Actual source code: plexdistribute.c
petsc-3.9.2 2018-05-20
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: DMPlexSetAdjacencyUseCone(), DMPlexSetAdjacencyUseClosure(), 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: DMPlexSetAdjacencyUseCone(), DMPlexSetAdjacencyUseClosure(), 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: DMPlexSetAdjacencyUseCone - Define adjacency in the mesh using either the cone or the support first
60: Input Parameters:
61: + dm - The DM object
62: - useCone - Flag to use the cone first
64: Level: intermediate
66: Notes:
67: $ FEM: Two points p and q are adjacent if q \in closure(star(p)), useCone = PETSC_FALSE, useClosure = PETSC_TRUE
68: $ FVM: Two points p and q are adjacent if q \in support(p+cone(p)), useCone = PETSC_TRUE, useClosure = PETSC_FALSE
69: $ FVM++: Two points p and q are adjacent if q \in star(closure(p)), useCone = PETSC_TRUE, useClosure = PETSC_TRUE
71: .seealso: DMPlexGetAdjacencyUseCone(), DMPlexSetAdjacencyUseClosure(), DMPlexGetAdjacencyUseClosure(), DMPlexDistribute(), DMPlexPreallocateOperator()
72: @*/
73: PetscErrorCode DMPlexSetAdjacencyUseCone(DM dm, PetscBool useCone)
74: {
75: PetscDS prob;
76: PetscBool useClosure;
77: PetscInt Nf;
81: DMGetDS(dm, &prob);
82: PetscDSGetNumFields(prob, &Nf);
83: if (!Nf) {
84: PetscDSGetAdjacency(prob, PETSC_DEFAULT, NULL, &useClosure);
85: PetscDSSetAdjacency(prob, PETSC_DEFAULT, useCone, useClosure);
86: } else {
87: PetscDSGetAdjacency(prob, 0, NULL, &useClosure);
88: PetscDSSetAdjacency(prob, 0, useCone, useClosure);
89: }
90: return(0);
91: }
93: /*@
94: DMPlexGetAdjacencyUseCone - Query whether adjacency in the mesh uses the cone or the support first
96: Input Parameter:
97: . dm - The DM object
99: Output Parameter:
100: . useCone - Flag to use the cone first
102: Level: intermediate
104: Notes:
105: $ FEM: Two points p and q are adjacent if q \in closure(star(p)), useCone = PETSC_FALSE, useClosure = PETSC_TRUE
106: $ FVM: Two points p and q are adjacent if q \in support(p+cone(p)), useCone = PETSC_TRUE, useClosure = PETSC_FALSE
107: $ FVM++: Two points p and q are adjacent if q \in star(closure(p)), useCone = PETSC_TRUE, useClosure = PETSC_TRUE
109: .seealso: DMPlexSetAdjacencyUseCone(), DMPlexSetAdjacencyUseClosure(), DMPlexGetAdjacencyUseClosure(), DMPlexDistribute(), DMPlexPreallocateOperator()
110: @*/
111: PetscErrorCode DMPlexGetAdjacencyUseCone(DM dm, PetscBool *useCone)
112: {
113: PetscDS prob;
114: PetscInt Nf;
118: DMGetDS(dm, &prob);
119: PetscDSGetNumFields(prob, &Nf);
120: if (!Nf) {
121: PetscDSGetAdjacency(prob, PETSC_DEFAULT, useCone, NULL);
122: } else {
123: PetscDSGetAdjacency(prob, 0, useCone, NULL);
124: }
125: return(0);
126: }
128: /*@
129: DMPlexSetAdjacencyUseClosure - Define adjacency in the mesh using the transitive closure
131: Input Parameters:
132: + dm - The DM object
133: - useClosure - Flag to use the closure
135: Level: intermediate
137: Notes:
138: $ FEM: Two points p and q are adjacent if q \in closure(star(p)), useCone = PETSC_FALSE, useClosure = PETSC_TRUE
139: $ FVM: Two points p and q are adjacent if q \in support(p+cone(p)), useCone = PETSC_TRUE, useClosure = PETSC_FALSE
140: $ FVM++: Two points p and q are adjacent if q \in star(closure(p)), useCone = PETSC_TRUE, useClosure = PETSC_TRUE
142: .seealso: DMPlexGetAdjacencyUseClosure(), DMPlexSetAdjacencyUseCone(), DMPlexGetAdjacencyUseCone(), DMPlexDistribute(), DMPlexPreallocateOperator()
143: @*/
144: PetscErrorCode DMPlexSetAdjacencyUseClosure(DM dm, PetscBool useClosure)
145: {
146: PetscDS prob;
147: PetscBool useCone;
148: PetscInt Nf;
152: DMGetDS(dm, &prob);
153: PetscDSGetNumFields(prob, &Nf);
154: if (!Nf) {
155: PetscDSGetAdjacency(prob, PETSC_DEFAULT, &useCone, NULL);
156: PetscDSSetAdjacency(prob, PETSC_DEFAULT, useCone, useClosure);
157: } else {
158: PetscDSGetAdjacency(prob, 0, &useCone, NULL);
159: PetscDSSetAdjacency(prob, 0, useCone, useClosure);
160: }
161: return(0);
162: }
164: /*@
165: DMPlexGetAdjacencyUseClosure - Query whether adjacency in the mesh uses the transitive closure
167: Input Parameter:
168: . dm - The DM object
170: Output Parameter:
171: . useClosure - Flag to use the closure
173: Level: intermediate
175: Notes:
176: $ FEM: Two points p and q are adjacent if q \in closure(star(p)), useCone = PETSC_FALSE, useClosure = PETSC_TRUE
177: $ FVM: Two points p and q are adjacent if q \in support(p+cone(p)), useCone = PETSC_TRUE, useClosure = PETSC_FALSE
178: $ FVM++: Two points p and q are adjacent if q \in star(closure(p)), useCone = PETSC_TRUE, useClosure = PETSC_TRUE
180: .seealso: DMPlexSetAdjacencyUseClosure(), DMPlexSetAdjacencyUseCone(), DMPlexGetAdjacencyUseCone(), DMPlexDistribute(), DMPlexPreallocateOperator()
181: @*/
182: PetscErrorCode DMPlexGetAdjacencyUseClosure(DM dm, PetscBool *useClosure)
183: {
184: PetscDS prob;
185: PetscInt Nf;
189: DMGetDS(dm, &prob);
190: PetscDSGetNumFields(prob, &Nf);
191: if (!Nf) {
192: PetscDSGetAdjacency(prob, PETSC_DEFAULT, NULL, useClosure);
193: } else {
194: PetscDSGetAdjacency(prob, 0, NULL, useClosure);
195: }
196: return(0);
197: }
199: /*@
200: DMPlexSetAdjacencyUseAnchors - Define adjacency in the mesh using the point-to-point constraints.
