Actual source code: mpiadj.c

petsc-master 2017-04-26
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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,owner,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,isvalue;
 16:   const PetscInt    *irows_indices,*icols_indices,*xadj, *adjncy;
 17:   Mat_MPIAdj        *a = (Mat_MPIAdj*)adj->data;
 18:   PetscLayout        rmap;
 19:   MPI_Comm           comm;
 20:   PetscSF            sf;
 21:   PetscSFNode       *iremote;
 22:   PetscBool          done;
 23:   PetscErrorCode     ierr;

 26:   PetscObjectGetComm((PetscObject)adj,&comm);
 27:   MatGetLayouts(adj,&rmap,NULL);
 28:   ISGetLocalSize(irows,&nlrows_is);
 29:   ISGetIndices(irows,&irows_indices);
 30:   PetscCalloc1(nlrows_is,&iremote);
 31:   /* construct sf graph*/
 32:   nleaves = nlrows_is;
 33:   for (i=0; i<nlrows_is; i++){
 34:     owner = -1;
 35:     rlocalindex = -1;
 36:     PetscLayoutFindOwnerIndex(rmap,irows_indices[i],&owner,&rlocalindex);
 37:     iremote[i].rank  = owner;
 38:     iremote[i].index = rlocalindex;
 39:   }
 40:   MatGetRowIJ(adj,0,PETSC_FALSE,PETSC_FALSE,&nlrows_mat,&xadj,&adjncy,&done);
 41:   PetscCalloc4(nlrows_mat,&ncols_send,nlrows_is,&xadj_recv,nlrows_is+1,&ncols_recv_offsets,nlrows_is,&ncols_recv);
 42:   nroots = nlrows_mat;
 43:   for (i=0; i<nlrows_mat; i++){
 44:     ncols_send[i] = xadj[i+1]-xadj[i];
 45:   }
 46:   PetscSFCreate(comm,&sf);
 47:   PetscSFSetGraph(sf,nroots,nleaves,NULL,PETSC_OWN_POINTER,iremote,PETSC_OWN_POINTER);
 48:   PetscSFSetType(sf,PETSCSFBASIC);
 49:   PetscSFSetFromOptions(sf);
 50:   PetscSFBcastBegin(sf,MPIU_INT,ncols_send,ncols_recv);
 51:   PetscSFBcastEnd(sf,MPIU_INT,ncols_send,ncols_recv);
 52:   PetscSFBcastBegin(sf,MPIU_INT,xadj,xadj_recv);
 53:   PetscSFBcastEnd(sf,MPIU_INT,xadj,xadj_recv);
 54:   PetscSFDestroy(&sf);
 55:   Ncols_recv =0;
 56:   for (i=0; i<nlrows_is; i++){
 57:     Ncols_recv             += ncols_recv[i];
 58:     ncols_recv_offsets[i+1] = ncols_recv[i]+ncols_recv_offsets[i];
 59:   }
 60:   Ncols_send = 0;
 61:   for(i=0; i<nlrows_mat; i++){
 62:     Ncols_send += ncols_send[i];
 63:   }
 64:   PetscCalloc1(Ncols_recv,&iremote);
 65:   PetscCalloc1(Ncols_recv,&adjncy_recv);
 66:   nleaves = Ncols_recv;
 67:   Ncols_recv = 0;
 68:   for (i=0; i<nlrows_is; i++){
 69:     PetscLayoutFindOwner(rmap,irows_indices[i],&owner);
 70:     for (j=0; j<ncols_recv[i]; j++){
 71:       iremote[Ncols_recv].rank    = owner;
 72:       iremote[Ncols_recv++].index = xadj_recv[i]+j;
 73:     }
 74:   }
 75:   ISRestoreIndices(irows,&irows_indices);
 76:   /*if we need to deal with edge weights ???*/
 77:   if (a->values){isvalue=1;} else {isvalue=0;}
 78:   /*involve a global communication */
 79:   /*MPIU_Allreduce(&isvalue,&isvalue,1,MPIU_INT,MPI_SUM,comm);*/
 80:   if (isvalue){PetscCalloc1(Ncols_recv,&values_recv);}
 81:   nroots = Ncols_send;
 82:   PetscSFCreate(comm,&sf);
 83:   PetscSFSetGraph(sf,nroots,nleaves,NULL,PETSC_OWN_POINTER,iremote,PETSC_OWN_POINTER);
 84:   PetscSFSetType(sf,PETSCSFBASIC);
 85:   PetscSFSetFromOptions(sf);
 86:   PetscSFBcastBegin(sf,MPIU_INT,adjncy,adjncy_recv);
 87:   PetscSFBcastEnd(sf,MPIU_INT,adjncy,adjncy_recv);
 88:   if (isvalue){
 89:     PetscSFBcastBegin(sf,MPIU_INT,a->values,values_recv);
 90:     PetscSFBcastEnd(sf,MPIU_INT,a->values,values_recv);
 91:   }
 92:   PetscSFDestroy(&sf);
 93:   MatRestoreRowIJ(adj,0,PETSC_FALSE,PETSC_FALSE,&nlrows_mat,&xadj,&adjncy,&done);
 94:   ISGetLocalSize(icols,&icols_n);
 95:   ISGetIndices(icols,&icols_indices);
 96:   rnclos = 0;
 97:   for (i=0; i<nlrows_is; i++){
 98:     for (j=ncols_recv_offsets[i]; j<ncols_recv_offsets[i+1]; j++){
 99:       PetscFindInt(adjncy_recv[j], icols_n, icols_indices, &loc);
100:       if (loc<0){
101:         adjncy_recv[j] = -1;
102:         if (isvalue) values_recv[j] = -1;
103:         ncols_recv[i]--;
104:       } else {
105:         rnclos++;
106:       }
107:     }
108:   }
109:   ISRestoreIndices(icols,&icols_indices);
110:   PetscCalloc1(rnclos,&sadjncy);
111:   if (isvalue) {PetscCalloc1(rnclos,&svalues);}
112:   PetscCalloc1(nlrows_is+1,&sxadj);
113:   rnclos = 0;
114:   for(i=0; i<nlrows_is; i++){
115:     for(j=ncols_recv_offsets[i]; j<ncols_recv_offsets[i+1]; j++){
116:       if (adjncy_recv[j]<0) continue;
117:       sadjncy[rnclos] = adjncy_recv[j];
118:       if (isvalue) svalues[rnclos] = values_recv[j];
119:       rnclos++;
120:     }
121:   }
122:   for(i=0; i<nlrows_is; i++){
123:     sxadj[i+1] = sxadj[i]+ncols_recv[i];
124:   }
125:   if (sadj_xadj)  { *sadj_xadj = sxadj;} else    { PetscFree(sxadj);}
126:   if (sadj_adjncy){ *sadj_adjncy = sadjncy;} else { PetscFree(sadjncy);}
127:   if (sadj_values){
128:     if (isvalue) *sadj_values = svalues; else *sadj_values=0;
129:   } else {
130:     if (isvalue) {PetscFree(svalues);}
131:   }
132:   PetscFree4(ncols_send,xadj_recv,ncols_recv_offsets,ncols_recv);
133:   PetscFree(adjncy_recv);
134:   if (isvalue) {PetscFree(values_recv);}
135:   return(0);
136: }

