Actual source code: iscoloring.c
petsc-3.8.4 2018-03-24
2: #include <petsc/private/isimpl.h>
3: #include <petscviewer.h>
4: #include <petscsf.h>
6: const char *const ISColoringTypes[] = {"global","ghosted","ISColoringType","IS_COLORING_",0};
8: PetscErrorCode ISColoringReference(ISColoring coloring)
9: {
11: (coloring)->refct++;
12: return(0);
13: }
15: PetscErrorCode ISColoringSetType(ISColoring coloring,ISColoringType type)
16: {
18: (coloring)->ctype = type;
19: return(0);
20: }
22: /*@
23: ISColoringDestroy - Destroys a coloring context.
25: Collective on ISColoring
27: Input Parameter:
28: . iscoloring - the coloring context
30: Level: advanced
32: .seealso: ISColoringView(), MatColoring
33: @*/
34: PetscErrorCode ISColoringDestroy(ISColoring *iscoloring)
35: {
36: PetscInt i;
40: if (!*iscoloring) return(0);
42: if (--(*iscoloring)->refct > 0) {*iscoloring = 0; return(0);}
44: if ((*iscoloring)->is) {
45: for (i=0; i<(*iscoloring)->n; i++) {
46: ISDestroy(&(*iscoloring)->is[i]);
47: }
48: PetscFree((*iscoloring)->is);
49: }
50: if ((*iscoloring)->allocated) {PetscFree((*iscoloring)->colors);}
51: PetscCommDestroy(&(*iscoloring)->comm);
52: PetscFree((*iscoloring));
53: return(0);
54: }
56: /*
57: ISColoringViewFromOptions - Processes command line options to determine if/how an ISColoring object is to be viewed.
59: Collective on ISColoring
61: Input Parameters:
62: + obj - the ISColoring object
63: . prefix - prefix to use for viewing, or NULL to use prefix of 'mat'
64: - optionname - option to activate viewing
66: Level: intermediate
68: Developer Note: This cannot use PetscObjectViewFromOptions() because ISColoring is not a PetscObject
70: */
71: PetscErrorCode ISColoringViewFromOptions(ISColoring obj,PetscObject bobj,const char optionname[])
72: {
73: PetscErrorCode ierr;
74: PetscViewer viewer;
75: PetscBool flg;
76: PetscViewerFormat format;
77: char *prefix;
80: prefix = bobj ? bobj->prefix : NULL;
81: PetscOptionsGetViewer(obj->comm,prefix,optionname,&viewer,&format,&flg);
82: if (flg) {
83: PetscViewerPushFormat(viewer,format);
84: ISColoringView(obj,viewer);
85: PetscViewerPopFormat(viewer);
86: PetscViewerDestroy(&viewer);
87: }
88: return(0);
89: }
91: /*@C
92: ISColoringView - Views a coloring context.
94: Collective on ISColoring
96: Input Parameters:
97: + iscoloring - the coloring context
98: - viewer - the viewer
100: Level: advanced
102: .seealso: ISColoringDestroy(), ISColoringGetIS(), MatColoring
103: @*/
104: PetscErrorCode ISColoringView(ISColoring iscoloring,PetscViewer viewer)
105: {
106: PetscInt i;
108: PetscBool iascii;
109: IS *is;
113: if (!viewer) {
114: PetscViewerASCIIGetStdout(iscoloring->comm,&viewer);
115: }
118: PetscObjectTypeCompare((PetscObject)viewer,PETSCVIEWERASCII,&iascii);
119: if (iascii) {
120: MPI_Comm comm;
121: PetscMPIInt size,rank;
123: PetscObjectGetComm((PetscObject)viewer,&comm);
124: MPI_Comm_size(comm,&size);
125: MPI_Comm_rank(comm,&rank);
126: PetscViewerASCIIPrintf(viewer,"ISColoring Object: %d MPI processes\n",size);
127: PetscViewerASCIIPushSynchronized(viewer);
128: PetscViewerASCIISynchronizedPrintf(viewer,"[%d] Number of colors %d\n",rank,iscoloring->n);
