Actual source code: plexdistribute.c
petsc-3.13.6 2020-09-29
1: #include <petsc/private/dmpleximpl.h>
2: #include <petsc/private/dmlabelimpl.h>
4: /*@C
5: DMPlexSetAdjacencyUser - Define adjacency in the mesh using a user-provided callback
7: Input Parameters:
8: + dm - The DM object
9: . user - The user callback, may be NULL (to clear the callback)
10: - ctx - context for callback evaluation, may be NULL
12: Level: advanced
14: Notes:
15: The caller of DMPlexGetAdjacency may need to arrange that a large enough array is available for the adjacency.
17: Any setting here overrides other configuration of DMPlex adjacency determination.
19: .seealso: DMSetAdjacency(), DMPlexDistribute(), DMPlexPreallocateOperator(), DMPlexGetAdjacency(), DMPlexGetAdjacencyUser()
20: @*/
21: PetscErrorCode DMPlexSetAdjacencyUser(DM dm,PetscErrorCode (*user)(DM,PetscInt,PetscInt*,PetscInt[],void*),void *ctx)
22: {
23: DM_Plex *mesh = (DM_Plex *)dm->data;
27: mesh->useradjacency = user;
28: mesh->useradjacencyctx = ctx;
29: return(0);
30: }
32: /*@C
33: DMPlexGetAdjacencyUser - get the user-defined adjacency callback
35: Input Parameter:
36: . dm - The DM object
38: Output Parameters:
39: - user - The user callback
40: - ctx - context for callback evaluation
42: Level: advanced
44: .seealso: DMSetAdjacency(), DMPlexDistribute(), DMPlexPreallocateOperator(), DMPlexGetAdjacency(), DMPlexSetAdjacencyUser()
45: @*/
46: PetscErrorCode DMPlexGetAdjacencyUser(DM dm, PetscErrorCode (**user)(DM,PetscInt,PetscInt*,PetscInt[],void*), void **ctx)
47: {
48: DM_Plex *mesh = (DM_Plex *)dm->data;
52: if (user) *user = mesh->useradjacency;
53: if (ctx) *ctx = mesh->useradjacencyctx;
54: return(0);
55: }
57: /*@
58: DMPlexSetAdjacencyUseAnchors - Define adjacency in the mesh using the point-to-point constraints.
60: Input Parameters:
61: + dm - The DM object
62: - useAnchors - Flag to use the constraints. If PETSC_TRUE, then constrained points are omitted from DMPlexGetAdjacency(), and their anchor points appear in their place.
64: Level: intermediate
66: .seealso: DMGetAdjacency(), DMSetAdjacency(), DMPlexDistribute(), DMPlexPreallocateOperator(), DMPlexSetAnchors()
67: @*/
68: PetscErrorCode DMPlexSetAdjacencyUseAnchors(DM dm, PetscBool useAnchors)
69: {
70: DM_Plex *mesh = (DM_Plex *) dm->data;
74: mesh->useAnchors = useAnchors;
75: return(0);
76: }
78: /*@
79: DMPlexGetAdjacencyUseAnchors - Query whether adjacency in the mesh uses the point-to-point constraints.
81: Input Parameter:
82: . dm - The DM object
84: Output Parameter:
85: . useAnchors - Flag to use the closure. If PETSC_TRUE, then constrained points are omitted from DMPlexGetAdjacency(), and their anchor points appear in their place.
87: Level: intermediate
89: .seealso: DMPlexSetAdjacencyUseAnchors(), DMSetAdjacency(), DMGetAdjacency(), DMPlexDistribute(), DMPlexPreallocateOperator(), DMPlexSetAnchors()
90: @*/
91: PetscErrorCode DMPlexGetAdjacencyUseAnchors(DM dm, PetscBool *useAnchors)
92: {
93: DM_Plex *mesh = (DM_Plex *) dm->data;
98: *useAnchors = mesh->useAnchors;
99: return(0);
100: }
102: static PetscErrorCode DMPlexGetAdjacency_Cone_Internal(DM dm, PetscInt p, PetscInt *adjSize, PetscInt adj[])
103: {
104: const PetscInt *cone = NULL;
105: PetscInt numAdj = 0, maxAdjSize = *adjSize, coneSize, c;
106: PetscErrorCode ierr;
109: DMPlexGetConeSize(dm, p, &coneSize);
110: DMPlexGetCone(dm, p, &cone);
111: for (c = 0; c <= coneSize; ++c) {
112: const PetscInt point = !c ? p : cone[c-1];
113: const PetscInt *support = NULL;
114: PetscInt supportSize, s, q;
116: DMPlexGetSupportSize(dm, point, &supportSize);
117: DMPlexGetSupport(dm, point, &support);
118: for (s = 0; s < supportSize; ++s) {
119: for (q = 0; q < numAdj || ((void)(adj[numAdj++] = support[s]),0); ++q) {
120: if (support[s] == adj[q]) break;
121: }
122: if (numAdj > maxAdjSize) SETERRQ1(PETSC_COMM_SELF, PETSC_ERR_PLIB, "Invalid mesh exceeded adjacency allocation (%D)", maxAdjSize);
123: }
124: }
125: *adjSize = numAdj;
126: return(0);
127: }
129: static PetscErrorCode DMPlexGetAdjacency_Support_Internal(DM dm, PetscInt p, PetscInt *adjSize, PetscInt adj[])
130: {
131: const PetscInt *support = NULL;
132: PetscInt numAdj = 0, maxAdjSize = *adjSize, supportSize, s;
133: PetscErrorCode ierr;
136: DMPlexGetSupportSize(dm, p, &supportSize);
137: DMPlexGetSupport(dm, p, &support);
138: for (s = 0; s <= supportSize; ++s) {
139: const PetscInt point = !s ? p : support[s-1];
140: const PetscInt *cone = NULL;
141: PetscInt coneSize, c, q;
143: DMPlexGetConeSize(dm, point, &coneSize);
144: DMPlexGetCone(dm, point, &cone);
145: for (c = 0; c < coneSize; ++c) {
146: for (q = 0; q < numAdj || ((void)(adj[numAdj++] = cone[c]),0); ++q) {
147: if (cone[c] == adj[q]) break;
148: }
149: if (numAdj > maxAdjSize) SETERRQ1(PETSC_COMM_SELF, PETSC_ERR_PLIB, "Invalid mesh exceeded adjacency allocation (%D)", maxAdjSize);
150: }
151: }
152: *adjSize = numAdj;
153: return(0);
154: }
156: static PetscErrorCode DMPlexGetAdjacency_Transitive_Internal(DM dm, PetscInt p, PetscBool useClosure, PetscInt *adjSize, PetscInt adj[])
157: {
158: PetscInt *star = NULL;
159: PetscInt numAdj = 0, maxAdjSize = *adjSize, starSize, s;
163: DMPlexGetTransitiveClosure(dm, p, useClosure, &starSize, &star);
164: for (s = 0; s < starSize*2; s += 2) {
165: const PetscInt *closure = NULL;
166: PetscInt closureSize, c, q;
168: DMPlexGetTransitiveClosure(dm, star[s], (PetscBool)!useClosure, &closureSize, (PetscInt**) &closure);
169: for (c = 0; c < closureSize*2; c += 2) {
170: for (q = 0; q < numAdj || ((void)(adj[numAdj++] = closure[c]),0); ++q) {
171: if (closure[c] == adj[q]) break;
172: }
173: if (numAdj > maxAdjSize) SETERRQ1(PETSC_COMM_SELF, PETSC_ERR_PLIB, "Invalid mesh exceeded adjacency allocation (%D)", maxAdjSize);
174: }
175: DMPlexRestoreTransitiveClosure(dm, star[s], (PetscBool)!useClosure, &closureSize, (PetscInt**) &closure);
176: }
177: DMPlexRestoreTransitiveClosure(dm, p, useClosure, &starSize, &star);
178: *adjSize = numAdj;
179: return(0);
180: }
182: PetscErrorCode DMPlexGetAdjacency_Internal(DM dm, PetscInt p, PetscBool useCone, PetscBool useTransitiveClosure, PetscBool useAnchors, PetscInt *adjSize, PetscInt *adj[])
183: {
184: static PetscInt asiz = 0;
185: PetscInt maxAnchors = 1;
186: PetscInt aStart = -1, aEnd = -1;
187: PetscInt maxAdjSize;
188: PetscSection aSec = NULL;
189: IS aIS = NULL;
190: const PetscInt *anchors;
191: DM_Plex *mesh = (DM_Plex *)dm->data;
192: PetscErrorCode ierr;
195: if (useAnchors) {
196: DMPlexGetAnchors(dm,&aSec,&aIS);
197: if (aSec) {
198: PetscSectionGetMaxDof(aSec,&maxAnchors);
199: maxAnchors = PetscMax(1,maxAnchors);
200: PetscSectionGetChart(aSec,&aStart,&aEnd);
201: ISGetIndices(aIS,&anchors);
202: }
203: }
204: if (!*adj) {
205: PetscInt depth, coneSeries, supportSeries, maxC, maxS, pStart, pEnd;
207: DMPlexGetChart(dm, &pStart,&pEnd);
208: DMPlexGetDepth(dm, &depth);
209: depth = PetscMax(depth, -depth);
210: DMPlexGetMaxSizes(dm, &maxC, &maxS);
211: coneSeries = (maxC > 1) ? ((PetscPowInt(maxC,depth+1)-1)/(maxC-1)) : depth+1;
212: supportSeries = (maxS > 1) ? ((PetscPowInt(maxS,depth+1)-1)/(maxS-1)) : depth+1;
213: asiz = PetscMax(PetscPowInt(maxS,depth)*coneSeries,PetscPowInt(maxC,depth)*supportSeries);
214: asiz *= maxAnchors;
215: asiz = PetscMin(asiz,pEnd-pStart);
216: PetscMalloc1(asiz,adj);
217: }
218: if (*adjSize < 0) *adjSize = asiz;
219: maxAdjSize = *adjSize;
220: if (mesh->useradjacency) {
221: (*mesh->useradjacency)(dm, p, adjSize, *adj, mesh->useradjacencyctx);
222: } else if (useTransitiveClosure) {
223: DMPlexGetAdjacency_Transitive_Internal(dm, p, useCone, adjSize, *adj);
224: } else if (useCone) {
225: DMPlexGetAdjacency_Cone_Internal(dm, p, adjSize, *adj);
226: } else {
227: DMPlexGetAdjacency_Support_Internal(dm, p, adjSize, *adj);
228: }
229: if (useAnchors && aSec) {
230: PetscInt origSize = *adjSize;
231: PetscInt numAdj = origSize;
232: PetscInt i = 0, j;
233: PetscInt *orig = *adj;
235: while (i < origSize) {
236: PetscInt p = orig[i];
237: PetscInt aDof = 0;
239: if (p >= aStart && p < aEnd) {
240: PetscSectionGetDof(aSec,p,&aDof);
241: }
242: if (aDof) {
243: PetscInt aOff;
244: PetscInt s, q;
246: for (j = i + 1; j < numAdj; j++) {
247: orig[j - 1] = orig[j];
248: }
249: origSize--;
250: numAdj--;
251: PetscSectionGetOffset(aSec,p,&aOff);
252: for (s = 0; s < aDof; ++s) {
253: for (q = 0; q < numAdj || ((void)(orig[numAdj++] = anchors[aOff+s]),0); ++q) {
254: if (anchors[aOff+s] == orig[q]) break;
255: }
256: if (numAdj > maxAdjSize) SETERRQ1(PETSC_COMM_SELF, PETSC_ERR_PLIB, "Invalid mesh exceeded adjacency allocation (%D)", maxAdjSize);
257: }
258: }
259: else {
260: i++;
261: }
262: }
263: *adjSize = numAdj;
264: ISRestoreIndices(aIS,&anchors);
265: }
266: return(0);
267: }
269: /*@
270: DMPlexGetAdjacency - Return all points adjacent to the given point
272: Input Parameters:
273: + dm - The DM object
274: . p - The point
275: . adjSize - The maximum size of adj if it is non-NULL, or PETSC_DETERMINE
276: - adj - Either NULL so that the array is allocated, or an existing array with size adjSize
278: Output Parameters:
279: + adjSize - The number of adjacent points
280: - adj - The adjacent points
282: Level: advanced
284: Notes:
285: The user must PetscFree the adj array if it was not passed in.