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

148:   nindx = 0;
149:   /*
150:    * Estimate a maximum number for allocating memory
151:    */
152:   for(i=0; i<n; i++){
153:     ISGetLocalSize(irow[i],&irow_n);
154:     ISGetLocalSize(icol[i],&icol_n);
155:     nindx = nindx>(irow_n+icol_n)? nindx:(irow_n+icol_n);
156:   }
157:   PetscCalloc1(nindx,&indices);
158:   /* construct a submat */
159:   for(i=0; i<n; i++){
160:     if (subcomm){
161:       PetscObjectGetComm((PetscObject)irow[i],&scomm_row);
162:       PetscObjectGetComm((PetscObject)icol[i],&scomm_col);
163:       MPI_Comm_compare(scomm_row,scomm_col,&issame);
164:       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");
165:       MPI_Comm_compare(scomm_row,PETSC_COMM_SELF,&issame);
166:       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");
167:     } else {
168:       scomm_row = PETSC_COMM_SELF;
169:     }
170:     /*get sub-matrix data*/
171:     sxadj=0; sadjncy=0; svalues=0;
172:     MatCreateSubMatrix_MPIAdj_data(mat,irow[i],icol[i],&sxadj,&sadjncy,&svalues);
173:     ISGetLocalSize(irow[i],&irow_n);
174:     ISGetLocalSize(icol[i],&icol_n);
175:     ISGetIndices(irow[i],&irow_indices);
176:     PetscMemcpy(indices,irow_indices,sizeof(PetscInt)*irow_n);
177:     ISRestoreIndices(irow[i],&irow_indices);
178:     ISGetIndices(icol[i],&icol_indices);
179:     PetscMemcpy(indices+irow_n,icol_indices,sizeof(PetscInt)*icol_n);
180:     ISRestoreIndices(icol[i],&icol_indices);
181:     nindx = irow_n+icol_n;
182:     PetscSortRemoveDupsInt(&nindx,indices);
183:     /* renumber columns */
184:     for(j=0; j<irow_n; j++){
185:       for(k=sxadj[j]; k<sxadj[j+1]; k++){
186:         PetscFindInt(sadjncy[k],nindx,indices,&loc);
187: #if PETSC_USE_DEBUG
188:         if (loc<0) SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONG,"can not find col %d \n",sadjncy[k]);
189: #endif
190:         sadjncy[k] = loc;
191:       }
192:     }
193:     if (scall==MAT_INITIAL_MATRIX){
194:       MatCreateMPIAdj(scomm_row,irow_n,icol_n,sxadj,sadjncy,svalues,submat[i]);
195:     } else {
196:        Mat                sadj = *(submat[i]);
197:        Mat_MPIAdj         *sa  = (Mat_MPIAdj*)((sadj)->data);
198:        PetscObjectGetComm((PetscObject)sadj,&scomm_mat);
199:        MPI_Comm_compare(scomm_row,scomm_mat,&issame);
200:        if (issame != MPI_IDENT) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_INCOMP,"submatrix  must have the same comm as the col index set\n");
201:        PetscMemcpy(sa->i,sxadj,sizeof(PetscInt)*(irow_n+1));
202:        PetscMemcpy(sa->j,sadjncy,sizeof(PetscInt)*sxadj[irow_n]);
203:        if (svalues){PetscMemcpy(sa->values,svalues,sizeof(PetscInt)*sxadj[irow_n]);}
204:        PetscFree(sxadj);
205:        PetscFree(sadjncy);
206:        if (svalues) {PetscFree(svalues);}
207:     }
208:   }
209:   PetscFree(indices);
210:   return(0);
211: }