202: Input Parameters:
203: + dm - The DM object
204: - useAnchors - Flag to use the constraints. If PETSC_TRUE, then constrained points are omitted from DMPlexGetAdjacency(), and their anchor points appear in their place.
206: Level: intermediate
208: .seealso: DMPlexGetAdjacencyUseClosure(), DMPlexSetAdjacencyUseCone(), DMPlexGetAdjacencyUseCone(), DMPlexDistribute(), DMPlexPreallocateOperator(), DMPlexSetAnchors()
209: @*/
210: PetscErrorCode DMPlexSetAdjacencyUseAnchors(DM dm, PetscBool useAnchors)
211: {
212: DM_Plex *mesh = (DM_Plex *) dm->data;
216: mesh->useAnchors = useAnchors;
217: return(0);
218: }
220: /*@
221: DMPlexGetAdjacencyUseAnchors - Query whether adjacency in the mesh uses the point-to-point constraints.
223: Input Parameter:
224: . dm - The DM object
226: Output Parameter:
227: . useAnchors - Flag to use the closure. If PETSC_TRUE, then constrained points are omitted from DMPlexGetAdjacency(), and their anchor points appear in their place.
229: Level: intermediate
231: .seealso: DMPlexSetAdjacencyUseAnchors(), DMPlexSetAdjacencyUseCone(), DMPlexGetAdjacencyUseCone(), DMPlexDistribute(), DMPlexPreallocateOperator(), DMPlexSetAnchors()
232: @*/
233: PetscErrorCode DMPlexGetAdjacencyUseAnchors(DM dm, PetscBool *useAnchors)
234: {
235: DM_Plex *mesh = (DM_Plex *) dm->data;
240: *useAnchors = mesh->useAnchors;
241: return(0);
242: }
244: static PetscErrorCode DMPlexGetAdjacency_Cone_Internal(DM dm, PetscInt p, PetscInt *adjSize, PetscInt adj[])
245: {
246: const PetscInt *cone = NULL;
247: PetscInt numAdj = 0, maxAdjSize = *adjSize, coneSize, c;
248: PetscErrorCode ierr;
251: DMPlexGetConeSize(dm, p, &coneSize);
252: DMPlexGetCone(dm, p, &cone);
253: for (c = 0; c <= coneSize; ++c) {
254: const PetscInt point = !c ? p : cone[c-1];
255: const PetscInt *support = NULL;
256: PetscInt supportSize, s, q;
258: DMPlexGetSupportSize(dm, point, &supportSize);
259: DMPlexGetSupport(dm, point, &support);
260: for (s = 0; s < supportSize; ++s) {
261: for (q = 0; q < numAdj || ((void)(adj[numAdj++] = support[s]),0); ++q) {
262: if (support[s] == adj[q]) break;
263: }
264: if (numAdj > maxAdjSize) SETERRQ1(PETSC_COMM_SELF, PETSC_ERR_PLIB, "Invalid mesh exceeded adjacency allocation (%D)", maxAdjSize);
265: }
266: }
267: *adjSize = numAdj;
268: return(0);
269: }
271: static PetscErrorCode DMPlexGetAdjacency_Support_Internal(DM dm, PetscInt p, PetscInt *adjSize, PetscInt adj[])
272: {
273: const PetscInt *support = NULL;
274: PetscInt numAdj = 0, maxAdjSize = *adjSize, supportSize, s;
275: PetscErrorCode ierr;
278: DMPlexGetSupportSize(dm, p, &supportSize);
279: DMPlexGetSupport(dm, p, &support);
280: for (s = 0; s <= supportSize; ++s) {
281: const PetscInt point = !s ? p : support[s-1];
282: const PetscInt *cone = NULL;
283: PetscInt coneSize, c, q;
285: DMPlexGetConeSize(dm, point, &coneSize);
286: DMPlexGetCone(dm, point, &cone);
287: for (c = 0; c < coneSize; ++c) {
288: for (q = 0; q < numAdj || ((void)(adj[numAdj++] = cone[c]),0); ++q) {
289: if (cone[c] == adj[q]) break;
290: }
291: if (numAdj > maxAdjSize) SETERRQ1(PETSC_COMM_SELF, PETSC_ERR_PLIB, "Invalid mesh exceeded adjacency allocation (%D)", maxAdjSize);
292: }
293: }
294: *adjSize = numAdj;
295: return(0);
296: }
298: static PetscErrorCode DMPlexGetAdjacency_Transitive_Internal(DM dm, PetscInt p, PetscBool useClosure, PetscInt *adjSize, PetscInt adj[])
299: {
300: PetscInt *star = NULL;
301: PetscInt numAdj = 0, maxAdjSize = *adjSize, starSize, s;
305: DMPlexGetTransitiveClosure(dm, p, useClosure, &starSize, &star);
306: for (s = 0; s < starSize*2; s += 2) {
307: const PetscInt *closure = NULL;
308: PetscInt closureSize, c, q;
310: DMPlexGetTransitiveClosure(dm, star[s], (PetscBool)!useClosure, &closureSize, (PetscInt**) &closure);
311: for (c = 0; c < closureSize*2; c += 2) {
312: for (q = 0; q < numAdj || ((void)(adj[numAdj++] = closure[c]),0); ++q) {
313: if (closure[c] == adj[q]) break;
314: }
315: if (numAdj > maxAdjSize) SETERRQ1(PETSC_COMM_SELF, PETSC_ERR_PLIB, "Invalid mesh exceeded adjacency allocation (%D)", maxAdjSize);
316: }
317: DMPlexRestoreTransitiveClosure(dm, star[s], (PetscBool)!useClosure, &closureSize, (PetscInt**) &closure);
318: }
319: DMPlexRestoreTransitiveClosure(dm, p, useClosure, &starSize, &star);
320: *adjSize = numAdj;
321: return(0);
322: }
324: PetscErrorCode DMPlexGetAdjacency_Internal(DM dm, PetscInt p, PetscBool useCone, PetscBool useTransitiveClosure, PetscBool useAnchors, PetscInt *adjSize, PetscInt *adj[])
325: {
326: static PetscInt asiz = 0;
327: PetscInt maxAnchors = 1;
328: PetscInt aStart = -1, aEnd = -1;
