Actual source code: mpiadj.c

petsc-master 2020-08-05
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  2: /*
  3:     Defines the basic matrix operations for the ADJ adjacency list matrix data-structure.
  4: */
  5:  #include <../src/mat/impls/adj/mpi/mpiadj.h>
  6:  #include <petscsf.h>

  8: /*
  9:  * The interface should be easy to use for both MatCreateSubMatrix (parallel sub-matrix) and MatCreateSubMatrices (sequential sub-matrices)
 10:  * */
 11: static PetscErrorCode MatCreateSubMatrix_MPIAdj_data(Mat adj,IS irows, IS icols, PetscInt **sadj_xadj,PetscInt **sadj_adjncy,PetscInt **sadj_values)
 12: {
 13:   PetscInt           nlrows_is,icols_n,i,j,nroots,nleaves,rlocalindex,*ncols_send,*ncols_recv;
 14:   PetscInt           nlrows_mat,*adjncy_recv,Ncols_recv,Ncols_send,*xadj_recv,*values_recv;
 15:   PetscInt          *ncols_recv_offsets,loc,rnclos,*sadjncy,*sxadj,*svalues;
 16:   const PetscInt    *irows_indices,*icols_indices,*xadj, *adjncy;
 17:   PetscMPIInt        owner;
 18:   Mat_MPIAdj        *a = (Mat_MPIAdj*)adj->data;
 19:   PetscLayout        rmap;
 20:   MPI_Comm           comm;
 21:   PetscSF            sf;
 22:   PetscSFNode       *iremote;
 23:   PetscBool          done;
 24:   PetscErrorCode     ierr;

 27:   PetscObjectGetComm((PetscObject)adj,&comm);
 28:   MatGetLayouts(adj,&rmap,NULL);
 29:   ISGetLocalSize(irows,&nlrows_is);
 30:   ISGetIndices(irows,&irows_indices);
 31:   PetscMalloc1(nlrows_is,&iremote);
 32:   /* construct sf graph*/
 33:   nleaves = nlrows_is;
 34:   for (i=0; i<nlrows_is; i++){
 35:     owner = -1;
 36:     rlocalindex = -1;
 37:     PetscLayoutFindOwnerIndex(rmap,irows_indices[i],&owner,&rlocalindex);
 38:     iremote[i].rank  = owner;
 39:     iremote[i].index = rlocalindex;
 40:   }
 41:   MatGetRowIJ(adj,0,PETSC_FALSE,PETSC_FALSE,&nlrows_mat,&xadj,&adjncy,&done);
 42:   PetscCalloc4(nlrows_mat,&ncols_send,nlrows_is,&xadj_recv,nlrows_is+1,&ncols_recv_offsets,nlrows_is,&ncols_recv);
 43:   nroots = nlrows_mat;
 44:   for (i=0; i<nlrows_mat; i++){
 45:     ncols_send[i] = xadj[i+1]-xadj[i];
 46:   }
 47:   PetscSFCreate(comm,&sf);
 48:   PetscSFSetGraph(sf,nroots,nleaves,NULL,PETSC_OWN_POINTER,iremote,PETSC_OWN_POINTER);
 49:   PetscSFSetType(sf,PETSCSFBASIC);
 50:   PetscSFSetFromOptions(sf);
 51:   PetscSFBcastBegin(sf,MPIU_INT,ncols_send,ncols_recv);
 52:   PetscSFBcastEnd(sf,MPIU_INT,ncols_send,ncols_recv);
 53:   PetscSFBcastBegin(sf,MPIU_INT,xadj,xadj_recv);
 54:   PetscSFBcastEnd(sf,MPIU_INT,xadj,xadj_recv);
 55:   PetscSFDestroy(&sf);
 56:   Ncols_recv =0;
 57:   for (i=0; i<nlrows_is; i++){
 58:     Ncols_recv             += ncols_recv[i];
 59:     ncols_recv_offsets[i+1] = ncols_recv[i]+ncols_recv_offsets[i];
 60:   }
 61:   Ncols_send = 0;
 62:   for(i=0; i<nlrows_mat; i++){
 63:     Ncols_send += ncols_send[i];