129: PetscViewerFlush(viewer);
130: PetscViewerASCIIPopSynchronized(viewer);
131: }
133: ISColoringGetIS(iscoloring,PETSC_IGNORE,&is);
134: for (i=0; i<iscoloring->n; i++) {
135: ISView(iscoloring->is[i],viewer);
136: }
137: ISColoringRestoreIS(iscoloring,&is);
138: return(0);
139: }
141: /*@C
142: ISColoringGetIS - Extracts index sets from the coloring context
144: Collective on ISColoring
146: Input Parameter:
147: . iscoloring - the coloring context
149: Output Parameters:
150: + nn - number of index sets in the coloring context
151: - is - array of index sets
153: Level: advanced
155: .seealso: ISColoringRestoreIS(), ISColoringView()
156: @*/
157: PetscErrorCode ISColoringGetIS(ISColoring iscoloring,PetscInt *nn,IS *isis[])
158: {
164: if (nn) *nn = iscoloring->n;
165: if (isis) {
166: if (!iscoloring->is) {
167: PetscInt *mcolors,**ii,nc = iscoloring->n,i,base, n = iscoloring->N;
168: ISColoringValue *colors = iscoloring->colors;
169: IS *is;
171: #if defined(PETSC_USE_DEBUG)
172: for (i=0; i<n; i++) {
173: 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);
174: }
175: #endif
177: /* generate the lists of nodes for each color */
178: PetscCalloc1(nc,&mcolors);
179: for (i=0; i<n; i++) mcolors[colors[i]]++;
181: PetscMalloc1(nc,&ii);
182: PetscMalloc1(n,&ii[0]);
183: for (i=1; i<nc; i++) ii[i] = ii[i-1] + mcolors[i-1];
184: PetscMemzero(mcolors,nc*sizeof(PetscInt));
186: if (iscoloring->ctype == IS_COLORING_GLOBAL) {
187: MPI_Scan(&iscoloring->N,&base,1,MPIU_INT,MPI_SUM,iscoloring->comm);
188: base -= iscoloring->N;
189: for (i=0; i<n; i++) ii[colors[i]][mcolors[colors[i]]++] = i + base; /* global idx */
190: } else if (iscoloring->ctype == IS_COLORING_LOCAL) {
191: for (i=0; i<n; i++) ii[colors[i]][mcolors[colors[i]]++] = i; /* local idx */
192: } else SETERRQ(PETSC_COMM_SELF,PETSC_ERR_SUP,"Not provided for this ISColoringType type");
194: PetscMalloc1(nc,&is);
195: for (i=0; i<nc; i++) {
196: ISCreateGeneral(iscoloring->comm,mcolors[i],ii[i],PETSC_COPY_VALUES,is+i);
197: }
199: iscoloring->is = is;
200: PetscFree(ii[0]);
201: PetscFree(ii);
202: PetscFree(mcolors);
203: }
204: *isis = iscoloring->is;
205: }
206: return(0);
207: }
209: /*@C
210: ISColoringRestoreIS - Restores the index sets extracted from the coloring context
212: Collective on ISColoring
214: Input Parameter:
215: + iscoloring - the coloring context
216: - is - array of index sets
218: Level: advanced
220: .seealso: ISColoringGetIS(), ISColoringView()
221: @*/
222: PetscErrorCode ISColoringRestoreIS(ISColoring iscoloring,IS *is[])
223: {
227: /* currently nothing is done here */
228: return(0);
229: }
232: /*@
233: ISColoringCreate - Generates an ISColoring context from lists (provided
234: by each processor) of colors for each node.
236: Collective on MPI_Comm
238: Input Parameters:
239: + comm - communicator for the processors creating the coloring
240: . ncolors - max color value
241: . n - number of nodes on this processor
242: . colors - array containing the colors for this processor, color numbers begin at 0.
243: - mode - see PetscCopyMode for meaning of this flag.