287: .seealso: DMSetAdjacency(), DMPlexDistribute(), DMCreateMatrix(), DMPlexPreallocateOperator()
288: @*/
289: PetscErrorCode DMPlexGetAdjacency(DM dm, PetscInt p, PetscInt *adjSize, PetscInt *adj[])
290: {
291: PetscBool useCone, useClosure, useAnchors;
298: DMGetBasicAdjacency(dm, &useCone, &useClosure);
299: DMPlexGetAdjacencyUseAnchors(dm, &useAnchors);
300: DMPlexGetAdjacency_Internal(dm, p, useCone, useClosure, useAnchors, adjSize, adj);
301: return(0);
302: }
304: /*@
305: DMPlexCreateTwoSidedProcessSF - Create an SF which just has process connectivity
307: Collective on dm
309: Input Parameters:
310: + dm - The DM
311: - sfPoint - The PetscSF which encodes point connectivity
313: Output Parameters:
314: + processRanks - A list of process neighbors, or NULL
315: - sfProcess - An SF encoding the two-sided process connectivity, or NULL
317: Level: developer
319: .seealso: PetscSFCreate(), DMPlexCreateProcessSF()
320: @*/
321: PetscErrorCode DMPlexCreateTwoSidedProcessSF(DM dm, PetscSF sfPoint, PetscSection rootRankSection, IS rootRanks, PetscSection leafRankSection, IS leafRanks, IS *processRanks, PetscSF *sfProcess)
322: {
323: const PetscSFNode *remotePoints;
324: PetscInt *localPointsNew;
325: PetscSFNode *remotePointsNew;
326: const PetscInt *nranks;
327: PetscInt *ranksNew;
328: PetscBT neighbors;
329: PetscInt pStart, pEnd, p, numLeaves, l, numNeighbors, n;
330: PetscMPIInt size, proc, rank;
331: PetscErrorCode ierr;
338: MPI_Comm_size(PetscObjectComm((PetscObject) dm), &size);
339: MPI_Comm_rank(PetscObjectComm((PetscObject) dm), &rank);
340: PetscSFGetGraph(sfPoint, NULL, &numLeaves, NULL, &remotePoints);
341: PetscBTCreate(size, &neighbors);
342: PetscBTMemzero(size, neighbors);
343: /* Compute root-to-leaf process connectivity */
344: PetscSectionGetChart(rootRankSection, &pStart, &pEnd);
345: ISGetIndices(rootRanks, &nranks);
346: for (p = pStart; p < pEnd; ++p) {
347: PetscInt ndof, noff, n;
349: PetscSectionGetDof(rootRankSection, p, &ndof);
350: PetscSectionGetOffset(rootRankSection, p, &noff);
351: for (n = 0; n < ndof; ++n) {PetscBTSet(neighbors, nranks[noff+n]);}
352: }
353: ISRestoreIndices(rootRanks, &nranks);
354: /* Compute leaf-to-neighbor process connectivity */
355: PetscSectionGetChart(leafRankSection, &pStart, &pEnd);
356: ISGetIndices(leafRanks, &nranks);
357: for (p = pStart; p < pEnd; ++p) {
358: PetscInt ndof, noff, n;
360: PetscSectionGetDof(leafRankSection, p, &ndof);
361: PetscSectionGetOffset(leafRankSection, p, &noff);
362: for (n = 0; n < ndof; ++n) {PetscBTSet(neighbors, nranks[noff+n]);}
363: }
364: ISRestoreIndices(leafRanks, &nranks);
365: /* Compute leaf-to-root process connectivity */
366: for (l = 0; l < numLeaves; ++l) {PetscBTSet(neighbors, remotePoints[l].rank);}
367: /* Calculate edges */
368: PetscBTClear(neighbors, rank);
369: for(proc = 0, numNeighbors = 0; proc < size; ++proc) {if (PetscBTLookup(neighbors, proc)) ++numNeighbors;}
370: PetscMalloc1(numNeighbors, &ranksNew);
371: PetscMalloc1(numNeighbors, &localPointsNew);
372: PetscMalloc1(numNeighbors, &remotePointsNew);
373: for(proc = 0, n = 0; proc < size; ++proc) {
374: if (PetscBTLookup(neighbors, proc)) {
375: ranksNew[n] = proc;
376: localPointsNew[n] = proc;
377: remotePointsNew[n].index = rank;
378: remotePointsNew[n].rank = proc;
379: ++n;
380: }
381: }
382: PetscBTDestroy(&neighbors);
383: if (processRanks) {ISCreateGeneral(PetscObjectComm((PetscObject)dm), numNeighbors, ranksNew, PETSC_OWN_POINTER, processRanks);}
384: else {PetscFree(ranksNew);}
385: if (sfProcess) {
386: PetscSFCreate(PetscObjectComm((PetscObject)dm), sfProcess);
387: PetscObjectSetName((PetscObject) *sfProcess, "Two-Sided Process SF");
388: PetscSFSetFromOptions(*sfProcess);
389: PetscSFSetGraph(*sfProcess, size, numNeighbors, localPointsNew, PETSC_OWN_POINTER, remotePointsNew, PETSC_OWN_POINTER);
390: }
391: return(0);
392: }
394: /*@
395: DMPlexDistributeOwnership - Compute owner information for shared points. This basically gets two-sided for an SF.
397: Collective on dm
399: Input Parameter:
400: . dm - The DM
402: Output Parameters:
403: + rootSection - The number of leaves for a given root point
404: . rootrank - The rank of each edge into the root point
405: . leafSection - The number of processes sharing a given leaf point
406: - leafrank - The rank of each process sharing a leaf point
408: Level: developer
410: .seealso: DMPlexCreateOverlapLabel(), DMPlexDistribute(), DMPlexDistributeOverlap()
411: @*/
412: PetscErrorCode DMPlexDistributeOwnership(DM dm, PetscSection rootSection, IS *rootrank, PetscSection leafSection, IS *leafrank)
413: {
414: MPI_Comm comm;
415: PetscSF sfPoint;
416: const PetscInt *rootdegree;
417: PetscInt *myrank, *remoterank;
418: PetscInt pStart, pEnd, p, nedges;
419: PetscMPIInt rank;
420: PetscErrorCode ierr;
423: PetscObjectGetComm((PetscObject) dm, &comm);
424: MPI_Comm_rank(comm, &rank);
425: DMPlexGetChart(dm, &pStart, &pEnd);
426: DMGetPointSF(dm, &sfPoint);
427: /* Compute number of leaves for each root */
428: PetscObjectSetName((PetscObject) rootSection, "Root Section");
429: PetscSectionSetChart(rootSection, pStart, pEnd);
430: PetscSFComputeDegreeBegin(sfPoint, &rootdegree);
431: PetscSFComputeDegreeEnd(sfPoint, &rootdegree);
432: for (p = pStart; p < pEnd; ++p) {PetscSectionSetDof(rootSection, p, rootdegree[p-pStart]);}
433: PetscSectionSetUp(rootSection);
434: /* Gather rank of each leaf to root */
435: PetscSectionGetStorageSize(rootSection, &nedges);
436: PetscMalloc1(pEnd-pStart, &myrank);
437: PetscMalloc1(nedges, &remoterank);
438: for (p = 0; p < pEnd-pStart; ++p) myrank[p] = rank;
439: PetscSFGatherBegin(sfPoint, MPIU_INT, myrank, remoterank);
440: PetscSFGatherEnd(sfPoint, MPIU_INT, myrank, remoterank);
441: PetscFree(myrank);
442: ISCreateGeneral(comm, nedges, remoterank, PETSC_OWN_POINTER, rootrank);
443: /* Distribute remote ranks to leaves */
444: PetscObjectSetName((PetscObject) leafSection, "Leaf Section");
445: DMPlexDistributeFieldIS(dm, sfPoint, rootSection, *rootrank, leafSection, leafrank);
446: return(0);
447: }
449: /*@C
450: DMPlexCreateOverlapLabel - Compute owner information for shared points. This basically gets two-sided for an SF.
452: Collective on dm
454: Input Parameters:
455: + dm - The DM
456: . levels - Number of overlap levels
457: . rootSection - The number of leaves for a given root point
458: . rootrank - The rank of each edge into the root point
459: . leafSection - The number of processes sharing a given leaf point
460: - leafrank - The rank of each process sharing a leaf point
462: Output Parameter:
463: . ovLabel - DMLabel containing remote overlap contributions as point/rank pairings
465: Level: developer
467: .seealso: DMPlexDistributeOwnership(), DMPlexDistribute()
468: @*/
469: PetscErrorCode DMPlexCreateOverlapLabel(DM dm, PetscInt levels, PetscSection rootSection, IS rootrank, PetscSection leafSection, IS leafrank, DMLabel *ovLabel)
470: {
471: MPI_Comm comm;
472: DMLabel ovAdjByRank; /* A DMLabel containing all points adjacent to shared points, separated by rank (value in label) */
473: PetscSF sfPoint;
474: const PetscSFNode *remote;
475: const PetscInt *local;
476: const PetscInt *nrank, *rrank;
477: PetscInt *adj = NULL;
478: PetscInt pStart, pEnd, p, sStart, sEnd, nleaves, l;
479: PetscMPIInt rank, size;
480: PetscBool flg;
481: PetscErrorCode ierr;
484: *ovLabel = NULL;
485: PetscObjectGetComm((PetscObject) dm, &comm);
486: MPI_Comm_size(comm, &size);
487: MPI_Comm_rank(comm, &rank);
488: if (size == 1) return(0);
489: DMGetPointSF(dm, &sfPoint);
490: DMPlexGetChart(dm, &pStart, &pEnd);
491: PetscSectionGetChart(leafSection, &sStart, &sEnd);
492: PetscSFGetGraph(sfPoint, NULL, &nleaves, &local, &remote);
493: DMLabelCreate(PETSC_COMM_SELF, "Overlap adjacency", &ovAdjByRank);
494: /* Handle leaves: shared with the root point */
495: for (l = 0; l < nleaves; ++l) {
496: PetscInt adjSize = PETSC_DETERMINE, a;
498: DMPlexGetAdjacency(dm, local ? local[l] : l, &adjSize, &adj);
499: for (a = 0; a < adjSize; ++a) {DMLabelSetValue(ovAdjByRank, adj[a], remote[l].rank);}
500: }
501: ISGetIndices(rootrank, &rrank);
502: ISGetIndices(leafrank, &nrank);
503: /* Handle roots */
504: for (p = pStart; p < pEnd; ++p) {
505: PetscInt adjSize = PETSC_DETERMINE, neighbors = 0, noff, n, a;
507: if ((p >= sStart) && (p < sEnd)) {
508: /* Some leaves share a root with other leaves on different processes */
509: PetscSectionGetDof(leafSection, p, &neighbors);
510: if (neighbors) {
511: PetscSectionGetOffset(leafSection, p, &noff);
512: DMPlexGetAdjacency(dm, p, &adjSize, &adj);
513: for (n = 0; n < neighbors; ++n) {
514: const PetscInt remoteRank = nrank[noff+n];
516: if (remoteRank == rank) continue;
517: for (a = 0; a < adjSize; ++a) {DMLabelSetValue(ovAdjByRank, adj[a], remoteRank);}
518: }
519: }
520: }
521: /* Roots are shared with leaves */
522: PetscSectionGetDof(rootSection, p, &neighbors);
523: if (!neighbors) continue;
524: PetscSectionGetOffset(rootSection, p, &noff);
525: DMPlexGetAdjacency(dm, p, &adjSize, &adj);
526: for (n = 0; n < neighbors; ++n) {
527: const PetscInt remoteRank = rrank[noff+n];
529: if (remoteRank == rank) continue;
530: for (a = 0; a < adjSize; ++a) {DMLabelSetValue(ovAdjByRank, adj[a], remoteRank);}
531: }
532: }
533: PetscFree(adj);
534: ISRestoreIndices(rootrank, &rrank);
535: ISRestoreIndices(leafrank, &nrank);
536: /* Add additional overlap levels */
537: for (l = 1; l < levels; l++) {
538: /* Propagate point donations over SF to capture remote connections */
539: DMPlexPartitionLabelPropagate(dm, ovAdjByRank);
540: /* Add next level of point donations to the label */