 64:   }
 65:   PetscCalloc1(Ncols_recv,&iremote);
 66:   PetscCalloc1(Ncols_recv,&adjncy_recv);
 67:   nleaves = Ncols_recv;
 68:   Ncols_recv = 0;
 69:   for (i=0; i<nlrows_is; i++){
 70:     PetscLayoutFindOwner(rmap,irows_indices[i],&owner);
 71:     for (j=0; j<ncols_recv[i]; j++){
 72:       iremote[Ncols_recv].rank    = owner;
 73:       iremote[Ncols_recv++].index = xadj_recv[i]+j;
 74:     }
 75:   }
 76:   ISRestoreIndices(irows,&irows_indices);
 77:   /*if we need to deal with edge weights ???*/
 78:   if (a->useedgeweights){PetscCalloc1(Ncols_recv,&values_recv);}
 79:   nroots = Ncols_send;
 80:   PetscSFCreate(comm,&sf);
 81:   PetscSFSetGraph(sf,nroots,nleaves,NULL,PETSC_OWN_POINTER,iremote,PETSC_OWN_POINTER);
 82:   PetscSFSetType(sf,PETSCSFBASIC);
 83:   PetscSFSetFromOptions(sf);
 84:   PetscSFBcastBegin(sf,MPIU_INT,adjncy,adjncy_recv);
 85:   PetscSFBcastEnd(sf,MPIU_INT,adjncy,adjncy_recv);
 86:   if (a->useedgeweights){
 87:     PetscSFBcastBegin(sf,MPIU_INT,a->values,values_recv);
 88:     PetscSFBcastEnd(sf,MPIU_INT,a->values,values_recv);
 89:   }
 90:   PetscSFDestroy(&sf);
 91:   MatRestoreRowIJ(adj,0,PETSC_FALSE,PETSC_FALSE,&nlrows_mat,&xadj,&adjncy,&done);
 92:   ISGetLocalSize(icols,&icols_n);
 93:   ISGetIndices(icols,&icols_indices);
 94:   rnclos = 0;
 95:   for (i=0; i<nlrows_is; i++){
 96:     for (j=ncols_recv_offsets[i]; j<ncols_recv_offsets[i+1]; j++){
 97:       PetscFindInt(adjncy_recv[j], icols_n, icols_indices, &loc);
 98:       if (loc<0){
 99:         adjncy_recv[j] = -1;
100:         if (a->useedgeweights) values_recv[j] = -1;
101:         ncols_recv[i]--;
102:       } else {
103:         rnclos++;
104:       }
105:     }
106:   }
107:   ISRestoreIndices(icols,&icols_indices);
108:   PetscCalloc1(rnclos,&sadjncy);
109:   if (a->useedgeweights) {PetscCalloc1(rnclos,&svalues);}
110:   PetscCalloc1(nlrows_is+1,&sxadj);
111:   rnclos = 0;
112:   for(i=0; i<nlrows_is; i++){
113:     for(j=ncols_recv_offsets[i]; j<ncols_recv_offsets[i+1]; j++){
114:       if (adjncy_recv[j]<0) continue;
115:       sadjncy[rnclos] = adjncy_recv[j];
116:       if (a->useedgeweights) svalues[rnclos] = values_recv[j];
117:       rnclos++;
118:     }
119:   }
120:   for(i=0; i<nlrows_is; i++){
121:     sxadj[i+1] = sxadj[i]+ncols_recv[i];
122:   }
123:   if (sadj_xadj)  { *sadj_xadj = sxadj;} else    { PetscFree(sxadj);}
124:   if (sadj_adjncy){ *sadj_adjncy = sadjncy;} else { PetscFree(sadjncy);}
125:   if (sadj_values){
126:     if (a->useedgeweights) *sadj_values = svalues; else *sadj_values=0;
127:   } else {
128:     if (a->useedgeweights) {PetscFree(svalues);}
129:   }
130:   PetscFree4(ncols_send,xadj_recv,ncols_recv_offsets,ncols_recv);
131:   PetscFree(adjncy_recv);
132:   if (a->useedgeweights) {PetscFree(values_recv);}
133:   return(0);
134: }