245: Output Parameter:
246: . iscoloring - the resulting coloring data structure
248: Options Database Key:
249: . -is_coloring_view - Activates ISColoringView()
251: Level: advanced
253: Notes: By default sets coloring type to IS_COLORING_GLOBAL
255: .seealso: MatColoringCreate(), ISColoringView(), ISColoringDestroy(), ISColoringSetType()
257: @*/
258: PetscErrorCode ISColoringCreate(MPI_Comm comm,PetscInt ncolors,PetscInt n,const ISColoringValue colors[],PetscCopyMode mode,ISColoring *iscoloring)
259: {
261: PetscMPIInt size,rank,tag;
262: PetscInt base,top,i;
263: PetscInt nc,ncwork;
264: MPI_Status status;
267: if (ncolors != PETSC_DECIDE && ncolors > IS_COLORING_MAX) {
268: 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);
269: 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);
270: }
271: PetscNew(iscoloring);
272: PetscCommDuplicate(comm,&(*iscoloring)->comm,&tag);
273: comm = (*iscoloring)->comm;
275: /* compute the number of the first node on my processor */
276: MPI_Comm_size(comm,&size);
278: /* should use MPI_Scan() */
279: MPI_Comm_rank(comm,&rank);
280: if (!rank) {
281: base = 0;
282: top = n;
283: } else {
284: MPI_Recv(&base,1,MPIU_INT,rank-1,tag,comm,&status);
285: top = base+n;
286: }
287: if (rank < size-1) {
288: MPI_Send(&top,1,MPIU_INT,rank+1,tag,comm);
289: }
291: /* compute the total number of colors */
292: ncwork = 0;
293: for (i=0; i<n; i++) {
294: if (ncwork < colors[i]) ncwork = colors[i];
295: }
296: ncwork++;
297: MPIU_Allreduce(&ncwork,&nc,1,MPIU_INT,MPI_MAX,comm);
298: 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);
299: (*iscoloring)->n = nc;
300: (*iscoloring)->is = 0;
301: (*iscoloring)->N = n;
302: (*iscoloring)->refct = 1;
303: (*iscoloring)->ctype = IS_COLORING_GLOBAL;
304: if (mode == PETSC_COPY_VALUES) {
305: PetscMalloc1(n,&(*iscoloring)->colors);
306: PetscLogObjectMemory((PetscObject)(*iscoloring),n*sizeof(ISColoringValue));
307: PetscMemcpy((*iscoloring)->colors,colors,n*sizeof(ISColoringValue));
308: (*iscoloring)->allocated = PETSC_TRUE;
309: } else if (mode == PETSC_OWN_POINTER) {
310: (*iscoloring)->colors = (ISColoringValue*)colors;
311: (*iscoloring)->allocated = PETSC_TRUE;
312: } else {
313: (*iscoloring)->colors = (ISColoringValue*)colors;
314: (*iscoloring)->allocated = PETSC_FALSE;
315: }
316: ISColoringViewFromOptions(*iscoloring,NULL,"-is_coloring_view");
317: PetscInfo1(0,"Number of colors %D\n",nc);
318: return(0);
319: }
321: /*@
322: ISBuildTwoSided - Takes an IS that describes where we will go. Generates an IS that contains new numbers from remote or local
323: on the IS.