329: PetscInt maxAdjSize;
330: PetscSection aSec = NULL;
331: IS aIS = NULL;
332: const PetscInt *anchors;
333: DM_Plex *mesh = (DM_Plex *)dm->data;
334: PetscErrorCode ierr;
337: if (useAnchors) {
338: DMPlexGetAnchors(dm,&aSec,&aIS);
339: if (aSec) {
340: PetscSectionGetMaxDof(aSec,&maxAnchors);
341: maxAnchors = PetscMax(1,maxAnchors);
342: PetscSectionGetChart(aSec,&aStart,&aEnd);
343: ISGetIndices(aIS,&anchors);
344: }
345: }
346: if (!*adj) {
347: PetscInt depth, coneSeries, supportSeries, maxC, maxS, pStart, pEnd;
349: DMPlexGetChart(dm, &pStart,&pEnd);
350: DMPlexGetDepth(dm, &depth);
351: DMPlexGetMaxSizes(dm, &maxC, &maxS);
352: coneSeries = (maxC > 1) ? ((PetscPowInt(maxC,depth+1)-1)/(maxC-1)) : depth+1;
353: supportSeries = (maxS > 1) ? ((PetscPowInt(maxS,depth+1)-1)/(maxS-1)) : depth+1;
354: asiz = PetscMax(PetscPowInt(maxS,depth)*coneSeries,PetscPowInt(maxC,depth)*supportSeries);
355: asiz *= maxAnchors;
356: asiz = PetscMin(asiz,pEnd-pStart);
357: PetscMalloc1(asiz,adj);
358: }
359: if (*adjSize < 0) *adjSize = asiz;
360: maxAdjSize = *adjSize;
361: if (mesh->useradjacency) {
362: mesh->useradjacency(dm, p, adjSize, *adj, mesh->useradjacencyctx);
363: } else if (useTransitiveClosure) {
364: DMPlexGetAdjacency_Transitive_Internal(dm, p, useCone, adjSize, *adj);
365: } else if (useCone) {
366: DMPlexGetAdjacency_Cone_Internal(dm, p, adjSize, *adj);
367: } else {
368: DMPlexGetAdjacency_Support_Internal(dm, p, adjSize, *adj);
369: }
370: if (useAnchors && aSec) {
371: PetscInt origSize = *adjSize;
372: PetscInt numAdj = origSize;
373: PetscInt i = 0, j;
374: PetscInt *orig = *adj;
376: while (i < origSize) {
377: PetscInt p = orig[i];
378: PetscInt aDof = 0;
380: if (p >= aStart && p < aEnd) {
381: PetscSectionGetDof(aSec,p,&aDof);
382: }
383: if (aDof) {
384: PetscInt aOff;
385: PetscInt s, q;
387: for (j = i + 1; j < numAdj; j++) {
388: orig[j - 1] = orig[j];
389: }
390: origSize--;
391: numAdj--;
392: PetscSectionGetOffset(aSec,p,&aOff);
393: for (s = 0; s < aDof; ++s) {
394: for (q = 0; q < numAdj || ((void)(orig[numAdj++] = anchors[aOff+s]),0); ++q) {
395: if (anchors[aOff+s] == orig[q]) break;
396: }
397: if (numAdj > maxAdjSize) SETERRQ1(PETSC_COMM_SELF, PETSC_ERR_PLIB, "Invalid mesh exceeded adjacency allocation (%D)", maxAdjSize);
398: }
399: }
400: else {
401: i++;
402: }
403: }
404: *adjSize = numAdj;
405: ISRestoreIndices(aIS,&anchors);
406: }
407: return(0);
408: }
410: /*@
411: DMPlexGetAdjacency - Return all points adjacent to the given point
413: Input Parameters:
414: + dm - The DM object
415: . p - The point
416: . adjSize - The maximum size of adj if it is non-NULL, or PETSC_DETERMINE
417: - adj - Either NULL so that the array is allocated, or an existing array with size adjSize
419: Output Parameters:
420: + adjSize - The number of adjacent points
421: - adj - The adjacent points
423: Level: advanced
425: Notes: The user must PetscFree the adj array if it was not passed in.
427: .seealso: DMPlexSetAdjacencyUseCone(), DMPlexSetAdjacencyUseClosure(), DMPlexDistribute(), DMCreateMatrix(), DMPlexPreallocateOperator()
428: @*/
429: PetscErrorCode DMPlexGetAdjacency(DM dm, PetscInt p, PetscInt *adjSize, PetscInt *adj[])
430: {
431: PetscBool useCone, useClosure, useAnchors;
438: DMPlexGetAdjacencyUseCone(dm, &useCone);
439: DMPlexGetAdjacencyUseClosure(dm, &useClosure);
440: DMPlexGetAdjacencyUseAnchors(dm, &useAnchors);
441: DMPlexGetAdjacency_Internal(dm, p, useCone, useClosure, useAnchors, adjSize, adj);
442: return(0);
443: }
445: /*@
446: DMPlexCreateTwoSidedProcessSF - Create an SF which just has process connectivity
448: Collective on DM
450: Input Parameters:
451: + dm - The DM
452: - sfPoint - The PetscSF which encodes point connectivity
454: Output Parameters:
455: + processRanks - A list of process neighbors, or NULL
456: - sfProcess - An SF encoding the two-sided process connectivity, or NULL
458: Level: developer
460: .seealso: PetscSFCreate(), DMPlexCreateProcessSF()
461: @*/
462: PetscErrorCode DMPlexCreateTwoSidedProcessSF(DM dm, PetscSF sfPoint, PetscSection rootRankSection, IS rootRanks, PetscSection leafRankSection, IS leafRanks, IS *processRanks, PetscSF *sfProcess)
463: {
464: const PetscSFNode *remotePoints;
465: PetscInt *localPointsNew;
466: PetscSFNode *remotePointsNew;
467: const PetscInt *nranks;
468: PetscInt *ranksNew;
469: PetscBT neighbors;
470: PetscInt pStart, pEnd, p, numLeaves, l, numNeighbors, n;
471: PetscMPIInt size, proc, rank;
472: PetscErrorCode ierr;
479: MPI_Comm_size(PetscObjectComm((PetscObject) dm), &size);
480: MPI_Comm_rank(PetscObjectComm((PetscObject) dm), &rank);
