Actual source code: iscoloring.c

petsc-3.4.4 2014-03-13
  2: #include <petsc-private/isimpl.h>    /*I "petscis.h"  I*/
  3: #include <petscviewer.h>

  5: const char *const ISColoringTypes[] = {"global","ghosted","ISColoringType","IS_COLORING_",0};

  9: PetscErrorCode ISColoringReference(ISColoring coloring)
 10: {
 12:   (coloring)->refct++;
 13:   return(0);
 14: }

 18: PetscErrorCode ISColoringSetType(ISColoring coloring,ISColoringType type)
 19: {
 21:   (coloring)->ctype = type;
 22:   return(0);
 23: }

 27: /*@
 28:    ISColoringDestroy - Destroys a coloring context.

 30:    Collective on ISColoring

 32:    Input Parameter:
 33: .  iscoloring - the coloring context

 35:    Level: advanced

 37: .seealso: ISColoringView(), MatGetColoring()
 38: @*/
 39: PetscErrorCode  ISColoringDestroy(ISColoring *iscoloring)
 40: {
 41:   PetscInt       i;

 45:   if (!*iscoloring) return(0);
 47:   if (--(*iscoloring)->refct > 0) {*iscoloring = 0; return(0);}

 49:   if ((*iscoloring)->is) {
 50:     for (i=0; i<(*iscoloring)->n; i++) {
 51:       ISDestroy(&(*iscoloring)->is[i]);
 52:     }
 53:     PetscFree((*iscoloring)->is);
 54:   }
 55:   PetscFree((*iscoloring)->colors);
 56:   PetscCommDestroy(&(*iscoloring)->comm);
 57:   PetscFree((*iscoloring));
 58:   return(0);
 59: }

 63: /*@C
 64:    ISColoringView - Views a coloring context.

 66:    Collective on ISColoring

 68:    Input Parameters:
 69: +  iscoloring - the coloring context
 70: -  viewer - the viewer

 72:    Level: advanced

 74: .seealso: ISColoringDestroy(), ISColoringGetIS(), MatGetColoring()
 75: @*/
 76: PetscErrorCode  ISColoringView(ISColoring iscoloring,PetscViewer viewer)
 77: {
 78:   PetscInt       i;
 80:   PetscBool      iascii;
 81:   IS             *is;

 85:   if (!viewer) {
 86:     PetscViewerASCIIGetStdout(iscoloring->comm,&viewer);
 87:   }

 90:   PetscObjectTypeCompare((PetscObject)viewer,PETSCVIEWERASCII,&iascii);
 91:   if (iascii) {
 92:     MPI_Comm    comm;
 93:     PetscMPIInt rank;
 94:     PetscObjectGetComm((PetscObject)viewer,&comm);
 95:     MPI_Comm_rank(comm,&rank);
 96:     PetscViewerASCIISynchronizedAllow(viewer,PETSC_TRUE);
 97:     PetscViewerASCIISynchronizedPrintf(viewer,"[%d] Number of colors %d\n",rank,iscoloring->n);
 98:     PetscViewerFlush(viewer);
 99:     PetscViewerASCIISynchronizedAllow(viewer,PETSC_FALSE);
100:   } else SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_SUP,"Viewer type %s not supported for ISColoring",((PetscObject)viewer)->type_name);

102:   ISColoringGetIS(iscoloring,PETSC_IGNORE,&is);
103:   for (i=0; i<iscoloring->n; i++) {
104:     ISView(iscoloring->is[i],viewer);
105:   }
106:   ISColoringRestoreIS(iscoloring,&is);
107:   return(0);
108: }

112: /*@C
113:    ISColoringGetIS - Extracts index sets from the coloring context

115:    Collective on ISColoring

117:    Input Parameter:
118: .  iscoloring - the coloring context

120:    Output Parameters:
121: +  nn - number of index sets in the coloring context
122: -  is - array of index sets

124:    Level: advanced

126: .seealso: ISColoringRestoreIS(), ISColoringView()
127: @*/
128: PetscErrorCode  ISColoringGetIS(ISColoring iscoloring,PetscInt *nn,IS *isis[])
129: {