325: Collective on IS
327: Input Parameters
328: . to - an IS describes where we will go. Negative target rank will be ignored
329: . toindx - an IS describes what indices should send. NULL means sending natural numbering
331: Output Parameter:
332: . rows - contains new numbers from remote or local
334: Level: advanced
336: .seealso: MatPartitioningCreate(), ISPartitioningToNumbering(), ISPartitioningCount()
338: @*/
339: PetscErrorCode ISBuildTwoSided(IS ito,IS toindx, IS *rows)
340: {
341: const PetscInt *ito_indices,*toindx_indices;
342: PetscInt *send_indices,rstart,*recv_indices,nrecvs,nsends;
343: PetscInt *tosizes,*fromsizes,i,j,*tosizes_tmp,*tooffsets_tmp,ito_ln;
344: PetscMPIInt *toranks,*fromranks,size,target_rank,*fromperm_newtoold,nto,nfrom;
345: PetscLayout isrmap;
346: MPI_Comm comm;
347: PetscSF sf;
348: PetscSFNode *iremote;
349: PetscErrorCode ierr;
352: PetscObjectGetComm((PetscObject)ito,&comm);
353: MPI_Comm_size(comm,&size);
354: ISGetLocalSize(ito,&ito_ln);
355: /* why we do not have ISGetLayout? */
356: isrmap = ito->map;
357: PetscLayoutGetRange(isrmap,&rstart,NULL);
358: ISGetIndices(ito,&ito_indices);
359: PetscCalloc2(size,&tosizes_tmp,size+1,&tooffsets_tmp);
360: for(i=0; i<ito_ln; i++){
361: if(ito_indices[i]<0) continue;
362: #if defined(PETSC_USE_DEBUG)
363: if(ito_indices[i]>=size) SETERRQ2(comm,PETSC_ERR_ARG_OUTOFRANGE,"target rank %d is larger than communicator size %d ",ito_indices[i],size);
364: #endif
365: tosizes_tmp[ito_indices[i]]++;
366: }
367: nto = 0;
368: for(i=0; i<size; i++){
369: tooffsets_tmp[i+1] = tooffsets_tmp[i]+tosizes_tmp[i];
370: if(tosizes_tmp[i]>0) nto++;
371: }
372: PetscCalloc2(nto,&toranks,2*nto,&tosizes);
373: nto = 0;
374: for(i=0; i<size; i++){
375: if(tosizes_tmp[i]>0){
376: toranks[nto] = i;
377: tosizes[2*nto] = tosizes_tmp[i];/* size */
378: tosizes[2*nto+1] = tooffsets_tmp[i];/* offset */
379: nto++;
380: }
381: }
382: nsends = tooffsets_tmp[size];
383: PetscCalloc1(nsends,&send_indices);
384: if(toindx){
385: ISGetIndices(toindx,&toindx_indices);
386: }
387: for(i=0; i<ito_ln; i++){
388: if(ito_indices[i]<0) continue;
389: target_rank = ito_indices[i];
390: send_indices[tooffsets_tmp[target_rank]] = toindx? toindx_indices[i]:(i+rstart);
391: tooffsets_tmp[target_rank]++;
392: }
393: if(toindx){
394: ISRestoreIndices(toindx,&toindx_indices);
395: }
396: ISRestoreIndices(ito,&ito_indices);
397: PetscFree2(tosizes_tmp,tooffsets_tmp);
398: PetscCommBuildTwoSided(comm,2,MPIU_INT,nto,toranks,tosizes,&nfrom,&fromranks,&fromsizes);
399: PetscFree2(toranks,tosizes);
400: PetscCalloc1(nfrom,&fromperm_newtoold);
401: for(i=0; i<nfrom; i++){
402: fromperm_newtoold[i] = i;
403: }
404: PetscSortMPIIntWithArray(nfrom,fromranks,fromperm_newtoold);
405: nrecvs = 0;
406: for(i=0; i<nfrom; i++){
407: nrecvs += fromsizes[i*2];
408: }
409: PetscCalloc1(nrecvs,&recv_indices);
410: PetscCalloc1(nrecvs,&iremote);
411: nrecvs = 0;
412: for(i=0; i<nfrom; i++){
413: for(j=0; j<fromsizes[2*fromperm_newtoold[i]]; j++){
414: iremote[nrecvs].rank = fromranks[i];
415: iremote[nrecvs++].index = fromsizes[2*fromperm_newtoold[i]+1]+j;
416: }
417: }
418: PetscSFCreate(comm,&sf);
419: PetscSFSetGraph(sf,nsends,nrecvs,NULL,PETSC_OWN_POINTER,iremote,PETSC_OWN_POINTER);
420: PetscSFSetType(sf,PETSCSFBASIC);
421: /* how to put a prefix ? */
422: PetscSFSetFromOptions(sf);
423: PetscSFBcastBegin(sf,MPIU_INT,send_indices,recv_indices);
424: PetscSFBcastEnd(sf,MPIU_INT,send_indices,recv_indices);
425: PetscSFDestroy(&sf);
426: PetscFree(fromranks);
427: PetscFree(fromsizes);
428: PetscFree(fromperm_newtoold);
429: PetscFree(send_indices);
430: if(rows){
431: PetscSortInt(nrecvs,recv_indices);
432: ISCreateGeneral(comm, nrecvs,recv_indices,PETSC_OWN_POINTER,rows);
433: }else{
434: PetscFree(recv_indices);
435: }
436: return(0);
437: }
440: /*@
441: ISPartitioningToNumbering - Takes an ISPartitioning and on each processor
442: generates an IS that contains a new global node number for each index based
443: on the partitioing.
