != ncol) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_SIZ,"Cannot reuse matrix. wrong size");

    1685:     subc    = (Mat_SeqAIJ*)submat->data;
    1686:     rmax    = subc->rmax;
    1687:     smatis1 = subc->submatis1;
    1688:     nrqs        = smatis1->nrqs;
    1689:     nrqr        = smatis1->nrqr;
    1690:     rbuf1       = smatis1->rbuf1;
    1691:     rbuf2       = smatis1->rbuf2;
    1692:     rbuf3       = smatis1->rbuf3;
    1693:     req_source2 = smatis1->req_source2;

    1695:     sbuf1     = smatis1->sbuf1;
    1696:     sbuf2     = smatis1->sbuf2;
    1697:     ptr       = smatis1->ptr;
    1698:     tmp       = smatis1->tmp;
    1699:     ctr       = smatis1->ctr;

    1701:     pa         = smatis1->pa;
    1702:     req_size   = smatis1->req_size;
    1703:     req_source1 = smatis1->req_source1;

    1705:     allcolumns = smatis1->allcolumns;
    1706:     row2proc   = smatis1->row2proc;
    1707:     rmap       = smatis1->rmap;
    1708:     cmap       = smatis1->cmap;
    1709: #if defined(PETSC_USE_CTABLE)
    1710:     rmap_loc   = smatis1->rmap_loc;
    1711:     cmap_loc   = smatis1->cmap_loc;
    1712: #endif
    1713:   }

    1715:   /* Post recv matrix values */
    1716:   PetscMalloc3(nrqs+1,&rbuf4, rmax,&subcols, rmax,&subvals);
    1717:   PetscMalloc4(nrqs+1,&r_waits4,nrqr+1,&s_waits4,nrqs+1,&r_status4,nrqr+1,&s_status4);
    1718:   PetscObjectGetNewTag((PetscObject)C,&tag4);
    1719:   for (i=0; i<nrqs; ++i) {
    1720:     PetscMalloc1(rbuf2[i][0]+1,&rbuf4[i]);
    1721:     MPI_Irecv(rbuf4[i],rbuf2[i][0],MPIU_SCALAR,req_source2[i],tag4,comm,r_waits4+i);
    1722:   }

    1724:   /* Allocate sending buffers for a->a, and send them off */
    1725:   PetscMalloc1(nrqr+1,&sbuf_aa);
    1726:   for (i=0,j=0; i<nrqr; i++) j += req_size[i];
    1727:   PetscMalloc1(j+1,&sbuf_aa[0]);
    1728:   for (i=1; i<nrqr; i++) sbuf_aa[i] = sbuf_aa[i-1] + req_size[i-1];

    1730:   for (i=0; i<nrqr; i++) {
    1731:     rbuf1_i   = rbuf1[i];
    1732:     sbuf_aa_i = sbuf_aa[i];
    1733:     ct1       = 2*rbuf1_i[0]+1;
    1734:     ct2       = 0;
    1735:     /* max1=rbuf1_i[0]; if (max1 != 1) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_PLIB,"max1 !=1"); */

    1737:     kmax = rbuf1_i[2];
    1738:     for (k=0; k<kmax; k++,ct1++) {
    1739:       row = rbuf1_i[ct1] - rstart;
    1740:       nzA = ai[row+1] - ai[row];
    1741:       nzB = bi[row+1] - bi[row];
    1742:       ncols  = nzA + nzB;
    1743:       cworkB = bj + bi[row];
    1744:       vworkA = a_a + ai[row];
    1745:       vworkB = b_a + bi[row];

    1747:       /* load the column values for this row into vals*/
    1748:       vals = sbuf_aa_i + ct2;

    1750:       lwrite = 0;
    1751:       for (l=0; l<nzB; l++) {
    1752:         if ((bmap[cworkB[l]]) < cstart) vals[lwrite++] = vworkB[l];
    1753:       }
    1754:       for (l=0; l<nzA; l++) vals[lwrite++] = vworkA[l];
    1755:       for (l=0; l<nzB; l++) {
    1756:         if ((bmap[cworkB[l]]) >= cend) vals[lwrite++] = vworkB[l];
    1757:       }

    1759:       ct2 += ncols;
    1760:     }
    1761:     MPI_Isend(sbuf_aa_i,req_size[i],MPIU_SCALAR,req_source1[i],tag4,comm,s_waits4+i);
    1762:   }

    1764:   /* Assemble submat */
    1765:   /* First assemble the local rows */
    1766:   for (j=0; j<nrow; j++) {
    1767:     row  = irow[j];
    1768:     proc = row2proc[j];
    1769:     if (proc == rank) {
    1770:       Crow = row - rstart;  /* local row index of C */
    1771: #if defined(PETSC_USE_CTABLE)
    1772:       row = rmap_loc[Crow]; /* row index of submat */
    1773: #else
    1774:       row = rmap[row];
    1775: #endif

    1777:       if (allcolumns) {
    1778:         /* diagonal part A = c->A */
    1779:         ncols = ai[Crow+1] - ai[Crow];
    1780:         cols  = aj + ai[Crow];
    1781:         vals  = a->a + ai[Crow];
    1782:         i     = 0;
    1783:         for (k=0; k<ncols; k++) {
    1784:           subcols[i]   = cols[k] + cstart;
    1785:           subvals[i++] = vals[k];
    1786:         }

    1788:         /* off-diagonal part B = c->B */
    1789:         ncols = bi[Crow+1] - bi[Crow];
    1790:         cols  = bj + bi[Crow];
    1791:         vals  = b->a + bi[Crow];
    1792:         for (k=0; k<ncols; k++) {
    1793:           subcols[i]   = bmap[cols[k]];
    1794:           subvals[i++] = vals[k];
    1795:         }

    1797:         MatSetValues_SeqAIJ(submat,1,&row,i,subcols,subvals,INSERT_VALUES);

    1799:       } else { /* !allcolumns */
    1800: #if defined(PETSC_USE_CTABLE)
    1801:         /* diagonal part A = c->A */
    1802:         ncols = ai[Crow+1] - ai[Crow];
    1803:         cols  = aj + ai[Crow];
    1804:         vals  = a->a + ai[Crow];
    1805:         i     = 0;
    1806:         for (k=0; k<ncols; k++) {
    1807:           tcol = cmap_loc[cols[k]];
    1808:           if (tcol) {
    1809:             subcols[i]   = --tcol;
    1810:             subvals[i++] = vals[k];
    1811:           }
    1812:         }

    1814:         /* off-diagonal part B = c->B */
    1815:         ncols = bi[Crow+1] - bi[Crow];
    1816:         cols  = bj + bi[Crow];
    1817:         vals  = b->a + bi[Crow];
    1818:         for (k=0; k<ncols; k++) {
    1819:           PetscTableFind(cmap,bmap[cols[k]]+1,&tcol);
    1820:           if (tcol) {
    1821:             subcols[i]   = --tcol;
    1822:             subvals[i++] = vals[k];
    1823:           }
    1824:         }
    1825: #else
    1826:         /* diagonal part A = c->A */
    1827:         ncols = ai[Crow+1] - ai[Crow];
    1828:         cols  = aj + ai[Crow];
    1829:         vals  = a->a + ai[Crow];
    1830:         i     = 0;
    1831:         for (k=0; k<ncols; k++) {
    1832:           tcol = cmap[cols[k]+cstart];
    1833:           if (tcol) {
    1834:             subcols[i]   = --tcol;
    1835:             subvals[i++] = vals[k];
    1836:           }
    1837:         }

    1839:         /* off-diagonal part B = c->B */
    1840:         ncols = bi[Crow+1] - bi[Crow];
    1841:         cols  = bj + bi[Crow];
    1842:         vals  = b->a + bi[Crow];
    1843:         for (k=0; k<ncols; k++) {
    1844:           tcol = cmap[bmap[cols[k]]];
    1845:           if (tcol) {
    1846:             subcols[i]   = --tcol;
    1847:             subvals[i++] = vals[k];
    1848:           }
    1849:         }
    1850: #endif
    1851:         MatSetValues_SeqAIJ(submat,1,&row,i,subcols,subvals,INSERT_VALUES);
    1852:       }
    1853:     }
    1854:   }

    1856:   /* Now assemble the off-proc rows */
    1857:   for (i=0; i<nrqs; i++) { /* for each requested message */
    1858:     /* recv values from other processes */
    1859:     MPI_Waitany(nrqs,r_waits4,&idex,r_status4+i);
    1860:     proc    = pa[idex];
    1861:     sbuf1_i = sbuf1[proc];
    1862:     /* jmax    = sbuf1_i[0]; if (jmax != 1)SETERRQ1(PETSC_COMM_SELF,0,"jmax %d != 1",jmax); */
    1863:     ct1     = 2 + 1;
    1864:     ct2     = 0; /* count of received C->j */
    1865:     ct3     = 0; /* count of received C->j that will be inserted into submat */
    1866:     rbuf2_i = rbuf2[idex]; /* int** received length of C->j from other processes */
    1867:     rbuf3_i = rbuf3[idex]; /* int** received C->j from other processes */
    1868:     rbuf4_i = rbuf4[idex]; /* scalar** received C->a from other processes */

    1870:     /* is_no = sbuf1_i[2*j-1]; if (is_no != 0) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_PLIB,"is_no !=0"); */
    1871:     max1 = sbuf1_i[2];             /* num of rows */
    1872:     for (k=0; k<max1; k++,ct1++) { /* for each recved row */
    1873:       row = sbuf1_i[ct1]; /* row index of submat */
    1874:       if (!allcolumns) {
    1875:         idex = 0;
    1876:         if (scall == MAT_INITIAL_MATRIX || !iscolsorted) {
    1877:           nnz  = rbuf2_i[ct1]; /* num of C entries in this row */
    1878:           for (l=0; l<nnz; l++,ct2++) { /* for each recved column */
    1879: #if defined(PETSC_USE_CTABLE)
    1880:             if (rbuf3_i[ct2] >= cstart && rbuf3_i[ct2] <cend) {
    1881:               tcol = cmap_loc[rbuf3_i[ct2] - cstart];
    1882:             } else {
    1883:               PetscTableFind(cmap,rbuf3_i[ct2]+1,&tcol);
    1884:             }
    1885: #else
    1886:             tcol = cmap[rbuf3_i[ct2]];
    1887: #endif
    1888:             if (tcol) {
    1889:               subcols[idex]   = --tcol; /* may not be sorted */
    1890:               subvals[idex++] = rbuf4_i[ct2];