136: static PetscErrorCode MatCreateSubMatrices_MPIAdj_Private(Mat mat,PetscInt n,const IS irow[],const IS icol[],PetscBool subcomm,MatReuse scall,Mat *submat[])
137: {
138:   PetscInt           i,irow_n,icol_n,*sxadj,*sadjncy,*svalues;
139:   PetscInt          *indices,nindx,j,k,loc;
140:   PetscMPIInt        issame;
141:   const PetscInt    *irow_indices,*icol_indices;
142:   MPI_Comm           scomm_row,scomm_col,scomm_mat;
143:   PetscErrorCode     ierr;

146:   nindx = 0;
147:   /*
148:    * Estimate a maximum number for allocating memory
149:    */
150:   for(i=0; i<n; i++){
151:     ISGetLocalSize(irow[i],&irow_n);
152:     ISGetLocalSize(icol[i],&icol_n);
153:     nindx = nindx>(irow_n+icol_n)? nindx:(irow_n+icol_n);
154:   }
155:   PetscMalloc1(nindx,&indices);
156:   /* construct a submat */
157:   for (i=0; i<n; i++){
158:     if (subcomm){
159:       PetscObjectGetComm((PetscObject)irow[i],&scomm_row);
160:       PetscObjectGetComm((PetscObject)icol[i],&scomm_col);
161:       MPI_Comm_compare(scomm_row,scomm_col,&issame);
162:       if (issame != MPI_IDENT) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_INCOMP,"row index set must have the same comm as the col index set\n");
163:       MPI_Comm_compare(scomm_row,PETSC_COMM_SELF,&issame);
164:       if (issame == MPI_IDENT) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_INCOMP," can not use PETSC_COMM_SELF as comm when extracting a parallel submatrix\n");
165:     } else {
166:       scomm_row = PETSC_COMM_SELF;
167:     }
168:     /*get sub-matrix data*/
169:     sxadj=0; sadjncy=0; svalues=0;
170:     MatCreateSubMatrix_MPIAdj_data(mat,irow[i],icol[i],&sxadj,&sadjncy,&svalues);
171:     ISGetLocalSize(irow[i],&irow_n);
172:     ISGetLocalSize(icol[i],&icol_n);
173:     ISGetIndices(irow[i],&irow_indices);
174:     PetscArraycpy(indices,irow_indices,irow_n);
175:     ISRestoreIndices(irow[i],&irow_indices);
176:     ISGetIndices(icol[i],&icol_indices);
177:     PetscArraycpy(indices+irow_n,icol_indices,icol_n);
178:     ISRestoreIndices(icol[i],&icol_indices);
179:     nindx = irow_n+icol_n;
180:     PetscSortRemoveDupsInt(&nindx,indices);
181:     /* renumber columns */
182:     for (j=0; j<irow_n; j++){
183:       for (k=sxadj[j]; k<sxadj[j+1]; k++){
184:         PetscFindInt(sadjncy[k],nindx,indices,&loc);
185:         if (loc<0) SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONG,"can not find col %D",sadjncy[k]);
186:         sadjncy[k] = loc;
187:       }
188:     }
189:     if (scall==MAT_INITIAL_MATRIX){
190:       MatCreateMPIAdj(scomm_row,irow_n,icol_n,sxadj,sadjncy,svalues,submat[i]);
191:     } else {
192:        Mat                sadj = *(submat[i]);
193:        Mat_MPIAdj         *sa  = (Mat_MPIAdj*)((sadj)->data);
194:        PetscObjectGetComm((PetscObject)sadj,&scomm_mat);
195:        MPI_Comm_compare(scomm_row,scomm_mat,&issame);
196:        if (issame != MPI_IDENT) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_INCOMP,"submatrix  must have the same comm as the col index set\n");
197:        PetscArraycpy(sa->i,sxadj,irow_n+1);
198:        PetscArraycpy(sa->j,sadjncy,sxadj[irow_n]);
199:        if (svalues){PetscArraycpy(sa->values,svalues,sxadj[irow_n]);}
200:        PetscFree(sxadj);
201:        PetscFree(sadjncy);
202:        if (svalues) {PetscFree(svalues);}
203:     }
204:   }
205:   PetscFree(indices);
206:   return(0);
207: }

209: static PetscErrorCode MatCreateSubMatricesMPI_MPIAdj(Mat mat,PetscInt n, const IS irow[],const IS icol[],MatReuse scall,Mat *submat[])
210: {
211:   PetscErrorCode     ierr;
212:   /*get sub-matrices across a sub communicator */
214:   MatCreateSubMatrices_MPIAdj_Private(mat,n,irow,icol,PETSC_TRUE,scall,submat);
215:   return(0);
216: }

218: static PetscErrorCode MatCreateSubMatrices_MPIAdj(Mat mat,PetscInt n,const IS irow[],const IS icol[],MatReuse scall,Mat *submat[])
219: {
220:   PetscErrorCode     ierr;

223:   /*get sub-matrices based on PETSC_COMM_SELF */
224:   MatCreateSubMatrices_MPIAdj_Private(mat,n,irow,icol,PETSC_FALSE,scall,submat);
225:   return(0);
226: }

228: static PetscErrorCode MatView_MPIAdj_ASCII(Mat A,PetscViewer viewer)
229: {
230:   Mat_MPIAdj        *a = (Mat_MPIAdj*)A->data;
231:   PetscErrorCode    ierr;
232:   PetscInt          i,j,m = A->rmap->n;
233:   const char        *name;
234:   PetscViewerFormat format;

237:   PetscObjectGetName((PetscObject)A,&name);
238:   PetscViewerGetFormat(viewer,&format);
239:   if (format == PETSC_VIEWER_ASCII_INFO) {
240:     return(0);
241:   } else if (format == PETSC_VIEWER_ASCII_MATLAB) SETERRQ(PetscObjectComm((PetscObject)A),PETSC_ERR_SUP,"MATLAB format not supported");
242:   else {
243:     PetscViewerASCIIUseTabs(viewer,PETSC_FALSE);
244:     PetscViewerASCIIPushSynchronized(viewer);
245:     for (i=0; i<m; i++) {
246:       PetscViewerASCIISynchronizedPrintf(viewer,"row %D:",i+A->rmap->rstart);
247:       for (j=a->i[i]; j<a->i[i+1]; j++) {
248:         if (a->values) {
249:           PetscViewerASCIISynchronizedPrintf(viewer," (%D, %D) ",a->j[j], a->values[j]);
250:         } else {
251:           PetscViewerASCIISynchronizedPrintf(viewer," %D ",a->j[j]);
252:         }
253:       }
254:       PetscViewerASCIISynchronizedPrintf(viewer,"\n");
255:     }
256:     PetscViewerASCIIUseTabs(viewer,PETSC_TRUE);
257:     PetscViewerFlush(viewer);
258:     PetscViewerASCIIPopSynchronized(viewer);
259:   }
260:   return(0);
261: }

263: static PetscErrorCode MatView_MPIAdj(Mat A,PetscViewer viewer)
264: {
266:   PetscBool      iascii;

269:   PetscObjectTypeCompare((PetscObject)viewer,PETSCVIEWERASCII,&iascii);
270:   if (iascii) {
271:     MatView_MPIAdj_ASCII(A,viewer);
272:   }
273:   return(0);
274: }

