Actual source code: mpiov.c

petsc-3.10.3 2018-12-18
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  1: /*
  2:    Routines to compute overlapping regions of a parallel MPI matrix
  3:   and to find submatrices that were shared across processors.
  4: */
  5:  #include <../src/mat/impls/aij/seq/aij.h>
  6:  #include <../src/mat/impls/aij/mpi/mpiaij.h>
  7:  #include <petscbt.h>
  8:  #include <petscsf.h>

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

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


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

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

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

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


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

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

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

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

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

255:   PetscObjectGetComm((PetscObject)mat,&comm);
256:   MPI_Comm_rank(comm,&rank);
257:   MatMPIAIJGetSeqAIJ(mat,&amat,&bmat,&gcols);
258:   /* Even if the mat is symmetric, we still assume it is not symmetric */
259:   MatGetRowIJ(amat,0,PETSC_FALSE,PETSC_FALSE,&an,&ai,&aj,&done);
260:   if (!done) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONGSTATE,"can not get row IJ \n");
261:   MatGetRowIJ(bmat,0,PETSC_FALSE,PETSC_FALSE,&bn,&bi,&bj,&done);
262:   if (!done) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONGSTATE,"can not get row IJ \n");
263:   /* total number of nonzero values is used to estimate the memory usage in the next step */
264:   tnz  = ai[an]+bi[bn];
265:   MatGetLayouts(mat,&rmap,&cmap);
266:   PetscLayoutGetRange(rmap,&rstart,NULL);
267:   PetscLayoutGetRange(cmap,&cstart,NULL);
268:   /* to find the longest message */
269:   max_fszs = 0;
270:   for (i=0; i<nfrom; i++) max_fszs = fromsizes[2*i]>max_fszs ? fromsizes[2*i]:max_fszs;
271:   /* better way to estimate number of nonzero in the mat??? */
272:   PetscCalloc5(max_fszs*nidx,&rows_data_ptr,nidx,&rows_data,nidx,&rows_pos_i,nfrom*nidx,&indv_counts,tnz,&indices_tmp);
273:   for (i=0; i<nidx; i++) rows_data[i] = rows_data_ptr+max_fszs*i;
274:   rows_pos  = 0;
275:   totalrows = 0;
276:   for (i=0; i<nfrom; i++){
277:     PetscMemzero(rows_pos_i,sizeof(PetscInt)*nidx);
278:     /* group data together */
279:     for (j=0; j<fromsizes[2*i]; j+=2){
280:       is_id                       = fromrows[rows_pos++];/* no of is */
281:       rows_i                      = rows_data[is_id];
282:       rows_i[rows_pos_i[is_id]++] = fromrows[rows_pos++];/* row */
283:     }
284:     /* estimate a space to avoid multiple allocations  */
285:     for (j=0; j<nidx; j++){
286:       indvc_ij = 0;
287:       rows_i   = rows_data[j];
288:       for (l=0; l<rows_pos_i[j]; l++){
289:         row    = rows_i[l]-rstart;
290:         start  = ai[row];
291:         end    = ai[row+1];
292:         for (k=start; k<end; k++){ /* Amat */
293:           col = aj[k] + cstart;
294:           indices_tmp[indvc_ij++] = col;/* do not count the rows from the original rank */
295:         }
296:         start = bi[row];
297:         end   = bi[row+1];
298:         for (k=start; k<end; k++) { /* Bmat */
299:           col = gcols[bj[k]];
300:           indices_tmp[indvc_ij++] = col;
301:         }
302:       }
303:       PetscSortRemoveDupsInt(&indvc_ij,indices_tmp);
304:       indv_counts[i*nidx+j] = indvc_ij;
305:       totalrows            += indvc_ij;
306:     }
307:   }
308:   /* message triple <no of is, number of rows, rows> */
309:   PetscCalloc2(totalrows+nidx*nfrom*2,&sbdata,2*nfrom,&sbsizes);
310:   totalrows = 0;
311:   rows_pos  = 0;
312:   /* use this code again */
313:   for (i=0;i<nfrom;i++){
314:     PetscMemzero(rows_pos_i,sizeof(PetscInt)*nidx);
315:     for (j=0; j<fromsizes[2*i]; j+=2){
316:       is_id                       = fromrows[rows_pos++];
317:       rows_i                      = rows_data[is_id];
318:       rows_i[rows_pos_i[is_id]++] = fromrows[rows_pos++];
319:     }
320:     /* add data  */
321:     for (j=0; j<nidx; j++){
322:       if (!indv_counts[i*nidx+j]) continue;
323:       indvc_ij = 0;
324:       sbdata[totalrows++] = j;
325:       sbdata[totalrows++] = indv_counts[i*nidx+j];
326:       sbsizes[2*i]       += 2;
327:       rows_i              = rows_data[j];
328:       for (l=0; l<rows_pos_i[j]; l++){
329:         row   = rows_i[l]-rstart;
330:         start = ai[row];
331:         end   = ai[row+1];
332:         for (k=start; k<end; k++){ /* Amat */
333:           col = aj[k] + cstart;
334:           indices_tmp[indvc_ij++] = col;
335:         }
336:         start = bi[row];
337:         end   = bi[row+1];
338:         for (k=start; k<end; k++) { /* Bmat */
339:           col = gcols[bj[k]];
340:           indices_tmp[indvc_ij++] = col;
341:         }
342:       }
343:       PetscSortRemoveDupsInt(&indvc_ij,indices_tmp);
344:       sbsizes[2*i]  += indvc_ij;
345:       PetscMemcpy(sbdata+totalrows,indices_tmp,sizeof(PetscInt)*indvc_ij);
346:       totalrows += indvc_ij;
347:     }
348:   }
349:   PetscCalloc1(nfrom+1,&offsets);
350:   for (i=0; i<nfrom; i++){
351:     offsets[i+1]   = offsets[i] + sbsizes[2*i];
352:     sbsizes[2*i+1] = offsets[i];
353:   }
354:   PetscFree(offsets);
355:   if (sbrowsizes) *sbrowsizes = sbsizes;
356:   if (sbrows) *sbrows = sbdata;
357:   PetscFree5(rows_data_ptr,rows_data,rows_pos_i,indv_counts,indices_tmp);
358:   MatRestoreRowIJ(amat,0,PETSC_FALSE,PETSC_FALSE,&an,&ai,&aj,&done);
359:   MatRestoreRowIJ(bmat,0,PETSC_FALSE,PETSC_FALSE,&bn,&bi,&bj,&done);
360:   return(0);
361: }