541: DMPlexPartitionLabelAdjacency(dm, ovAdjByRank);
542: }
543: /* We require the closure in the overlap */
544: DMPlexPartitionLabelClosure(dm, ovAdjByRank);
545: PetscOptionsHasName(((PetscObject) dm)->options,((PetscObject) dm)->prefix, "-overlap_view", &flg);
546: if (flg) {
547: PetscViewer viewer;
548: PetscViewerASCIIGetStdout(PetscObjectComm((PetscObject)dm), &viewer);
549: DMLabelView(ovAdjByRank, viewer);
550: }
551: /* Invert sender to receiver label */
552: DMLabelCreate(PETSC_COMM_SELF, "Overlap label", ovLabel);
553: DMPlexPartitionLabelInvert(dm, ovAdjByRank, NULL, *ovLabel);
554: /* Add owned points, except for shared local points */
555: for (p = pStart; p < pEnd; ++p) {DMLabelSetValue(*ovLabel, p, rank);}
556: for (l = 0; l < nleaves; ++l) {
557: DMLabelClearValue(*ovLabel, local[l], rank);
558: DMLabelSetValue(*ovLabel, remote[l].index, remote[l].rank);
559: }
560: /* Clean up */
561: DMLabelDestroy(&ovAdjByRank);
562: return(0);
563: }
565: /*@C
566: DMPlexCreateOverlapMigrationSF - Create an SF describing the new mesh distribution to make the overlap described by the input SF
568: Collective on dm
570: Input Parameters:
571: + dm - The DM
572: - overlapSF - The SF mapping ghost points in overlap to owner points on other processes
574: Output Parameter:
575: . migrationSF - An SF that maps original points in old locations to points in new locations
577: Level: developer
579: .seealso: DMPlexCreateOverlapLabel(), DMPlexDistributeOverlap(), DMPlexDistribute()
580: @*/
581: PetscErrorCode DMPlexCreateOverlapMigrationSF(DM dm, PetscSF overlapSF, PetscSF *migrationSF)
582: {
583: MPI_Comm comm;
584: PetscMPIInt rank, size;
585: PetscInt d, dim, p, pStart, pEnd, nroots, nleaves, newLeaves, point, numSharedPoints;
586: PetscInt *pointDepths, *remoteDepths, *ilocal;
587: PetscInt *depthRecv, *depthShift, *depthIdx;
588: PetscSFNode *iremote;
589: PetscSF pointSF;
590: const PetscInt *sharedLocal;
591: const PetscSFNode *overlapRemote, *sharedRemote;
592: PetscErrorCode ierr;
596: PetscObjectGetComm((PetscObject)dm, &comm);
597: MPI_Comm_rank(comm, &rank);
598: MPI_Comm_size(comm, &size);
599: DMGetDimension(dm, &dim);
601: /* Before building the migration SF we need to know the new stratum offsets */
602: PetscSFGetGraph(overlapSF, &nroots, &nleaves, NULL, &overlapRemote);
603: PetscMalloc2(nroots, &pointDepths, nleaves, &remoteDepths);
604: for (d=0; d<dim+1; d++) {
605: DMPlexGetDepthStratum(dm, d, &pStart, &pEnd);
606: for (p=pStart; p<pEnd; p++) pointDepths[p] = d;
607: }
608: for (p=0; p<nleaves; p++) remoteDepths[p] = -1;
609: PetscSFBcastBegin(overlapSF, MPIU_INT, pointDepths, remoteDepths);
610: PetscSFBcastEnd(overlapSF, MPIU_INT, pointDepths, remoteDepths);
612: /* Count received points in each stratum and compute the internal strata shift */
613: PetscMalloc3(dim+1, &depthRecv, dim+1, &depthShift, dim+1, &depthIdx);
614: for (d=0; d<dim+1; d++) depthRecv[d]=0;
615: for (p=0; p<nleaves; p++) depthRecv[remoteDepths[p]]++;
616: depthShift[dim] = 0;
617: for (d=0; d<dim; d++) depthShift[d] = depthRecv[dim];
618: for (d=1; d<dim; d++) depthShift[d] += depthRecv[0];
619: for (d=dim-2; d>0; d--) depthShift[d] += depthRecv[d+1];
620: for (d=0; d<dim+1; d++) {
621: DMPlexGetDepthStratum(dm, d, &pStart, &pEnd);
622: depthIdx[d] = pStart + depthShift[d];
623: }
625: /* Form the overlap SF build an SF that describes the full overlap migration SF */
626: DMPlexGetChart(dm, &pStart, &pEnd);
627: newLeaves = pEnd - pStart + nleaves;
628: PetscMalloc1(newLeaves, &ilocal);
629: PetscMalloc1(newLeaves, &iremote);
630: /* First map local points to themselves */
631: for (d=0; d<dim+1; d++) {
632: DMPlexGetDepthStratum(dm, d, &pStart, &pEnd);
633: for (p=pStart; p<pEnd; p++) {
634: point = p + depthShift[d];
635: ilocal[point] = point;
636: iremote[point].index = p;
637: iremote[point].rank = rank;
638: depthIdx[d]++;
639: }
640: }
642: /* Add in the remote roots for currently shared points */
643: DMGetPointSF(dm, &pointSF);
644: PetscSFGetGraph(pointSF, NULL, &numSharedPoints, &sharedLocal, &sharedRemote);
645: for (d=0; d<dim+1; d++) {
646: DMPlexGetDepthStratum(dm, d, &pStart, &pEnd);
647: for (p=0; p<numSharedPoints; p++) {
648: if (pStart <= sharedLocal[p] && sharedLocal[p] < pEnd) {
649: point = sharedLocal[p] + depthShift[d];
650: iremote[point].index = sharedRemote[p].index;
651: iremote[point].rank = sharedRemote[p].rank;
652: }
653: }
654: }
656: /* Now add the incoming overlap points */
657: for (p=0; p<nleaves; p++) {
658: point = depthIdx[remoteDepths[p]];
659: ilocal[point] = point;
660: iremote[point].index = overlapRemote[p].index;
661: iremote[point].rank = overlapRemote[p].rank;
662: depthIdx[remoteDepths[p]]++;
663: }
664: PetscFree2(pointDepths,remoteDepths);
666: PetscSFCreate(comm, migrationSF);
667: PetscObjectSetName((PetscObject) *migrationSF, "Overlap Migration SF");
668: PetscSFSetFromOptions(*migrationSF);
669: DMPlexGetChart(dm, &pStart, &pEnd);
670: PetscSFSetGraph(*migrationSF, pEnd-pStart, newLeaves, ilocal, PETSC_OWN_POINTER, iremote, PETSC_OWN_POINTER);
672: PetscFree3(depthRecv, depthShift, depthIdx);
673: return(0);
674: }
676: /*@
677: DMPlexStratifyMigrationSF - Rearrange the leaves of a migration sf for stratification.
679: Input Parameters:
680: + dm - The DM
681: - sf - A star forest with non-ordered leaves, usually defining a DM point migration
683: Output Parameter:
684: . migrationSF - A star forest with added leaf indirection that ensures the resulting DM is stratified
686: Note:
687: This lexicographically sorts by (depth, cellType)
689: Level: developer
691: .seealso: DMPlexPartitionLabelCreateSF(), DMPlexDistribute(), DMPlexDistributeOverlap()
692: @*/
693: PetscErrorCode DMPlexStratifyMigrationSF(DM dm, PetscSF sf, PetscSF *migrationSF)
694: {
695: MPI_Comm comm;
696: PetscMPIInt rank, size;
697: PetscInt d, ldepth, depth, dim, p, pStart, pEnd, nroots, nleaves;
698: PetscSFNode *pointDepths, *remoteDepths;
699: PetscInt *ilocal;
700: PetscInt *depthRecv, *depthShift, *depthIdx;
701: PetscInt *ctRecv, *ctShift, *ctIdx;
702: const PetscSFNode *iremote;
703: PetscErrorCode ierr;
707: PetscObjectGetComm((PetscObject) dm, &comm);
708: MPI_Comm_rank(comm, &rank);
709: MPI_Comm_size(comm, &size);
710: DMPlexGetDepth(dm, &ldepth);
711: DMGetDimension(dm, &dim);
712: MPIU_Allreduce(&ldepth, &depth, 1, MPIU_INT, MPI_MAX, comm);
713: if ((ldepth >= 0) && (depth != ldepth)) SETERRQ2(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Inconsistent Plex depth %d != %d", ldepth, depth);
714: PetscLogEventBegin(DMPLEX_PartStratSF,dm,0,0,0);
716: /* Before building the migration SF we need to know the new stratum offsets */
717: PetscSFGetGraph(sf, &nroots, &nleaves, NULL, &iremote);
718: PetscMalloc2(nroots, &pointDepths, nleaves, &remoteDepths);
719: for (d = 0; d < depth+1; ++d) {
720: DMPlexGetDepthStratum(dm, d, &pStart, &pEnd);
721: for (p = pStart; p < pEnd; ++p) {
722: DMPolytopeType ct;
724: DMPlexGetCellType(dm, p, &ct);
725: pointDepths[p].index = d;
726: pointDepths[p].rank = ct;
727: }
728: }
729: for (p = 0; p < nleaves; ++p) {remoteDepths[p].index = -1; remoteDepths[p].rank = -1;}
730: PetscSFBcastBegin(sf, MPIU_2INT, pointDepths, remoteDepths);
731: PetscSFBcastEnd(sf, MPIU_2INT, pointDepths, remoteDepths);
732: /* Count received points in each stratum and compute the internal strata shift */
733: PetscCalloc6(depth+1, &depthRecv, depth+1, &depthShift, depth+1, &depthIdx, DM_NUM_POLYTOPES, &ctRecv, DM_NUM_POLYTOPES, &ctShift, DM_NUM_POLYTOPES, &ctIdx);
734: for (p = 0; p < nleaves; ++p) {
735: if (remoteDepths[p].rank < 0) {
736: ++depthRecv[remoteDepths[p].index];
737: } else {
738: ++ctRecv[remoteDepths[p].rank];
739: }
740: }
741: {
742: PetscInt depths[4], dims[4], shift = 0, i, c;
744: /* Cells (depth), Vertices (0), Faces (depth-1), Edges (1) */
745: depths[0] = depth; depths[1] = 0; depths[2] = depth-1; depths[3] = 1;
746: dims[0] = dim; dims[1] = 0; dims[2] = dim-1; dims[3] = 1;
747: for (i = 0; i <= depth; ++i) {
748: const PetscInt dep = depths[i];
749: const PetscInt dim = dims[i];
751: for (c = 0; c < DM_NUM_POLYTOPES; ++c) {
752: if (DMPolytopeTypeGetDim((DMPolytopeType) c) != dim && !(i == 0 && c == DM_POLYTOPE_FV_GHOST)) continue;
753: ctShift[c] = shift;
754: shift += ctRecv[c];
755: }
756: depthShift[dep] = shift;
757: shift += depthRecv[dep];
758: }
759: for (c = 0; c < DM_NUM_POLYTOPES; ++c) {
760: const PetscInt ctDim = DMPolytopeTypeGetDim((DMPolytopeType) c);
762: if ((ctDim < 0 || ctDim > dim) && c != DM_POLYTOPE_FV_GHOST) {
763: ctShift[c] = shift;
764: shift += ctRecv[c];
765: }
766: }
767: }
768: /* Derive a new local permutation based on stratified indices */
769: PetscMalloc1(nleaves, &ilocal);
770: for (p = 0; p < nleaves; ++p) {
771: const PetscInt dep = remoteDepths[p].index;
772: const DMPolytopeType ct = (DMPolytopeType) remoteDepths[p].rank;
774: if ((PetscInt) ct < 0) {
775: ilocal[p] = depthShift[dep] + depthIdx[dep];
776: ++depthIdx[dep];
777: } else {
778: ilocal[p] = ctShift[ct] + ctIdx[ct];
779: ++ctIdx[ct];
780: }
781: }
782: PetscSFCreate(comm, migrationSF);
783: PetscObjectSetName((PetscObject) *migrationSF, "Migration SF");
784: PetscSFSetGraph(*migrationSF, nroots, nleaves, ilocal, PETSC_OWN_POINTER, iremote, PETSC_COPY_VALUES);
785: PetscFree2(pointDepths,remoteDepths);
786: PetscFree6(depthRecv, depthShift, depthIdx, ctRecv, ctShift, ctIdx);
787: PetscLogEventEnd(DMPLEX_PartStratSF,dm,0,0,0);
788: return(0);
789: }
791: /*@
792: DMPlexDistributeField - Distribute field data to match a given PetscSF, usually the SF from mesh distribution
794: Collective on dm
796: Input Parameters:
797: + dm - The DMPlex object
798: . pointSF - The PetscSF describing the communication pattern
799: . originalSection - The PetscSection for existing data layout
800: - originalVec - The existing data in a local vector
802: Output Parameters:
803: + newSection - The PetscSF describing the new data layout
804: - newVec - The new data in a local vector
806: Level: developer
808: .seealso: DMPlexDistribute(), DMPlexDistributeFieldIS(), DMPlexDistributeData()
809: @*/
810: PetscErrorCode DMPlexDistributeField(DM dm, PetscSF pointSF, PetscSection originalSection, Vec originalVec, PetscSection newSection, Vec newVec)
811: {
812: PetscSF fieldSF;
813: PetscInt *remoteOffsets, fieldSize;
814: PetscScalar *originalValues, *newValues;
818: PetscLogEventBegin(DMPLEX_DistributeField,dm,0,0,0);
819: PetscSFDistributeSection(pointSF, originalSection, &remoteOffsets, newSection);
821: PetscSectionGetStorageSize(newSection, &fieldSize);
822: VecSetSizes(newVec, fieldSize, PETSC_DETERMINE);
823: VecSetType(newVec,dm->vectype);
825: VecGetArray(originalVec, &originalValues);
826: VecGetArray(newVec, &newValues);
827: PetscSFCreateSectionSF(pointSF, originalSection, remoteOffsets, newSection, &fieldSF);
828: PetscFree(remoteOffsets);
829: PetscSFBcastBegin(fieldSF, MPIU_SCALAR, originalValues, newValues);
830: PetscSFBcastEnd(fieldSF, MPIU_SCALAR, originalValues, newValues);
831: PetscSFDestroy(&fieldSF);
832: VecRestoreArray(newVec, &newValues);
833: VecRestoreArray(originalVec, &originalValues);
834: PetscLogEventEnd(DMPLEX_DistributeField,dm,0,0,0);
835: return(0);
836: }
838: /*@
839: DMPlexDistributeFieldIS - Distribute field data to match a given PetscSF, usually the SF from mesh distribution
841: Collective on dm
843: Input Parameters:
844: + dm - The DMPlex object
845: . pointSF - The PetscSF describing the communication pattern
846: . originalSection - The PetscSection for existing data layout
847: - originalIS - The existing data
849: Output Parameters:
850: + newSection - The PetscSF describing the new data layout
851: - newIS - The new data
853: Level: developer
855: .seealso: DMPlexDistribute(), DMPlexDistributeField(), DMPlexDistributeData()
856: @*/
857: PetscErrorCode DMPlexDistributeFieldIS(DM dm, PetscSF pointSF, PetscSection originalSection, IS originalIS, PetscSection newSection, IS *newIS)
858: {
859: PetscSF fieldSF;
860: PetscInt *newValues, *remoteOffsets, fieldSize;
861: const PetscInt *originalValues;
862: PetscErrorCode ierr;
865: PetscLogEventBegin(DMPLEX_DistributeField,dm,0,0,0);
866: PetscSFDistributeSection(pointSF, originalSection, &remoteOffsets, newSection);
868: PetscSectionGetStorageSize(newSection, &fieldSize);
869: PetscMalloc1(fieldSize, &newValues);
871: ISGetIndices(originalIS, &originalValues);
872: PetscSFCreateSectionSF(pointSF, originalSection, remoteOffsets, newSection, &fieldSF);
873: PetscFree(remoteOffsets);
874: PetscSFBcastBegin(fieldSF, MPIU_INT, (PetscInt *) originalValues, newValues);
875: PetscSFBcastEnd(fieldSF, MPIU_INT, (PetscInt *) originalValues, newValues);
876: PetscSFDestroy(&fieldSF);
877: ISRestoreIndices(originalIS, &originalValues);
878: ISCreateGeneral(PetscObjectComm((PetscObject) pointSF), fieldSize, newValues, PETSC_OWN_POINTER, newIS);
879: PetscLogEventEnd(DMPLEX_DistributeField,dm,0,0,0);
880: return(0);
881: }
883: /*@
884: DMPlexDistributeData - Distribute field data to match a given PetscSF, usually the SF from mesh distribution
886: Collective on dm
888: Input Parameters:
889: + dm - The DMPlex object
890: . pointSF - The PetscSF describing the communication pattern
891: . originalSection - The PetscSection for existing data layout
892: . datatype - The type of data
893: - originalData - The existing data
895: Output Parameters:
896: + newSection - The PetscSection describing the new data layout
897: - newData - The new data
899: Level: developer
901: .seealso: DMPlexDistribute(), DMPlexDistributeField()
902: @*/
903: PetscErrorCode DMPlexDistributeData(DM dm, PetscSF pointSF, PetscSection originalSection, MPI_Datatype datatype, void *originalData, PetscSection newSection, void **newData)
904: {
905: PetscSF fieldSF;
906: PetscInt *remoteOffsets, fieldSize;
907: PetscMPIInt dataSize;
911: PetscLogEventBegin(DMPLEX_DistributeData,dm,0,0,0);
912: PetscSFDistributeSection(pointSF, originalSection, &remoteOffsets, newSection);
914: PetscSectionGetStorageSize(newSection, &fieldSize);
915: MPI_Type_size(datatype, &dataSize);
916: PetscMalloc(fieldSize * dataSize, newData);
918: PetscSFCreateSectionSF(pointSF, originalSection, remoteOffsets, newSection, &fieldSF);
919: PetscFree(remoteOffsets);
920: PetscSFBcastBegin(fieldSF, datatype, originalData, *newData);
921: PetscSFBcastEnd(fieldSF, datatype, originalData, *newData);
922: PetscSFDestroy(&fieldSF);
923: PetscLogEventEnd(DMPLEX_DistributeData,dm,0,0,0);
924: return(0);
925: }
927: static PetscErrorCode DMPlexDistributeCones(DM dm, PetscSF migrationSF, ISLocalToGlobalMapping original, ISLocalToGlobalMapping renumbering, DM dmParallel)
928: {
929: DM_Plex *pmesh = (DM_Plex*) (dmParallel)->data;
930: MPI_Comm comm;
931: PetscSF coneSF;
932: PetscSection originalConeSection, newConeSection;
933: PetscInt *remoteOffsets, *cones, *globCones, *newCones, newConesSize;
934: PetscBool flg;
935: PetscErrorCode ierr;
940: PetscLogEventBegin(DMPLEX_DistributeCones,dm,0,0,0);
941: /* Distribute cone section */
942: PetscObjectGetComm((PetscObject)dm, &comm);
943: DMPlexGetConeSection(dm, &originalConeSection);
944: DMPlexGetConeSection(dmParallel, &newConeSection);
945: PetscSFDistributeSection(migrationSF, originalConeSection, &remoteOffsets, newConeSection);
946: DMSetUp(dmParallel);
947: {
948: PetscInt pStart, pEnd, p;
950: PetscSectionGetChart(newConeSection, &pStart, &pEnd);
951: for (p = pStart; p < pEnd; ++p) {
952: PetscInt coneSize;
953: PetscSectionGetDof(newConeSection, p, &coneSize);
954: pmesh->maxConeSize = PetscMax(pmesh->maxConeSize, coneSize);
955: }
956: }
957: /* Communicate and renumber cones */
958: PetscSFCreateSectionSF(migrationSF, originalConeSection, remoteOffsets, newConeSection, &coneSF);
959: PetscFree(remoteOffsets);
960: DMPlexGetCones(dm, &cones);
961: if (original) {
962: PetscInt numCones;
964: PetscSectionGetStorageSize(originalConeSection,&numCones);
965: PetscMalloc1(numCones,&globCones);
966: ISLocalToGlobalMappingApplyBlock(original, numCones, cones, globCones);
967: } else {
968: globCones = cones;
969: }
970: DMPlexGetCones(dmParallel, &newCones);
971: PetscSFBcastBegin(coneSF, MPIU_INT, globCones, newCones);
972: PetscSFBcastEnd(coneSF, MPIU_INT, globCones, newCones);
973: if (original) {
974: PetscFree(globCones);
975: }
976: PetscSectionGetStorageSize(newConeSection, &newConesSize);
977: ISGlobalToLocalMappingApplyBlock(renumbering, IS_GTOLM_MASK, newConesSize, newCones, NULL, newCones);
978: #if defined(PETSC_USE_DEBUG)
979: {
980: PetscInt p;
981: PetscBool valid = PETSC_TRUE;
982: for (p = 0; p < newConesSize; ++p) {
983: if (newCones[p] < 0) {valid = PETSC_FALSE; PetscPrintf(PETSC_COMM_SELF, "[%d] Point %D not in overlap SF\n", PetscGlobalRank,p);}
984: }
985: if (!valid) SETERRQ(PETSC_COMM_SELF, PETSC_ERR_ARG_OUTOFRANGE, "Invalid global to local map");
986: }
987: #endif
988: PetscOptionsHasName(((PetscObject) dm)->options,((PetscObject) dm)->prefix, "-cones_view", &flg);
989: if (flg) {
990: PetscPrintf(comm, "Serial Cone Section:\n");
991: PetscSectionView(originalConeSection, PETSC_VIEWER_STDOUT_(comm));
992: PetscPrintf(comm, "Parallel Cone Section:\n");
993: PetscSectionView(newConeSection, PETSC_VIEWER_STDOUT_(comm));
994: PetscSFView(coneSF, NULL);
995: }
996: DMPlexGetConeOrientations(dm, &cones);
997: DMPlexGetConeOrientations(dmParallel, &newCones);
998: PetscSFBcastBegin(coneSF, MPIU_INT, cones, newCones);
999: PetscSFBcastEnd(coneSF, MPIU_INT, cones, newCones);
1000: PetscSFDestroy(&coneSF);
1001: PetscLogEventEnd(DMPLEX_DistributeCones,dm,0,0,0);
1002: /* Create supports and stratify DMPlex */
1003: {
1004: PetscInt pStart, pEnd;
1006: PetscSectionGetChart(pmesh->coneSection, &pStart, &pEnd);
1007: PetscSectionSetChart(pmesh->supportSection, pStart, pEnd);
1008: }
1009: DMPlexSymmetrize(dmParallel);
1010: DMPlexStratify(dmParallel);
1011: {
1012: PetscBool useCone, useClosure, useAnchors;
1014: DMGetBasicAdjacency(dm, &useCone, &useClosure);
1015: DMSetBasicAdjacency(dmParallel, useCone, useClosure);
1016: DMPlexGetAdjacencyUseAnchors(dm, &useAnchors);
1017: DMPlexSetAdjacencyUseAnchors(dmParallel, useAnchors);
1018: }
1019: return(0);
1020: }
1022: static PetscErrorCode DMPlexDistributeCoordinates(DM dm, PetscSF migrationSF, DM dmParallel)
1023: {
1024: MPI_Comm comm;
1025: PetscSection originalCoordSection, newCoordSection;
1026: Vec originalCoordinates, newCoordinates;
1027: PetscInt bs;
1028: PetscBool isper;
1029: const char *name;
1030: const PetscReal *maxCell, *L;
1031: const DMBoundaryType *bd;
1032: PetscErrorCode ierr;
1038: PetscObjectGetComm((PetscObject)dm, &comm);
1039: DMGetCoordinateSection(dm, &originalCoordSection);
1040: DMGetCoordinateSection(dmParallel, &newCoordSection);
1041: DMGetCoordinatesLocal(dm, &originalCoordinates);
1042: if (originalCoordinates) {
1043: VecCreate(PETSC_COMM_SELF, &newCoordinates);
1044: PetscObjectGetName((PetscObject) originalCoordinates, &name);
1045: PetscObjectSetName((PetscObject) newCoordinates, name);
1047: DMPlexDistributeField(dm, migrationSF, originalCoordSection, originalCoordinates, newCoordSection, newCoordinates);
1048: DMSetCoordinatesLocal(dmParallel, newCoordinates);
1049: VecGetBlockSize(originalCoordinates, &bs);
1050: VecSetBlockSize(newCoordinates, bs);