276: static PetscErrorCode MatDestroy_MPIAdj(Mat mat)
277: {
278:   Mat_MPIAdj     *a = (Mat_MPIAdj*)mat->data;

282: #if defined(PETSC_USE_LOG)
283:   PetscLogObjectState((PetscObject)mat,"Rows=%D, Cols=%D, NZ=%D",mat->rmap->n,mat->cmap->n,a->nz);
284: #endif
285:   PetscFree(a->diag);
286:   if (a->freeaij) {
287:     if (a->freeaijwithfree) {
288:       if (a->i) free(a->i);
289:       if (a->j) free(a->j);
290:     } else {
291:       PetscFree(a->i);
292:       PetscFree(a->j);
293:       PetscFree(a->values);
294:     }
295:   }
296:   PetscFree(a->rowvalues);
297:   PetscFree(mat->data);
298:   PetscObjectChangeTypeName((PetscObject)mat,0);
299:   PetscObjectComposeFunction((PetscObject)mat,"MatMPIAdjSetPreallocation_C",NULL);
300:   PetscObjectComposeFunction((PetscObject)mat,"MatMPIAdjCreateNonemptySubcommMat_C",NULL);
301:   return(0);
302: }

304: static PetscErrorCode MatSetOption_MPIAdj(Mat A,MatOption op,PetscBool flg)
305: {
306:   Mat_MPIAdj     *a = (Mat_MPIAdj*)A->data;

310:   switch (op) {
311:   case MAT_SYMMETRIC:
312:   case MAT_STRUCTURALLY_SYMMETRIC:
313:   case MAT_HERMITIAN:
314:     a->symmetric = flg;
315:     break;
316:   case MAT_SYMMETRY_ETERNAL:
317:     break;
318:   default:
319:     PetscInfo1(A,"Option %s ignored\n",MatOptions[op]);
320:     break;
321:   }
322:   return(0);
323: }

325: static PetscErrorCode MatGetRow_MPIAdj(Mat A,PetscInt row,PetscInt *nz,PetscInt **idx,PetscScalar **v)
326: {
327:   Mat_MPIAdj *a = (Mat_MPIAdj*)A->data;

331:   row -= A->rmap->rstart;
332:   if (row < 0 || row >= A->rmap->n) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Row out of range");
333:   *nz = a->i[row+1] - a->i[row];
334:   if (v) {
335:     PetscInt j;
336:     if (a->rowvalues_alloc < *nz) {
337:       PetscFree(a->rowvalues);
338:       a->rowvalues_alloc = PetscMax(a->rowvalues_alloc*2, *nz);
339:       PetscMalloc1(a->rowvalues_alloc,&a->rowvalues);
340:     }
341:     for (j=0; j<*nz; j++){
342:       a->rowvalues[j] = a->values ? a->values[a->i[row]+j]:1.0;
343:     }
344:     *v = (*nz) ? a->rowvalues : NULL;
345:   }
346:   if (idx) *idx = (*nz) ? a->j + a->i[row] : NULL;
347:   return(0);
348: }

350: static PetscErrorCode MatRestoreRow_MPIAdj(Mat A,PetscInt row,PetscInt *nz,PetscInt **idx,PetscScalar **v)
351: {
353:   return(0);
354: }

356: static PetscErrorCode MatEqual_MPIAdj(Mat A,Mat B,PetscBool * flg)
357: {
358:   Mat_MPIAdj     *a = (Mat_MPIAdj*)A->data,*b = (Mat_MPIAdj*)B->data;
360:   PetscBool      flag;

363:   /* If the  matrix dimensions are not equal,or no of nonzeros */
364:   if ((A->rmap->n != B->rmap->n) ||(a->nz != b->nz)) {
365:     flag = PETSC_FALSE;
366:   }

368:   /* if the a->i are the same */
369:   PetscArraycmp(a->i,b->i,A->rmap->n+1,&flag);

371:   /* if a->j are the same */
372:   PetscMemcmp(a->j,b->j,(a->nz)*sizeof(PetscInt),&flag);

374:   MPIU_Allreduce(&flag,flg,1,MPIU_BOOL,MPI_LAND,PetscObjectComm((PetscObject)A));
375:   return(0);
376: }

378: static PetscErrorCode MatGetRowIJ_MPIAdj(Mat A,PetscInt oshift,PetscBool symmetric,PetscBool blockcompressed,PetscInt *m,const PetscInt *inia[],const PetscInt *inja[],PetscBool  *done)
379: {
380:   PetscInt   i;
381:   Mat_MPIAdj *a   = (Mat_MPIAdj*)A->data;
382:   PetscInt   **ia = (PetscInt**)inia,**ja = (PetscInt**)inja;

385:   *m    = A->rmap->n;
386:   *ia   = a->i;
387:   *ja   = a->j;
388:   *done = PETSC_TRUE;
389:   if (oshift) {
390:     for (i=0; i<(*ia)[*m]; i++) {
391:       (*ja)[i]++;
392:     }
393:     for (i=0; i<=(*m); i++) (*ia)[i]++;
394:   }
395:   return(0);
396: }