213: static PetscErrorCode MatCreateSubMatricesMPI_MPIAdj(Mat mat,PetscInt n, const IS irow[],const IS icol[],MatReuse scall,Mat *submat[])
214: {
215:   PetscErrorCode     ierr;
216:   /*get sub-matrices across a sub communicator */
218:   MatCreateSubMatrices_MPIAdj_Private(mat,n,irow,icol,PETSC_TRUE,scall,submat);
219:   return(0);
220: }

222: static PetscErrorCode MatCreateSubMatrices_MPIAdj(Mat mat,PetscInt n,const IS irow[],const IS icol[],MatReuse scall,Mat *submat[])
223: {
224:   PetscErrorCode     ierr;

227:   /*get sub-matrices based on PETSC_COMM_SELF */
228:   MatCreateSubMatrices_MPIAdj_Private(mat,n,irow,icol,PETSC_FALSE,scall,submat);
229:   return(0);
230: }

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

241:   PetscObjectGetName((PetscObject)A,&name);
242:   PetscViewerGetFormat(viewer,&format);
243:   if (format == PETSC_VIEWER_ASCII_INFO) {
244:     return(0);
245:   } else if (format == PETSC_VIEWER_ASCII_MATLAB) SETERRQ(PetscObjectComm((PetscObject)A),PETSC_ERR_SUP,"MATLAB format not supported");
246:   else {
247:     PetscViewerASCIIUseTabs(viewer,PETSC_FALSE);
248:     PetscViewerASCIIPushSynchronized(viewer);
249:     for (i=0; i<m; i++) {
250:       PetscViewerASCIISynchronizedPrintf(viewer,"row %D:",i+A->rmap->rstart);
251:       for (j=a->i[i]; j<a->i[i+1]; j++) {
252:         PetscViewerASCIISynchronizedPrintf(viewer," %D ",a->j[j]);
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:   PetscMemcmp(a->i,b->i,(A->rmap->n+1)*sizeof(PetscInt),&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;
626: #if defined(PETSC_USE_DEBUG)
627:   PetscInt ii;
628: #endif

631:   PetscLayoutSetUp(B->rmap);
632:   PetscLayoutSetUp(B->cmap);

634: #if defined(PETSC_USE_DEBUG)
635:   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]);
636:   for (ii=1; ii<B->rmap->n; ii++) {
637:     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]);
638:   }
639:   for (ii=0; ii<i[B->rmap->n]; ii++) {
640:     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]);
641:   }
642: #endif
643:   B->preallocated = PETSC_TRUE;

645:   b->j      = j;
646:   b->i      = i;
647:   b->values = values;

649:   b->nz        = i[B->rmap->n];
650:   b->diag      = 0;
651:   b->symmetric = PETSC_FALSE;
652:   b->freeaij   = PETSC_TRUE;