445: Collective on IS
447: Input Parameters
448: . partitioning - a partitioning as generated by MatPartitioningApply()
450: Output Parameter:
451: . is - on each processor the index set that defines the global numbers
452: (in the new numbering) for all the nodes currently (before the partitioning)
453: on that processor
455: Level: advanced
457: .seealso: MatPartitioningCreate(), AOCreateBasic(), ISPartitioningCount()
459: @*/
460: PetscErrorCode ISPartitioningToNumbering(IS part,IS *is)
461: {
462: MPI_Comm comm;
463: PetscInt i,np,npt,n,*starts = NULL,*sums = NULL,*lsizes = NULL,*newi = NULL;
464: const PetscInt *indices = NULL;
468: PetscObjectGetComm((PetscObject)part,&comm);
470: /* count the number of partitions, i.e., virtual processors */
471: ISGetLocalSize(part,&n);
472: ISGetIndices(part,&indices);
473: np = 0;
474: for (i=0; i<n; i++) np = PetscMax(np,indices[i]);
475: MPIU_Allreduce(&np,&npt,1,MPIU_INT,MPI_MAX,comm);
476: np = npt+1; /* so that it looks like a MPI_Comm_size output */
478: /*
479: lsizes - number of elements of each partition on this particular processor
480: sums - total number of "previous" nodes for any particular partition
481: starts - global number of first element in each partition on this processor
482: */
483: PetscMalloc3(np,&lsizes,np,&starts,np,&sums);
484: PetscMemzero(lsizes,np*sizeof(PetscInt));
485: for (i=0; i<n; i++) lsizes[indices[i]]++;
486: MPIU_Allreduce(lsizes,sums,np,MPIU_INT,MPI_SUM,comm);
487: MPI_Scan(lsizes,starts,np,MPIU_INT,MPI_SUM,comm);
488: for (i=0; i<np; i++) starts[i] -= lsizes[i];
489: for (i=1; i<np; i++) {
490: sums[i] += sums[i-1];
491: starts[i] += sums[i-1];
492: }
494: /*
495: For each local index give it the new global number
496: */
497: PetscMalloc1(n,&newi);
498: for (i=0; i<n; i++) newi[i] = starts[indices[i]]++;
499: PetscFree3(lsizes,starts,sums);
501: ISRestoreIndices(part,&indices);
502: ISCreateGeneral(comm,n,newi,PETSC_OWN_POINTER,is);
503: ISSetPermutation(*is);
504: return(0);
505: }
507: /*@
508: ISPartitioningCount - Takes a ISPartitioning and determines the number of
509: resulting elements on each (partition) process
511: Collective on IS
513: Input Parameters:
514: + partitioning - a partitioning as generated by MatPartitioningApply()
515: - len - length of the array count, this is the total number of partitions
517: Output Parameter:
518: . count - array of length size, to contain the number of elements assigned
519: to each partition, where size is the number of partitions generated
520: (see notes below).
522: Level: advanced
524: Notes:
525: By default the number of partitions generated (and thus the length
526: of count) is the size of the communicator associated with IS,
527: but it can be set by MatPartitioningSetNParts. The resulting array
528: of lengths can for instance serve as input of PCBJacobiSetTotalBlocks.