398: static PetscErrorCode MatRestoreRowIJ_MPIAdj(Mat A,PetscInt oshift,PetscBool symmetric,PetscBool blockcompressed,PetscInt *m,const PetscInt *inia[],const PetscInt *inja[],PetscBool  *done)
399: {
400:   PetscInt   i;
401:   Mat_MPIAdj *a   = (Mat_MPIAdj*)A->data;
402:   PetscInt   **ia = (PetscInt**)inia,**ja = (PetscInt**)inja;

405:   if (ia && a->i != *ia) SETERRQ(PetscObjectComm((PetscObject)A),PETSC_ERR_ARG_WRONGSTATE,"ia passed back is not one obtained with MatGetRowIJ()");
406:   if (ja && a->j != *ja) SETERRQ(PetscObjectComm((PetscObject)A),PETSC_ERR_ARG_WRONGSTATE,"ja passed back is not one obtained with MatGetRowIJ()");
407:   if (oshift) {
408:     if (!ia) SETERRQ(PetscObjectComm((PetscObject)A),PETSC_ERR_ARG_WRONGSTATE,"If oshift then you must passed in inia[] argument");
409:     if (!ja) SETERRQ(PetscObjectComm((PetscObject)A),PETSC_ERR_ARG_WRONGSTATE,"If oshift then you must passed in inja[] argument");
410:     for (i=0; i<=(*m); i++) (*ia)[i]--;
411:     for (i=0; i<(*ia)[*m]; i++) {
412:       (*ja)[i]--;
413:     }
414:   }
415:   return(0);
416: }

418: PetscErrorCode  MatConvertFrom_MPIAdj(Mat A,MatType type,MatReuse reuse,Mat *newmat)
419: {
420:   Mat               B;
421:   PetscErrorCode    ierr;
422:   PetscInt          i,m,N,nzeros = 0,*ia,*ja,len,rstart,cnt,j,*a;
423:   const PetscInt    *rj;
424:   const PetscScalar *ra;
425:   MPI_Comm          comm;

428:   MatGetSize(A,NULL,&N);
429:   MatGetLocalSize(A,&m,NULL);
430:   MatGetOwnershipRange(A,&rstart,NULL);

432:   /* count the number of nonzeros per row */
433:   for (i=0; i<m; i++) {
434:     MatGetRow(A,i+rstart,&len,&rj,NULL);
435:     for (j=0; j<len; j++) {
436:       if (rj[j] == i+rstart) {len--; break;}    /* don't count diagonal */
437:     }
438:     nzeros += len;
439:     MatRestoreRow(A,i+rstart,&len,&rj,NULL);
440:   }

442:   /* malloc space for nonzeros */
443:   PetscMalloc1(nzeros+1,&a);
444:   PetscMalloc1(N+1,&ia);
445:   PetscMalloc1(nzeros+1,&ja);

447:   nzeros = 0;
448:   ia[0]  = 0;
449:   for (i=0; i<m; i++) {
450:     MatGetRow(A,i+rstart,&len,&rj,&ra);
451:     cnt  = 0;
452:     for (j=0; j<len; j++) {
453:       if (rj[j] != i+rstart) { /* if not diagonal */
454:         a[nzeros+cnt]    = (PetscInt) PetscAbsScalar(ra[j]);
455:         ja[nzeros+cnt++] = rj[j];
456:       }
457:     }
458:     MatRestoreRow(A,i+rstart,&len,&rj,&ra);
459:     nzeros += cnt;
460:     ia[i+1] = nzeros;
461:   }

463:   PetscObjectGetComm((PetscObject)A,&comm);
464:   MatCreate(comm,&B);
465:   MatSetSizes(B,m,PETSC_DETERMINE,PETSC_DETERMINE,N);
466:   MatSetType(B,type);
467:   MatMPIAdjSetPreallocation(B,ia,ja,a);

469:   if (reuse == MAT_INPLACE_MATRIX) {
470:     MatHeaderReplace(A,&B);
471:   } else {
472:     *newmat = B;
473:   }
474:   return(0);
475: }