1051: VecDestroy(&newCoordinates);
1052: }
1053: DMGetPeriodicity(dm, &isper, &maxCell, &L, &bd);
1054: DMSetPeriodicity(dmParallel, isper, maxCell, L, bd);
1055: return(0);
1056: }
1058: static PetscErrorCode DMPlexDistributeLabels(DM dm, PetscSF migrationSF, DM dmParallel)
1059: {
1060: DM_Plex *mesh = (DM_Plex*) dm->data;
1061: MPI_Comm comm;
1062: DMLabel depthLabel;
1063: PetscMPIInt rank;
1064: PetscInt depth, d, numLabels, numLocalLabels, l;
1065: PetscBool hasLabels = PETSC_FALSE, lsendDepth, sendDepth;
1066: PetscObjectState depthState = -1;
1067: PetscErrorCode ierr;
1073: PetscLogEventBegin(DMPLEX_DistributeLabels,dm,0,0,0);
1074: PetscObjectGetComm((PetscObject)dm, &comm);
1075: MPI_Comm_rank(comm, &rank);
1077: /* If the user has changed the depth label, communicate it instead */
1078: DMPlexGetDepth(dm, &depth);
1079: DMPlexGetDepthLabel(dm, &depthLabel);
1080: if (depthLabel) {PetscObjectStateGet((PetscObject) depthLabel, &depthState);}
1081: lsendDepth = mesh->depthState != depthState ? PETSC_TRUE : PETSC_FALSE;
1082: MPIU_Allreduce(&lsendDepth, &sendDepth, 1, MPIU_BOOL, MPI_LOR, comm);
1083: if (sendDepth) {
1084: DMPlexGetDepthLabel(dmParallel, &dmParallel->depthLabel);
1085: DMRemoveLabelBySelf(dmParallel, &dmParallel->depthLabel, PETSC_FALSE);
1086: }
1087: /* Everyone must have either the same number of labels, or none */
1088: DMGetNumLabels(dm, &numLocalLabels);
1089: numLabels = numLocalLabels;
1090: MPI_Bcast(&numLabels, 1, MPIU_INT, 0, comm);
1091: if (numLabels == numLocalLabels) hasLabels = PETSC_TRUE;
1092: for (l = 0; l < numLabels; ++l) {
1093: DMLabel label = NULL, labelNew = NULL;
1094: PetscBool isDepth, lisOutput = PETSC_TRUE, isOutput;
1095: const char *name = NULL;
1097: if (hasLabels) {
1098: DMGetLabelByNum(dm, l, &label);
1099: /* Skip "depth" because it is recreated */
1100: PetscObjectGetName((PetscObject) label, &name);
1101: PetscStrcmp(name, "depth", &isDepth);
1102: }
1103: MPI_Bcast(&isDepth, 1, MPIU_BOOL, 0, comm);
1104: if (isDepth && !sendDepth) continue;
1105: DMLabelDistribute(label, migrationSF, &labelNew);
1106: if (isDepth) {
1107: /* Put in any missing strata which can occur if users are managing the depth label themselves */
1108: PetscInt gdepth;
1110: MPIU_Allreduce(&depth, &gdepth, 1, MPIU_INT, MPI_MAX, comm);
1111: if ((depth >= 0) && (gdepth != depth)) SETERRQ2(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Inconsistent Plex depth %d != %d", depth, gdepth);
1112: for (d = 0; d <= gdepth; ++d) {
1113: PetscBool has;
1115: DMLabelHasStratum(labelNew, d, &has);
1116: if (!has) {DMLabelAddStratum(labelNew, d);}
1117: }
1118: }
1119: DMAddLabel(dmParallel, labelNew);
1120: /* Put the output flag in the new label */
1121: if (hasLabels) {DMGetLabelOutput(dm, name, &lisOutput);}
1122: MPIU_Allreduce(&lisOutput, &isOutput, 1, MPIU_BOOL, MPI_LAND, comm);
1123: PetscObjectGetName((PetscObject) labelNew, &name);
1124: DMSetLabelOutput(dmParallel, name, isOutput);
1125: DMLabelDestroy(&labelNew);
1126: }
1127: PetscLogEventEnd(DMPLEX_DistributeLabels,dm,0,0,0);
1128: return(0);
1129: }
1131: static PetscErrorCode DMPlexDistributeSetupTree(DM dm, PetscSF migrationSF, ISLocalToGlobalMapping original, ISLocalToGlobalMapping renumbering, DM dmParallel)
1132: {
1133: DM_Plex *mesh = (DM_Plex*) dm->data;
1134: DM_Plex *pmesh = (DM_Plex*) (dmParallel)->data;
1135: MPI_Comm comm;
1136: DM refTree;
1137: PetscSection origParentSection, newParentSection;
1138: PetscInt *origParents, *origChildIDs;
1139: PetscBool flg;
1140: PetscErrorCode ierr;
1145: PetscObjectGetComm((PetscObject)dm, &comm);
1147: /* Set up tree */
1148: DMPlexGetReferenceTree(dm,&refTree);
1149: DMPlexSetReferenceTree(dmParallel,refTree);
1150: DMPlexGetTree(dm,&origParentSection,&origParents,&origChildIDs,NULL,NULL);
1151: if (origParentSection) {
1152: PetscInt pStart, pEnd;
1153: PetscInt *newParents, *newChildIDs, *globParents;
1154: PetscInt *remoteOffsetsParents, newParentSize;
1155: PetscSF parentSF;
1157: DMPlexGetChart(dmParallel, &pStart, &pEnd);
1158: PetscSectionCreate(PetscObjectComm((PetscObject)dmParallel),&newParentSection);
1159: PetscSectionSetChart(newParentSection,pStart,pEnd);
1160: PetscSFDistributeSection(migrationSF, origParentSection, &remoteOffsetsParents, newParentSection);
1161: PetscSFCreateSectionSF(migrationSF, origParentSection, remoteOffsetsParents, newParentSection, &parentSF);
1162: PetscFree(remoteOffsetsParents);
1163: PetscSectionGetStorageSize(newParentSection,&newParentSize);
1164: PetscMalloc2(newParentSize,&newParents,newParentSize,&newChildIDs);
1165: if (original) {
1166: PetscInt numParents;
1168: PetscSectionGetStorageSize(origParentSection,&numParents);
1169: PetscMalloc1(numParents,&globParents);
1170: ISLocalToGlobalMappingApplyBlock(original, numParents, origParents, globParents);
1171: }
1172: else {
1173: globParents = origParents;
1174: }
1175: PetscSFBcastBegin(parentSF, MPIU_INT, globParents, newParents);
1176: PetscSFBcastEnd(parentSF, MPIU_INT, globParents, newParents);
1177: if (original) {
1178: PetscFree(globParents);
1179: }
1180: PetscSFBcastBegin(parentSF, MPIU_INT, origChildIDs, newChildIDs);
1181: PetscSFBcastEnd(parentSF, MPIU_INT, origChildIDs, newChildIDs);
1182: ISGlobalToLocalMappingApplyBlock(renumbering,IS_GTOLM_MASK, newParentSize, newParents, NULL, newParents);
1183: #if defined(PETSC_USE_DEBUG)
1184: {
1185: PetscInt p;
1186: PetscBool valid = PETSC_TRUE;
1187: for (p = 0; p < newParentSize; ++p) {
1188: if (newParents[p] < 0) {valid = PETSC_FALSE; PetscPrintf(PETSC_COMM_SELF, "Point %d not in overlap SF\n", p);}
1189: }
1190: if (!valid) SETERRQ(PETSC_COMM_SELF, PETSC_ERR_ARG_OUTOFRANGE, "Invalid global to local map");
1191: }
1192: #endif
1193: PetscOptionsHasName(((PetscObject) dm)->options,((PetscObject) dm)->prefix, "-parents_view", &flg);
1194: if (flg) {
1195: PetscPrintf(comm, "Serial Parent Section: \n");
1196: PetscSectionView(origParentSection, PETSC_VIEWER_STDOUT_(comm));
1197: PetscPrintf(comm, "Parallel Parent Section: \n");
1198: PetscSectionView(newParentSection, PETSC_VIEWER_STDOUT_(comm));
1199: PetscSFView(parentSF, NULL);
1200: }
1201: DMPlexSetTree(dmParallel,newParentSection,newParents,newChildIDs);
1202: PetscSectionDestroy(&newParentSection);
1203: PetscFree2(newParents,newChildIDs);
1204: PetscSFDestroy(&parentSF);
1205: }
1206: pmesh->useAnchors = mesh->useAnchors;
1207: return(0);
1208: }
1210: PETSC_UNUSED static PetscErrorCode DMPlexDistributeSF(DM dm, PetscSF migrationSF, DM dmParallel)
1211: {
1212: PetscMPIInt rank, size;
1213: MPI_Comm comm;
1214: PetscErrorCode ierr;
1220: /* Create point SF for parallel mesh */
1221: PetscLogEventBegin(DMPLEX_DistributeSF,dm,0,0,0);
1222: PetscObjectGetComm((PetscObject)dm, &comm);
1223: MPI_Comm_rank(comm, &rank);
1224: MPI_Comm_size(comm, &size);
1225: {
1226: const PetscInt *leaves;
1227: PetscSFNode *remotePoints, *rowners, *lowners;
1228: PetscInt numRoots, numLeaves, numGhostPoints = 0, p, gp, *ghostPoints;
1229: PetscInt pStart, pEnd;
1231: DMPlexGetChart(dmParallel, &pStart, &pEnd);
1232: PetscSFGetGraph(migrationSF, &numRoots, &numLeaves, &leaves, NULL);
1233: PetscMalloc2(numRoots,&rowners,numLeaves,&lowners);
1234: for (p=0; p<numRoots; p++) {
1235: rowners[p].rank = -1;
1236: rowners[p].index = -1;
1237: }
1238: PetscSFBcastBegin(migrationSF, MPIU_2INT, rowners, lowners);
1239: PetscSFBcastEnd(migrationSF, MPIU_2INT, rowners, lowners);
1240: for (p = 0; p < numLeaves; ++p) {
1241: if (lowners[p].rank < 0 || lowners[p].rank == rank) { /* Either put in a bid or we know we own it */
1242: lowners[p].rank = rank;
1243: lowners[p].index = leaves ? leaves[p] : p;
1244: } else if (lowners[p].rank >= 0) { /* Point already claimed so flag so that MAXLOC does not listen to us */
1245: lowners[p].rank = -2;
1246: lowners[p].index = -2;
1247: }
1248: }
1249: for (p=0; p<numRoots; p++) { /* Root must not participate in the rediction, flag so that MAXLOC does not use */
1250: rowners[p].rank = -3;
1251: rowners[p].index = -3;
1252: }
1253: PetscSFReduceBegin(migrationSF, MPIU_2INT, lowners, rowners, MPI_MAXLOC);
1254: PetscSFReduceEnd(migrationSF, MPIU_2INT, lowners, rowners, MPI_MAXLOC);
1255: PetscSFBcastBegin(migrationSF, MPIU_2INT, rowners, lowners);
1256: PetscSFBcastEnd(migrationSF, MPIU_2INT, rowners, lowners);
1257: for (p = 0; p < numLeaves; ++p) {
1258: if (lowners[p].rank < 0 || lowners[p].index < 0) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_PLIB,"Cell partition corrupt: point not claimed");
1259: if (lowners[p].rank != rank) ++numGhostPoints;
1260: }
1261: PetscMalloc1(numGhostPoints, &ghostPoints);
1262: PetscMalloc1(numGhostPoints, &remotePoints);
1263: for (p = 0, gp = 0; p < numLeaves; ++p) {
1264: if (lowners[p].rank != rank) {
1265: ghostPoints[gp] = leaves ? leaves[p] : p;
1266: remotePoints[gp].rank = lowners[p].rank;
1267: remotePoints[gp].index = lowners[p].index;
1268: ++gp;
1269: }
1270: }
1271: PetscFree2(rowners,lowners);
1272: PetscSFSetGraph((dmParallel)->sf, pEnd - pStart, numGhostPoints, ghostPoints, PETSC_OWN_POINTER, remotePoints, PETSC_OWN_POINTER);
1273: PetscSFSetFromOptions((dmParallel)->sf);
1274: }
1275: {
1276: PetscBool useCone, useClosure, useAnchors;
1278: DMGetBasicAdjacency(dm, &useCone, &useClosure);
1279: DMSetBasicAdjacency(dmParallel, useCone, useClosure);
1280: DMPlexGetAdjacencyUseAnchors(dm, &useAnchors);
1281: DMPlexSetAdjacencyUseAnchors(dmParallel, useAnchors);
1282: }
1283: PetscLogEventEnd(DMPLEX_DistributeSF,dm,0,0,0);
1284: return(0);
1285: }
1287: /*@
1288: DMPlexSetPartitionBalance - Should distribution of the DM attempt to balance the shared point partition?
