Actual source code: mpiadj.c

petsc-3.5.2 2014-09-08
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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>    /*I "petscmat.h" I*/

  9: PetscErrorCode MatView_MPIAdj_ASCII(Mat A,PetscViewer viewer)
 10: {
 11:   Mat_MPIAdj        *a = (Mat_MPIAdj*)A->data;
 12:   PetscErrorCode    ierr;
 13:   PetscInt          i,j,m = A->rmap->n;
 14:   const char        *name;
 15:   PetscViewerFormat format;

 18:   PetscObjectGetName((PetscObject)A,&name);
 19:   PetscViewerGetFormat(viewer,&format);
 20:   if (format == PETSC_VIEWER_ASCII_INFO) {
 21:     return(0);
 22:   } else if (format == PETSC_VIEWER_ASCII_MATLAB) {
 23:     SETERRQ(PetscObjectComm((PetscObject)A),PETSC_ERR_SUP,"MATLAB format not supported");
 24:   } else {
 25:     PetscViewerASCIIUseTabs(viewer,PETSC_FALSE);
 26:     PetscViewerASCIISynchronizedAllow(viewer,PETSC_TRUE);
 27:     for (i=0; i<m; i++) {
 28:       PetscViewerASCIISynchronizedPrintf(viewer,"row %D:",i+A->rmap->rstart);
 29:       for (j=a->i[i]; j<a->i[i+1]; j++) {
 30:         PetscViewerASCIISynchronizedPrintf(viewer," %D ",a->j[j]);
 31:       }
 32:       PetscViewerASCIISynchronizedPrintf(viewer,"\n");
 33:     }
 34:     PetscViewerASCIIUseTabs(viewer,PETSC_TRUE);
 35:     PetscViewerFlush(viewer);
 36:     PetscViewerASCIISynchronizedAllow(viewer,PETSC_FALSE);
 37:   }
 38:   return(0);
 39: }

 43: PetscErrorCode MatView_MPIAdj(Mat A,PetscViewer viewer)
 44: {
 46:   PetscBool      iascii;

 49:   PetscObjectTypeCompare((PetscObject)viewer,PETSCVIEWERASCII,&iascii);
 50:   if (iascii) {
 51:     MatView_MPIAdj_ASCII(A,viewer);
 52:   }
 53:   return(0);
 54: }

 58: PetscErrorCode MatDestroy_MPIAdj(Mat mat)
 59: {
 60:   Mat_MPIAdj     *a = (Mat_MPIAdj*)mat->data;

 64: #if defined(PETSC_USE_LOG)
 65:   PetscLogObjectState((PetscObject)mat,"Rows=%D, Cols=%D, NZ=%D",mat->rmap->n,mat->cmap->n,a->nz);
 66: #endif
 67:   PetscFree(a->diag);
 68:   if (a->freeaij) {
 69:     if (a->freeaijwithfree) {
 70:       if (a->i) free(a->i);
 71:       if (a->j) free(a->j);
 72:     } else {
 73:       PetscFree(a->i);
 74:       PetscFree(a->j);
 75:       PetscFree(a->values);
 76:     }
 77:   }
 78:   PetscFree(a->rowvalues);
 79:   PetscFree(mat->data);
 80:   PetscObjectChangeTypeName((PetscObject)mat,0);
 81:   PetscObjectComposeFunction((PetscObject)mat,"MatMPIAdjSetPreallocation_C",NULL);
 82:   PetscObjectComposeFunction((PetscObject)mat,"MatMPIAdjCreateNonemptySubcommMat_C",NULL);
 83:   return(0);
 84: }

 88: PetscErrorCode MatSetOption_MPIAdj(Mat A,MatOption op,PetscBool flg)
 89: {
 90:   Mat_MPIAdj     *a = (Mat_MPIAdj*)A->data;

 94:   switch (op) {
 95:   case MAT_SYMMETRIC:
 96:   case MAT_STRUCTURALLY_SYMMETRIC:
 97:   case MAT_HERMITIAN:
 98:     a->symmetric = flg;
 99:     break;
100:   case MAT_SYMMETRY_ETERNAL:
101:     break;
102:   default:
103:     PetscInfo1(A,"Option %s ignored\n",MatOptions[op]);
104:     break;
105:   }
106:   return(0);
107: }


110: /*
111:      Adds diagonal pointers to sparse matrix structure.
112: */

116: PetscErrorCode MatMarkDiagonal_MPIAdj(Mat A)
117: {
118:   Mat_MPIAdj     *a = (Mat_MPIAdj*)A->data;
120:   PetscInt       i,j,m = A->rmap->n;