477: /* -------------------------------------------------------------------*/
478: static struct _MatOps MatOps_Values = {0,
479:                                        MatGetRow_MPIAdj,
480:                                        MatRestoreRow_MPIAdj,
481:                                        0,
482:                                 /* 4*/ 0,
483:                                        0,
484:                                        0,
485:                                        0,
486:                                        0,
487:                                        0,
488:                                 /*10*/ 0,
489:                                        0,
490:                                        0,
491:                                        0,
492:                                        0,
493:                                 /*15*/ 0,
494:                                        MatEqual_MPIAdj,
495:                                        0,
496:                                        0,
497:                                        0,
498:                                 /*20*/ 0,
499:                                        0,
500:                                        MatSetOption_MPIAdj,
501:                                        0,
502:                                 /*24*/ 0,
503:                                        0,
504:                                        0,
505:                                        0,
506:                                        0,
507:                                 /*29*/ 0,
508:                                        0,
509:                                        0,
510:                                        0,
511:                                        0,
512:                                 /*34*/ 0,
513:                                        0,
514:                                        0,
515:                                        0,
516:                                        0,
517:                                 /*39*/ 0,
518:                                        MatCreateSubMatrices_MPIAdj,
519:                                        0,
520:                                        0,
521:                                        0,
522:                                 /*44*/ 0,
523:                                        0,
524:                                        MatShift_Basic,
525:                                        0,
526:                                        0,
527:                                 /*49*/ 0,
528:                                        MatGetRowIJ_MPIAdj,
529:                                        MatRestoreRowIJ_MPIAdj,
530:                                        0,
531:                                        0,
532:                                 /*54*/ 0,
533:                                        0,
534:                                        0,
535:                                        0,
536:                                        0,
537:                                 /*59*/ 0,
538:                                        MatDestroy_MPIAdj,
539:                                        MatView_MPIAdj,
540:                                        MatConvertFrom_MPIAdj,
541:                                        0,
542:                                 /*64*/ 0,
543:                                        0,
544:                                        0,
545:                                        0,
546:                                        0,
547:                                 /*69*/ 0,
548:                                        0,
549:                                        0,
550:                                        0,
551:                                        0,
552:                                 /*74*/ 0,
553:                                        0,
554:                                        0,
555:                                        0,
556:                                        0,
557:                                 /*79*/ 0,
558:                                        0,
559:                                        0,
560:                                        0,
561:                                        0,
562:                                 /*84*/ 0,
563:                                        0,
564:                                        0,
565:                                        0,
566:                                        0,
567:                                 /*89*/ 0,
568:                                        0,
569:                                        0,
570:                                        0,
571:                                        0,
572:                                 /*94*/ 0,
573:                                        0,
574:                                        0,
575:                                        0,
576:                                        0,
577:                                 /*99*/ 0,
578:                                        0,
579:                                        0,
580:                                        0,
581:                                        0,
582:                                /*104*/ 0,
583:                                        0,
584:                                        0,
585:                                        0,
586:                                        0,
587:                                /*109*/ 0,
588:                                        0,
589:                                        0,
590:                                        0,
591:                                        0,
592:                                /*114*/ 0,
593:                                        0,
594:                                        0,
595:                                        0,
596:                                        0,
597:                                /*119*/ 0,
598:                                        0,
599:                                        0,
600:                                        0,
601:                                        0,
602:                                /*124*/ 0,
603:                                        0,
604:                                        0,
605:                                        0,
606:                                        MatCreateSubMatricesMPI_MPIAdj,
607:                                /*129*/ 0,
608:                                        0,
609:                                        0,
610:                                        0,
611:                                        0,
612:                                /*134*/ 0,
613:                                        0,
614:                                        0,
615:                                        0,
616:                                        0,
617:                                /*139*/ 0,
618:                                        0,
619:                                        0
620: };

622: static PetscErrorCode  MatMPIAdjSetPreallocation_MPIAdj(Mat B,PetscInt *i,PetscInt *j,PetscInt *values)
623: {
624:   Mat_MPIAdj     *b = (Mat_MPIAdj*)B->data;
625:   PetscBool       useedgeweights;

629:   PetscLayoutSetUp(B->rmap);
630:   PetscLayoutSetUp(B->cmap);
631:   if (values) useedgeweights = PETSC_TRUE; else useedgeweights = PETSC_FALSE;
632:   /* Make everybody knows if they are using edge weights or not */
633:   MPIU_Allreduce((int*)&useedgeweights,(int*)&b->useedgeweights,1,MPI_INT,MPI_MAX,PetscObjectComm((PetscObject)B));

635:   if (PetscDefined(USE_DEBUG)) {
636:     PetscInt ii;

638:     if (i[0] != 0) SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"First i[] index must be zero, instead it is %D\n",i[0]);
639:     for (ii=1; ii<B->rmap->n; ii++) {
640:       if (i[ii] < 0 || i[ii] < i[ii-1]) SETERRQ4(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"i[%D]=%D index is out of range: i[%D]=%D",ii,i[ii],ii-1,i[ii-1]);
641:     }
642:     for (ii=0; ii<i[B->rmap->n]; ii++) {
643:       if (j[ii] < 0 || j[ii] >= B->cmap->N) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Column index %D out of range %D\n",ii,j[ii]);
644:     }
645:   }
646:   B->preallocated = PETSC_TRUE;

648:   b->j      = j;
649:   b->i      = i;
650:   b->values = values;

652:   b->nz        = i[B->rmap->n];
653:   b->diag      = 0;
654:   b->symmetric = PETSC_FALSE;
655:   b->freeaij   = PETSC_TRUE;

657:   MatAssemblyBegin(B,MAT_FINAL_ASSEMBLY);
658:   MatAssemblyEnd(B,MAT_FINAL_ASSEMBLY);
659:   return(0);
660: }

662: static PetscErrorCode MatMPIAdjCreateNonemptySubcommMat_MPIAdj(Mat A,Mat *B)
663: {
664:   Mat_MPIAdj     *a = (Mat_MPIAdj*)A->data;
666:   const PetscInt *ranges;
667:   MPI_Comm       acomm,bcomm;
668:   MPI_Group      agroup,bgroup;
669:   PetscMPIInt    i,rank,size,nranks,*ranks;