1290: Input Parameters:
1291: + dm - The DMPlex object
1292: - flg - Balance the partition?
1294: Level: intermediate
1296: .seealso: DMPlexDistribute(), DMPlexGetPartitionBalance()
1297: @*/
1298: PetscErrorCode DMPlexSetPartitionBalance(DM dm, PetscBool flg)
1299: {
1300: DM_Plex *mesh = (DM_Plex *)dm->data;
1303: mesh->partitionBalance = flg;
1304: return(0);
1305: }
1307: /*@
1308: DMPlexGetPartitionBalance - Does distribution of the DM attempt to balance the shared point partition?
1310: Input Parameter:
1311: . dm - The DMPlex object
1313: Output Parameter:
1314: . flg - Balance the partition?
1316: Level: intermediate
1318: .seealso: DMPlexDistribute(), DMPlexSetPartitionBalance()
1319: @*/
1320: PetscErrorCode DMPlexGetPartitionBalance(DM dm, PetscBool *flg)
1321: {
1322: DM_Plex *mesh = (DM_Plex *)dm->data;
1327: *flg = mesh->partitionBalance;
1328: return(0);
1329: }
1331: typedef struct {
1332: PetscInt vote, rank, index;
1333: } Petsc3Int;
1335: /* MaxLoc, but carry a third piece of information around */
1336: static void MPIAPI MaxLocCarry(void *in_, void *inout_, PetscMPIInt *len_, MPI_Datatype *dtype)
1337: {
1338: Petsc3Int *a = (Petsc3Int *)inout_;
1339: Petsc3Int *b = (Petsc3Int *)in_;
1340: PetscInt i, len = *len_;
1341: for (i = 0; i < len; i++) {
1342: if (a[i].vote < b[i].vote) {
1343: a[i].vote = b[i].vote;
1344: a[i].rank = b[i].rank;
1345: a[i].index = b[i].index;
1346: } else if (a[i].vote <= b[i].vote) {
1347: if (a[i].rank >= b[i].rank) {
1348: a[i].rank = b[i].rank;
1349: a[i].index = b[i].index;
1350: }
1351: }
1352: }
1353: }
1355: /*@C
1356: DMPlexCreatePointSF - Build a point SF from an SF describing a point migration
1358: Input Parameters:
1359: + dm - The source DMPlex object
1360: . migrationSF - The star forest that describes the parallel point remapping
1361: . ownership - Flag causing a vote to determine point ownership
1363: Output Parameter:
1364: - pointSF - The star forest describing the point overlap in the remapped DM
1366: Notes:
1367: Output pointSF is guaranteed to have the array of local indices (leaves) sorted.
1369: Level: developer
1371: .seealso: DMPlexDistribute(), DMPlexDistributeOverlap()
1372: @*/
1373: PetscErrorCode DMPlexCreatePointSF(DM dm, PetscSF migrationSF, PetscBool ownership, PetscSF *pointSF)
1374: {
1375: PetscMPIInt rank, size;
1376: PetscInt p, nroots, nleaves, idx, npointLeaves;
1377: PetscInt *pointLocal;
1378: const PetscInt *leaves;
1379: const PetscSFNode *roots;
1380: PetscSFNode *rootNodes, *leafNodes, *pointRemote;
1381: Vec shifts;
1382: const PetscInt numShifts = 13759;
1383: const PetscScalar *shift = NULL;
1384: const PetscBool shiftDebug = PETSC_FALSE;
1385: PetscBool balance;
1386: PetscErrorCode ierr;
1390: MPI_Comm_rank(PetscObjectComm((PetscObject) dm), &rank);
1391: MPI_Comm_size(PetscObjectComm((PetscObject) dm), &size);
1392: PetscLogEventBegin(DMPLEX_CreatePointSF,dm,0,0,0);
1394: DMPlexGetPartitionBalance(dm, &balance);
1395: PetscSFGetGraph(migrationSF, &nroots, &nleaves, &leaves, &roots);
1396: PetscMalloc2(nroots, &rootNodes, nleaves, &leafNodes);
1397: if (ownership) {
1398: MPI_Op op;
1399: MPI_Datatype datatype;
1400: Petsc3Int *rootVote = NULL, *leafVote = NULL;
1401: /* If balancing, we compute a random cyclic shift of the rank for each remote point. That way, the max will evenly distribute among ranks. */
1402: if (balance) {
1403: PetscRandom r;
1405: PetscRandomCreate(PETSC_COMM_SELF, &r);
1406: PetscRandomSetInterval(r, 0, 2467*size);
1407: VecCreate(PETSC_COMM_SELF, &shifts);
1408: VecSetSizes(shifts, numShifts, numShifts);
1409: VecSetType(shifts, VECSTANDARD);
1410: VecSetRandom(shifts, r);
1411: PetscRandomDestroy(&r);
1412: VecGetArrayRead(shifts, &shift);
1413: }
1415: PetscMalloc1(nroots, &rootVote);
1416: PetscMalloc1(nleaves, &leafVote);
1417: /* Point ownership vote: Process with highest rank owns shared points */
1418: for (p = 0; p < nleaves; ++p) {
1419: if (shiftDebug) {
1420: PetscSynchronizedPrintf(PetscObjectComm((PetscObject) dm), "[%d] Point %D RemotePoint %D Shift %D MyRank %D\n", rank, leaves ? leaves[p] : p, roots[p].index, (PetscInt) PetscRealPart(shift[roots[p].index%numShifts]), (rank + (shift ? (PetscInt) PetscRealPart(shift[roots[p].index%numShifts]) : 0))%size);
1421: }
1422: /* Either put in a bid or we know we own it */
1423: leafVote[p].vote = (rank + (shift ? (PetscInt) PetscRealPart(shift[roots[p].index%numShifts]) : 0))%size;
1424: leafVote[p].rank = rank;
1425: leafVote[p].index = p;
1426: }
1427: for (p = 0; p < nroots; p++) {
1428: /* Root must not participate in the reduction, flag so that MAXLOC does not use */
1429: rootVote[p].vote = -3;
1430: rootVote[p].rank = -3;
1431: rootVote[p].index = -3;
1432: }
1433: MPI_Type_contiguous(3, MPIU_INT, &datatype);
1434: MPI_Type_commit(&datatype);
1435: MPI_Op_create(&MaxLocCarry, 1, &op);
1436: PetscSFReduceBegin(migrationSF, datatype, leafVote, rootVote, op);
1437: PetscSFReduceEnd(migrationSF, datatype, leafVote, rootVote, op);
1438: MPI_Op_free(&op);
1439: MPI_Type_free(&datatype);
1440: for (p = 0; p < nroots; p++) {
1441: rootNodes[p].rank = rootVote[p].rank;
1442: rootNodes[p].index = rootVote[p].index;
1443: }
1444: PetscFree(leafVote);
1445: PetscFree(rootVote);
1446: } else {
1447: for (p = 0; p < nroots; p++) {
1448: rootNodes[p].index = -1;
1449: rootNodes[p].rank = rank;
1450: }
1451: for (p = 0; p < nleaves; p++) {
1452: /* Write new local id into old location */
1453: if (roots[p].rank == rank) {
1454: rootNodes[roots[p].index].index = leaves ? leaves[p] : p;
1455: }
1456: }
1457: }
1458: PetscSFBcastBegin(migrationSF, MPIU_2INT, rootNodes, leafNodes);
1459: PetscSFBcastEnd(migrationSF, MPIU_2INT, rootNodes, leafNodes);
1461: for (npointLeaves = 0, p = 0; p < nleaves; p++) {
1462: if (leafNodes[p].rank != rank) npointLeaves++;
1463: }
1464: PetscMalloc1(npointLeaves, &pointLocal);
1465: PetscMalloc1(npointLeaves, &pointRemote);
1466: for (idx = 0, p = 0; p < nleaves; p++) {
1467: if (leafNodes[p].rank != rank) {
1468: /* Note that pointLocal is automatically sorted as it is sublist of 0, ..., nleaves-1 */
1469: pointLocal[idx] = p;
1470: pointRemote[idx] = leafNodes[p];
1471: idx++;
1472: }
1473: }
1474: if (shift) {
1475: VecRestoreArrayRead(shifts, &shift);
1476: VecDestroy(&shifts);
1477: }
1478: if (shiftDebug) {PetscSynchronizedFlush(PetscObjectComm((PetscObject) dm), PETSC_STDOUT);}
1479: PetscSFCreate(PetscObjectComm((PetscObject) dm), pointSF);
1480: PetscSFSetFromOptions(*pointSF);
1481: PetscSFSetGraph(*pointSF, nleaves, npointLeaves, pointLocal, PETSC_OWN_POINTER, pointRemote, PETSC_OWN_POINTER);
1482: PetscFree2(rootNodes, leafNodes);
1483: PetscLogEventEnd(DMPLEX_CreatePointSF,dm,0,0,0);
1484: return(0);
1485: }
1487: /*@C
1488: DMPlexMigrate - Migrates internal DM data over the supplied star forest
1490: Collective on dm
1492: Input Parameters:
1493: + dm - The source DMPlex object
1494: . sf - The star forest communication context describing the migration pattern
1496: Output Parameter:
1497: - targetDM - The target DMPlex object
1499: Level: intermediate
1501: .seealso: DMPlexDistribute(), DMPlexDistributeOverlap()
1502: @*/
1503: PetscErrorCode DMPlexMigrate(DM dm, PetscSF sf, DM targetDM)
1504: {
1505: MPI_Comm comm;
1506: PetscInt dim, cdim, nroots;
1507: PetscSF sfPoint;
1508: ISLocalToGlobalMapping ltogMigration;
1509: ISLocalToGlobalMapping ltogOriginal = NULL;
1510: PetscBool flg;
1511: PetscErrorCode ierr;
1515: PetscLogEventBegin(DMPLEX_Migrate, dm, 0, 0, 0);
1516: PetscObjectGetComm((PetscObject) dm, &comm);
1517: DMGetDimension(dm, &dim);
1518: DMSetDimension(targetDM, dim);
1519: DMGetCoordinateDim(dm, &cdim);
1520: DMSetCoordinateDim(targetDM, cdim);
1522: /* Check for a one-to-all distribution pattern */
1523: DMGetPointSF(dm, &sfPoint);
1524: PetscSFGetGraph(sfPoint, &nroots, NULL, NULL, NULL);
1525: if (nroots >= 0) {
1526: IS isOriginal;
1527: PetscInt n, size, nleaves;
1528: PetscInt *numbering_orig, *numbering_new;
1530: /* Get the original point numbering */
1531: DMPlexCreatePointNumbering(dm, &isOriginal);
1532: ISLocalToGlobalMappingCreateIS(isOriginal, <ogOriginal);
1533: ISLocalToGlobalMappingGetSize(ltogOriginal, &size);
1534: ISLocalToGlobalMappingGetBlockIndices(ltogOriginal, (const PetscInt**)&numbering_orig);
1535: /* Convert to positive global numbers */
1536: for (n=0; n<size; n++) {if (numbering_orig[n] < 0) numbering_orig[n] = -(numbering_orig[n]+1);}
1537: /* Derive the new local-to-global mapping from the old one */
1538: PetscSFGetGraph(sf, NULL, &nleaves, NULL, NULL);
1539: PetscMalloc1(nleaves, &numbering_new);
1540: PetscSFBcastBegin(sf, MPIU_INT, numbering_orig, numbering_new);
1541: PetscSFBcastEnd(sf, MPIU_INT, numbering_orig, numbering_new);
1542: ISLocalToGlobalMappingCreate(comm, 1, nleaves, numbering_new, PETSC_OWN_POINTER, <ogMigration);
1543: ISLocalToGlobalMappingRestoreIndices(ltogOriginal, (const PetscInt**)&numbering_orig);
1544: ISDestroy(&isOriginal);
1545: } else {
1546: /* One-to-all distribution pattern: We can derive LToG from SF */
1547: ISLocalToGlobalMappingCreateSF(sf, 0, <ogMigration);
1548: }
1549: PetscOptionsHasName(((PetscObject) dm)->options,((PetscObject) dm)->prefix, "-partition_view", &flg);
1550: if (flg) {
1551: PetscPrintf(comm, "Point renumbering for DM migration:\n");
1552: ISLocalToGlobalMappingView(ltogMigration, NULL);
1553: }
1554: /* Migrate DM data to target DM */
1555: DMPlexDistributeCones(dm, sf, ltogOriginal, ltogMigration, targetDM);
1556: DMPlexDistributeLabels(dm, sf, targetDM);
1557: DMPlexDistributeCoordinates(dm, sf, targetDM);
1558: DMPlexDistributeSetupTree(dm, sf, ltogOriginal, ltogMigration, targetDM);
1559: ISLocalToGlobalMappingDestroy(<ogOriginal);
1560: ISLocalToGlobalMappingDestroy(<ogMigration);
1561: PetscLogEventEnd(DMPLEX_Migrate, dm, 0, 0, 0);
1562: return(0);
1563: }
1565: /*@C
1566: DMPlexDistribute - Distributes the mesh and any associated sections.