531: .seealso: MatPartitioningCreate(), AOCreateBasic(), ISPartitioningToNumbering(),
532: MatPartitioningSetNParts(), MatPartitioningApply()
534: @*/
535: PetscErrorCode ISPartitioningCount(IS part,PetscInt len,PetscInt count[])
536: {
537: MPI_Comm comm;
538: PetscInt i,n,*lsizes;
539: const PetscInt *indices;
541: PetscMPIInt npp;
544: PetscObjectGetComm((PetscObject)part,&comm);
545: if (len == PETSC_DEFAULT) {
546: PetscMPIInt size;
547: MPI_Comm_size(comm,&size);
548: len = (PetscInt) size;
549: }
551: /* count the number of partitions */
552: ISGetLocalSize(part,&n);
553: ISGetIndices(part,&indices);
554: #if defined(PETSC_USE_DEBUG)
555: {
556: PetscInt np = 0,npt;
557: for (i=0; i<n; i++) np = PetscMax(np,indices[i]);
558: MPIU_Allreduce(&np,&npt,1,MPIU_INT,MPI_MAX,comm);
559: np = npt+1; /* so that it looks like a MPI_Comm_size output */
560: 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);
561: }
562: #endif
564: /*
565: lsizes - number of elements of each partition on this particular processor
566: sums - total number of "previous" nodes for any particular partition
567: starts - global number of first element in each partition on this processor
568: */
569: PetscCalloc1(len,&lsizes);
570: for (i=0; i<n; i++) lsizes[indices[i]]++;
571: ISRestoreIndices(part,&indices);
572: PetscMPIIntCast(len,&npp);
573: MPIU_Allreduce(lsizes,count,npp,MPIU_INT,MPI_SUM,comm);
574: PetscFree(lsizes);
575: return(0);
576: }
578: /*@
579: ISAllGather - Given an index set (IS) on each processor, generates a large
580: index set (same on each processor) by concatenating together each
581: processors index set.
583: Collective on IS
585: Input Parameter:
586: . is - the distributed index set
588: Output Parameter:
589: . isout - the concatenated index set (same on all processors)
591: Notes:
592: ISAllGather() is clearly not scalable for large index sets.
594: The IS created on each processor must be created with a common
595: communicator (e.g., PETSC_COMM_WORLD). If the index sets were created
596: with PETSC_COMM_SELF, this routine will not work as expected, since
597: each process will generate its own new IS that consists only of
598: itself.
600: The communicator for this new IS is PETSC_COMM_SELF
602: Level: intermediate
604: Concepts: gather^index sets
605: Concepts: index sets^gathering to all processors
606: Concepts: IS^gathering to all processors
608: .seealso: ISCreateGeneral(), ISCreateStride(), ISCreateBlock()
609: @*/
610: PetscErrorCode ISAllGather(IS is,IS *isout)
611: {
613: PetscInt *indices,n,i,N,step,first;
614: const PetscInt *lindices;
615: MPI_Comm comm;
616: PetscMPIInt size,*sizes = NULL,*offsets = NULL,nn;
617: PetscBool stride;
623: PetscObjectGetComm((PetscObject)is,&comm);
624: MPI_Comm_size(comm,&size);
625: ISGetLocalSize(is,&n);
626: PetscObjectTypeCompare((PetscObject)is,ISSTRIDE,&stride);
627: if (size == 1 && stride) { /* should handle parallel ISStride also */
628: ISStrideGetInfo(is,&first,&step);
629: ISCreateStride(PETSC_COMM_SELF,n,first,step,isout);
630: } else {
631: PetscMalloc2(size,&sizes,size,&offsets);
633: PetscMPIIntCast(n,&nn);
634: MPI_Allgather(&nn,1,MPI_INT,sizes,1,MPI_INT,comm);
635: offsets[0] = 0;
636: for (i=1; i<size; i++) {
637: PetscInt s = offsets[i-1] + sizes[i-1];
638: PetscMPIIntCast(s,&offsets[i]);
639: }
640: N = offsets[size-1] + sizes[size-1];
642: PetscMalloc1(N,&indices);
643: ISGetIndices(is,&lindices);
644: MPI_Allgatherv((void*)lindices,nn,MPIU_INT,indices,sizes,offsets,MPIU_INT,comm);
645: ISRestoreIndices(is,&lindices);
646: PetscFree2(sizes,offsets);
648: ISCreateGeneral(PETSC_COMM_SELF,N,indices,PETSC_OWN_POINTER,isout);
649: }
650: return(0);
651: }
653: /*@C
654: ISAllGatherColors - Given a a set of colors on each processor, generates a large
655: set (same on each processor) by concatenating together each processors colors
657: Collective on MPI_Comm
659: Input Parameter:
660: + comm - communicator to share the indices
661: . n - local size of set
662: - lindices - local colors
664: Output Parameter:
665: + outN - total number of indices
666: - outindices - all of the colors
668: Notes:
669: ISAllGatherColors() is clearly not scalable for large index sets.