    1892:               /* We receive an entire column of C, but a subset of it needs to be inserted into submat.
    1893:                For reuse, we replace received C->j with index that should be inserted to submat */
    1894:               if (iscolsorted) rbuf3_i[ct3++] = ct2;
    1895:             }
    1896:           }
    1897:           MatSetValues_SeqAIJ(submat,1,&row,idex,subcols,subvals,INSERT_VALUES);
    1898:         } else { /* scall == MAT_REUSE_MATRIX */
    1899:           submat = submats[0];
    1900:           subc   = (Mat_SeqAIJ*)submat->data;

    1902:           nnz = subc->i[row+1] - subc->i[row]; /* num of submat entries in this row */
    1903:           for (l=0; l<nnz; l++) {
    1904:             ct2 = rbuf3_i[ct3++]; /* index of rbuf4_i[] which needs to be inserted into submat */
    1905:             subvals[idex++] = rbuf4_i[ct2];
    1906:           }

    1908:           bj = subc->j + subc->i[row]; /* sorted column indices */
    1909:           MatSetValues_SeqAIJ(submat,1,&row,nnz,bj,subvals,INSERT_VALUES);
    1910:         }
    1911:       } else { /* allcolumns */
    1912:         nnz  = rbuf2_i[ct1]; /* num of C entries in this row */
    1913:         MatSetValues_SeqAIJ(submat,1,&row,nnz,rbuf3_i+ct2,rbuf4_i+ct2,INSERT_VALUES);
    1914:         ct2 += nnz;
    1915:       }
    1916:     }
    1917:   }

    1919:   /* sending a->a are done */
    1920:   MPI_Waitall(nrqr,s_waits4,s_status4);
    1921:   PetscFree4(r_waits4,s_waits4,r_status4,s_status4);

    1923:   MatAssemblyBegin(submat,MAT_FINAL_ASSEMBLY);
    1924:   MatAssemblyEnd(submat,MAT_FINAL_ASSEMBLY);
    1925:   submats[0] = submat;

    1927:   /* Restore the indices */
    1928:   ISRestoreIndices(isrow[0],&irow);
    1929:   if (!allcolumns) {
    1930:     ISRestoreIndices(iscol[0],&icol);
    1931:   }

    1933:   /* Destroy allocated memory */
    1934:   for (i=0; i<nrqs; ++i) {
    1935:     PetscFree3(rbuf4[i],subcols,subvals);
    1936:   }
    1937:   PetscFree3(rbuf4,subcols,subvals);
    1938:   PetscFree(sbuf_aa[0]);
    1939:   PetscFree(sbuf_aa);

    1941:   if (scall == MAT_INITIAL_MATRIX) {
    1942:     PetscFree(lens);
    1943:     PetscFree(sbuf_aj[0]);
    1944:     PetscFree(sbuf_aj);
    1945:   }
    1946:   return(0);
    1947: }

    1949: PetscErrorCode MatCreateSubMatrices_MPIAIJ_SingleIS(Mat C,PetscInt ismax,const IS isrow[],const IS iscol[],MatReuse scall,Mat *submat[])
    1950: {
    1952:   PetscInt       ncol;
    1953:   PetscBool      colflag,allcolumns=PETSC_FALSE;

    1956:   /* Allocate memory to hold all the submatrices */
    1957:   if (scall == MAT_INITIAL_MATRIX) {
    1958:     PetscCalloc1(2,submat);
    1959:   }

    1961:   /* Check for special case: each processor gets entire matrix columns */
    1962:   ISIdentity(iscol[0],&colflag);
    1963:   ISGetLocalSize(iscol[0],&ncol);
    1964:   if (colflag && ncol == C->cmap->N) allcolumns = PETSC_TRUE;

    1966:   MatCreateSubMatrices_MPIAIJ_SingleIS_Local(C,ismax,isrow,iscol,scall,allcolumns,*submat);
    1967:   return(0);
    1968: }

    1970: PetscErrorCode MatCreateSubMatrices_MPIAIJ(Mat C,PetscInt ismax,const IS isrow[],const IS iscol[],MatReuse scall,Mat *submat[])
    1971: {
    1973:   PetscInt       nmax,nstages=0,i,pos,max_no,nrow,ncol,in[2],out[2];
    1974:   PetscBool      rowflag,colflag,wantallmatrix=PETSC_FALSE;
    1975:   Mat_SeqAIJ     *subc;
    1976:   Mat_SubSppt    *smat;

    1979:   /* Check for special case: each processor has a single IS */
    1980:   if (C->submat_singleis) { /* flag is set in PCSetUp_ASM() to skip MPIU_Allreduce() */
    1981:     MatCreateSubMatrices_MPIAIJ_SingleIS(C,ismax,isrow,iscol,scall,submat);
    1982:     C->submat_singleis = PETSC_FALSE; /* resume its default value in case C will be used for non-single IS */
    1983:     return(0);
    1984:   }

    1986:   /* Collect global wantallmatrix and nstages */
    1987:   if (!C->cmap->N) nmax=20*1000000/sizeof(PetscInt);
    1988:   else nmax = 20*1000000 / (C->cmap->N * sizeof(PetscInt));
    1989:   if (!nmax) nmax = 1;

    1991:   if (scall == MAT_INITIAL_MATRIX) {
    1992:     /* Collect global wantallmatrix and nstages */
    1993:     if (ismax == 1 && C->rmap->N == C->cmap->N) {
    1994:       ISIdentity(*isrow,&rowflag);
    1995:       ISIdentity(*iscol,&colflag);
    1996:       ISGetLocalSize(*isrow,&nrow);
    1997:       ISGetLocalSize(*iscol,&ncol);
    1998:       if (rowflag && colflag && nrow == C->rmap->N && ncol == C->cmap->N) {
    1999:         wantallmatrix = PETSC_TRUE;

    2001:         PetscOptionsGetBool(((PetscObject)C)->options,((PetscObject)C)->prefix,"-use_fast_submatrix",&wantallmatrix,NULL);
    2002:       }
    2003:     }

    2005:     /* Determine the number of stages through which submatrices are done
    2006:        Each stage will extract nmax submatrices.
    2007:        nmax is determined by the matrix column dimension.
    2008:        If the original matrix has 20M columns, only one submatrix per stage is allowed, etc.
    2009:     */
    2010:     nstages = ismax/nmax + ((ismax % nmax) ? 1 : 0); /* local nstages */

    2012:     in[0] = -1*(PetscInt)wantallmatrix;
    2013:     in[1] = nstages;
    2014:     MPIU_Allreduce(in,out,2,MPIU_INT,MPI_MAX,PetscObjectComm((PetscObject)C));
    2015:     wantallmatrix = (PetscBool)(-out[0]);
    2016:     nstages       = out[1]; /* Make sure every processor loops through the global nstages */

    2018:   } else { /* MAT_REUSE_MATRIX */
    2019:     if (ismax) {
    2020:       subc = (Mat_SeqAIJ*)(*submat)[0]->data;
    2021:       smat = subc->submatis1;
    2022:     } else { /* (*submat)[0] is a dummy matrix */
    2023:       smat = (Mat_SubSppt*)(*submat)[0]->data;
    2024:     }
    2025:     if (!smat) {
    2026:       /* smat is not generated by MatCreateSubMatrix_MPIAIJ_All(...,MAT_INITIAL_MATRIX,...) */
    2027:       wantallmatrix = PETSC_TRUE;
    2028:     } else if (smat->singleis) {
    2029:       MatCreateSubMatrices_MPIAIJ_SingleIS(C,ismax,isrow,iscol,scall,submat);
    2030:       return(0);
    2031:     } else {
    2032:       nstages = smat->nstages;
    2033:     }
    2034:   }

    2036:   if (wantallmatrix) {
    2037:     MatCreateSubMatrix_MPIAIJ_All(C,MAT_GET_VALUES,scall,submat);
    2038:     return(0);
    2039:   }

    2041:   /* Allocate memory to hold all the submatrices and dummy submatrices */
    2042:   if (scall == MAT_INITIAL_MATRIX) {
    2043:     PetscCalloc1(ismax+nstages,submat);
    2044:   }

    2046:   for (i=0,pos=0; i<nstages; i++) {
    2047:     if (pos+nmax <= ismax) max_no = nmax;
    2048:     else if (pos >= ismax) max_no = 0;
    2049:     else                   max_no = ismax-pos;

    2051:     MatCreateSubMatrices_MPIAIJ_Local(C,max_no,isrow+pos,iscol+pos,scall,*submat+pos);
    2052:     if (!max_no && scall == MAT_INITIAL_MATRIX) { /* submat[pos] is a dummy matrix */
    2053:       smat = (Mat_SubSppt*)(*submat)[pos]->data; pos++;
    2054:       smat->nstages = nstages;
    2055:     }
    2056:     pos += max_no;
    2057:   }

    2059:   if (ismax && scall == MAT_INITIAL_MATRIX) {
    2060:     /* save nstages for reuse */
    2061:     subc = (Mat_SeqAIJ*)(*submat)[0]->data;
    2062:     smat = subc->submatis1;
    2063:     smat->nstages = nstages;
    2064:   }
    2065:   return(0);
    2066: }