672:   *B    = NULL;
673:   PetscObjectGetComm((PetscObject)A,&acomm);
674:   MPI_Comm_size(acomm,&size);
675:   MPI_Comm_size(acomm,&rank);
676:   MatGetOwnershipRanges(A,&ranges);
677:   for (i=0,nranks=0; i<size; i++) {
678:     if (ranges[i+1] - ranges[i] > 0) nranks++;
679:   }
680:   if (nranks == size) {         /* All ranks have a positive number of rows, so we do not need to create a subcomm; */
681:     PetscObjectReference((PetscObject)A);
682:     *B   = A;
683:     return(0);
684:   }

686:   PetscMalloc1(nranks,&ranks);
687:   for (i=0,nranks=0; i<size; i++) {
688:     if (ranges[i+1] - ranges[i] > 0) ranks[nranks++] = i;
689:   }
690:   MPI_Comm_group(acomm,&agroup);
691:   MPI_Group_incl(agroup,nranks,ranks,&bgroup);
692:   PetscFree(ranks);
693:   MPI_Comm_create(acomm,bgroup,&bcomm);
694:   MPI_Group_free(&agroup);
695:   MPI_Group_free(&bgroup);
696:   if (bcomm != MPI_COMM_NULL) {
697:     PetscInt   m,N;
698:     Mat_MPIAdj *b;
699:     MatGetLocalSize(A,&m,NULL);
700:     MatGetSize(A,NULL,&N);
701:     MatCreateMPIAdj(bcomm,m,N,a->i,a->j,a->values,B);
702:     b          = (Mat_MPIAdj*)(*B)->data;
703:     b->freeaij = PETSC_FALSE;
704:     MPI_Comm_free(&bcomm);
705:   }
706:   return(0);
707: }

709: PetscErrorCode  MatMPIAdjToSeq_MPIAdj(Mat A,Mat *B)
710: {
712:   PetscInt       M,N,*II,*J,NZ,nz,m,nzstart,i;
713:   PetscInt       *Values = NULL;
714:   Mat_MPIAdj     *adj = (Mat_MPIAdj*)A->data;
715:   PetscMPIInt    mnz,mm,*allnz,*allm,size,*dispnz,*dispm;

718:   MPI_Comm_size(PetscObjectComm((PetscObject)A),&size);
719:   MatGetSize(A,&M,&N);
720:   MatGetLocalSize(A,&m,NULL);
721:   nz   = adj->nz;
722:   if (adj->i[m] != nz) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_PLIB,"nz %D not correct i[m] %d",nz,adj->i[m]);
723:   MPI_Allreduce(&nz,&NZ,1,MPIU_INT,MPI_SUM,PetscObjectComm((PetscObject)A));

725:   PetscMPIIntCast(nz,&mnz);
726:   PetscMalloc2(size,&allnz,size,&dispnz);
727:   MPI_Allgather(&mnz,1,MPI_INT,allnz,1,MPI_INT,PetscObjectComm((PetscObject)A));
728:   dispnz[0] = 0; for (i=1; i<size; i++) dispnz[i] = dispnz[i-1]+ allnz[i-1];
729:   if (adj->values) {
730:     PetscMalloc1(NZ,&Values);
731:     MPI_Allgatherv(adj->values,mnz,MPIU_INT,Values,allnz,dispnz,MPIU_INT,PetscObjectComm((PetscObject)A));
732:   }
733:   PetscMalloc1(NZ,&J);
734:   MPI_Allgatherv(adj->j,mnz,MPIU_INT,J,allnz,dispnz,MPIU_INT,PetscObjectComm((PetscObject)A));
735:   PetscFree2(allnz,dispnz);
736:   MPI_Scan(&nz,&nzstart,1,MPIU_INT,MPI_SUM,PetscObjectComm((PetscObject)A));
737:   nzstart -= nz;
738:   /* shift the i[] values so they will be correct after being received */
739:   for (i=0; i<m; i++) adj->i[i] += nzstart;
740:   PetscMalloc1(M+1,&II);
741:   PetscMPIIntCast(m,&mm);
742:   PetscMalloc2(size,&allm,size,&dispm);
743:   MPI_Allgather(&mm,1,MPI_INT,allm,1,MPI_INT,PetscObjectComm((PetscObject)A));
744:   dispm[0] = 0; for (i=1; i<size; i++) dispm[i] = dispm[i-1]+ allm[i-1];
745:   MPI_Allgatherv(adj->i,mm,MPIU_INT,II,allm,dispm,MPIU_INT,PetscObjectComm((PetscObject)A));
746:   PetscFree2(allm,dispm);
747:   II[M] = NZ;
748:   /* shift the i[] values back */
749:   for (i=0; i<m; i++) adj->i[i] -= nzstart;
750:   MatCreateMPIAdj(PETSC_COMM_SELF,M,N,II,J,Values,B);
751:   return(0);
752: }

754: /*@
755:    MatMPIAdjCreateNonemptySubcommMat - create the same MPIAdj matrix on a subcommunicator containing only processes owning a positive number of rows

757:    Collective

759:    Input Arguments:
760: .  A - original MPIAdj matrix

762:    Output Arguments:
763: .  B - matrix on subcommunicator, NULL on ranks that owned zero rows of A

765:    Level: developer

767:    Note:
768:    This function is mostly useful for internal use by mesh partitioning packages that require that every process owns at least one row.