123:   PetscMalloc1(m,&a->diag);
124:   PetscLogObjectMemory((PetscObject)A,m*sizeof(PetscInt));
125:   for (i=0; i<A->rmap->n; i++) {
126:     for (j=a->i[i]; j<a->i[i+1]; j++) {
127:       if (a->j[j] == i) {
128:         a->diag[i] = j;
129:         break;
130:       }
131:     }
132:   }
133:   return(0);
134: }

138: PetscErrorCode MatGetRow_MPIAdj(Mat A,PetscInt row,PetscInt *nz,PetscInt **idx,PetscScalar **v)
139: {
140:   Mat_MPIAdj *a = (Mat_MPIAdj*)A->data;

144:   row -= A->rmap->rstart;

146:   if (row < 0 || row >= A->rmap->n) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Row out of range");

148:   *nz = a->i[row+1] - a->i[row];
149:   if (v) {
150:     PetscInt j;
151:     if (a->rowvalues_alloc < *nz) {
152:       PetscFree(a->rowvalues);
153:       a->rowvalues_alloc = PetscMax(a->rowvalues_alloc*2, *nz);
154:       PetscMalloc1(a->rowvalues_alloc,&a->rowvalues);
155:     }
156:     for (j=0; j<*nz; j++) a->rowvalues[j] = a->values[a->i[row]+j];
157:     *v = (*nz) ? a->rowvalues : NULL;
158:   }
159:   if (idx) *idx = (*nz) ? a->j + a->i[row] : NULL;
160:   return(0);
161: }

165: PetscErrorCode MatRestoreRow_MPIAdj(Mat A,PetscInt row,PetscInt *nz,PetscInt **idx,PetscScalar **v)
166: {
168:   return(0);
169: }

173: PetscErrorCode MatEqual_MPIAdj(Mat A,Mat B,PetscBool * flg)
174: {
175:   Mat_MPIAdj     *a = (Mat_MPIAdj*)A->data,*b = (Mat_MPIAdj*)B->data;
177:   PetscBool      flag;

180:   /* If the  matrix dimensions are not equal,or no of nonzeros */
181:   if ((A->rmap->n != B->rmap->n) ||(a->nz != b->nz)) {
182:     flag = PETSC_FALSE;
183:   }

185:   /* if the a->i are the same */
186:   PetscMemcmp(a->i,b->i,(A->rmap->n+1)*sizeof(PetscInt),&flag);

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

191:   MPI_Allreduce(&flag,flg,1,MPIU_BOOL,MPI_LAND,PetscObjectComm((PetscObject)A));
192:   return(0);
193: }

197: PetscErrorCode MatGetRowIJ_MPIAdj(Mat A,PetscInt oshift,PetscBool symmetric,PetscBool blockcompressed,PetscInt *m,const PetscInt *inia[],const PetscInt *inja[],PetscBool  *done)
198: {
199:   PetscInt   i;
200:   Mat_MPIAdj *a   = (Mat_MPIAdj*)A->data;
201:   PetscInt   **ia = (PetscInt**)inia,**ja = (PetscInt**)inja;

204:   *m    = A->rmap->n;
205:   *ia   = a->i;
206:   *ja   = a->j;
207:   *done = PETSC_TRUE;
208:   if (oshift) {
209:     for (i=0; i<(*ia)[*m]; i++) {
210:       (*ja)[i]++;
211:     }
212:     for (i=0; i<=(*m); i++) (*ia)[i]++;
213:   }
214:   return(0);
215: }

219: PetscErrorCode MatRestoreRowIJ_MPIAdj(Mat A,PetscInt oshift,PetscBool symmetric,PetscBool blockcompressed,PetscInt *m,const PetscInt *inia[],const PetscInt *inja[],PetscBool  *done)
220: {
221:   PetscInt   i;
222:   Mat_MPIAdj *a   = (Mat_MPIAdj*)A->data;
223:   PetscInt   **ia = (PetscInt**)inia,**ja = (PetscInt**)inja;

226:   if (ia && a->i != *ia) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONGSTATE,"ia passed back is not one obtained with MatGetRowIJ()");
227:   if (ja && a->j != *ja) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONGSTATE,"ja passed back is not one obtained with MatGetRowIJ()");
228:   if (oshift) {
229:     for (i=0; i<=(*m); i++) (*ia)[i]--;
230:     for (i=0; i<(*ia)[*m]; i++) {
231:       (*ja)[i]--;
232:     }
233:   }
234:   return(0);
235: }