672: Level: intermediate
674: Concepts: gather^index sets
675: Concepts: index sets^gathering to all processors
676: Concepts: IS^gathering to all processors
678: .seealso: ISCreateGeneral(), ISCreateStride(), ISCreateBlock(), ISAllGather()
679: @*/
680: PetscErrorCode ISAllGatherColors(MPI_Comm comm,PetscInt n,ISColoringValue *lindices,PetscInt *outN,ISColoringValue *outindices[])
681: {
682: ISColoringValue *indices;
683: PetscErrorCode ierr;
684: PetscInt i,N;
685: PetscMPIInt size,*offsets = NULL,*sizes = NULL, nn = n;
688: MPI_Comm_size(comm,&size);
689: PetscMalloc2(size,&sizes,size,&offsets);
691: MPI_Allgather(&nn,1,MPI_INT,sizes,1,MPI_INT,comm);
692: offsets[0] = 0;
693: for (i=1; i<size; i++) offsets[i] = offsets[i-1] + sizes[i-1];
694: N = offsets[size-1] + sizes[size-1];
695: PetscFree2(sizes,offsets);
697: PetscMalloc1(N+1,&indices);
698: MPI_Allgatherv(lindices,(PetscMPIInt)n,MPIU_COLORING_VALUE,indices,sizes,offsets,MPIU_COLORING_VALUE,comm);
700: *outindices = indices;
701: if (outN) *outN = N;
702: return(0);
703: }
705: /*@
706: ISComplement - Given an index set (IS) generates the complement index set. That is all
707: all indices that are NOT in the given set.
709: Collective on IS
711: Input Parameter:
712: + is - the index set
713: . nmin - the first index desired in the local part of the complement
714: - 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)
716: Output Parameter:
717: . isout - the complement
719: Notes: The communicator for this new IS is the same as for the input IS
721: For a parallel IS, this will generate the local part of the complement on each process
723: To generate the entire complement (on each process) of a parallel IS, first call ISAllGather() and then
724: call this routine.
726: Level: intermediate
728: Concepts: gather^index sets
729: Concepts: index sets^gathering to all processors
730: Concepts: IS^gathering to all processors
732: .seealso: ISCreateGeneral(), ISCreateStride(), ISCreateBlock(), ISAllGather()
733: @*/
734: PetscErrorCode ISComplement(IS is,PetscInt nmin,PetscInt nmax,IS *isout)
735: {
737: const PetscInt *indices;
738: PetscInt n,i,j,unique,cnt,*nindices;
739: PetscBool sorted;
744: if (nmin < 0) SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"nmin %D cannot be negative",nmin);
745: if (nmin > nmax) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"nmin %D cannot be greater than nmax %D",nmin,nmax);
746: ISSorted(is,&sorted);
747: if (!sorted) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONG,"Index set must be sorted");
749: ISGetLocalSize(is,&n);
750: ISGetIndices(is,&indices);
751: #if defined(PETSC_USE_DEBUG)
752: for (i=0; i<n; i++) {
753: 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);
754: 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);
755: }
756: #endif
757: /* Count number of unique entries */
758: unique = (n>0);
759: for (i=0; i<n-1; i++) {
760: if (indices[i+1] != indices[i]) unique++;
761: }
762: PetscMalloc1(nmax-nmin-unique,&nindices);
763: cnt = 0;
764: for (i=nmin,j=0; i<nmax; i++) {
765: if (j<n && i==indices[j]) do { j++; } while (j<n && i==indices[j]);
766: else nindices[cnt++] = i;
767: }
768: 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);
769: ISCreateGeneral(PetscObjectComm((PetscObject)is),cnt,nindices,PETSC_OWN_POINTER,isout);
770: ISRestoreIndices(is,&indices);
771: return(0);
772: }