770:    The matrix B should be destroyed with MatDestroy(). The arrays are not copied, so B should be destroyed before A is destroyed.

772: .seealso: MatCreateMPIAdj()
773: @*/
774: PetscErrorCode MatMPIAdjCreateNonemptySubcommMat(Mat A,Mat *B)
775: {

780:   PetscUseMethod(A,"MatMPIAdjCreateNonemptySubcommMat_C",(Mat,Mat*),(A,B));
781:   return(0);
782: }

784: /*MC
785:    MATMPIADJ - MATMPIADJ = "mpiadj" - A matrix type to be used for distributed adjacency matrices,
786:    intended for use constructing orderings and partitionings.

788:   Level: beginner

790: .seealso: MatCreateMPIAdj
791: M*/

793: PETSC_EXTERN PetscErrorCode MatCreate_MPIAdj(Mat B)
794: {
795:   Mat_MPIAdj     *b;

799:   PetscNewLog(B,&b);
800:   B->data      = (void*)b;
801:   PetscMemcpy(B->ops,&MatOps_Values,sizeof(struct _MatOps));
802:   B->assembled = PETSC_FALSE;

804:   PetscObjectComposeFunction((PetscObject)B,"MatMPIAdjSetPreallocation_C",MatMPIAdjSetPreallocation_MPIAdj);
805:   PetscObjectComposeFunction((PetscObject)B,"MatMPIAdjCreateNonemptySubcommMat_C",MatMPIAdjCreateNonemptySubcommMat_MPIAdj);
806:   PetscObjectComposeFunction((PetscObject)B,"MatMPIAdjToSeq_C",MatMPIAdjToSeq_MPIAdj);
807:   PetscObjectChangeTypeName((PetscObject)B,MATMPIADJ);
808:   return(0);
809: }

811: /*@C
812:    MatMPIAdjToSeq - Converts an parallel MPIAdj matrix to complete MPIAdj on each process (needed by sequential preconditioners)

814:    Logically Collective

816:    Input Parameter:
817: .  A - the matrix

819:    Output Parameter:
820: .  B - the same matrix on all processes

822:    Level: intermediate

824: .seealso: MatCreate(), MatCreateMPIAdj(), MatSetValues()
825: @*/
826: PetscErrorCode  MatMPIAdjToSeq(Mat A,Mat *B)
827: {

831:   PetscUseMethod(A,"MatMPIAdjToSeq_C",(Mat,Mat*),(A,B));
832:   return(0);
833: }

835: /*@C
836:    MatMPIAdjSetPreallocation - Sets the array used for storing the matrix elements

838:    Logically Collective

840:    Input Parameters:
841: +  A - the matrix
842: .  i - the indices into j for the start of each row
843: .  j - the column indices for each row (sorted for each row).
844:        The indices in i and j start with zero (NOT with one).
845: -  values - [optional] edge weights

847:    Level: intermediate

849: .seealso: MatCreate(), MatCreateMPIAdj(), MatSetValues()
850: @*/
851: PetscErrorCode  MatMPIAdjSetPreallocation(Mat B,PetscInt *i,PetscInt *j,PetscInt *values)
852: {

856:   PetscTryMethod(B,"MatMPIAdjSetPreallocation_C",(Mat,PetscInt*,PetscInt*,PetscInt*),(B,i,j,values));
857:   return(0);
858: }

860: /*@C
861:    MatCreateMPIAdj - Creates a sparse matrix representing an adjacency list.
862:    The matrix does not have numerical values associated with it, but is
863:    intended for ordering (to reduce bandwidth etc) and partitioning.

865:    Collective

867:    Input Parameters:
868: +  comm - MPI communicator
869: .  m - number of local rows
870: .  N - number of global columns
871: .  i - the indices into j for the start of each row
872: .  j - the column indices for each row (sorted for each row).
873:        The indices in i and j start with zero (NOT with one).
874: -  values -[optional] edge weights

876:    Output Parameter:
877: .  A - the matrix

879:    Level: intermediate

881:    Notes:
882:     This matrix object does not support most matrix operations, include
883:    MatSetValues().
884:    You must NOT free the ii, values and jj arrays yourself. PETSc will free them
885:    when the matrix is destroyed; you must allocate them with PetscMalloc(). If you
886:     call from Fortran you need not create the arrays with PetscMalloc().
887:    Should not include the matrix diagonals.

889:    If you already have a matrix, you can create its adjacency matrix by a call
890:    to MatConvert, specifying a type of MATMPIADJ.

892:    Possible values for MatSetOption() - MAT_STRUCTURALLY_SYMMETRIC

894: .seealso: MatCreate(), MatConvert(), MatGetOrdering()
895: @*/
896: PetscErrorCode  MatCreateMPIAdj(MPI_Comm comm,PetscInt m,PetscInt N,PetscInt *i,PetscInt *j,PetscInt *values,Mat *A)
897: {

901:   MatCreate(comm,A);
902:   MatSetSizes(*A,m,PETSC_DETERMINE,PETSC_DETERMINE,N);
903:   MatSetType(*A,MATMPIADJ);
904:   MatMPIAdjSetPreallocation(*A,i,j,values);
905:   return(0);
906: }