239: PetscErrorCode  MatConvertFrom_MPIAdj(Mat A,MatType type,MatReuse reuse,Mat *newmat)
240: {
241:   Mat               B;
242:   PetscErrorCode    ierr;
243:   PetscInt          i,m,N,nzeros = 0,*ia,*ja,len,rstart,cnt,j,*a;
244:   const PetscInt    *rj;
245:   const PetscScalar *ra;
246:   MPI_Comm          comm;

249:   MatGetSize(A,NULL,&N);
250:   MatGetLocalSize(A,&m,NULL);
251:   MatGetOwnershipRange(A,&rstart,NULL);

253:   /* count the number of nonzeros per row */
254:   for (i=0; i<m; i++) {
255:     MatGetRow(A,i+rstart,&len,&rj,NULL);
256:     for (j=0; j<len; j++) {
257:       if (rj[j] == i+rstart) {len--; break;}    /* don't count diagonal */
258:     }
259:     nzeros += len;
260:     MatRestoreRow(A,i+rstart,&len,&rj,NULL);
261:   }

263:   /* malloc space for nonzeros */
264:   PetscMalloc1((nzeros+1),&a);
265:   PetscMalloc1((N+1),&ia);
266:   PetscMalloc1((nzeros+1),&ja);

268:   nzeros = 0;
269:   ia[0]  = 0;
270:   for (i=0; i<m; i++) {
271:     MatGetRow(A,i+rstart,&len,&rj,&ra);
272:     cnt  = 0;
273:     for (j=0; j<len; j++) {
274:       if (rj[j] != i+rstart) { /* if not diagonal */
275:         a[nzeros+cnt]    = (PetscInt) PetscAbsScalar(ra[j]);
276:         ja[nzeros+cnt++] = rj[j];
277:       }
278:     }
279:     MatRestoreRow(A,i+rstart,&len,&rj,&ra);
280:     nzeros += cnt;
281:     ia[i+1] = nzeros;
282:   }

284:   PetscObjectGetComm((PetscObject)A,&comm);
285:   MatCreate(comm,&B);
286:   MatSetSizes(B,m,PETSC_DETERMINE,PETSC_DETERMINE,N);
287:   MatSetType(B,type);
288:   MatMPIAdjSetPreallocation(B,ia,ja,a);

290:   if (reuse == MAT_REUSE_MATRIX) {
291:     MatHeaderReplace(A,B);
292:   } else {
293:     *newmat = B;
294:   }
295:   return(0);
296: }

298: /* -------------------------------------------------------------------*/
299: static struct _MatOps MatOps_Values = {0,
300:                                        MatGetRow_MPIAdj,
301:                                        MatRestoreRow_MPIAdj,
302:                                        0,
303:                                 /* 4*/ 0,
304:                                        0,
305:                                        0,
306:                                        0,
307:                                        0,
308:                                        0,
309:                                 /*10*/ 0,
310:                                        0,
311:                                        0,
312:                                        0,
313:                                        0,
314:                                 /*15*/ 0,
315:                                        MatEqual_MPIAdj,
316:                                        0,
317:                                        0,
318:                                        0,
319:                                 /*20*/ 0,
320:                                        0,
321:                                        MatSetOption_MPIAdj,
322:                                        0,
323:                                 /*24*/ 0,
324:                                        0,
325:                                        0,
326:                                        0,
327:                                        0,
328:                                 /*29*/ 0,
329:                                        0,
330:                                        0,
331:                                        0,
332:                                        0,
333:                                 /*34*/ 0,
334:                                        0,
335:                                        0,
336:                                        0,
337:                                        0,
338:                                 /*39*/ 0,
339:                                        0,
340:                                        0,
341:                                        0,
342:                                        0,
343:                                 /*44*/ 0,
344:                                        0,
345:                                        0,
346:                                        0,
347:                                        0,
348:                                 /*49*/ 0,
349:                                        MatGetRowIJ_MPIAdj,
350:                                        MatRestoreRowIJ_MPIAdj,
351:                                        0,
352:                                        0,
353:                                 /*54*/ 0,
354:                                        0,
355:                                        0,
356:                                        0,
357:                                        0,
358:                                 /*59*/ 0,
359:                                        MatDestroy_MPIAdj,
360:                                        MatView_MPIAdj,
361:                                        MatConvertFrom_MPIAdj,
362:                                        0,
363:                                 /*64*/ 0,
364:                                        0,
365:                                        0,
366:                                        0,
367:                                        0,
368:                                 /*69*/ 0,
369:                                        0,
370:                                        0,
371:                                        0,
372:                                        0,
373:                                 /*74*/ 0,
374:                                        0,
375:                                        0,
376:                                        0,
377:                                        0,
378:                                 /*79*/ 0,
379:                                        0,
380:                                        0,
381:                                        0,
382:                                        0,
383:                                 /*84*/ 0,
384:                                        0,
385:                                        0,
386:                                        0,
387:                                        0,
388:                                 /*89*/ 0,
389:                                        0,
390:                                        0,
391:                                        0,
392:                                        0,
393:                                 /*94*/ 0,
394:                                        0,
395:                                        0,
396:                                        0,
397:                                        0,
398:                                 /*99*/ 0,
399:                                        0,
400:                                        0,
401:                                        0,
402:                                        0,
403:                                /*104*/ 0,
404:                                        0,
405:                                        0,
406:                                        0,
407:                                        0,
408:                                /*109*/ 0,
409:                                        0,
410:                                        0,
411:                                        0,
412:                                        0,
413:                                /*114*/ 0,
414:                                        0,
415:                                        0,
416:                                        0,
417:                                        0,
418:                                /*119*/ 0,
419:                                        0,
420:                                        0,
421:                                        0,
422:                                        0,
423:                                /*124*/ 0,
424:                                        0,
425:                                        0,
426:                                        0,
427:                                        0,
428:                                /*129*/ 0,
429:                                        0,
430:                                        0,
431:                                        0,
432:                                        0,
433:                                /*134*/ 0,
434:                                        0,
435:                                        0,
436:                                        0,
437:                                        0,
438:                                /*139*/ 0,
439:                                        0,
440:                                        0
441: };