    2068: /* -------------------------------------------------------------------------*/
    2069: PetscErrorCode MatCreateSubMatrices_MPIAIJ_Local(Mat C,PetscInt ismax,const IS isrow[],const IS iscol[],MatReuse scall,Mat *submats)
    2070: {
    2071:   Mat_MPIAIJ     *c = (Mat_MPIAIJ*)C->data;
    2072:   Mat            A  = c->A;
    2073:   Mat_SeqAIJ     *a = (Mat_SeqAIJ*)A->data,*b = (Mat_SeqAIJ*)c->B->data,*subc;
    2074:   const PetscInt **icol,**irow;
    2075:   PetscInt       *nrow,*ncol,start;
    2077:   PetscMPIInt    rank,size,tag0,tag2,tag3,tag4,*w1,*w2,*w3,*w4,nrqr;
    2078:   PetscInt       **sbuf1,**sbuf2,i,j,k,l,ct1,ct2,**rbuf1,row,proc=-1;
    2079:   PetscInt       nrqs=0,msz,**ptr=NULL,*req_size=NULL,*ctr=NULL,*pa,*tmp=NULL,tcol;
    2080:   PetscInt       **rbuf3=NULL,*req_source1=NULL,*req_source2,**sbuf_aj,**rbuf2=NULL,max1,max2;
    2081:   PetscInt       **lens,is_no,ncols,*cols,mat_i,*mat_j,tmp2,jmax;
    2082: #if defined(PETSC_USE_CTABLE)
    2083:   PetscTable     *cmap,cmap_i=NULL,*rmap,rmap_i;
    2084: #else
    2085:   PetscInt       **cmap,*cmap_i=NULL,**rmap,*rmap_i;
    2086: #endif
    2087:   const PetscInt *irow_i;
    2088:   PetscInt       ctr_j,*sbuf1_j,*sbuf_aj_i,*rbuf1_i,kmax,*lens_i;
    2089:   MPI_Request    *s_waits1,*r_waits1,*s_waits2,*r_waits2,*r_waits3;
    2090:   MPI_Request    *r_waits4,*s_waits3,*s_waits4;
    2091:   MPI_Status     *r_status1,*r_status2,*s_status1,*s_status3,*s_status2;
    2092:   MPI_Status     *r_status3,*r_status4,*s_status4;
    2093:   MPI_Comm       comm;
    2094:   PetscScalar    **rbuf4,*rbuf4_i,**sbuf_aa,*vals,*mat_a,*imat_a,*sbuf_aa_i;
    2095:   PetscMPIInt    *onodes1,*olengths1,end;
    2096:   PetscInt       **row2proc,*row2proc_i,ilen_row,*imat_ilen,*imat_j,*imat_i,old_row;
    2097:   Mat_SubSppt    *smat_i;
    2098:   PetscBool      *issorted,*allcolumns,colflag,iscsorted=PETSC_TRUE;
    2099:   PetscInt       *sbuf1_i,*rbuf2_i,*rbuf3_i,ilen;

    2102:   PetscObjectGetComm((PetscObject)C,&comm);
    2103:   size = c->size;
    2104:   rank = c->rank;

    2106:   PetscMalloc4(ismax,&row2proc,ismax,&cmap,ismax,&rmap,ismax+1,&allcolumns);
    2107:   PetscMalloc5(ismax,(PetscInt***)&irow,ismax,(PetscInt***)&icol,ismax,&nrow,ismax,&ncol,ismax,&issorted);

    2109:   for (i=0; i<ismax; i++) {
    2110:     ISSorted(iscol[i],&issorted[i]);
    2111:     if (!issorted[i]) iscsorted = issorted[i];

    2113:     ISSorted(isrow[i],&issorted[i]);

    2115:     ISGetIndices(isrow[i],&irow[i]);
    2116:     ISGetLocalSize(isrow[i],&nrow[i]);

    2118:     /* Check for special case: allcolumn */
    2119:     ISIdentity(iscol[i],&colflag);
    2120:     ISGetLocalSize(iscol[i],&ncol[i]);
    2121:     if (colflag && ncol[i] == C->cmap->N) {
    2122:       allcolumns[i] = PETSC_TRUE;
    2123:       icol[i] = NULL;
    2124:     } else {
    2125:       allcolumns[i] = PETSC_FALSE;
    2126:       ISGetIndices(iscol[i],&icol[i]);
    2127:     }
    2128:   }

    2130:   if (scall == MAT_REUSE_MATRIX) {
    2131:     /* Assumes new rows are same length as the old rows */
    2132:     for (i=0; i<ismax; i++) {
    2133:       if (!submats[i]) SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_ARG_NULL,"submats[%D] is null, cannot reuse",i);
    2134:       subc = (Mat_SeqAIJ*)submats[i]->data;
    2135:       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");

    2137:       /* Initial matrix as if empty */
    2138:       PetscArrayzero(subc->ilen,submats[i]->rmap->n);

    2140:       smat_i   = subc->submatis1;

    2142:       nrqs        = smat_i->nrqs;
    2143:       nrqr        = smat_i->nrqr;
    2144:       rbuf1       = smat_i->rbuf1;
    2145:       rbuf2       = smat_i->rbuf2;
    2146:       rbuf3       = smat_i->rbuf3;
    2147:       req_source2 = smat_i->req_source2;

    2149:       sbuf1     = smat_i->sbuf1;
    2150:       sbuf2     = smat_i->sbuf2;
    2151:       ptr       = smat_i->ptr;
    2152:       tmp       = smat_i->tmp;
    2153:       ctr       = smat_i->ctr;

    2155:       pa          = smat_i->pa;
    2156:       req_size    = smat_i->req_size;
    2157:       req_source1 = smat_i->req_source1;

    2159:       allcolumns[i] = smat_i->allcolumns;
    2160:       row2proc[i]   = smat_i->row2proc;
    2161:       rmap[i]       = smat_i->rmap;
    2162:       cmap[i]       = smat_i->cmap;
    2163:     }

    2165:     if (!ismax){ /* Get dummy submatrices and retrieve struct submatis1 */
    2166:       if (!submats[0]) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_NULL,"submats are null, cannot reuse");
    2167:       smat_i = (Mat_SubSppt*)submats[0]->data;

    2169:       nrqs        = smat_i->nrqs;
    2170:       nrqr        = smat_i->nrqr;
    2171:       rbuf1       = smat_i->rbuf1;
    2172:       rbuf2       = smat_i->rbuf2;
    2173:       rbuf3       = smat_i->rbuf3;
    2174:       req_source2 = smat_i->req_source2;

    2176:       sbuf1       = smat_i->sbuf1;
    2177:       sbuf2       = smat_i->sbuf2;
    2178:       ptr         = smat_i->ptr;
    2179:       tmp         = smat_i->tmp;
    2180:       ctr         = smat_i->ctr;

    2182:       pa          = smat_i->pa;
    2183:       req_size    = smat_i->req_size;
    2184:       req_source1 = smat_i->req_source1;

    2186:       allcolumns[0] = PETSC_FALSE;
    2187:     }
    2188:   } else { /* scall == MAT_INITIAL_MATRIX */
    2189:     /* Get some new tags to keep the communication clean */
    2190:     PetscObjectGetNewTag((PetscObject)C,&tag2);
    2191:     PetscObjectGetNewTag((PetscObject)C,&tag3);

    2193:     /* evaluate communication - mesg to who, length of mesg, and buffer space
    2194:      required. Based on this, buffers are allocated, and data copied into them*/
    2195:     PetscCalloc4(size,&w1,size,&w2,size,&w3,size,&w4);   /* mesg size, initialize work vectors */

    2197:     for (i=0; i<ismax; i++) {
    2198:       jmax   = nrow[i];
    2199:       irow_i = irow[i];

    2201:       PetscMalloc1(jmax,&row2proc_i);
    2202:       row2proc[i] = row2proc_i;

    2204:       if (issorted[i]) proc = 0;
    2205:       for (j=0; j<jmax; j++) {
    2206:         if (!issorted[i]) proc = 0;
    2207:         row = irow_i[j];
    2208:         while (row >= C->rmap->range[proc+1]) proc++;
    2209:         w4[proc]++;
    2210:         row2proc_i[j] = proc; /* map row index to proc */
    2211:       }
    2212:       for (j=0; j<size; j++) {
    2213:         if (w4[j]) { w1[j] += w4[j];  w3[j]++; w4[j] = 0;}
    2214:       }
    2215:     }

    2217:     nrqs     = 0;              /* no of outgoing messages */
    2218:     msz      = 0;              /* total mesg length (for all procs) */
    2219:     w1[rank] = 0;              /* no mesg sent to self */
    2220:     w3[rank] = 0;
    2221:     for (i=0; i<size; i++) {
    2222:       if (w1[i])  { w2[i] = 1; nrqs++;} /* there exists a message to proc i */
    2223:     }
    2224:     PetscMalloc1(nrqs+1,&pa); /*(proc -array)*/
    2225:     for (i=0,j=0; i<size; i++) {
    2226:       if (w1[i]) { pa[j] = i; j++; }
    2227:     }

    2229:     /* Each message would have a header = 1 + 2*(no of IS) + data */
    2230:     for (i=0; i<nrqs; i++) {
    2231:       j      = pa[i];
    2232:       w1[j] += w2[j] + 2* w3[j];
    2233:       msz   += w1[j];
    2234:     }
    2235:     PetscInfo2(0,"Number of outgoing messages %D Total message length %D\n",nrqs,msz);

    2237:     /* Determine the number of messages to expect, their lengths, from from-ids */
    2238:     PetscGatherNumberOfMessages(comm,w2,w1,&nrqr);
    2239:     PetscGatherMessageLengths(comm,nrqs,nrqr,w1,&onodes1,&olengths1);

    2241:     /* Now post the Irecvs corresponding to these messages */
    2242:     tag0 = ((PetscObject)C)->tag;
    2243:     PetscPostIrecvInt(comm,tag0,nrqr,onodes1,olengths1,&rbuf1,&r_waits1);

    2245:     PetscFree(onodes1);
    2246:     PetscFree(olengths1);

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

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

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

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

    2297:     /*  Now  post the sends */
    2298:     PetscMalloc1(nrqs+1,&s_waits1);
    2299:     for (i=0; i<nrqs; ++i) {
    2300:       j    = pa[i];
    2301:       MPI_Isend(sbuf1[j],w1[j],MPIU_INT,j,tag0,comm,s_waits1+i);
    2302:     }