135:   if (nn) *nn = iscoloring->n;
136:   if (isis) {
137:     if (!iscoloring->is) {
138:       PetscInt        *mcolors,**ii,nc = iscoloring->n,i,base, n = iscoloring->N;
139:       ISColoringValue *colors = iscoloring->colors;
140:       IS              *is;

142: #if defined(PETSC_USE_DEBUG)
143:       for (i=0; i<n; i++) {
144:         if (((PetscInt)colors[i]) >= nc) SETERRQ3(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Coloring is our of range index %d value %d number colors %d",(int)i,(int)colors[i],(int)nc);
145:       }
146: #endif

148:       /* generate the lists of nodes for each color */
149:       PetscMalloc(nc*sizeof(PetscInt),&mcolors);
150:       PetscMemzero(mcolors,nc*sizeof(PetscInt));
151:       for (i=0; i<n; i++) mcolors[colors[i]]++;

153:       PetscMalloc(nc*sizeof(PetscInt*),&ii);
154:       PetscMalloc(n*sizeof(PetscInt),&ii[0]);
155:       for (i=1; i<nc; i++) ii[i] = ii[i-1] + mcolors[i-1];
156:       PetscMemzero(mcolors,nc*sizeof(PetscInt));

158:       if (iscoloring->ctype == IS_COLORING_GLOBAL) {
159:         MPI_Scan(&iscoloring->N,&base,1,MPIU_INT,MPI_SUM,iscoloring->comm);
160:         base -= iscoloring->N;
161:         for (i=0; i<n; i++) ii[colors[i]][mcolors[colors[i]]++] = i + base; /* global idx */
162:       } else if (iscoloring->ctype == IS_COLORING_GHOSTED) {
163:         for (i=0; i<n; i++) ii[colors[i]][mcolors[colors[i]]++] = i;   /* local idx */
164:       } else SETERRQ(PETSC_COMM_SELF,PETSC_ERR_SUP,"Not provided for this ISColoringType type");

166:       PetscMalloc(nc*sizeof(IS),&is);
167:       for (i=0; i<nc; i++) {
168:         ISCreateGeneral(iscoloring->comm,mcolors[i],ii[i],PETSC_COPY_VALUES,is+i);
169:       }

171:       iscoloring->is = is;
172:       PetscFree(ii[0]);
173:       PetscFree(ii);
174:       PetscFree(mcolors);
175:     }
176:     *isis = iscoloring->is;
177:   }
178:   return(0);
179: }

183: /*@C
184:    ISColoringRestoreIS - Restores the index sets extracted from the coloring context

186:    Collective on ISColoring

188:    Input Parameter:
189: +  iscoloring - the coloring context
190: -  is - array of index sets

192:    Level: advanced

194: .seealso: ISColoringGetIS(), ISColoringView()
195: @*/
196: PetscErrorCode  ISColoringRestoreIS(ISColoring iscoloring,IS *is[])
197: {

201:   /* currently nothing is done here */
202:   return(0);
203: }


208: /*@C
209:     ISColoringCreate - Generates an ISColoring context from lists (provided
210:     by each processor) of colors for each node.

212:     Collective on MPI_Comm

214:     Input Parameters:
215: +   comm - communicator for the processors creating the coloring
216: .   ncolors - max color value
217: .   n - number of nodes on this processor
218: -   colors - array containing the colors for this processor, color
219:              numbers begin at 0. In C/C++ this array must have been obtained with PetscMalloc()
220:              and should NOT be freed (The ISColoringDestroy() will free it).