445: static PetscErrorCode  MatMPIAdjSetPreallocation_MPIAdj(Mat B,PetscInt *i,PetscInt *j,PetscInt *values)
446: {
447:   Mat_MPIAdj     *b = (Mat_MPIAdj*)B->data;
449: #if defined(PETSC_USE_DEBUG)
450:   PetscInt ii;
451: #endif

454:   PetscLayoutSetUp(B->rmap);
455:   PetscLayoutSetUp(B->cmap);

457: #if defined(PETSC_USE_DEBUG)
458:   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]);
459:   for (ii=1; ii<B->rmap->n; ii++) {
460:     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]);
461:   }
462:   for (ii=0; ii<i[B->rmap->n]; ii++) {
463:     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]);
464:   }
465: #endif
466:   B->preallocated = PETSC_TRUE;

468:   b->j      = j;
469:   b->i      = i;
470:   b->values = values;

472:   b->nz        = i[B->rmap->n];
473:   b->diag      = 0;
474:   b->symmetric = PETSC_FALSE;
475:   b->freeaij   = PETSC_TRUE;

477:   MatAssemblyBegin(B,MAT_FINAL_ASSEMBLY);
478:   MatAssemblyEnd(B,MAT_FINAL_ASSEMBLY);
479:   return(0);
480: }

484: static PetscErrorCode MatMPIAdjCreateNonemptySubcommMat_MPIAdj(Mat A,Mat *B)
485: {
486:   Mat_MPIAdj     *a = (Mat_MPIAdj*)A->data;
488:   const PetscInt *ranges;
489:   MPI_Comm       acomm,bcomm;
490:   MPI_Group      agroup,bgroup;
491:   PetscMPIInt    i,rank,size,nranks,*ranks;

494:   *B    = NULL;
495:   PetscObjectGetComm((PetscObject)A,&acomm);
496:   MPI_Comm_size(acomm,&size);
497:   MPI_Comm_size(acomm,&rank);
498:   MatGetOwnershipRanges(A,&ranges);
499:   for (i=0,nranks=0; i<size; i++) {
500:     if (ranges[i+1] - ranges[i] > 0) nranks++;
501:   }
502:   if (nranks == size) {         /* All ranks have a positive number of rows, so we do not need to create a subcomm; */
503:     PetscObjectReference((PetscObject)A);
504:     *B   = A;
505:     return(0);
506:   }

508:   PetscMalloc1(nranks,&ranks);
509:   for (i=0,nranks=0; i<size; i++) {
510:     if (ranges[i+1] - ranges[i] > 0) ranks[nranks++] = i;
511:   }
512:   MPI_Comm_group(acomm,&agroup);
513:   MPI_Group_incl(agroup,nranks,ranks,&bgroup);
514:   PetscFree(ranks);
515:   MPI_Comm_create(acomm,bgroup,&bcomm);
516:   MPI_Group_free(&agroup);
517:   MPI_Group_free(&bgroup);
518:   if (bcomm != MPI_COMM_NULL) {
519:     PetscInt   m,N;
520:     Mat_MPIAdj *b;
521:     MatGetLocalSize(A,&m,NULL);
522:     MatGetSize(A,NULL,&N);
523:     MatCreateMPIAdj(bcomm,m,N,a->i,a->j,a->values,B);
524:     b          = (Mat_MPIAdj*)(*B)->data;
525:     b->freeaij = PETSC_FALSE;
526:     MPI_Comm_free(&bcomm);
527:   }
528:   return(0);
529: }