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

    2316:     /* Send to other procs the buf size they should allocate */
    2317:     /* Receive messages*/
    2318:     PetscMalloc1(nrqr+1,&s_waits2);
    2319:     PetscMalloc1(nrqr+1,&r_status1);
    2320:     PetscMalloc3(nrqr,&sbuf2,nrqr,&req_size,nrqr,&req_source1);
    2321:     {
    2322:       PetscInt   *sAi = a->i,*sBi = b->i,id,rstart = C->rmap->rstart;
    2323:       PetscInt   *sbuf2_i;

    2325:       MPI_Waitall(nrqr,r_waits1,r_status1);
    2326:       for (i=0; i<nrqr; ++i) {
    2327:         req_size[i] = 0;
    2328:         rbuf1_i        = rbuf1[i];
    2329:         start          = 2*rbuf1_i[0] + 1;
    2330:         MPI_Get_count(r_status1+i,MPIU_INT,&end);
    2331:         PetscMalloc1(end+1,&sbuf2[i]);
    2332:         sbuf2_i        = sbuf2[i];
    2333:         for (j=start; j<end; j++) {
    2334:           id              = rbuf1_i[j] - rstart;
    2335:           ncols           = sAi[id+1] - sAi[id] + sBi[id+1] - sBi[id];
    2336:           sbuf2_i[j]      = ncols;
    2337:           req_size[i] += ncols;
    2338:         }
    2339:         req_source1[i] = r_status1[i].MPI_SOURCE;
    2340:         /* form the header */
    2341:         sbuf2_i[0] = req_size[i];
    2342:         for (j=1; j<start; j++) sbuf2_i[j] = rbuf1_i[j];

    2344:         MPI_Isend(sbuf2_i,end,MPIU_INT,req_source1[i],tag2,comm,s_waits2+i);
    2345:       }
    2346:     }
    2347:     PetscFree(r_status1);
    2348:     PetscFree(r_waits1);
    2349:     PetscFree4(w1,w2,w3,w4);

    2351:     /* Receive messages*/
    2352:     PetscMalloc1(nrqs+1,&r_waits3);
    2353:     PetscMalloc1(nrqs+1,&r_status2);

    2355:     MPI_Waitall(nrqs,r_waits2,r_status2);
    2356:     for (i=0; i<nrqs; ++i) {
    2357:       PetscMalloc1(rbuf2[i][0]+1,&rbuf3[i]);
    2358:       req_source2[i] = r_status2[i].MPI_SOURCE;
    2359:       MPI_Irecv(rbuf3[i],rbuf2[i][0],MPIU_INT,req_source2[i],tag3,comm,r_waits3+i);
    2360:     }
    2361:     PetscFree(r_status2);
    2362:     PetscFree(r_waits2);

    2364:     /* Wait on sends1 and sends2 */
    2365:     PetscMalloc1(nrqs+1,&s_status1);
    2366:     PetscMalloc1(nrqr+1,&s_status2);

    2368:     if (nrqs) {MPI_Waitall(nrqs,s_waits1,s_status1);}
    2369:     if (nrqr) {MPI_Waitall(nrqr,s_waits2,s_status2);}
    2370:     PetscFree(s_status1);
    2371:     PetscFree(s_status2);
    2372:     PetscFree(s_waits1);
    2373:     PetscFree(s_waits2);

    2375:     /* Now allocate sending buffers for a->j, and send them off */
    2376:     PetscMalloc1(nrqr+1,&sbuf_aj);
    2377:     for (i=0,j=0; i<nrqr; i++) j += req_size[i];
    2378:     PetscMalloc1(j+1,&sbuf_aj[0]);
    2379:     for (i=1; i<nrqr; i++) sbuf_aj[i] = sbuf_aj[i-1] + req_size[i-1];

    2381:     PetscMalloc1(nrqr+1,&s_waits3);
    2382:     {
    2383:       PetscInt nzA,nzB,*a_i = a->i,*b_i = b->i,lwrite;
    2384:       PetscInt *cworkA,*cworkB,cstart = C->cmap->rstart,rstart = C->rmap->rstart,*bmap = c->garray;
    2385:       PetscInt cend = C->cmap->rend;
    2386:       PetscInt *a_j = a->j,*b_j = b->j,ctmp;

    2388:       for (i=0; i<nrqr; i++) {
    2389:         rbuf1_i   = rbuf1[i];
    2390:         sbuf_aj_i = sbuf_aj[i];
    2391:         ct1       = 2*rbuf1_i[0] + 1;
    2392:         ct2       = 0;
    2393:         for (j=1,max1=rbuf1_i[0]; j<=max1; j++) {
    2394:           kmax = rbuf1[i][2*j];
    2395:           for (k=0; k<kmax; k++,ct1++) {
    2396:             row    = rbuf1_i[ct1] - rstart;
    2397:             nzA    = a_i[row+1] - a_i[row]; nzB = b_i[row+1] - b_i[row];
    2398:             ncols  = nzA + nzB;
    2399:             cworkA = a_j + a_i[row]; cworkB = b_j + b_i[row];

    2401:             /* load the column indices for this row into cols */
    2402:             cols = sbuf_aj_i + ct2;

    2404:             lwrite = 0;
    2405:             for (l=0; l<nzB; l++) {
    2406:               if ((ctmp = bmap[cworkB[l]]) < cstart) cols[lwrite++] = ctmp;
    2407:             }
    2408:             for (l=0; l<nzA; l++) cols[lwrite++] = cstart + cworkA[l];
    2409:             for (l=0; l<nzB; l++) {
    2410:               if ((ctmp = bmap[cworkB[l]]) >= cend) cols[lwrite++] = ctmp;
    2411:             }

    2413:             ct2 += ncols;
    2414:           }
    2415:         }
    2416:         MPI_Isend(sbuf_aj_i,req_size[i],MPIU_INT,req_source1[i],tag3,comm,s_waits3+i);
    2417:       }
    2418:     }
    2419:     PetscMalloc2(nrqs+1,&r_status3,nrqr+1,&s_status3);

    2421:     /* create col map: global col of C -> local col of submatrices */
    2422:     {
    2423:       const PetscInt *icol_i;
    2424: #if defined(PETSC_USE_CTABLE)
    2425:       for (i=0; i<ismax; i++) {
    2426:         if (!allcolumns[i]) {
    2427:           PetscTableCreate(ncol[i]+1,C->cmap->N+1,&cmap[i]);

    2429:           jmax   = ncol[i];
    2430:           icol_i = icol[i];
    2431:           cmap_i = cmap[i];
    2432:           for (j=0; j<jmax; j++) {
    2433:             PetscTableAdd(cmap[i],icol_i[j]+1,j+1,INSERT_VALUES);
    2434:           }
    2435:         } else cmap[i] = NULL;
    2436:       }
    2437: #else
    2438:       for (i=0; i<ismax; i++) {
    2439:         if (!allcolumns[i]) {
    2440:           PetscCalloc1(C->cmap->N,&cmap[i]);
    2441:           jmax   = ncol[i];
    2442:           icol_i = icol[i];
    2443:           cmap_i = cmap[i];
    2444:           for (j=0; j<jmax; j++) {
    2445:             cmap_i[icol_i[j]] = j+1;
    2446:           }
    2447:         } else cmap[i] = NULL;
    2448:       }
    2449: #endif
    2450:     }

    2452:     /* Create lens which is required for MatCreate... */
    2453:     for (i=0,j=0; i<ismax; i++) j += nrow[i];
    2454:     PetscMalloc1(ismax,&lens);

    2456:     if (ismax) {
    2457:       PetscCalloc1(j,&lens[0]);
    2458:     }
    2459:     for (i=1; i<ismax; i++) lens[i] = lens[i-1] + nrow[i-1];

    2461:     /* Update lens from local data */
    2462:     for (i=0; i<ismax; i++) {
    2463:       row2proc_i = row2proc[i];
    2464:       jmax = nrow[i];
    2465:       if (!allcolumns[i]) cmap_i = cmap[i];
    2466:       irow_i = irow[i];
    2467:       lens_i = lens[i];
    2468:       for (j=0; j<jmax; j++) {
    2469:         row = irow_i[j];
    2470:         proc = row2proc_i[j];
    2471:         if (proc == rank) {
    2472:           MatGetRow_MPIAIJ(C,row,&ncols,&cols,0);
    2473:           if (!allcolumns[i]) {
    2474:             for (k=0; k<ncols; k++) {
    2475: #if defined(PETSC_USE_CTABLE)
    2476:               PetscTableFind(cmap_i,cols[k]+1,&tcol);
    2477: #else
    2478:               tcol = cmap_i[cols[k]];
    2479: #endif
    2480:               if (tcol) lens_i[j]++;
    2481:             }
    2482:           } else { /* allcolumns */
    2483:             lens_i[j] = ncols;
    2484:           }
    2485:           MatRestoreRow_MPIAIJ(C,row,&ncols,&cols,0);
    2486:         }
    2487:       }
    2488:     }

    2490:     /* Create row map: global row of C -> local row of submatrices */
    2491: #if defined(PETSC_USE_CTABLE)
    2492:     for (i=0; i<ismax; i++) {
    2493:       PetscTableCreate(nrow[i]+1,C->rmap->N+1,&rmap[i]);
    2494:       irow_i = irow[i];
    2495:       jmax   = nrow[i];
    2496:       for (j=0; j<jmax; j++) {
    2497:       PetscTableAdd(rmap[i],irow_i[j]+1,j+1,INSERT_VALUES);
    2498:       }
    2499:     }
    2500: #else
    2501:     for (i=0; i<ismax; i++) {
    2502:       PetscCalloc1(C->rmap->N,&rmap[i]);
    2503:       rmap_i = rmap[i];
    2504:       irow_i = irow[i];
    2505:       jmax   = nrow[i];
    2506:       for (j=0; j<jmax; j++) {
    2507:         rmap_i[irow_i[j]] = j;
    2508:       }
    2509:     }
    2510: #endif

    2512:     /* Update lens from offproc data */
    2513:     {
    2514:       PetscInt *rbuf2_i,*rbuf3_i,*sbuf1_i;