222:     Output Parameter:
223: .   iscoloring - the resulting coloring data structure

225:     Options Database Key:
226: .   -is_coloring_view - Activates ISColoringView()

228:    Level: advanced

230:     Notes: By default sets coloring type to  IS_COLORING_GLOBAL

232: .seealso: MatColoringCreate(), ISColoringView(), ISColoringDestroy(), ISColoringSetType()

234: @*/
235: PetscErrorCode  ISColoringCreate(MPI_Comm comm,PetscInt ncolors,PetscInt n,const ISColoringValue colors[],ISColoring *iscoloring)
236: {
238:   PetscMPIInt    size,rank,tag;
239:   PetscInt       base,top,i;
240:   PetscInt       nc,ncwork;
241:   PetscBool      flg = PETSC_FALSE;
242:   MPI_Status     status;

245:   if (ncolors != PETSC_DECIDE && ncolors > IS_COLORING_MAX) {
246:     if (ncolors > 65535) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Max color value exeeds 65535 limit. This number is unrealistic. Perhaps a bug in code?\nCurrent max: %d user rewuested: %d",IS_COLORING_MAX,ncolors);
247:     else                 SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Max color value exeeds limit. Perhaps reconfigure PETSc with --with-is-color-value-type=short?\n Current max: %d user rewuested: %d",IS_COLORING_MAX,ncolors);
248:   }
249:   PetscNew(struct _n_ISColoring,iscoloring);
250:   PetscCommDuplicate(comm,&(*iscoloring)->comm,&tag);
251:   comm = (*iscoloring)->comm;

253:   /* compute the number of the first node on my processor */
254:   MPI_Comm_size(comm,&size);

256:   /* should use MPI_Scan() */
257:   MPI_Comm_rank(comm,&rank);
258:   if (!rank) {
259:     base = 0;
260:     top  = n;
261:   } else {
262:     MPI_Recv(&base,1,MPIU_INT,rank-1,tag,comm,&status);
263:     top  = base+n;
264:   }
265:   if (rank < size-1) {
266:     MPI_Send(&top,1,MPIU_INT,rank+1,tag,comm);
267:   }

269:   /* compute the total number of colors */
270:   ncwork = 0;
271:   for (i=0; i<n; i++) {
272:     if (ncwork < colors[i]) ncwork = colors[i];
273:   }
274:   ncwork++;
275:   MPI_Allreduce(&ncwork,&nc,1,MPIU_INT,MPI_MAX,comm);
276:   if (nc > ncolors) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_INCOMP,"Number of colors passed in %D is less then the actual number of colors in array %D",ncolors,nc);
277:   (*iscoloring)->n      = nc;
278:   (*iscoloring)->is     = 0;
279:   (*iscoloring)->colors = (ISColoringValue*)colors;
280:   (*iscoloring)->N      = n;
281:   (*iscoloring)->refct  = 1;
282:   (*iscoloring)->ctype  = IS_COLORING_GLOBAL;

284:   PetscOptionsGetBool(NULL,"-is_coloring_view",&flg,NULL);
285:   if (flg) {
286:     PetscViewer viewer;
287:     PetscViewerASCIIGetStdout((*iscoloring)->comm,&viewer);
288:     ISColoringView(*iscoloring,viewer);
289:   }
290:   PetscInfo1(0,"Number of colors %D\n",nc);
291:   return(0);
292: }

296: /*@
297:     ISPartitioningToNumbering - Takes an ISPartitioning and on each processor
298:     generates an IS that contains a new global node number for each index based
299:     on the partitioing.

301:     Collective on IS

303:     Input Parameters
304: .   partitioning - a partitioning as generated by MatPartitioningApply()

306:     Output Parameter:
307: .   is - on each processor the index set that defines the global numbers
308:          (in the new numbering) for all the nodes currently (before the partitioning)
309:          on that processor

311:    Level: advanced

313: .seealso: MatPartitioningCreate(), AOCreateBasic(), ISPartitioningCount()

315: @*/
316: PetscErrorCode  ISPartitioningToNumbering(IS part,IS *is)
317: {
318:   MPI_Comm       comm;
319:   PetscInt       i,np,npt,n,*starts = NULL,*sums = NULL,*lsizes = NULL,*newi = NULL;
320:   const PetscInt *indices = NULL;

324:   PetscObjectGetComm((PetscObject)part,&comm);

326:   /* count the number of partitions, i.e., virtual processors */
327:   ISGetLocalSize(part,&n);
328:   ISGetIndices(part,&indices);
329:   np   = 0;
330:   for (i=0; i<n; i++) np = PetscMax(np,indices[i]);
331:   MPI_Allreduce(&np,&npt,1,MPIU_INT,MPI_MAX,comm);
332:   np   = npt+1; /* so that it looks like a MPI_Comm_size output */