1568: Collective on dm
1570: Input Parameters:
1571: + dm - The original DMPlex object
1572: - overlap - The overlap of partitions, 0 is the default
1574: Output Parameters:
1575: + sf - The PetscSF used for point distribution, or NULL if not needed
1576: - dmParallel - The distributed DMPlex object
1578: Note: If the mesh was not distributed, the output dmParallel will be NULL.
1580: The user can control the definition of adjacency for the mesh using DMSetAdjacency(). They should choose the combination appropriate for the function
1581: representation on the mesh.
1583: Level: intermediate
1585: .seealso: DMPlexCreate(), DMSetAdjacency(), DMPlexGetOverlap()
1586: @*/
1587: PetscErrorCode DMPlexDistribute(DM dm, PetscInt overlap, PetscSF *sf, DM *dmParallel)
1588: {
1589: MPI_Comm comm;
1590: PetscPartitioner partitioner;
1591: IS cellPart;
1592: PetscSection cellPartSection;
1593: DM dmCoord;
1594: DMLabel lblPartition, lblMigration;
1595: PetscSF sfMigration, sfStratified, sfPoint;
1596: PetscBool flg, balance;
1597: PetscMPIInt rank, size;
1598: PetscErrorCode ierr;
1606: if (sf) *sf = NULL;
1607: *dmParallel = NULL;
1608: PetscObjectGetComm((PetscObject)dm,&comm);
1609: MPI_Comm_rank(comm, &rank);
1610: MPI_Comm_size(comm, &size);
1611: if (size == 1) return(0);
1613: PetscLogEventBegin(DMPLEX_Distribute,dm,0,0,0);
1614: /* Create cell partition */
1615: PetscLogEventBegin(DMPLEX_Partition,dm,0,0,0);
1616: PetscSectionCreate(comm, &cellPartSection);
1617: DMPlexGetPartitioner(dm, &partitioner);
1618: PetscPartitionerDMPlexPartition(partitioner, dm, NULL, cellPartSection, &cellPart);
1619: PetscLogEventBegin(DMPLEX_PartSelf,dm,0,0,0);
1620: {
1621: /* Convert partition to DMLabel */
1622: IS is;
1623: PetscHSetI ht;
1624: const PetscInt *points;
1625: PetscInt *iranks;
1626: PetscInt pStart, pEnd, proc, npoints, poff = 0, nranks;
1628: DMLabelCreate(PETSC_COMM_SELF, "Point Partition", &lblPartition);
1629: /* Preallocate strata */
1630: PetscHSetICreate(&ht);
1631: PetscSectionGetChart(cellPartSection, &pStart, &pEnd);
1632: for (proc = pStart; proc < pEnd; proc++) {
1633: PetscSectionGetDof(cellPartSection, proc, &npoints);
1634: if (npoints) {PetscHSetIAdd(ht, proc);}
1635: }
1636: PetscHSetIGetSize(ht, &nranks);
1637: PetscMalloc1(nranks, &iranks);
1638: PetscHSetIGetElems(ht, &poff, iranks);
1639: PetscHSetIDestroy(&ht);
1640: DMLabelAddStrata(lblPartition, nranks, iranks);
1641: PetscFree(iranks);
1642: /* Inline DMPlexPartitionLabelClosure() */
1643: ISGetIndices(cellPart, &points);
1644: PetscSectionGetChart(cellPartSection, &pStart, &pEnd);
1645: for (proc = pStart; proc < pEnd; proc++) {
1646: PetscSectionGetDof(cellPartSection, proc, &npoints);
1647: if (!npoints) continue;
1648: PetscSectionGetOffset(cellPartSection, proc, &poff);
1649: DMPlexClosurePoints_Private(dm, npoints, points+poff, &is);
1650: DMLabelSetStratumIS(lblPartition, proc, is);
1651: ISDestroy(&is);
1652: }
1653: ISRestoreIndices(cellPart, &points);
1654: }
1655: PetscLogEventEnd(DMPLEX_PartSelf,dm,0,0,0);
1657: DMLabelCreate(PETSC_COMM_SELF, "Point migration", &lblMigration);
1658: DMPlexPartitionLabelInvert(dm, lblPartition, NULL, lblMigration);
1659: DMPlexPartitionLabelCreateSF(dm, lblMigration, &sfMigration);
1660: DMPlexStratifyMigrationSF(dm, sfMigration, &sfStratified);
1661: PetscSFDestroy(&sfMigration);
1662: sfMigration = sfStratified;
1663: PetscSFSetUp(sfMigration);
1664: PetscLogEventEnd(DMPLEX_Partition,dm,0,0,0);
1665: PetscOptionsHasName(((PetscObject) dm)->options,((PetscObject) dm)->prefix, "-partition_view", &flg);
1666: if (flg) {
1667: DMLabelView(lblPartition, PETSC_VIEWER_STDOUT_(comm));
1668: PetscSFView(sfMigration, PETSC_VIEWER_STDOUT_(comm));
1669: }
1671: /* Create non-overlapping parallel DM and migrate internal data */
1672: DMPlexCreate(comm, dmParallel);
1673: PetscObjectSetName((PetscObject) *dmParallel, "Parallel Mesh");
1674: DMPlexMigrate(dm, sfMigration, *dmParallel);
1676: /* Build the point SF without overlap */
1677: DMPlexGetPartitionBalance(dm, &balance);
1678: DMPlexSetPartitionBalance(*dmParallel, balance);
1679: DMPlexCreatePointSF(*dmParallel, sfMigration, PETSC_TRUE, &sfPoint);
1680: DMSetPointSF(*dmParallel, sfPoint);
1681: DMGetCoordinateDM(*dmParallel, &dmCoord);
1682: if (dmCoord) {DMSetPointSF(dmCoord, sfPoint);}
1683: if (flg) {PetscSFView(sfPoint, NULL);}
1685: if (overlap > 0) {
1686: DM dmOverlap;
1687: PetscInt nroots, nleaves, noldleaves, l;
1688: const PetscInt *oldLeaves;
1689: PetscSFNode *newRemote, *permRemote;
1690: const PetscSFNode *oldRemote;
1691: PetscSF sfOverlap, sfOverlapPoint;
1693: /* Add the partition overlap to the distributed DM */
1694: DMPlexDistributeOverlap(*dmParallel, overlap, &sfOverlap, &dmOverlap);
1695: DMDestroy(dmParallel);
1696: *dmParallel = dmOverlap;
1697: if (flg) {
1698: PetscPrintf(comm, "Overlap Migration SF:\n");
1699: PetscSFView(sfOverlap, NULL);
1700: }
1702: /* Re-map the migration SF to establish the full migration pattern */
1703: PetscSFGetGraph(sfMigration, &nroots, &noldleaves, &oldLeaves, &oldRemote);
1704: PetscSFGetGraph(sfOverlap, NULL, &nleaves, NULL, NULL);
1705: PetscMalloc1(nleaves, &newRemote);
1706: /* oldRemote: original root point mapping to original leaf point
1707: newRemote: original leaf point mapping to overlapped leaf point */
1708: if (oldLeaves) {
1709: /* After stratification, the migration remotes may not be in root (canonical) order, so we reorder using the leaf numbering */
1710: PetscMalloc1(noldleaves, &permRemote);
1711: for (l = 0; l < noldleaves; ++l) permRemote[oldLeaves[l]] = oldRemote[l];
1712: oldRemote = permRemote;
1713: }
1714: PetscSFBcastBegin(sfOverlap, MPIU_2INT, oldRemote, newRemote);
1715: PetscSFBcastEnd(sfOverlap, MPIU_2INT, oldRemote, newRemote);
1716: if (oldLeaves) {PetscFree(oldRemote);}
1717: PetscSFCreate(comm, &sfOverlapPoint);
1718: PetscSFSetGraph(sfOverlapPoint, nroots, nleaves, NULL, PETSC_OWN_POINTER, newRemote, PETSC_OWN_POINTER);
1719: PetscSFDestroy(&sfOverlap);
1720: PetscSFDestroy(&sfMigration);
1721: sfMigration = sfOverlapPoint;
1722: }
1723: /* Cleanup Partition */
1724: DMLabelDestroy(&lblPartition);
1725: DMLabelDestroy(&lblMigration);
1726: PetscSectionDestroy(&cellPartSection);
1727: ISDestroy(&cellPart);
1728: /* Copy BC */
1729: DMCopyBoundary(dm, *dmParallel);
1730: /* Create sfNatural */
1731: if (dm->useNatural) {
1732: PetscSection section;
1734: DMGetLocalSection(dm, §ion);
1735: DMPlexCreateGlobalToNaturalSF(*dmParallel, section, sfMigration, &(*dmParallel)->sfNatural);
1736: DMSetUseNatural(*dmParallel, PETSC_TRUE);
1737: }
1738: /* Cleanup */
1739: if (sf) {*sf = sfMigration;}
1740: else {PetscSFDestroy(&sfMigration);}
1741: PetscSFDestroy(&sfPoint);
1742: PetscLogEventEnd(DMPLEX_Distribute,dm,0,0,0);
1743: return(0);
1744: }
1746: /*@C
1747: DMPlexDistributeOverlap - Add partition overlap to a distributed non-overlapping DM.