481: PetscSFGetGraph(sfPoint, NULL, &numLeaves, NULL, &remotePoints);
482: PetscBTCreate(size, &neighbors);
483: PetscBTMemzero(size, neighbors);
484: /* Compute root-to-leaf process connectivity */
485: PetscSectionGetChart(rootRankSection, &pStart, &pEnd);
486: ISGetIndices(rootRanks, &nranks);
487: for (p = pStart; p < pEnd; ++p) {
488: PetscInt ndof, noff, n;
490: PetscSectionGetDof(rootRankSection, p, &ndof);
491: PetscSectionGetOffset(rootRankSection, p, &noff);
492: for (n = 0; n < ndof; ++n) {PetscBTSet(neighbors, nranks[noff+n]);}
493: }
494: ISRestoreIndices(rootRanks, &nranks);
495: /* Compute leaf-to-neighbor process connectivity */
496: PetscSectionGetChart(leafRankSection, &pStart, &pEnd);
497: ISGetIndices(leafRanks, &nranks);
498: for (p = pStart; p < pEnd; ++p) {
499: PetscInt ndof, noff, n;
501: PetscSectionGetDof(leafRankSection, p, &ndof);
502: PetscSectionGetOffset(leafRankSection, p, &noff);
503: for (n = 0; n < ndof; ++n) {PetscBTSet(neighbors, nranks[noff+n]);}
504: }
505: ISRestoreIndices(leafRanks, &nranks);
506: /* Compute leaf-to-root process connectivity */
507: for (l = 0; l < numLeaves; ++l) {PetscBTSet(neighbors, remotePoints[l].rank);}
508: /* Calculate edges */
509: PetscBTClear(neighbors, rank);
510: for(proc = 0, numNeighbors = 0; proc < size; ++proc) {if (PetscBTLookup(neighbors, proc)) ++numNeighbors;}
511: PetscMalloc1(numNeighbors, &ranksNew);
512: PetscMalloc1(numNeighbors, &localPointsNew);
513: PetscMalloc1(numNeighbors, &remotePointsNew);
514: for(proc = 0, n = 0; proc < size; ++proc) {
515: if (PetscBTLookup(neighbors, proc)) {
516: ranksNew[n] = proc;
517: localPointsNew[n] = proc;
518: remotePointsNew[n].index = rank;
519: remotePointsNew[n].rank = proc;
520: ++n;
521: }
522: }
523: PetscBTDestroy(&neighbors);
524: if (processRanks) {ISCreateGeneral(PetscObjectComm((PetscObject)dm), numNeighbors, ranksNew, PETSC_OWN_POINTER, processRanks);}
525: else {PetscFree(ranksNew);}
526: if (sfProcess) {
527: PetscSFCreate(PetscObjectComm((PetscObject)dm), sfProcess);
528: PetscObjectSetName((PetscObject) *sfProcess, "Two-Sided Process SF");
529: PetscSFSetFromOptions(*sfProcess);
530: PetscSFSetGraph(*sfProcess, size, numNeighbors, localPointsNew, PETSC_OWN_POINTER, remotePointsNew, PETSC_OWN_POINTER);
531: }
532: return(0);
533: }
535: /*@
536: DMPlexDistributeOwnership - Compute owner information for shared points. This basically gets two-sided for an SF.
538: Collective on DM
540: Input Parameter:
541: . dm - The DM
543: Output Parameters:
544: + rootSection - The number of leaves for a given root point
545: . rootrank - The rank of each edge into the root point
546: . leafSection - The number of processes sharing a given leaf point
547: - leafrank - The rank of each process sharing a leaf point
549: Level: developer
551: .seealso: DMPlexCreateOverlap()
552: @*/
553: PetscErrorCode DMPlexDistributeOwnership(DM dm, PetscSection rootSection, IS *rootrank, PetscSection leafSection, IS *leafrank)
554: {
555: MPI_Comm comm;
556: PetscSF sfPoint;
557: const PetscInt *rootdegree;
558: PetscInt *myrank, *remoterank;
559: PetscInt pStart, pEnd, p, nedges;
560: PetscMPIInt rank;
561: PetscErrorCode ierr;
564: PetscObjectGetComm((PetscObject) dm, &comm);
565: MPI_Comm_rank(comm, &rank);
566: DMPlexGetChart(dm, &pStart, &pEnd);
567: DMGetPointSF(dm, &sfPoint);
568: /* Compute number of leaves for each root */
569: PetscObjectSetName((PetscObject) rootSection, "Root Section");
570: PetscSectionSetChart(rootSection, pStart, pEnd);
571: PetscSFComputeDegreeBegin(sfPoint, &rootdegree);
572: PetscSFComputeDegreeEnd(sfPoint, &rootdegree);
573: for (p = pStart; p < pEnd; ++p) {PetscSectionSetDof(rootSection, p, rootdegree[p-pStart]);}
574: PetscSectionSetUp(rootSection);
575: /* Gather rank of each leaf to root */
576: PetscSectionGetStorageSize(rootSection, &nedges);
577: PetscMalloc1(pEnd-pStart, &myrank);
578: PetscMalloc1(nedges, &remoterank);
579: for (p = 0; p < pEnd-pStart; ++p) myrank[p] = rank;
580: PetscSFGatherBegin(sfPoint, MPIU_INT, myrank, remoterank);
581: PetscSFGatherEnd(sfPoint, MPIU_INT, myrank, remoterank);
582: PetscFree(myrank);
583: ISCreateGeneral(comm, nedges, remoterank, PETSC_OWN_POINTER, rootrank);
584: /* Distribute remote ranks to leaves */
585: PetscObjectSetName((PetscObject) leafSection, "Leaf Section");
586: DMPlexDistributeFieldIS(dm, sfPoint, rootSection, *rootrank, leafSection, leafrank);
587: return(0);
588: }
590: /*@C
591: DMPlexCreateOverlap - Compute owner information for shared points. This basically gets two-sided for an SF.