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

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

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


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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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


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

685:     PetscCalloc1(size,&rw1);

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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


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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

1405:     PetscFree2(w1,w2);

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

2139:       smat_i   = subc->submatis1;

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

2315:     /* Send to other procs the buf size they should allocate */
2316:     /* Receive messages*/
2317:     PetscMalloc1(nrqr+1,&s_waits2);
2318:     PetscMalloc1(nrqr+1,&r_status1);
2319:     PetscMalloc3(nrqr,&sbuf2,nrqr,&req_size,nrqr,&req_source1);
2320:     {
2321:       PetscInt   *sAi = a->i,*sBi = b->i,id,rstart = C->rmap->rstart;
2322:       PetscInt   *sbuf2_i;

2324:       MPI_Waitall(nrqr,r_waits1,r_status1);
2325:       for (i=0; i<nrqr; ++i) {
2326:         req_size[i] = 0;
2327:         rbuf1_i        = rbuf1[i];
2328:         start          = 2*rbuf1_i[0] + 1;
2329:         MPI_Get_count(r_status1+i,MPIU_INT,&end);
2330:         PetscMalloc1(end+1,&sbuf2[i]);
2331:         sbuf2_i        = sbuf2[i];
2332:         for (j=start; j<end; j++) {
2333:           id              = rbuf1_i[j] - rstart;
2334:           ncols           = sAi[id+1] - sAi[id] + sBi[id+1] - sBi[id];
2335:           sbuf2_i[j]      = ncols;
2336:           req_size[i] += ncols;
2337:         }
2338:         req_source1[i] = r_status1[i].MPI_SOURCE;
2339:         /* form the header */
2340:         sbuf2_i[0] = req_size[i];
2341:         for (j=1; j<start; j++) sbuf2_i[j] = rbuf1_i[j];

2343:         MPI_Isend(sbuf2_i,end,MPIU_INT,req_source1[i],tag2,comm,s_waits2+i);
2344:       }
2345:     }
2346:     PetscFree(r_status1);
2347:     PetscFree(r_waits1);
2348:     PetscFree4(w1,w2,w3,w4);