533: /*@
534:    MatMPIAdjCreateNonemptySubcommMat - create the same MPIAdj matrix on a subcommunicator containing only processes owning a positive number of rows

536:    Collective

538:    Input Arguments:
539: .  A - original MPIAdj matrix

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

544:    Level: developer

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

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

551: .seealso: MatCreateMPIAdj()
552: @*/
553: PetscErrorCode MatMPIAdjCreateNonemptySubcommMat(Mat A,Mat *B)
554: {

559:   PetscUseMethod(A,"MatMPIAdjCreateNonemptySubcommMat_C",(Mat,Mat*),(A,B));
560:   return(0);
561: }

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

567:   Level: beginner

569: .seealso: MatCreateMPIAdj
570: M*/

574: PETSC_EXTERN PetscErrorCode MatCreate_MPIAdj(Mat B)
575: {
576:   Mat_MPIAdj     *b;

580:   PetscNewLog(B,&b);
581:   B->data      = (void*)b;
582:   PetscMemcpy(B->ops,&MatOps_Values,sizeof(struct _MatOps));
583:   B->assembled = PETSC_FALSE;

585:   PetscObjectComposeFunction((PetscObject)B,"MatMPIAdjSetPreallocation_C",MatMPIAdjSetPreallocation_MPIAdj);
586:   PetscObjectComposeFunction((PetscObject)B,"MatMPIAdjCreateNonemptySubcommMat_C",MatMPIAdjCreateNonemptySubcommMat_MPIAdj);
587:   PetscObjectChangeTypeName((PetscObject)B,MATMPIADJ);
588:   return(0);
589: }

593: /*@C
594:    MatMPIAdjSetPreallocation - Sets the array used for storing the matrix elements

596:    Logically Collective on MPI_Comm

598:    Input Parameters:
599: +  A - the matrix
600: .  i - the indices into j for the start of each row
601: .  j - the column indices for each row (sorted for each row).
602:        The indices in i and j start with zero (NOT with one).
603: -  values - [optional] edge weights

605:    Level: intermediate

607: .seealso: MatCreate(), MatCreateMPIAdj(), MatSetValues()
608: @*/
609: PetscErrorCode  MatMPIAdjSetPreallocation(Mat B,PetscInt *i,PetscInt *j,PetscInt *values)
610: {

614:   PetscTryMethod(B,"MatMPIAdjSetPreallocation_C",(Mat,PetscInt*,PetscInt*,PetscInt*),(B,i,j,values));
615:   return(0);
616: }

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

625:    Collective on MPI_Comm

627:    Input Parameters:
628: +  comm - MPI communicator
629: .  m - number of local rows
630: .  N - number of global columns
631: .  i - the indices into j for the start of each row
632: .  j - the column indices for each row (sorted for each row).
633:        The indices in i and j start with zero (NOT with one).
634: -  values -[optional] edge weights

636:    Output Parameter:
637: .  A - the matrix

639:    Level: intermediate

641:    Notes: This matrix object does not support most matrix operations, include
642:    MatSetValues().
643:    You must NOT free the ii, values and jj arrays yourself. PETSc will free them
644:    when the matrix is destroyed; you must allocate them with PetscMalloc(). If you
645:     call from Fortran you need not create the arrays with PetscMalloc().
646:    Should not include the matrix diagonals.

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

651:    Possible values for MatSetOption() - MAT_STRUCTURALLY_SYMMETRIC

653: .seealso: MatCreate(), MatConvert(), MatGetOrdering()
654: @*/
655: PetscErrorCode  MatCreateMPIAdj(MPI_Comm comm,PetscInt m,PetscInt N,PetscInt *i,PetscInt *j,PetscInt *values,Mat *A)
656: {

660:   MatCreate(comm,A);
661:   MatSetSizes(*A,m,PETSC_DETERMINE,PETSC_DETERMINE,N);
662:   MatSetType(*A,MATMPIADJ);
663:   MatMPIAdjSetPreallocation(*A,i,j,values);
664:   return(0);
665: }