593: Collective on DM
595: Input Parameters:
596: + dm - The DM
597: . levels - Number of overlap levels
598: . rootSection - The number of leaves for a given root point
599: . rootrank - The rank of each edge into the root point
600: . leafSection - The number of processes sharing a given leaf point
601: - leafrank - The rank of each process sharing a leaf point
603: Output Parameters:
604: + ovLabel - DMLabel containing remote overlap contributions as point/rank pairings
606: Level: developer
608: .seealso: DMPlexDistributeOwnership(), DMPlexDistribute()
609: @*/
610: PetscErrorCode DMPlexCreateOverlap(DM dm, PetscInt levels, PetscSection rootSection, IS rootrank, PetscSection leafSection, IS leafrank, DMLabel *ovLabel)
611: {
612: MPI_Comm comm;
613: DMLabel ovAdjByRank; /* A DMLabel containing all points adjacent to shared points, separated by rank (value in label) */
614: PetscSF sfPoint, sfProc;
615: const PetscSFNode *remote;
616: const PetscInt *local;
617: const PetscInt *nrank, *rrank;
618: PetscInt *adj = NULL;
619: PetscInt pStart, pEnd, p, sStart, sEnd, nleaves, l;
620: PetscMPIInt rank, size;
621: PetscBool useCone, useClosure, flg;
622: PetscErrorCode ierr;
625: PetscObjectGetComm((PetscObject) dm, &comm);
626: MPI_Comm_size(comm, &size);
627: MPI_Comm_rank(comm, &rank);
628: DMGetPointSF(dm, &sfPoint);
629: DMPlexGetChart(dm, &pStart, &pEnd);
630: PetscSectionGetChart(leafSection, &sStart, &sEnd);
631: PetscSFGetGraph(sfPoint, NULL, &nleaves, &local, &remote);
632: DMLabelCreate("Overlap adjacency", &ovAdjByRank);
633: /* Handle leaves: shared with the root point */
634: for (l = 0; l < nleaves; ++l) {
635: PetscInt adjSize = PETSC_DETERMINE, a;
637: DMPlexGetAdjacency(dm, local[l], &adjSize, &adj);
638: for (a = 0; a < adjSize; ++a) {DMLabelSetValue(ovAdjByRank, adj[a], remote[l].rank);}
639: }
640: ISGetIndices(rootrank, &rrank);
641: ISGetIndices(leafrank, &nrank);
642: /* Handle roots */
643: for (p = pStart; p < pEnd; ++p) {
644: PetscInt adjSize = PETSC_DETERMINE, neighbors = 0, noff, n, a;
646: if ((p >= sStart) && (p < sEnd)) {
647: /* Some leaves share a root with other leaves on different processes */
648: PetscSectionGetDof(leafSection, p, &neighbors);
649: if (neighbors) {
650: PetscSectionGetOffset(leafSection, p, &noff);
651: DMPlexGetAdjacency(dm, p, &adjSize, &adj);
652: for (n = 0; n < neighbors; ++n) {
653: const PetscInt remoteRank = nrank[noff+n];
655: if (remoteRank == rank) continue;
656: for (a = 0; a < adjSize; ++a) {DMLabelSetValue(ovAdjByRank, adj[a], remoteRank);}
657: }
658: }
659: }
660: /* Roots are shared with leaves */
661: PetscSectionGetDof(rootSection, p, &neighbors);
662: if (!neighbors) continue;
663: PetscSectionGetOffset(rootSection, p, &noff);
664: DMPlexGetAdjacency(dm, p, &adjSize, &adj);
665: for (n = 0; n < neighbors; ++n) {
666: const PetscInt remoteRank = rrank[noff+n];
668: if (remoteRank == rank) continue;
669: for (a = 0; a < adjSize; ++a) {DMLabelSetValue(ovAdjByRank, adj[a], remoteRank);}
670: }
671: }
672: PetscFree(adj);
673: ISRestoreIndices(rootrank, &rrank);
674: ISRestoreIndices(leafrank, &nrank);
675: /* Add additional overlap levels */
676: for (l = 1; l < levels; l++) {
677: /* Propagate point donations over SF to capture remote connections */
678: DMPlexPartitionLabelPropagate(dm, ovAdjByRank);
679: /* Add next level of point donations to the label */
680: DMPlexPartitionLabelAdjacency(dm, ovAdjByRank);
681: }
682: /* We require the closure in the overlap */
683: DMPlexGetAdjacencyUseCone(dm, &useCone);
684: DMPlexGetAdjacencyUseClosure(dm, &useClosure);
685: if (useCone || !useClosure) {
686: DMPlexPartitionLabelClosure(dm, ovAdjByRank);
687: }
688: PetscOptionsHasName(((PetscObject) dm)->options,((PetscObject) dm)->prefix, "-overlap_view", &flg);
689: if (flg) {
690: DMLabelView(ovAdjByRank, PETSC_VIEWER_STDOUT_WORLD);
691: }
692: /* Make global process SF and invert sender to receiver label */
693: {
694: /* Build a global process SF */
695: PetscSFNode *remoteProc;
696: PetscMalloc1(size, &remoteProc);
697: for (p = 0; p < size; ++p) {
698: remoteProc[p].rank = p;
699: remoteProc[p].index = rank;
700: }
701: PetscSFCreate(comm, &sfProc);
702: PetscObjectSetName((PetscObject) sfProc, "Process SF");
703: PetscSFSetGraph(sfProc, size, size, NULL, PETSC_OWN_POINTER, remoteProc, PETSC_OWN_POINTER);
704: }
705: DMLabelCreate("Overlap label", ovLabel);
706: DMPlexPartitionLabelInvert(dm, ovAdjByRank, sfProc, *ovLabel);
707: /* Add owned points, except for shared local points */
708: for (p = pStart; p < pEnd; ++p) {DMLabelSetValue(*ovLabel, p, rank);}
709: for (l = 0; l < nleaves; ++l) {
710: DMLabelClearValue(*ovLabel, local[l], rank);
711: DMLabelSetValue(*ovLabel, remote[l].index, remote[l].rank);
712: }
713: /* Clean up */
714: DMLabelDestroy(&ovAdjByRank);
715: PetscSFDestroy(&sfProc);
716: return(0);
717: }
719: /*@C
720: DMPlexCreateOverlapMigrationSF - Create an SF describing the new mesh distribution to make the overlap described by the input SF
722: Collective on DM
724: Input Parameters:
725: + dm - The DM
726: - overlapSF - The SF mapping ghost points in overlap to owner points on other processes
728: Output Parameters:
729: + migrationSF - An SF that maps original points in old locations to points in new locations
731: Level: developer
733: .seealso: DMPlexCreateOverlap(), DMPlexDistribute()
734: @*/
735: PetscErrorCode DMPlexCreateOverlapMigrationSF(DM dm, PetscSF overlapSF, PetscSF *migrationSF)
736: {
737: MPI_Comm comm;
738: PetscMPIInt rank, size;
739: PetscInt d, dim, p, pStart, pEnd, nroots, nleaves, newLeaves, point, numSharedPoints;
740: PetscInt *pointDepths, *remoteDepths, *ilocal;