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

2901:   /* Check to make sure the component matrices (and embeddings) are compatible with C. */
2902:   if (A) {
2903:     PetscObjectBaseTypeCompare((PetscObject)A,MATSEQAIJ,&seqaij);
2904:     if (!seqaij) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_PLIB,"Diagonal matrix is of wrong type");
2905:     if (rowemb) {
2906:       ISGetLocalSize(rowemb,&m);
2907:       if (m != A->rmap->n) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_PLIB,"Row IS of size %D is incompatible with diag matrix row size %D",m,A->rmap->n);
2908:     } else {
2909:       if (C->rmap->n != A->rmap->n) {
2910:         SETERRQ(PETSC_COMM_SELF,PETSC_ERR_PLIB,"Diag seq matrix is row-incompatible with the MPIAIJ matrix");
2911:       }
2912:     }
2913:     if (dcolemb) {
2914:       ISGetLocalSize(dcolemb,&n);
2915:       if (n != A->cmap->n) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_PLIB,"Diag col IS of size %D is incompatible with diag matrix col size %D",n,A->cmap->n);
2916:     } else {
2917:       if (C->cmap->n != A->cmap->n) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_PLIB,"Diag seq matrix is col-incompatible with the MPIAIJ matrix");
2918:     }
2919:   }
2920:   if (B) {
2921:     PetscObjectBaseTypeCompare((PetscObject)B,MATSEQAIJ,&seqaij);
2922:     if (!seqaij) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_PLIB,"Off-diagonal matrix is of wrong type");
2923:     if (rowemb) {
2924:       ISGetLocalSize(rowemb,&m);
2925:       if (m != B->rmap->n) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_PLIB,"Row IS of size %D is incompatible with off-diag matrix row size %D",m,A->rmap->n);
2926:     } else {
2927:       if (C->rmap->n != B->rmap->n) {
2928:         SETERRQ(PETSC_COMM_SELF,PETSC_ERR_PLIB,"Off-diag seq matrix is row-incompatible with the MPIAIJ matrix");
2929:       }
2930:     }
2931:     if (ocolemb) {
2932:       ISGetLocalSize(ocolemb,&n);
2933:       if (n != B->cmap->n) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_PLIB,"Off-diag col IS of size %D is incompatible with off-diag matrix col size %D",n,B->cmap->n);
2934:     } else {
2935:       if (C->cmap->N - C->cmap->n != B->cmap->n) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_PLIB,"Off-diag seq matrix is col-incompatible with the MPIAIJ matrix");
2936:     }
2937:   }

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

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

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

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

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

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

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

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

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

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

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

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

3145:     /*
3146:        Permute the indices into a nondecreasing order. Reject row and col indices with duplicates.
3147:      */
3148:     ISSortPermutation(isrow[i],PETSC_FALSE,isrow_p+i);
3149:     ISSort(isrow[i]);
3150:     ISGetLocalSize(isrow[i],&issize);
3151:     ISGetIndices(isrow[i],&indices);
3152:     for (j = 1; j < issize; ++j) {
3153:       if (indices[j] == indices[j-1]) {
3154:         SETERRQ4(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONG,"Repeated indices in row IS %D: indices at %D and %D are both %D",i,j-1,j,indices[j]);
3155:       }
3156:     }
3157:     ISRestoreIndices(isrow[i],&indices);


3160:     ISSortPermutation(iscol[i],PETSC_FALSE,iscol_p+i);
3161:     ISSort(iscol[i]);
3162:     ISGetLocalSize(iscol[i],&issize);
3163:     ISGetIndices(iscol[i],&indices);
3164:     for (j = 1; j < issize; ++j) {
3165:       if (indices[j-1] == indices[j]) {
3166:         SETERRQ4(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONG,"Repeated indices in col IS %D: indices at %D and %D are both %D",i,j-1,j,indices[j]);
3167:       }
3168:     }
3169:     ISRestoreIndices(iscol[i],&indices);
3170:     MPI_Comm_size(((PetscObject)isrow[i])->comm,&isize);
3171:     if (isize > 1) {
3172:       cisrow[ii] = isrow[i];
3173:       ++ii;
3174:     }
3175:   }
3176:   /*
3177:     Allocate the necessary arrays to hold the resulting parallel matrices as well as the intermediate
3178:     array of sequential matrices underlying the resulting parallel matrices.
3179:     Which arrays to allocate is based on the value of MatReuse scall and whether ISs are sorted and/or
3180:     contain duplicates.

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

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

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

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

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

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

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

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