1749: Collective on dm
1751: Input Parameters:
1752: + dm - The non-overlapping distributed DMPlex object
1753: - overlap - The overlap of partitions (the same on all ranks)
1755: Output Parameters:
1756: + sf - The PetscSF used for point distribution
1757: - dmOverlap - The overlapping distributed DMPlex object, or NULL
1759: Notes:
1760: If the mesh was not distributed, the return value is NULL.
1762: The user can control the definition of adjacency for the mesh using DMSetAdjacency(). They should choose the combination appropriate for the function
1763: representation on the mesh.
1765: Level: advanced
1767: .seealso: DMPlexCreate(), DMSetAdjacency(), DMPlexDistribute(), DMPlexCreateOverlapLabel(), DMPlexGetOverlap()
1768: @*/
1769: PetscErrorCode DMPlexDistributeOverlap(DM dm, PetscInt overlap, PetscSF *sf, DM *dmOverlap)
1770: {
1771: MPI_Comm comm;
1772: PetscMPIInt size, rank;
1773: PetscSection rootSection, leafSection;
1774: IS rootrank, leafrank;
1775: DM dmCoord;
1776: DMLabel lblOverlap;
1777: PetscSF sfOverlap, sfStratified, sfPoint;
1778: PetscErrorCode ierr;
1786: if (sf) *sf = NULL;
1787: *dmOverlap = NULL;
1788: PetscObjectGetComm((PetscObject)dm,&comm);
1789: MPI_Comm_size(comm, &size);
1790: MPI_Comm_rank(comm, &rank);
1791: if (size == 1) return(0);
1793: PetscLogEventBegin(DMPLEX_DistributeOverlap, dm, 0, 0, 0);
1794: /* Compute point overlap with neighbouring processes on the distributed DM */
1795: PetscLogEventBegin(DMPLEX_Partition,dm,0,0,0);
1796: PetscSectionCreate(comm, &rootSection);
1797: PetscSectionCreate(comm, &leafSection);
1798: DMPlexDistributeOwnership(dm, rootSection, &rootrank, leafSection, &leafrank);
1799: DMPlexCreateOverlapLabel(dm, overlap, rootSection, rootrank, leafSection, leafrank, &lblOverlap);
1800: /* Convert overlap label to stratified migration SF */
1801: DMPlexPartitionLabelCreateSF(dm, lblOverlap, &sfOverlap);
1802: DMPlexStratifyMigrationSF(dm, sfOverlap, &sfStratified);
1803: PetscSFDestroy(&sfOverlap);
1804: sfOverlap = sfStratified;
1805: PetscObjectSetName((PetscObject) sfOverlap, "Overlap SF");
1806: PetscSFSetFromOptions(sfOverlap);
1808: PetscSectionDestroy(&rootSection);
1809: PetscSectionDestroy(&leafSection);
1810: ISDestroy(&rootrank);
1811: ISDestroy(&leafrank);
1812: PetscLogEventEnd(DMPLEX_Partition,dm,0,0,0);
1814: /* Build the overlapping DM */
1815: DMPlexCreate(comm, dmOverlap);
1816: PetscObjectSetName((PetscObject) *dmOverlap, "Parallel Mesh");
1817: DMPlexMigrate(dm, sfOverlap, *dmOverlap);
1818: /* Store the overlap in the new DM */
1819: ((DM_Plex*)(*dmOverlap)->data)->overlap = overlap + ((DM_Plex*)dm->data)->overlap;
1820: /* Build the new point SF */
1821: DMPlexCreatePointSF(*dmOverlap, sfOverlap, PETSC_FALSE, &sfPoint);
1822: DMSetPointSF(*dmOverlap, sfPoint);
1823: DMGetCoordinateDM(*dmOverlap, &dmCoord);
1824: if (dmCoord) {DMSetPointSF(dmCoord, sfPoint);}
1825: PetscSFDestroy(&sfPoint);
1826: /* Cleanup overlap partition */
1827: DMLabelDestroy(&lblOverlap);
1828: if (sf) *sf = sfOverlap;
1829: else {PetscSFDestroy(&sfOverlap);}
1830: PetscLogEventEnd(DMPLEX_DistributeOverlap, dm, 0, 0, 0);
1831: return(0);
1832: }
1834: PetscErrorCode DMPlexGetOverlap_Plex(DM dm, PetscInt *overlap)
1835: {
1836: DM_Plex *mesh = (DM_Plex*) dm->data;
1839: *overlap = mesh->overlap;
1840: return(0);
1841: }
1843: /*@
1844: DMPlexGetOverlap - Get the DMPlex partition overlap.
1846: Not collective
1848: Input Parameter:
1849: . dm - The DM
1851: Output Parameter:
1852: . overlap - The overlap of this DM
1854: Level: intermediate
1856: .seealso: DMPlexDistribute(), DMPlexDistributeOverlap(), DMPlexCreateOverlapLabel()
1857: @*/
1858: PetscErrorCode DMPlexGetOverlap(DM dm, PetscInt *overlap)
1859: {
1860: PetscErrorCode ierr;
1864: PetscUseMethod(dm,"DMPlexGetOverlap_C",(DM,PetscInt*),(dm,overlap));
1865: return(0);
1866: }
1869: /*@C
1870: DMPlexGetGatherDM - Get a copy of the DMPlex that gathers all points on the
1871: root process of the original's communicator.
1873: Collective on dm
1875: Input Parameter:
1876: . dm - the original DMPlex object
1878: Output Parameters:
1879: + sf - the PetscSF used for point distribution (optional)
1880: - gatherMesh - the gathered DM object, or NULL
1882: Level: intermediate
1884: .seealso: DMPlexDistribute(), DMPlexGetRedundantDM()
1885: @*/
1886: PetscErrorCode DMPlexGetGatherDM(DM dm, PetscSF *sf, DM *gatherMesh)
1887: {
1888: MPI_Comm comm;
1889: PetscMPIInt size;
1890: PetscPartitioner oldPart, gatherPart;
1896: *gatherMesh = NULL;
1897: if (sf) *sf = NULL;
1898: comm = PetscObjectComm((PetscObject)dm);
1899: MPI_Comm_size(comm,&size);
1900: if (size == 1) return(0);
1901: DMPlexGetPartitioner(dm,&oldPart);
1902: PetscObjectReference((PetscObject)oldPart);
1903: PetscPartitionerCreate(comm,&gatherPart);
1904: PetscPartitionerSetType(gatherPart,PETSCPARTITIONERGATHER);
1905: DMPlexSetPartitioner(dm,gatherPart);
1906: DMPlexDistribute(dm,0,sf,gatherMesh);
1908: DMPlexSetPartitioner(dm,oldPart);
1909: PetscPartitionerDestroy(&gatherPart);
1910: PetscPartitionerDestroy(&oldPart);
1911: return(0);
1912: }
1914: /*@C
1915: DMPlexGetRedundantDM - Get a copy of the DMPlex that is completely copied on each process.
1917: Collective on dm
1919: Input Parameter:
1920: . dm - the original DMPlex object
1922: Output Parameters:
1923: + sf - the PetscSF used for point distribution (optional)
1924: - redundantMesh - the redundant DM object, or NULL
1926: Level: intermediate
1928: .seealso: DMPlexDistribute(), DMPlexGetGatherDM()
1929: @*/
1930: PetscErrorCode DMPlexGetRedundantDM(DM dm, PetscSF *sf, DM *redundantMesh)
1931: {
1932: MPI_Comm comm;
1933: PetscMPIInt size, rank;
1934: PetscInt pStart, pEnd, p;
1935: PetscInt numPoints = -1;
1936: PetscSF migrationSF, sfPoint, gatherSF;
1937: DM gatherDM, dmCoord;
1938: PetscSFNode *points;
1944: *redundantMesh = NULL;
1945: comm = PetscObjectComm((PetscObject)dm);
1946: MPI_Comm_size(comm,&size);
1947: if (size == 1) {
1948: PetscObjectReference((PetscObject) dm);
1949: *redundantMesh = dm;
1950: if (sf) *sf = NULL;
1951: return(0);
1952: }
1953: DMPlexGetGatherDM(dm,&gatherSF,&gatherDM);
1954: if (!gatherDM) return(0);
1955: MPI_Comm_rank(comm,&rank);
1956: DMPlexGetChart(gatherDM,&pStart,&pEnd);
1957: numPoints = pEnd - pStart;
1958: MPI_Bcast(&numPoints,1,MPIU_INT,0,comm);
1959: PetscMalloc1(numPoints,&points);
1960: PetscSFCreate(comm,&migrationSF);
1961: for (p = 0; p < numPoints; p++) {
1962: points[p].index = p;
1963: points[p].rank = 0;
1964: }
1965: PetscSFSetGraph(migrationSF,pEnd-pStart,numPoints,NULL,PETSC_OWN_POINTER,points,PETSC_OWN_POINTER);
1966: DMPlexCreate(comm, redundantMesh);
1967: PetscObjectSetName((PetscObject) *redundantMesh, "Redundant Mesh");
1968: DMPlexMigrate(gatherDM, migrationSF, *redundantMesh);
1969: DMPlexCreatePointSF(*redundantMesh, migrationSF, PETSC_FALSE, &sfPoint);
1970: DMSetPointSF(*redundantMesh, sfPoint);
1971: DMGetCoordinateDM(*redundantMesh, &dmCoord);
1972: if (dmCoord) {DMSetPointSF(dmCoord, sfPoint);}
1973: PetscSFDestroy(&sfPoint);
1974: if (sf) {
1975: PetscSF tsf;
1977: PetscSFCompose(gatherSF,migrationSF,&tsf);
1978: DMPlexStratifyMigrationSF(dm, tsf, sf);
1979: PetscSFDestroy(&tsf);
1980: }
1981: PetscSFDestroy(&migrationSF);
1982: PetscSFDestroy(&gatherSF);
1983: DMDestroy(&gatherDM);
1984: return(0);
1985: }
1987: /*@
1988: DMPlexIsDistributed - Find out whether this DM is distributed, i.e. more than one rank owns some points.
1990: Collective
1992: Input Parameter:
1993: . dm - The DM object
1995: Output Parameter:
1996: . distributed - Flag whether the DM is distributed
1998: Level: intermediate
2000: Notes:
2001: This currently finds out whether at least two ranks have any DAG points.
2002: This involves MPI_Allreduce() with one integer.
2003: The result is currently not stashed so every call to this routine involves this global communication.
2005: .seealso: DMPlexDistribute(), DMPlexGetOverlap(), DMPlexIsInterpolated()
2006: @*/
2007: PetscErrorCode DMPlexIsDistributed(DM dm, PetscBool *distributed)
2008: {
2009: PetscInt pStart, pEnd, count;
2010: MPI_Comm comm;
2011: PetscErrorCode ierr;
2016: PetscObjectGetComm((PetscObject)dm,&comm);
2017: DMPlexGetChart(dm, &pStart, &pEnd);
2018: count = !!(pEnd - pStart);
2019: MPI_Allreduce(MPI_IN_PLACE, &count, 1, MPIU_INT, MPI_SUM, comm);
2020: *distributed = count > 1 ? PETSC_TRUE : PETSC_FALSE;
2021: return(0);
2022: }