741: PetscInt *depthRecv, *depthShift, *depthIdx;
742: PetscSFNode *iremote;
743: PetscSF pointSF;
744: const PetscInt *sharedLocal;
745: const PetscSFNode *overlapRemote, *sharedRemote;
746: PetscErrorCode ierr;
750: PetscObjectGetComm((PetscObject)dm, &comm);
751: MPI_Comm_rank(comm, &rank);
752: MPI_Comm_size(comm, &size);
753: DMGetDimension(dm, &dim);
755: /* Before building the migration SF we need to know the new stratum offsets */
756: PetscSFGetGraph(overlapSF, &nroots, &nleaves, NULL, &overlapRemote);
757: PetscMalloc2(nroots, &pointDepths, nleaves, &remoteDepths);
758: for (d=0; d<dim+1; d++) {
759: DMPlexGetDepthStratum(dm, d, &pStart, &pEnd);
760: for (p=pStart; p<pEnd; p++) pointDepths[p] = d;
761: }
762: for (p=0; p<nleaves; p++) remoteDepths[p] = -1;
763: PetscSFBcastBegin(overlapSF, MPIU_INT, pointDepths, remoteDepths);
764: PetscSFBcastEnd(overlapSF, MPIU_INT, pointDepths, remoteDepths);
766: /* Count recevied points in each stratum and compute the internal strata shift */
767: PetscMalloc3(dim+1, &depthRecv, dim+1, &depthShift, dim+1, &depthIdx);
768: for (d=0; d<dim+1; d++) depthRecv[d]=0;
769: for (p=0; p<nleaves; p++) depthRecv[remoteDepths[p]]++;
770: depthShift[dim] = 0;
771: for (d=0; d<dim; d++) depthShift[d] = depthRecv[dim];
772: for (d=1; d<dim; d++) depthShift[d] += depthRecv[0];
773: for (d=dim-2; d>0; d--) depthShift[d] += depthRecv[d+1];
774: for (d=0; d<dim+1; d++) {
775: DMPlexGetDepthStratum(dm, d, &pStart, &pEnd);
776: depthIdx[d] = pStart + depthShift[d];
777: }
779: /* Form the overlap SF build an SF that describes the full overlap migration SF */
780: DMPlexGetChart(dm, &pStart, &pEnd);
781: newLeaves = pEnd - pStart + nleaves;
782: PetscMalloc1(newLeaves, &ilocal);
783: PetscMalloc1(newLeaves, &iremote);
784: /* First map local points to themselves */
785: for (d=0; d<dim+1; d++) {
786: DMPlexGetDepthStratum(dm, d, &pStart, &pEnd);
787: for (p=pStart; p<pEnd; p++) {
788: point = p + depthShift[d];
789: ilocal[point] = point;
790: iremote[point].index = p;
791: iremote[point].rank = rank;
792: depthIdx[d]++;
793: }
794: }
796: /* Add in the remote roots for currently shared points */
797: DMGetPointSF(dm, &pointSF);
798: PetscSFGetGraph(pointSF, NULL, &numSharedPoints, &sharedLocal, &sharedRemote);
799: for (d=0; d<dim+1; d++) {
800: DMPlexGetDepthStratum(dm, d, &pStart, &pEnd);
801: for (p=0; p<numSharedPoints; p++) {
802: if (pStart <= sharedLocal[p] && sharedLocal[p] < pEnd) {
803: point = sharedLocal[p] + depthShift[d];
804: iremote[point].index = sharedRemote[p].index;
805: iremote[point].rank = sharedRemote[p].rank;
806: }
807: }
808: }
810: /* Now add the incoming overlap points */
811: for (p=0; p<nleaves; p++) {
812: point = depthIdx[remoteDepths[p]];
813: ilocal[point] = point;
814: iremote[point].index = overlapRemote[p].index;
815: iremote[point].rank = overlapRemote[p].rank;
816: depthIdx[remoteDepths[p]]++;
817: }
818: PetscFree2(pointDepths,remoteDepths);
820: PetscSFCreate(comm, migrationSF);
821: PetscObjectSetName((PetscObject) *migrationSF, "Overlap Migration SF");
822: PetscSFSetFromOptions(*migrationSF);
823: DMPlexGetChart(dm, &pStart, &pEnd);
824: PetscSFSetGraph(*migrationSF, pEnd-pStart, newLeaves, ilocal, PETSC_OWN_POINTER, iremote, PETSC_OWN_POINTER);
826: PetscFree3(depthRecv, depthShift, depthIdx);
827: return(0);
828: }
830: /*@
831: DMPlexStratifyMigrationSF - Rearrange the leaves of a migration sf for stratification.
833: Input Parameter:
834: + dm - The DM
835: - sf - A star forest with non-ordered leaves, usually defining a DM point migration
837: Output Parameter:
838: . migrationSF - A star forest with added leaf indirection that ensures the resulting DM is stratified
840: Level: developer
842: .seealso: DMPlexPartitionLabelCreateSF(), DMPlexDistribute(), DMPlexDistributeOverlap()
843: @*/
844: PetscErrorCode DMPlexStratifyMigrationSF(DM dm, PetscSF sf, PetscSF *migrationSF)
845: {
846: MPI_Comm comm;
847: PetscMPIInt rank, size;
848: PetscInt d, ldepth, depth, p, pStart, pEnd, nroots, nleaves;
849: PetscInt *pointDepths, *remoteDepths, *ilocal;
850: PetscInt *depthRecv, *depthShift, *depthIdx;
851: PetscInt hybEnd[4];
852: const PetscSFNode *iremote;
853: PetscErrorCode ierr;
857: PetscObjectGetComm((PetscObject) dm, &comm);
858: MPI_Comm_rank(comm, &rank);
859: MPI_Comm_size(comm, &size);
860: DMPlexGetDepth(dm, &ldepth);
861: MPIU_Allreduce(&ldepth, &depth, 1, MPIU_INT, MPI_MAX, comm);
862: if ((ldepth >= 0) && (depth != ldepth)) SETERRQ2(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Inconsistent Plex depth %d != %d", ldepth, depth);
864: /* Before building the migration SF we need to know the new stratum offsets */
865: PetscSFGetGraph(sf, &nroots, &nleaves, NULL, &iremote);
866: PetscMalloc2(nroots, &pointDepths, nleaves, &remoteDepths);
867: DMPlexGetHybridBounds(dm,&hybEnd[depth],&hybEnd[depth-1],&hybEnd[1],&hybEnd[0]);
868: for (d = 0; d < depth+1; ++d) {
869: DMPlexGetDepthStratum(dm, d, &pStart, &pEnd);
870: for (p = pStart; p < pEnd; ++p) {
871: if (hybEnd[d] >= 0 && p >= hybEnd[d]) { /* put in a separate value for hybrid points */
872: pointDepths[p] = 2 * d;
873: } else {
874: pointDepths[p] = 2 * d + 1;
875: }
876: }
877: }
878: for (p = 0; p < nleaves; ++p) remoteDepths[p] = -1;
879: PetscSFBcastBegin(sf, MPIU_INT, pointDepths, remoteDepths);
880: PetscSFBcastEnd(sf, MPIU_INT, pointDepths, remoteDepths);
881: /* Count recevied points in each stratum and compute the internal strata shift */
882: PetscMalloc3(2*(depth+1), &depthRecv, 2*(depth+1), &depthShift, 2*(depth+1), &depthIdx);
883: for (d = 0; d < 2*(depth+1); ++d) depthRecv[d] = 0;