    2516:       MPI_Waitall(nrqs,r_waits3,r_status3);
    2517:       for (tmp2=0; tmp2<nrqs; tmp2++) {
    2518:         sbuf1_i = sbuf1[pa[tmp2]];
    2519:         jmax    = sbuf1_i[0];
    2520:         ct1     = 2*jmax+1;
    2521:         ct2     = 0;
    2522:         rbuf2_i = rbuf2[tmp2];
    2523:         rbuf3_i = rbuf3[tmp2];
    2524:         for (j=1; j<=jmax; j++) {
    2525:           is_no  = sbuf1_i[2*j-1];
    2526:           max1   = sbuf1_i[2*j];
    2527:           lens_i = lens[is_no];
    2528:           if (!allcolumns[is_no]) cmap_i = cmap[is_no];
    2529:           rmap_i = rmap[is_no];
    2530:           for (k=0; k<max1; k++,ct1++) {
    2531: #if defined(PETSC_USE_CTABLE)
    2532:             PetscTableFind(rmap_i,sbuf1_i[ct1]+1,&row);
    2533:             row--;
    2534:             if (row < 0) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_PLIB,"row not found in table");
    2535: #else
    2536:             row = rmap_i[sbuf1_i[ct1]]; /* the val in the new matrix to be */
    2537: #endif
    2538:             max2 = rbuf2_i[ct1];
    2539:             for (l=0; l<max2; l++,ct2++) {
    2540:               if (!allcolumns[is_no]) {
    2541: #if defined(PETSC_USE_CTABLE)
    2542:                 PetscTableFind(cmap_i,rbuf3_i[ct2]+1,&tcol);
    2543: #else
    2544:                 tcol = cmap_i[rbuf3_i[ct2]];
    2545: #endif
    2546:                 if (tcol) lens_i[row]++;
    2547:               } else { /* allcolumns */
    2548:                 lens_i[row]++; /* lens_i[row] += max2 ? */
    2549:               }
    2550:             }
    2551:           }
    2552:         }
    2553:       }
    2554:     }
    2555:     PetscFree(r_waits3);
    2556:     if (nrqr) {MPI_Waitall(nrqr,s_waits3,s_status3);}
    2557:     PetscFree2(r_status3,s_status3);
    2558:     PetscFree(s_waits3);

    2560:     /* Create the submatrices */
    2561:     for (i=0; i<ismax; i++) {
    2562:       PetscInt    rbs,cbs;

    2564:       ISGetBlockSize(isrow[i],&rbs);
    2565:       ISGetBlockSize(iscol[i],&cbs);

    2567:       MatCreate(PETSC_COMM_SELF,submats+i);
    2568:       MatSetSizes(submats[i],nrow[i],ncol[i],PETSC_DETERMINE,PETSC_DETERMINE);

    2570:       MatSetBlockSizes(submats[i],rbs,cbs);
    2571:       MatSetType(submats[i],((PetscObject)A)->type_name);
    2572:       MatSeqAIJSetPreallocation(submats[i],0,lens[i]);

    2574:       /* create struct Mat_SubSppt and attached it to submat */
    2575:       PetscNew(&smat_i);
    2576:       subc = (Mat_SeqAIJ*)submats[i]->data;
    2577:       subc->submatis1 = smat_i;

    2579:       smat_i->destroy          = submats[i]->ops->destroy;
    2580:       submats[i]->ops->destroy = MatDestroySubMatrix_SeqAIJ;
    2581:       submats[i]->factortype   = C->factortype;

    2583:       smat_i->id          = i;
    2584:       smat_i->nrqs        = nrqs;
    2585:       smat_i->nrqr        = nrqr;
    2586:       smat_i->rbuf1       = rbuf1;
    2587:       smat_i->rbuf2       = rbuf2;
    2588:       smat_i->rbuf3       = rbuf3;
    2589:       smat_i->sbuf2       = sbuf2;
    2590:       smat_i->req_source2 = req_source2;

    2592:       smat_i->sbuf1       = sbuf1;
    2593:       smat_i->ptr         = ptr;
    2594:       smat_i->tmp         = tmp;
    2595:       smat_i->ctr         = ctr;

    2597:       smat_i->pa           = pa;
    2598:       smat_i->req_size     = req_size;
    2599:       smat_i->req_source1  = req_source1;

    2601:       smat_i->allcolumns  = allcolumns[i];
    2602:       smat_i->singleis    = PETSC_FALSE;
    2603:       smat_i->row2proc    = row2proc[i];
    2604:       smat_i->rmap        = rmap[i];
    2605:       smat_i->cmap        = cmap[i];
    2606:     }

    2608:     if (!ismax) { /* Create dummy submats[0] for reuse struct subc */
    2609:       MatCreate(PETSC_COMM_SELF,&submats[0]);
    2610:       MatSetSizes(submats[0],0,0,PETSC_DETERMINE,PETSC_DETERMINE);
    2611:       MatSetType(submats[0],MATDUMMY);

    2613:       /* create struct Mat_SubSppt and attached it to submat */
    2614:       PetscNewLog(submats[0],&smat_i);
    2615:       submats[0]->data = (void*)smat_i;

    2617:       smat_i->destroy          = submats[0]->ops->destroy;
    2618:       submats[0]->ops->destroy = MatDestroySubMatrix_Dummy;
    2619:       submats[0]->factortype   = C->factortype;

    2621:       smat_i->id          = 0;
    2622:       smat_i->nrqs        = nrqs;
    2623:       smat_i->nrqr        = nrqr;
    2624:       smat_i->rbuf1       = rbuf1;
    2625:       smat_i->rbuf2       = rbuf2;
    2626:       smat_i->rbuf3       = rbuf3;
    2627:       smat_i->sbuf2       = sbuf2;
    2628:       smat_i->req_source2 = req_source2;

    2630:       smat_i->sbuf1       = sbuf1;
    2631:       smat_i->ptr         = ptr;
    2632:       smat_i->tmp         = tmp;
    2633:       smat_i->ctr         = ctr;

    2635:       smat_i->pa           = pa;
    2636:       smat_i->req_size     = req_size;
    2637:       smat_i->req_source1  = req_source1;

    2639:       smat_i->allcolumns  = PETSC_FALSE;
    2640:       smat_i->singleis    = PETSC_FALSE;
    2641:       smat_i->row2proc    = NULL;
    2642:       smat_i->rmap        = NULL;
    2643:       smat_i->cmap        = NULL;
    2644:     }

    2646:     if (ismax) {PetscFree(lens[0]);}
    2647:     PetscFree(lens);
    2648:     PetscFree(sbuf_aj[0]);
    2649:     PetscFree(sbuf_aj);

    2651:   } /* endof scall == MAT_INITIAL_MATRIX */

    2653:   /* Post recv matrix values */
    2654:   PetscObjectGetNewTag((PetscObject)C,&tag4);
    2655:   PetscMalloc1(nrqs+1,&rbuf4);
    2656:   PetscMalloc1(nrqs+1,&r_waits4);
    2657:   PetscMalloc1(nrqs+1,&r_status4);
    2658:   PetscMalloc1(nrqr+1,&s_status4);
    2659:   for (i=0; i<nrqs; ++i) {
    2660:     PetscMalloc1(rbuf2[i][0]+1,&rbuf4[i]);
    2661:     MPI_Irecv(rbuf4[i],rbuf2[i][0],MPIU_SCALAR,req_source2[i],tag4,comm,r_waits4+i);
    2662:   }

    2664:   /* Allocate sending buffers for a->a, and send them off */
    2665:   PetscMalloc1(nrqr+1,&sbuf_aa);
    2666:   for (i=0,j=0; i<nrqr; i++) j += req_size[i];
    2667:   PetscMalloc1(j+1,&sbuf_aa[0]);
    2668:   for (i=1; i<nrqr; i++) sbuf_aa[i] = sbuf_aa[i-1] + req_size[i-1];

    2670:   PetscMalloc1(nrqr+1,&s_waits4);
    2671:   {
    2672:     PetscInt    nzA,nzB,*a_i = a->i,*b_i = b->i, *cworkB,lwrite;
    2673:     PetscInt    cstart = C->cmap->rstart,rstart = C->rmap->rstart,*bmap = c->garray;
    2674:     PetscInt    cend   = C->cmap->rend;
    2675:     PetscInt    *b_j   = b->j;
    2676:     PetscScalar *vworkA,*vworkB,*a_a = a->a,*b_a = b->a;

    2678:     for (i=0; i<nrqr; i++) {
    2679:       rbuf1_i   = rbuf1[i];
    2680:       sbuf_aa_i = sbuf_aa[i];
    2681:       ct1       = 2*rbuf1_i[0]+1;
    2682:       ct2       = 0;
    2683:       for (j=1,max1=rbuf1_i[0]; j<=max1; j++) {
    2684:         kmax = rbuf1_i[2*j];
    2685:         for (k=0; k<kmax; k++,ct1++) {
    2686:           row    = rbuf1_i[ct1] - rstart;
    2687:           nzA    = a_i[row+1] - a_i[row];     nzB = b_i[row+1] - b_i[row];
    2688:           ncols  = nzA + nzB;
    2689:           cworkB = b_j + b_i[row];
    2690:           vworkA = a_a + a_i[row];
    2691:           vworkB = b_a + b_i[row];

    2693:           /* load the column values for this row into vals*/
    2694:           vals = sbuf_aa_i+ct2;

    2696:           lwrite = 0;
    2697:           for (l=0; l<nzB; l++) {
    2698:             if ((bmap[cworkB[l]]) < cstart) vals[lwrite++] = vworkB[l];
    2699:           }
    2700:           for (l=0; l<nzA; l++) vals[lwrite++] = vworkA[l];
    2701:           for (l=0; l<nzB; l++) {
    2702:             if ((bmap[cworkB[l]]) >= cend) vals[lwrite++] = vworkB[l];
    2703:           }

    2705:           ct2 += ncols;
    2706:         }
    2707:       }
    2708:       MPI_Isend(sbuf_aa_i,req_size[i],MPIU_SCALAR,req_source1[i],tag4,comm,s_waits4+i);
    2709:     }
    2710:   }