334:   /*
335:         lsizes - number of elements of each partition on this particular processor
336:         sums - total number of "previous" nodes for any particular partition
337:         starts - global number of first element in each partition on this processor
338:   */
339:   PetscMalloc3(np,PetscInt,&lsizes,np,PetscInt,&starts,np,PetscInt,&sums);
340:   PetscMemzero(lsizes,np*sizeof(PetscInt));
341:   for (i=0; i<n; i++) lsizes[indices[i]]++;
342:   MPI_Allreduce(lsizes,sums,np,MPIU_INT,MPI_SUM,comm);
343:   MPI_Scan(lsizes,starts,np,MPIU_INT,MPI_SUM,comm);
344:   for (i=0; i<np; i++) starts[i] -= lsizes[i];
345:   for (i=1; i<np; i++) {
346:     sums[i]   += sums[i-1];
347:     starts[i] += sums[i-1];
348:   }

350:   /*
351:       For each local index give it the new global number
352:   */
353:   PetscMalloc(n*sizeof(PetscInt),&newi);
354:   for (i=0; i<n; i++) newi[i] = starts[indices[i]]++;
355:   PetscFree3(lsizes,starts,sums);

357:   ISRestoreIndices(part,&indices);
358:   ISCreateGeneral(comm,n,newi,PETSC_OWN_POINTER,is);
359:   ISSetPermutation(*is);
360:   return(0);
361: }

365: /*@
366:     ISPartitioningCount - Takes a ISPartitioning and determines the number of
367:     resulting elements on each (partition) process

369:     Collective on IS

371:     Input Parameters:
372: +   partitioning - a partitioning as generated by MatPartitioningApply()
373: -   len - length of the array count, this is the total number of partitions

375:     Output Parameter:
376: .   count - array of length size, to contain the number of elements assigned
377:         to each partition, where size is the number of partitions generated
378:          (see notes below).

380:    Level: advanced

382:     Notes:
383:         By default the number of partitions generated (and thus the length
384:         of count) is the size of the communicator associated with IS,
385:         but it can be set by MatPartitioningSetNParts. The resulting array
386:         of lengths can for instance serve as input of PCBJacobiSetTotalBlocks.


389: .seealso: MatPartitioningCreate(), AOCreateBasic(), ISPartitioningToNumbering(),
390:         MatPartitioningSetNParts(), MatPartitioningApply()

392: @*/
393: PetscErrorCode  ISPartitioningCount(IS part,PetscInt len,PetscInt count[])
394: {
395:   MPI_Comm       comm;
396:   PetscInt       i,n,*lsizes;
397:   const PetscInt *indices;
399:   PetscMPIInt    npp;

402:   PetscObjectGetComm((PetscObject)part,&comm);
403:   if (len == PETSC_DEFAULT) {
404:     PetscMPIInt size;
405:     MPI_Comm_size(comm,&size);
406:     len  = (PetscInt) size;
407:   }

409:   /* count the number of partitions */
410:   ISGetLocalSize(part,&n);
411:   ISGetIndices(part,&indices);
412: #if defined(PETSC_USE_DEBUG)
413:   {
414:     PetscInt np = 0,npt;
415:     for (i=0; i<n; i++) np = PetscMax(np,indices[i]);
416:     MPI_Allreduce(&np,&npt,1,MPIU_INT,MPI_MAX,comm);
417:     np   = npt+1; /* so that it looks like a MPI_Comm_size output */
418:     if (np > len) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_SIZ,"Length of count array %D is less than number of partitions %D",len,np);
419:   }
420: #endif

422:   /*
423:         lsizes - number of elements of each partition on this particular processor
424:         sums - total number of "previous" nodes for any particular partition
425:         starts - global number of first element in each partition on this processor
426:   */
427:   PetscMalloc(len*sizeof(PetscInt),&lsizes);
428:   PetscMemzero(lsizes,len*sizeof(PetscInt));
429:   for (i=0; i<n; i++) lsizes[indices[i]]++;
430:   ISRestoreIndices(part,&indices);
431:   PetscMPIIntCast(len,&npp);
432:   MPI_Allreduce(lsizes,count,npp,MPIU_INT,MPI_SUM,comm);
433:   PetscFree(lsizes);
434:   return(0);
435: }

439: /*@
440:     ISAllGather - Given an index set (IS) on each processor, generates a large
441:     index set (same on each processor) by concatenating together each
442:     processors index set.