884: for (p = 0; p < nleaves; ++p) depthRecv[remoteDepths[p]]++;
885: depthShift[2*depth+1] = 0;
886: for (d = 0; d < 2*depth+1; ++d) depthShift[d] = depthRecv[2 * depth + 1];
887: for (d = 0; d < 2*depth; ++d) depthShift[d] += depthRecv[2 * depth];
888: depthShift[0] += depthRecv[1];
889: for (d = 2; d < 2*depth; ++d) depthShift[d] += depthRecv[1];
890: for (d = 2; d < 2*depth; ++d) depthShift[d] += depthRecv[0];
891: for (d = 2 * depth-1; d > 2; --d) {
892: PetscInt e;
894: for (e = d -1; e > 1; --e) depthShift[e] += depthRecv[d];
895: }
896: for (d = 0; d < 2*(depth+1); ++d) {depthIdx[d] = 0;}
897: /* Derive a new local permutation based on stratified indices */
898: PetscMalloc1(nleaves, &ilocal);
899: for (p = 0; p < nleaves; ++p) {
900: const PetscInt dep = remoteDepths[p];
902: ilocal[p] = depthShift[dep] + depthIdx[dep];
903: depthIdx[dep]++;
904: }
905: PetscSFCreate(comm, migrationSF);
906: PetscObjectSetName((PetscObject) *migrationSF, "Migration SF");
907: PetscSFSetGraph(*migrationSF, nroots, nleaves, ilocal, PETSC_OWN_POINTER, iremote, PETSC_COPY_VALUES);
908: PetscFree2(pointDepths,remoteDepths);
909: PetscFree3(depthRecv, depthShift, depthIdx);
910: return(0);
911: }
913: /*@
914: DMPlexDistributeField - Distribute field data to match a given PetscSF, usually the SF from mesh distribution
916: Collective on DM
918: Input Parameters:
919: + dm - The DMPlex object
920: . pointSF - The PetscSF describing the communication pattern
921: . originalSection - The PetscSection for existing data layout
922: - originalVec - The existing data
924: Output Parameters:
925: + newSection - The PetscSF describing the new data layout
926: - newVec - The new data
928: Level: developer
930: .seealso: DMPlexDistribute(), DMPlexDistributeFieldIS(), DMPlexDistributeData()
931: @*/
932: PetscErrorCode DMPlexDistributeField(DM dm, PetscSF pointSF, PetscSection originalSection, Vec originalVec, PetscSection newSection, Vec newVec)
933: {
934: PetscSF fieldSF;
935: PetscInt *remoteOffsets, fieldSize;
936: PetscScalar *originalValues, *newValues;
940: PetscLogEventBegin(DMPLEX_DistributeField,dm,0,0,0);
941: PetscSFDistributeSection(pointSF, originalSection, &remoteOffsets, newSection);
943: PetscSectionGetStorageSize(newSection, &fieldSize);
944: VecSetSizes(newVec, fieldSize, PETSC_DETERMINE);
945: VecSetType(newVec,dm->vectype);
947: VecGetArray(originalVec, &originalValues);
948: VecGetArray(newVec, &newValues);
949: PetscSFCreateSectionSF(pointSF, originalSection, remoteOffsets, newSection, &fieldSF);
950: PetscFree(remoteOffsets);
951: PetscSFBcastBegin(fieldSF, MPIU_SCALAR, originalValues, newValues);
952: PetscSFBcastEnd(fieldSF, MPIU_SCALAR, originalValues, newValues);
953: PetscSFDestroy(&fieldSF);
954: VecRestoreArray(newVec, &newValues);
955: VecRestoreArray(originalVec, &originalValues);
956: PetscLogEventEnd(DMPLEX_DistributeField,dm,0,0,0);
957: return(0);
958: }
960: /*@
961: DMPlexDistributeFieldIS - Distribute field data to match a given PetscSF, usually the SF from mesh distribution
963: Collective on DM
965: Input Parameters:
966: + dm - The DMPlex object
967: . pointSF - The PetscSF describing the communication pattern
968: . originalSection - The PetscSection for existing data layout
969: - originalIS - The existing data
971: Output Parameters:
972: + newSection - The PetscSF describing the new data layout
973: - newIS - The new data
975: Level: developer
977: .seealso: DMPlexDistribute(), DMPlexDistributeField(), DMPlexDistributeData()
978: @*/
979: PetscErrorCode DMPlexDistributeFieldIS(DM dm, PetscSF pointSF, PetscSection originalSection, IS originalIS, PetscSection newSection, IS *newIS)
980: {
981: PetscSF fieldSF;
982: PetscInt *newValues, *remoteOffsets, fieldSize;
983: const PetscInt *originalValues;
984: PetscErrorCode ierr;
987: PetscLogEventBegin(DMPLEX_DistributeField,dm,0,0,0);
988: PetscSFDistributeSection(pointSF, originalSection, &remoteOffsets, newSection);
990: PetscSectionGetStorageSize(newSection, &fieldSize);
991: PetscMalloc1(fieldSize, &newValues);
993: ISGetIndices(originalIS, &originalValues);
994: PetscSFCreateSectionSF(pointSF, originalSection, remoteOffsets, newSection, &fieldSF);
995: PetscFree(remoteOffsets);
996: PetscSFBcastBegin(fieldSF, MPIU_INT, (PetscInt *) originalValues, newValues);
997: PetscSFBcastEnd(fieldSF, MPIU_INT, (PetscInt *) originalValues, newValues);
998: PetscSFDestroy(&fieldSF);
999: ISRestoreIndices(originalIS, &originalValues);
1000: ISCreateGeneral(PetscObjectComm((PetscObject) pointSF), fieldSize, newValues, PETSC_OWN_POINTER, newIS);
1001: PetscLogEventEnd(DMPLEX_DistributeField,dm,0,0,0);
1002: return(0);
1003: }
1005: /*@
1006: DMPlexDistributeData - Distribute field data to match a given PetscSF, usually the SF from mesh distribution
1008: Collective on DM
1010: Input Parameters:
1011: + dm - The DMPlex object
1012: . pointSF - The PetscSF describing the communication pattern
1013: . originalSection - The PetscSection for existing data layout
1014: . datatype - The type of data
1015: - originalData - The existing data
1017: Output Parameters:
1018: + newSection - The PetscSection describing the new data layout
1019: - newData - The new data
1021: Level: developer
1023: .seealso: DMPlexDistribute(), DMPlexDistributeField()
1024: @*/
1025: PetscErrorCode DMPlexDistributeData(DM dm, PetscSF pointSF, PetscSection originalSection, MPI_Datatype datatype, void *originalData, PetscSection newSection, void **newData)
1026: {
1027: PetscSF fieldSF;
1028: PetscInt *remoteOffsets, fieldSize;
1029: PetscMPIInt dataSize;
1033: PetscLogEventBegin(DMPLEX_DistributeData,dm,0,0,0);
1034: PetscSFDistributeSection(pointSF, originalSection, &remoteOffsets, newSection);