    2712:   /* Assemble the matrices */
    2713:   /* First assemble the local rows */
    2714:   for (i=0; i<ismax; i++) {
    2715:     row2proc_i = row2proc[i];
    2716:     subc      = (Mat_SeqAIJ*)submats[i]->data;
    2717:     imat_ilen = subc->ilen;
    2718:     imat_j    = subc->j;
    2719:     imat_i    = subc->i;
    2720:     imat_a    = subc->a;

    2722:     if (!allcolumns[i]) cmap_i = cmap[i];
    2723:     rmap_i = rmap[i];
    2724:     irow_i = irow[i];
    2725:     jmax   = nrow[i];
    2726:     for (j=0; j<jmax; j++) {
    2727:       row  = irow_i[j];
    2728:       proc = row2proc_i[j];
    2729:       if (proc == rank) {
    2730:         old_row = row;
    2731: #if defined(PETSC_USE_CTABLE)
    2732:         PetscTableFind(rmap_i,row+1,&row);
    2733:         row--;
    2734: #else
    2735:         row = rmap_i[row];
    2736: #endif
    2737:         ilen_row = imat_ilen[row];
    2738:         MatGetRow_MPIAIJ(C,old_row,&ncols,&cols,&vals);
    2739:         mat_i    = imat_i[row];
    2740:         mat_a    = imat_a + mat_i;
    2741:         mat_j    = imat_j + mat_i;
    2742:         if (!allcolumns[i]) {
    2743:           for (k=0; k<ncols; k++) {
    2744: #if defined(PETSC_USE_CTABLE)
    2745:             PetscTableFind(cmap_i,cols[k]+1,&tcol);
    2746: #else
    2747:             tcol = cmap_i[cols[k]];
    2748: #endif
    2749:             if (tcol) {
    2750:               *mat_j++ = tcol - 1;
    2751:               *mat_a++ = vals[k];
    2752:               ilen_row++;
    2753:             }
    2754:           }
    2755:         } else { /* allcolumns */
    2756:           for (k=0; k<ncols; k++) {
    2757:             *mat_j++ = cols[k];  /* global col index! */
    2758:             *mat_a++ = vals[k];
    2759:             ilen_row++;
    2760:           }
    2761:         }
    2762:         MatRestoreRow_MPIAIJ(C,old_row,&ncols,&cols,&vals);

    2764:         imat_ilen[row] = ilen_row;
    2765:       }
    2766:     }
    2767:   }

    2769:   /* Now assemble the off proc rows */
    2770:   MPI_Waitall(nrqs,r_waits4,r_status4);
    2771:   for (tmp2=0; tmp2<nrqs; tmp2++) {
    2772:     sbuf1_i = sbuf1[pa[tmp2]];
    2773:     jmax    = sbuf1_i[0];
    2774:     ct1     = 2*jmax + 1;
    2775:     ct2     = 0;
    2776:     rbuf2_i = rbuf2[tmp2];
    2777:     rbuf3_i = rbuf3[tmp2];
    2778:     rbuf4_i = rbuf4[tmp2];
    2779:     for (j=1; j<=jmax; j++) {
    2780:       is_no     = sbuf1_i[2*j-1];
    2781:       rmap_i    = rmap[is_no];
    2782:       if (!allcolumns[is_no]) cmap_i = cmap[is_no];
    2783:       subc      = (Mat_SeqAIJ*)submats[is_no]->data;
    2784:       imat_ilen = subc->ilen;
    2785:       imat_j    = subc->j;
    2786:       imat_i    = subc->i;
    2787:       imat_a    = subc->a;
    2788:       max1      = sbuf1_i[2*j];
    2789:       for (k=0; k<max1; k++,ct1++) {
    2790:         row = sbuf1_i[ct1];
    2791: #if defined(PETSC_USE_CTABLE)
    2792:         PetscTableFind(rmap_i,row+1,&row);
    2793:         row--;
    2794: #else
    2795:         row = rmap_i[row];
    2796: #endif
    2797:         ilen  = imat_ilen[row];
    2798:         mat_i = imat_i[row];
    2799:         mat_a = imat_a + mat_i;
    2800:         mat_j = imat_j + mat_i;
    2801:         max2  = rbuf2_i[ct1];
    2802:         if (!allcolumns[is_no]) {
    2803:           for (l=0; l<max2; l++,ct2++) {
    2804: #if defined(PETSC_USE_CTABLE)
    2805:             PetscTableFind(cmap_i,rbuf3_i[ct2]+1,&tcol);
    2806: #else
    2807:             tcol = cmap_i[rbuf3_i[ct2]];
    2808: #endif
    2809:             if (tcol) {
    2810:               *mat_j++ = tcol - 1;
    2811:               *mat_a++ = rbuf4_i[ct2];
    2812:               ilen++;
    2813:             }
    2814:           }
    2815:         } else { /* allcolumns */
    2816:           for (l=0; l<max2; l++,ct2++) {
    2817:             *mat_j++ = rbuf3_i[ct2]; /* same global column index of C */
    2818:             *mat_a++ = rbuf4_i[ct2];
    2819:             ilen++;
    2820:           }
    2821:         }
    2822:         imat_ilen[row] = ilen;
    2823:       }
    2824:     }
    2825:   }

    2827:   if (!iscsorted) { /* sort column indices of the rows */
    2828:     for (i=0; i<ismax; i++) {
    2829:       subc      = (Mat_SeqAIJ*)submats[i]->data;
    2830:       imat_j    = subc->j;
    2831:       imat_i    = subc->i;
    2832:       imat_a    = subc->a;
    2833:       imat_ilen = subc->ilen;

    2835:       if (allcolumns[i]) continue;
    2836:       jmax = nrow[i];
    2837:       for (j=0; j<jmax; j++) {
    2838:         mat_i = imat_i[j];
    2839:         mat_a = imat_a + mat_i;
    2840:         mat_j = imat_j + mat_i;
    2841:         PetscSortIntWithScalarArray(imat_ilen[j],mat_j,mat_a);
    2842:       }
    2843:     }
    2844:   }

    2846:   PetscFree(r_status4);
    2847:   PetscFree(r_waits4);
    2848:   if (nrqr) {MPI_Waitall(nrqr,s_waits4,s_status4);}
    2849:   PetscFree(s_waits4);
    2850:   PetscFree(s_status4);

    2852:   /* Restore the indices */
    2853:   for (i=0; i<ismax; i++) {
    2854:     ISRestoreIndices(isrow[i],irow+i);
    2855:     if (!allcolumns[i]) {
    2856:       ISRestoreIndices(iscol[i],icol+i);
    2857:     }
    2858:   }

    2860:   for (i=0; i<ismax; i++) {
    2861:     MatAssemblyBegin(submats[i],MAT_FINAL_ASSEMBLY);
    2862:     MatAssemblyEnd(submats[i],MAT_FINAL_ASSEMBLY);
    2863:   }

    2865:   /* Destroy allocated memory */
    2866:   PetscFree(sbuf_aa[0]);
    2867:   PetscFree(sbuf_aa);
    2868:   PetscFree5(*(PetscInt***)&irow,*(PetscInt***)&icol,nrow,ncol,issorted);

    2870:   for (i=0; i<nrqs; ++i) {
    2871:     PetscFree(rbuf4[i]);
    2872:   }
    2873:   PetscFree(rbuf4);

    2875:   PetscFree4(row2proc,cmap,rmap,allcolumns);
    2876:   return(0);
    2877: }

    2879: /*
    2880:  Permute A & B into C's *local* index space using rowemb,dcolemb for A and rowemb,ocolemb for B.
    2881:  Embeddings are supposed to be injections and the above implies that the range of rowemb is a subset
    2882:  of [0,m), dcolemb is in [0,n) and ocolemb is in [N-n).
    2883:  If pattern == DIFFERENT_NONZERO_PATTERN, C is preallocated according to A&B.
    2884:  After that B's columns are mapped into C's global column space, so that C is in the "disassembled"
    2885:  state, and needs to be "assembled" later by compressing B's column space.

    2887:  This function may be called in lieu of preallocation, so C should not be expected to be preallocated.
    2888:  Following this call, C->A & C->B have been created, even if empty.
    2889:  */
    2890: PetscErrorCode MatSetSeqMats_MPIAIJ(Mat C,IS rowemb,IS dcolemb,IS ocolemb,MatStructure pattern,Mat A,Mat B)
    2891: {
    2892:   /* If making this function public, change the error returned in this function away from _PLIB. */
    2894:   Mat_MPIAIJ     *aij;
    2895:   Mat_SeqAIJ     *Baij;
    2896:   PetscBool      seqaij,Bdisassembled;
    2897:   PetscInt       m,n,*nz,i,j,ngcol,col,rstart,rend,shift,count;
    2898:   PetscScalar    v;
    2899:   const PetscInt *rowindices,*colindices;

    2902:   /* Check to make sure the component matrices (and embeddings) are compatible with C. */
    2903:   if (A) {
    2904:     PetscObjectBaseTypeCompare((PetscObject)A,MATSEQAIJ,&seqaij);
    2905:     if (!seqaij) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_PLIB,"Diagonal matrix is of wrong type");
    2906:     if (rowemb) {
    2907:       ISGetLocalSize(rowemb,&m);
    2908:       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);
    2909:     } else {
    2910:       if (C->rmap->n != A->rmap->n) {
    2911:         SETERRQ(PETSC_COMM_SELF,PETSC_ERR_PLIB,"Diag seq matrix is row-incompatible with the MPIAIJ matrix");
    2912:       }
    2913:     }
    2914:     if (dcolemb) {
    2915:       ISGetLocalSize(dcolemb,&n);
    2916:       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);
    2917:     } else {
    2918:       if (C->cmap->n != A->cmap->n) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_PLIB,"Diag seq matrix is col-incompatible with the MPIAIJ matrix");
    2919:     }
    2920:   }
    2921:   if (B) {
    2922:     PetscObjectBaseTypeCompare((PetscObject)B,MATSEQAIJ,&seqaij);
    2923:     if (!seqaij) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_PLIB,"Off-diagonal matrix is of wrong type");
    2924:     if (rowemb) {
    2925:       ISGetLocalSize(rowemb,&m);
    2926:       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);
    2927:     } else {
    2928:       if (C->rmap->n != B->rmap->n) {
    2929:         SETERRQ(PETSC_COMM_SELF,PETSC_ERR_PLIB,"Off-diag seq matrix is row-incompatible with the MPIAIJ matrix");
    2930:       }
    2931:     }
    2932:     if (ocolemb) {
    2933:       ISGetLocalSize(ocolemb,&n);
    2934:       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);
    2935:     } else {
    2936:       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");
    2937:     }
    2938:   }