444:     Collective on IS

446:     Input Parameter:
447: .   is - the distributed index set

449:     Output Parameter:
450: .   isout - the concatenated index set (same on all processors)

452:     Notes:
453:     ISAllGather() is clearly not scalable for large index sets.

455:     The IS created on each processor must be created with a common
456:     communicator (e.g., PETSC_COMM_WORLD). If the index sets were created
457:     with PETSC_COMM_SELF, this routine will not work as expected, since
458:     each process will generate its own new IS that consists only of
459:     itself.

461:     The communicator for this new IS is PETSC_COMM_SELF

463:     Level: intermediate

465:     Concepts: gather^index sets
466:     Concepts: index sets^gathering to all processors
467:     Concepts: IS^gathering to all processors

469: .seealso: ISCreateGeneral(), ISCreateStride(), ISCreateBlock()
470: @*/
471: PetscErrorCode  ISAllGather(IS is,IS *isout)
472: {
474:   PetscInt       *indices,n,i,N,step,first;
475:   const PetscInt *lindices;
476:   MPI_Comm       comm;
477:   PetscMPIInt    size,*sizes = NULL,*offsets = NULL,nn;
478:   PetscBool      stride;


484:   PetscObjectGetComm((PetscObject)is,&comm);
485:   MPI_Comm_size(comm,&size);
486:   ISGetLocalSize(is,&n);
487:   PetscObjectTypeCompare((PetscObject)is,ISSTRIDE,&stride);
488:   if (size == 1 && stride) { /* should handle parallel ISStride also */
489:     ISStrideGetInfo(is,&first,&step);
490:     ISCreateStride(PETSC_COMM_SELF,n,first,step,isout);
491:   } else {
492:     PetscMalloc2(size,PetscMPIInt,&sizes,size,PetscMPIInt,&offsets);

494:     PetscMPIIntCast(n,&nn);
495:     MPI_Allgather(&nn,1,MPI_INT,sizes,1,MPI_INT,comm);
496:     offsets[0] = 0;
497:     for (i=1; i<size; i++) offsets[i] = offsets[i-1] + sizes[i-1];
498:     N = offsets[size-1] + sizes[size-1];

500:     PetscMalloc(N*sizeof(PetscInt),&indices);
501:     ISGetIndices(is,&lindices);
502:     MPI_Allgatherv((void*)lindices,nn,MPIU_INT,indices,sizes,offsets,MPIU_INT,comm);
503:     ISRestoreIndices(is,&lindices);
504:     PetscFree2(sizes,offsets);

506:     ISCreateGeneral(PETSC_COMM_SELF,N,indices,PETSC_OWN_POINTER,isout);
507:   }
508:   return(0);
509: }

513: /*@C
514:     ISAllGatherColors - Given a a set of colors on each processor, generates a large
515:     set (same on each processor) by concatenating together each processors colors

517:     Collective on MPI_Comm

519:     Input Parameter:
520: +   comm - communicator to share the indices
521: .   n - local size of set
522: -   lindices - local colors

524:     Output Parameter:
525: +   outN - total number of indices
526: -   outindices - all of the colors

528:     Notes:
529:     ISAllGatherColors() is clearly not scalable for large index sets.