654:   MatAssemblyBegin(B,MAT_FINAL_ASSEMBLY);
655:   MatAssemblyEnd(B,MAT_FINAL_ASSEMBLY);
656:   return(0);
657: }

659: static PetscErrorCode MatMPIAdjCreateNonemptySubcommMat_MPIAdj(Mat A,Mat *B)
660: {
661:   Mat_MPIAdj     *a = (Mat_MPIAdj*)A->data;
663:   const PetscInt *ranges;
664:   MPI_Comm       acomm,bcomm;
665:   MPI_Group      agroup,bgroup;
666:   PetscMPIInt    i,rank,size,nranks,*ranks;

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

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

706: /*@
707:    MatMPIAdjCreateNonemptySubcommMat - create the same MPIAdj matrix on a subcommunicator containing only processes owning a positive number of rows

709:    Collective

711:    Input Arguments:
712: .  A - original MPIAdj matrix

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

717:    Level: developer

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

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

724: .seealso: MatCreateMPIAdj()
725: @*/
726: PetscErrorCode MatMPIAdjCreateNonemptySubcommMat(Mat A,Mat *B)
727: {

732:   PetscUseMethod(A,"MatMPIAdjCreateNonemptySubcommMat_C",(Mat,Mat*),(A,B));
733:   return(0);
734: }

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

740:   Level: beginner

742: .seealso: MatCreateMPIAdj
743: M*/

745: PETSC_EXTERN PetscErrorCode MatCreate_MPIAdj(Mat B)
746: {
747:   Mat_MPIAdj     *b;

751:   PetscNewLog(B,&b);
752:   B->data      = (void*)b;
753:   PetscMemcpy(B->ops,&MatOps_Values,sizeof(struct _MatOps));
754:   B->assembled = PETSC_FALSE;

756:   PetscObjectComposeFunction((PetscObject)B,"MatMPIAdjSetPreallocation_C",MatMPIAdjSetPreallocation_MPIAdj);
757:   PetscObjectComposeFunction((PetscObject)B,"MatMPIAdjCreateNonemptySubcommMat_C",MatMPIAdjCreateNonemptySubcommMat_MPIAdj);
758:   PetscObjectChangeTypeName((PetscObject)B,MATMPIADJ);
759:   return(0);
760: }

762: /*@C
763:    MatMPIAdjSetPreallocation - Sets the array used for storing the matrix elements

765:    Logically Collective on MPI_Comm

767:    Input Parameters:
768: +  A - the matrix
769: .  i - the indices into j for the start of each row
770: .  j - the column indices for each row (sorted for each row).
771:        The indices in i and j start with zero (NOT with one).
772: -  values - [optional] edge weights

774:    Level: intermediate

776: .seealso: MatCreate(), MatCreateMPIAdj(), MatSetValues()
777: @*/
778: PetscErrorCode  MatMPIAdjSetPreallocation(Mat B,PetscInt *i,PetscInt *j,PetscInt *values)
779: {

783:   PetscTryMethod(B,"MatMPIAdjSetPreallocation_C",(Mat,PetscInt*,PetscInt*,PetscInt*),(B,i,j,values));
784:   return(0);
785: }

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

792:    Collective on MPI_Comm

794:    Input Parameters:
795: +  comm - MPI communicator
796: .  m - number of local rows
797: .  N - number of global columns
798: .  i - the indices into j for the start of each row
799: .  j - the column indices for each row (sorted for each row).
800:        The indices in i and j start with zero (NOT with one).
801: -  values -[optional] edge weights

803:    Output Parameter:
804: .  A - the matrix

806:    Level: intermediate

808:    Notes: This matrix object does not support most matrix operations, include
809:    MatSetValues().
810:    You must NOT free the ii, values and jj arrays yourself. PETSc will free them
811:    when the matrix is destroyed; you must allocate them with PetscMalloc(). If you
812:     call from Fortran you need not create the arrays with PetscMalloc().
813:    Should not include the matrix diagonals.

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

818:    Possible values for MatSetOption() - MAT_STRUCTURALLY_SYMMETRIC

820: .seealso: MatCreate(), MatConvert(), MatGetOrdering()
821: @*/
822: PetscErrorCode  MatCreateMPIAdj(MPI_Comm comm,PetscInt m,PetscInt N,PetscInt *i,PetscInt *j,PetscInt *values,Mat *A)
823: {

827:   MatCreate(comm,A);
828:   MatSetSizes(*A,m,PETSC_DETERMINE,PETSC_DETERMINE,N);
829:   MatSetType(*A,MATMPIADJ);
830:   MatMPIAdjSetPreallocation(*A,i,j,values);
831:   return(0);
832: }