    2940:   aij = (Mat_MPIAIJ*)C->data;
    2941:   if (!aij->A) {
    2942:     /* Mimic parts of MatMPIAIJSetPreallocation() */
    2943:     MatCreate(PETSC_COMM_SELF,&aij->A);
    2944:     MatSetSizes(aij->A,C->rmap->n,C->cmap->n,C->rmap->n,C->cmap->n);
    2945:     MatSetBlockSizesFromMats(aij->A,C,C);
    2946:     MatSetType(aij->A,MATSEQAIJ);
    2947:     PetscLogObjectParent((PetscObject)C,(PetscObject)aij->A);
    2948:   }
    2949:   if (A) {
    2950:     MatSetSeqMat_SeqAIJ(aij->A,rowemb,dcolemb,pattern,A);
    2951:   } else {
    2952:     MatSetUp(aij->A);
    2953:   }
    2954:   if (B) { /* Destroy the old matrix or the column map, depending on the sparsity pattern. */
    2955:     /*
    2956:       If pattern == DIFFERENT_NONZERO_PATTERN, we reallocate B and
    2957:       need to "disassemble" B -- convert it to using C's global indices.
    2958:       To insert the values we take the safer, albeit more expensive, route of MatSetValues().

    2960:       If pattern == SUBSET_NONZERO_PATTERN, we do not "disassemble" B and do not reallocate;
    2961:       we MatZeroValues(B) first, so there may be a bunch of zeros that, perhaps, could be compacted out.

    2963:       TODO: Put B's values into aij->B's aij structure in place using the embedding ISs?
    2964:       At least avoid calling MatSetValues() and the implied searches?
    2965:     */

    2967:     if (B && pattern == DIFFERENT_NONZERO_PATTERN) {
    2968: #if defined(PETSC_USE_CTABLE)
    2969:       PetscTableDestroy(&aij->colmap);
    2970: #else
    2971:       PetscFree(aij->colmap);
    2972:       /* A bit of a HACK: ideally we should deal with case aij->B all in one code block below. */
    2973:       if (aij->B) {
    2974:         PetscLogObjectMemory((PetscObject)C,-aij->B->cmap->n*sizeof(PetscInt));
    2975:       }
    2976: #endif
    2977:       ngcol = 0;
    2978:       if (aij->lvec) {
    2979:         VecGetSize(aij->lvec,&ngcol);
    2980:       }
    2981:       if (aij->garray) {
    2982:         PetscFree(aij->garray);
    2983:         PetscLogObjectMemory((PetscObject)C,-ngcol*sizeof(PetscInt));
    2984:       }
    2985:       VecDestroy(&aij->lvec);
    2986:       VecScatterDestroy(&aij->Mvctx);
    2987:     }
    2988:     if (aij->B && B && pattern == DIFFERENT_NONZERO_PATTERN) {
    2989:       MatDestroy(&aij->B);
    2990:     }
    2991:     if (aij->B && B && pattern == SUBSET_NONZERO_PATTERN) {
    2992:       MatZeroEntries(aij->B);
    2993:     }
    2994:   }
    2995:   Bdisassembled = PETSC_FALSE;
    2996:   if (!aij->B) {
    2997:     MatCreate(PETSC_COMM_SELF,&aij->B);
    2998:     PetscLogObjectParent((PetscObject)C,(PetscObject)aij->B);
    2999:     MatSetSizes(aij->B,C->rmap->n,C->cmap->N,C->rmap->n,C->cmap->N);
    3000:     MatSetBlockSizesFromMats(aij->B,B,B);
    3001:     MatSetType(aij->B,MATSEQAIJ);
    3002:     Bdisassembled = PETSC_TRUE;
    3003:   }
    3004:   if (B) {
    3005:     Baij = (Mat_SeqAIJ*)B->data;
    3006:     if (pattern == DIFFERENT_NONZERO_PATTERN) {
    3007:       PetscMalloc1(B->rmap->n,&nz);
    3008:       for (i=0; i<B->rmap->n; i++) {
    3009:         nz[i] = Baij->i[i+1] - Baij->i[i];
    3010:       }
    3011:       MatSeqAIJSetPreallocation(aij->B,0,nz);
    3012:       PetscFree(nz);
    3013:     }

    3015:     PetscLayoutGetRange(C->rmap,&rstart,&rend);
    3016:     shift = rend-rstart;
    3017:     count = 0;
    3018:     rowindices = NULL;
    3019:     colindices = NULL;
    3020:     if (rowemb) {
    3021:       ISGetIndices(rowemb,&rowindices);
    3022:     }
    3023:     if (ocolemb) {
    3024:       ISGetIndices(ocolemb,&colindices);
    3025:     }
    3026:     for (i=0; i<B->rmap->n; i++) {
    3027:       PetscInt row;
    3028:       row = i;
    3029:       if (rowindices) row = rowindices[i];
    3030:       for (j=Baij->i[i]; j<Baij->i[i+1]; j++) {
    3031:         col  = Baij->j[count];
    3032:         if (colindices) col = colindices[col];
    3033:         if (Bdisassembled && col>=rstart) col += shift;
    3034:         v    = Baij->a[count];
    3035:         MatSetValues(aij->B,1,&row,1,&col,&v,INSERT_VALUES);
    3036:         ++count;
    3037:       }
    3038:     }
    3039:     /* No assembly for aij->B is necessary. */
    3040:     /* FIXME: set aij->B's nonzerostate correctly. */
    3041:   } else {
    3042:     MatSetUp(aij->B);
    3043:   }
    3044:   C->preallocated  = PETSC_TRUE;
    3045:   C->was_assembled = PETSC_FALSE;
    3046:   C->assembled     = PETSC_FALSE;
    3047:    /*
    3048:       C will need to be assembled so that aij->B can be compressed into local form in MatSetUpMultiply_MPIAIJ().
    3049:       Furthermore, its nonzerostate will need to be based on that of aij->A's and aij->B's.
    3050:    */
    3051:   return(0);
    3052: }

    3054: /*
    3055:   B uses local indices with column indices ranging between 0 and N-n; they  must be interpreted using garray.
    3056:  */
    3057: PetscErrorCode MatGetSeqMats_MPIAIJ(Mat C,Mat *A,Mat *B)
    3058: {
    3059:   Mat_MPIAIJ *aij = (Mat_MPIAIJ*)C->data;

    3064:   /* FIXME: make sure C is assembled */
    3065:   *A = aij->A;
    3066:   *B = aij->B;
    3067:   /* Note that we don't incref *A and *B, so be careful! */
    3068:   return(0);
    3069: }

    3071: /*
    3072:   Extract MPI submatrices encoded by pairs of IS that may live on subcomms of C.
    3073:   NOT SCALABLE due to the use of ISGetNonlocalIS() (see below).
    3074: */
    3075: PetscErrorCode MatCreateSubMatricesMPI_MPIXAIJ(Mat C,PetscInt ismax,const IS isrow[],const IS iscol[],MatReuse scall,Mat *submat[],
    3076:                                                  PetscErrorCode(*getsubmats_seq)(Mat,PetscInt,const IS[],const IS[],MatReuse,Mat**),
    3077:                                                  PetscErrorCode(*getlocalmats)(Mat,Mat*,Mat*),
    3078:                                                  PetscErrorCode(*setseqmat)(Mat,IS,IS,MatStructure,Mat),
    3079:                                                  PetscErrorCode(*setseqmats)(Mat,IS,IS,IS,MatStructure,Mat,Mat))
    3080: {
    3082:   PetscMPIInt    isize,flag;
    3083:   PetscInt       i,ii,cismax,ispar;
    3084:   Mat            *A,*B;
    3085:   IS             *isrow_p,*iscol_p,*cisrow,*ciscol,*ciscol_p;

    3088:   if (!ismax) return(0);

    3090:   for (i = 0, cismax = 0; i < ismax; ++i) {
    3091:     PetscMPIInt isize;
    3092:     MPI_Comm_compare(((PetscObject)isrow[i])->comm,((PetscObject)iscol[i])->comm,&flag);
    3093:     if (flag != MPI_IDENT) SETERRQ(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Row and column index sets must have the same communicator");
    3094:     MPI_Comm_size(((PetscObject)isrow[i])->comm, &isize);
    3095:     if (isize > 1) ++cismax;
    3096:   }

    3098:   /*
    3099:      If cismax is zero on all C's ranks, then and only then can we use purely sequential matrix extraction.
    3100:      ispar counts the number of parallel ISs across C's comm.
    3101:   */
    3102:   MPIU_Allreduce(&cismax,&ispar,1,MPIU_INT,MPI_MAX,PetscObjectComm((PetscObject)C));
    3103:   if (!ispar) { /* Sequential ISs only across C's comm, so can call the sequential matrix extraction subroutine. */
    3104:     (*getsubmats_seq)(C,ismax,isrow,iscol,scall,submat);
    3105:     return(0);
    3106:   }