532:     Level: intermediate

534:     Concepts: gather^index sets
535:     Concepts: index sets^gathering to all processors
536:     Concepts: IS^gathering to all processors

538: .seealso: ISCreateGeneral(), ISCreateStride(), ISCreateBlock(), ISAllGather()
539: @*/
540: PetscErrorCode  ISAllGatherColors(MPI_Comm comm,PetscInt n,ISColoringValue *lindices,PetscInt *outN,ISColoringValue *outindices[])
541: {
542:   ISColoringValue *indices;
543:   PetscErrorCode  ierr;
544:   PetscInt        i,N;
545:   PetscMPIInt     size,*offsets = NULL,*sizes = NULL, nn = n;

548:   MPI_Comm_size(comm,&size);
549:   PetscMalloc2(size,PetscMPIInt,&sizes,size,PetscMPIInt,&offsets);

551:   MPI_Allgather(&nn,1,MPI_INT,sizes,1,MPI_INT,comm);
552:   offsets[0] = 0;
553:   for (i=1; i<size; i++) offsets[i] = offsets[i-1] + sizes[i-1];
554:   N    = offsets[size-1] + sizes[size-1];
555:   PetscFree2(sizes,offsets);

557:   PetscMalloc((N+1)*sizeof(ISColoringValue),&indices);
558:   MPI_Allgatherv(lindices,(PetscMPIInt)n,MPIU_COLORING_VALUE,indices,sizes,offsets,MPIU_COLORING_VALUE,comm);

560:   *outindices = indices;
561:   if (outN) *outN = N;
562:   return(0);
563: }

567: /*@
568:     ISComplement - Given an index set (IS) generates the complement index set. That is all
569:        all indices that are NOT in the given set.

571:     Collective on IS

573:     Input Parameter:
574: +   is - the index set
575: .   nmin - the first index desired in the local part of the complement
576: -   nmax - the largest index desired in the local part of the complement (note that all indices in is must be greater or equal to nmin and less than nmax)

578:     Output Parameter:
579: .   isout - the complement

581:     Notes:  The communicator for this new IS is the same as for the input IS

583:       For a parallel IS, this will generate the local part of the complement on each process

585:       To generate the entire complement (on each process) of a parallel IS, first call ISAllGather() and then
586:     call this routine.

588:     Level: intermediate

590:     Concepts: gather^index sets
591:     Concepts: index sets^gathering to all processors
592:     Concepts: IS^gathering to all processors

594: .seealso: ISCreateGeneral(), ISCreateStride(), ISCreateBlock(), ISAllGather()
595: @*/
596: PetscErrorCode  ISComplement(IS is,PetscInt nmin,PetscInt nmax,IS *isout)
597: {
599:   const PetscInt *indices;
600:   PetscInt       n,i,j,unique,cnt,*nindices;
601:   PetscBool      sorted;

606:   if (nmin < 0) SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"nmin %D cannot be negative",nmin);
607:   if (nmin > nmax) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"nmin %D cannot be greater than nmax %D",nmin,nmax);
608:   ISSorted(is,&sorted);
609:   if (!sorted) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONG,"Index set must be sorted");

611:   ISGetLocalSize(is,&n);
612:   ISGetIndices(is,&indices);
613: #if defined(PETSC_USE_DEBUG)
614:   for (i=0; i<n; i++) {
615:     if (indices[i] <  nmin) SETERRQ3(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Index %D's value %D is smaller than minimum given %D",i,indices[i],nmin);
616:     if (indices[i] >= nmax) SETERRQ3(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Index %D's value %D is larger than maximum given %D",i,indices[i],nmax);
617:   }
618: #endif
619:   /* Count number of unique entries */
620:   unique = (n>0);
621:   for (i=0; i<n-1; i++) {
622:     if (indices[i+1] != indices[i]) unique++;
623:   }
624:   PetscMalloc((nmax-nmin-unique)*sizeof(PetscInt),&nindices);
625:   cnt  = 0;
626:   for (i=nmin,j=0; i<nmax; i++) {
627:     if (j<n && i==indices[j]) do { j++; } while (j<n && i==indices[j]);
628:     else nindices[cnt++] = i;
629:   }
630:   if (cnt != nmax-nmin-unique) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_PLIB,"Number of entries found in complement %D does not match expected %D",cnt,nmax-nmin-unique);
631:   ISCreateGeneral(PetscObjectComm((PetscObject)is),cnt,nindices,PETSC_OWN_POINTER,isout);
632:   ISRestoreIndices(is,&indices);
633:   return(0);
634: }