    3108:   /* if (ispar) */
    3109:   /*
    3110:     Construct the "complements" -- the off-processor indices -- of the iscol ISs for parallel ISs only.
    3111:     These are used to extract the off-diag portion of the resulting parallel matrix.
    3112:     The row IS for the off-diag portion is the same as for the diag portion,
    3113:     so we merely alias (without increfing) the row IS, while skipping those that are sequential.
    3114:   */
    3115:   PetscMalloc2(cismax,&cisrow,cismax,&ciscol);
    3116:   PetscMalloc1(cismax,&ciscol_p);
    3117:   for (i = 0, ii = 0; i < ismax; ++i) {
    3118:     MPI_Comm_size(((PetscObject)isrow[i])->comm,&isize);
    3119:     if (isize > 1) {
    3120:       /*
    3121:          TODO: This is the part that's ***NOT SCALABLE***.
    3122:          To fix this we need to extract just the indices of C's nonzero columns
    3123:          that lie on the intersection of isrow[i] and ciscol[ii] -- the nonlocal
    3124:          part of iscol[i] -- without actually computing ciscol[ii]. This also has
    3125:          to be done without serializing on the IS list, so, most likely, it is best
    3126:          done by rewriting MatCreateSubMatrices_MPIAIJ() directly.
    3127:       */
    3128:       ISGetNonlocalIS(iscol[i],&(ciscol[ii]));
    3129:       /* Now we have to
    3130:          (a) make sure ciscol[ii] is sorted, since, even if the off-proc indices
    3131:              were sorted on each rank, concatenated they might no longer be sorted;
    3132:          (b) Use ISSortPermutation() to construct ciscol_p, the mapping from the
    3133:              indices in the nondecreasing order to the original index positions.
    3134:          If ciscol[ii] is strictly increasing, the permutation IS is NULL.
    3135:       */
    3136:       ISSortPermutation(ciscol[ii],PETSC_FALSE,ciscol_p+ii);
    3137:       ISSort(ciscol[ii]);
    3138:       ++ii;
    3139:     }
    3140:   }
    3141:   PetscMalloc2(ismax,&isrow_p,ismax,&iscol_p);
    3142:   for (i = 0, ii = 0; i < ismax; ++i) {
    3143:     PetscInt       j,issize;
    3144:     const PetscInt *indices;

    3146:     /*
    3147:        Permute the indices into a nondecreasing order. Reject row and col indices with duplicates.
    3148:      */
    3149:     ISSortPermutation(isrow[i],PETSC_FALSE,isrow_p+i);
    3150:     ISSort(isrow[i]);
    3151:     ISGetLocalSize(isrow[i],&issize);
    3152:     ISGetIndices(isrow[i],&indices);
    3153:     for (j = 1; j < issize; ++j) {
    3154:       if (indices[j] == indices[j-1]) {
    3155:         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]);
    3156:       }
    3157:     }
    3158:     ISRestoreIndices(isrow[i],&indices);

    3161:     ISSortPermutation(iscol[i],PETSC_FALSE,iscol_p+i);
    3162:     ISSort(iscol[i]);
    3163:     ISGetLocalSize(iscol[i],&issize);
    3164:     ISGetIndices(iscol[i],&indices);
    3165:     for (j = 1; j < issize; ++j) {
    3166:       if (indices[j-1] == indices[j]) {
    3167:         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]);
    3168:       }
    3169:     }
    3170:     ISRestoreIndices(iscol[i],&indices);
    3171:     MPI_Comm_size(((PetscObject)isrow[i])->comm,&isize);
    3172:     if (isize > 1) {
    3173:       cisrow[ii] = isrow[i];
    3174:       ++ii;
    3175:     }
    3176:   }
    3177:   /*
    3178:     Allocate the necessary arrays to hold the resulting parallel matrices as well as the intermediate
    3179:     array of sequential matrices underlying the resulting parallel matrices.
    3180:     Which arrays to allocate is based on the value of MatReuse scall and whether ISs are sorted and/or
    3181:     contain duplicates.

    3183:     There are as many diag matrices as there are original index sets. There are only as many parallel
    3184:     and off-diag matrices, as there are parallel (comm size > 1) index sets.

    3186:     ARRAYS that can hold Seq matrices get allocated in any event -- either here or by getsubmats_seq():
    3187:     - If the array of MPI matrices already exists and is being reused, we need to allocate the array
    3188:       and extract the underlying seq matrices into it to serve as placeholders, into which getsubmats_seq
    3189:       will deposite the extracted diag and off-diag parts. Thus, we allocate the A&B arrays and fill them
    3190:       with A[i] and B[ii] extracted from the corresponding MPI submat.
    3191:     - However, if the rows, A's column indices or B's column indices are not sorted, the extracted A[i] & B[ii]
    3192:       will have a different order from what getsubmats_seq expects.  To handle this case -- indicated
    3193:       by a nonzero isrow_p[i], iscol_p[i], or ciscol_p[ii] -- we duplicate A[i] --> AA[i], B[ii] --> BB[ii]
    3194:       (retrieve composed AA[i] or BB[ii]) and reuse them here. AA[i] and BB[ii] are then used to permute its
    3195:       values into A[i] and B[ii] sitting inside the corresponding submat.
    3196:     - If no reuse is taking place then getsubmats_seq will allocate the A&B arrays and create the corresponding
    3197:       A[i], B[ii], AA[i] or BB[ii] matrices.
    3198:   */
    3199:   /* Parallel matrix array is allocated here only if no reuse is taking place. If reused, it is passed in by the caller. */
    3200:   if (scall == MAT_INITIAL_MATRIX) {
    3201:     PetscMalloc1(ismax,submat);
    3202:   }

    3204:   /* Now obtain the sequential A and B submatrices separately. */
    3205:   /* scall=MAT_REUSE_MATRIX is not handled yet, because getsubmats_seq() requires reuse of A and B */
    3206:   (*getsubmats_seq)(C,ismax,isrow,iscol,MAT_INITIAL_MATRIX,&A);
    3207:   (*getsubmats_seq)(C,cismax,cisrow,ciscol,MAT_INITIAL_MATRIX,&B);

    3209:   /*
    3210:     If scall == MAT_REUSE_MATRIX AND the permutations are NULL, we are done, since the sequential
    3211:     matrices A & B have been extracted directly into the parallel matrices containing them, or
    3212:     simply into the sequential matrix identical with the corresponding A (if isize == 1).
    3213:     Note that in that case colmap doesn't need to be rebuilt, since the matrices are expected
    3214:     to have the same sparsity pattern.
    3215:     Otherwise, A and/or B have to be properly embedded into C's index spaces and the correct colmap
    3216:     must be constructed for C. This is done by setseqmat(s).
    3217:   */
    3218:   for (i = 0, ii = 0; i < ismax; ++i) {
    3219:     /*
    3220:        TODO: cache ciscol, permutation ISs and maybe cisrow? What about isrow & iscol?
    3221:        That way we can avoid sorting and computing permutations when reusing.
    3222:        To this end:
    3223:         - remove the old cache, if it exists, when extracting submatrices with MAT_INITIAL_MATRIX
    3224:         - if caching arrays to hold the ISs, make and compose a container for them so that it can
    3225:           be destroyed upon destruction of C (use PetscContainerUserDestroy() to clear out the contents).
    3226:     */
    3227:     MatStructure pattern;
    3228:     pattern = DIFFERENT_NONZERO_PATTERN;

    3230:     MPI_Comm_size(((PetscObject)isrow[i])->comm,&isize);
    3231:     /* Construct submat[i] from the Seq pieces A (and B, if necessary). */
    3232:     if (isize > 1) {
    3233:       if (scall == MAT_INITIAL_MATRIX) {
    3234:         MatCreate(((PetscObject)isrow[i])->comm,(*submat)+i);
    3235:         MatSetSizes((*submat)[i],A[i]->rmap->n,A[i]->cmap->n,PETSC_DETERMINE,PETSC_DETERMINE);
    3236:         MatSetType((*submat)[i],MATMPIAIJ);
    3237:         PetscLayoutSetUp((*submat)[i]->rmap);
    3238:         PetscLayoutSetUp((*submat)[i]->cmap);
    3239:       }
    3240:       /*
    3241:         For each parallel isrow[i], insert the extracted sequential matrices into the parallel matrix.
    3242:       */
    3243:       {
    3244:         Mat AA,BB;
    3245:         AA = A[i];
    3246:         BB = B[ii];
    3247:         if (AA || BB) {
    3248:           setseqmats((*submat)[i],isrow_p[i],iscol_p[i],ciscol_p[ii],pattern,AA,BB);
    3249:           MatAssemblyBegin((*submat)[i],MAT_FINAL_ASSEMBLY);
    3250:           MatAssemblyEnd((*submat)[i],MAT_FINAL_ASSEMBLY);
    3251:         }

    3253:         MatDestroy(&AA);
    3254:       }
    3255:       ISDestroy(ciscol+ii);
    3256:       ISDestroy(ciscol_p+ii);
    3257:       ++ii;
    3258:     } else { /* if (isize == 1) */
    3259:       if (scall == MAT_REUSE_MATRIX) {
    3260:         MatDestroy(&(*submat)[i]);
    3261:       }
    3262:       if (isrow_p[i] || iscol_p[i]) {
    3263:         MatDuplicate(A[i],MAT_DO_NOT_COPY_VALUES,(*submat)+i);
    3264:         setseqmat((*submat)[i],isrow_p[i],iscol_p[i],pattern,A[i]);
    3265:         /* Otherwise A is extracted straight into (*submats)[i]. */
    3266:         /* TODO: Compose A[i] on (*submat([i] for future use, if ((isrow_p[i] || iscol_p[i]) && MAT_INITIAL_MATRIX). */
    3267:         MatDestroy(A+i);
    3268:       } else (*submat)[i] = A[i];
    3269:     }
    3270:     ISDestroy(&isrow_p[i]);
    3271:     ISDestroy(&iscol_p[i]);
    3272:   }
    3273:   PetscFree2(cisrow,ciscol);
    3274:   PetscFree2(isrow_p,iscol_p);
    3275:   PetscFree(ciscol_p);
    3276:   PetscFree(A);
    3277:   MatDestroySubMatrices(cismax,&B);
    3278:   return(0);
    3279: }

    3281: PetscErrorCode MatCreateSubMatricesMPI_MPIAIJ(Mat C,PetscInt ismax,const IS isrow[],const IS iscol[],MatReuse scall,Mat *submat[])
    3282: {

    3286:   MatCreateSubMatricesMPI_MPIXAIJ(C,ismax,isrow,iscol,scall,submat,MatCreateSubMatrices_MPIAIJ,MatGetSeqMats_MPIAIJ,MatSetSeqMat_SeqAIJ,MatSetSeqMats_MPIAIJ);
    3287:   return(0);
    3288: }