1036: PetscSectionGetStorageSize(newSection, &fieldSize);
1037: MPI_Type_size(datatype, &dataSize);
1038: PetscMalloc(fieldSize * dataSize, newData);
1040: PetscSFCreateSectionSF(pointSF, originalSection, remoteOffsets, newSection, &fieldSF);
1041: PetscFree(remoteOffsets);
1042: PetscSFBcastBegin(fieldSF, datatype, originalData, *newData);
1043: PetscSFBcastEnd(fieldSF, datatype, originalData, *newData);
1044: PetscSFDestroy(&fieldSF);
1045: PetscLogEventEnd(DMPLEX_DistributeData,dm,0,0,0);
1046: return(0);
1047: }
1049: static PetscErrorCode DMPlexDistributeCones(DM dm, PetscSF migrationSF, ISLocalToGlobalMapping original, ISLocalToGlobalMapping renumbering, DM dmParallel)
1050: {
1051: DM_Plex *pmesh = (DM_Plex*) (dmParallel)->data;
1052: MPI_Comm comm;
1053: PetscSF coneSF;
1054: PetscSection originalConeSection, newConeSection;
1055: PetscInt *remoteOffsets, *cones, *globCones, *newCones, newConesSize;
1056: PetscBool flg;
1057: PetscErrorCode ierr;
1062: PetscLogEventBegin(DMPLEX_DistributeCones,dm,0,0,0);
1064: /* Distribute cone section */
1065: PetscObjectGetComm((PetscObject)dm, &comm);
1066: DMPlexGetConeSection(dm, &originalConeSection);
1067: DMPlexGetConeSection(dmParallel, &newConeSection);
1068: PetscSFDistributeSection(migrationSF, originalConeSection, &remoteOffsets, newConeSection);
1069: DMSetUp(dmParallel);
1070: {
1071: PetscInt pStart, pEnd, p;
1073: PetscSectionGetChart(newConeSection, &pStart, &pEnd);
1074: for (p = pStart; p < pEnd; ++p) {
1075: PetscInt coneSize;
1076: PetscSectionGetDof(newConeSection, p, &coneSize);
1077: pmesh->maxConeSize = PetscMax(pmesh->maxConeSize, coneSize);
1078: }
1079: }
1080: /* Communicate and renumber cones */
1081: PetscSFCreateSectionSF(migrationSF, originalConeSection, remoteOffsets, newConeSection, &coneSF);
1082: PetscFree(remoteOffsets);
1083: DMPlexGetCones(dm, &cones);
1084: if (original) {
1085: PetscInt numCones;
1087: PetscSectionGetStorageSize(originalConeSection,&numCones); PetscMalloc1(numCones,&globCones);
1088: ISLocalToGlobalMappingApplyBlock(original, numCones, cones, globCones);
1089: }
1090: else {
1091: globCones = cones;
1092: }
1093: DMPlexGetCones(dmParallel, &newCones);
1094: PetscSFBcastBegin(coneSF, MPIU_INT, globCones, newCones);
1095: PetscSFBcastEnd(coneSF, MPIU_INT, globCones, newCones);
1096: if (original) {
1097: PetscFree(globCones);
1098: }
1099: PetscSectionGetStorageSize(newConeSection, &newConesSize);
1100: ISGlobalToLocalMappingApplyBlock(renumbering, IS_GTOLM_MASK, newConesSize, newCones, NULL, newCones);
1101: #if PETSC_USE_DEBUG
1102: {
1103: PetscInt p;
1104: PetscBool valid = PETSC_TRUE;
1105: for (p = 0; p < newConesSize; ++p) {
1106: if (newCones[p] < 0) {valid = PETSC_FALSE; PetscPrintf(PETSC_COMM_SELF, "Point %d not in overlap SF\n", p);}
1107: }
1108: if (!valid) SETERRQ(PETSC_COMM_SELF, PETSC_ERR_ARG_OUTOFRANGE, "Invalid global to local map");
1109: }
1110: #endif
1111: PetscOptionsHasName(((PetscObject) dm)->options,((PetscObject) dm)->prefix, "-cones_view", &flg);
1112: if (flg) {
1113: PetscPrintf(comm, "Serial Cone Section:\n");
1114: PetscSectionView(originalConeSection, PETSC_VIEWER_STDOUT_WORLD);
1115: PetscPrintf(comm, "Parallel Cone Section:\n");
1116: PetscSectionView(newConeSection, PETSC_VIEWER_STDOUT_WORLD);
1117: PetscSFView(coneSF, NULL);
1118: }
1119: DMPlexGetConeOrientations(dm, &cones);
1120: DMPlexGetConeOrientations(dmParallel, &newCones);
1121: PetscSFBcastBegin(coneSF, MPIU_INT, cones, newCones);
1122: PetscSFBcastEnd(coneSF, MPIU_INT, cones, newCones);
1123: PetscSFDestroy(&coneSF);
1124: PetscLogEventEnd(DMPLEX_DistributeCones,dm,0,0,0);
1125: /* Create supports and stratify DMPlex */
1126: {
1127: PetscInt pStart, pEnd;
1129: PetscSectionGetChart(pmesh->coneSection, &pStart, &pEnd);
1130: PetscSectionSetChart(pmesh->supportSection, pStart, pEnd);
1131: }
1132: DMPlexSymmetrize(dmParallel);
1133: DMPlexStratify(dmParallel);
1134: {
1135: PetscBool useCone, useClosure, useAnchors;
1137: DMPlexGetAdjacencyUseCone(dm, &useCone);
1138: DMPlexGetAdjacencyUseClosure(dm, &useClosure);
1139: DMPlexGetAdjacencyUseAnchors(dm, &useAnchors);
1140: DMPlexSetAdjacencyUseCone(dmParallel, useCone);
1141: DMPlexSetAdjacencyUseClosure(dmParallel, useClosure);
1142: DMPlexSetAdjacencyUseAnchors(dmParallel, useAnchors);
1143: }
1144: return(0);
1145: }
1147: static PetscErrorCode DMPlexDistributeCoordinates(DM dm, PetscSF migrationSF, DM dmParallel)
1148: {
1149: MPI_Comm comm;
1150: PetscSection originalCoordSection, newCoordSection;
1151: Vec originalCoordinates, newCoordinates;
1152: PetscInt bs;
1153: PetscBool isper;
1154: const char *name;
1155: const PetscReal *maxCell, *L;
1156: const DMBoundaryType *bd;
1157: PetscErrorCode ierr;
1163: PetscObjectGetComm((PetscObject)dm, &comm);
1164: DMGetCoordinateSection(dm, &originalCoordSection);
1165: DMGetCoordinateSection(dmParallel, &newCoordSection);
1166: DMGetCoordinatesLocal(dm, &originalCoordinates);
1167: if (originalCoordinates) {
1168: VecCreate(PETSC_COMM_SELF, &newCoordinates);
1169: PetscObjectGetName((PetscObject) originalCoordinates, &name);
1170: PetscObjectSetName((PetscObject) newCoordinates, name);
1172: DMPlexDistributeField(dm, migrationSF, originalCoordSection, originalCoordinates, newCoordSection, newCoordinates);
1173: DMSetCoordinatesLocal(dmParallel, newCoordinates);
1174: VecGetBlockSize(originalCoordinates, &bs);
1175: VecSetBlockSize(newCoordinates, bs);
1176: VecDestroy(&newCoordinates);
1177: }
1178: DMGetPeriodicity(dm, &isper, &maxCell, &L, &bd);
1179: DMSetPeriodicity(dmParallel, isper, maxCell, L, bd);
1180: return(0);
1181: }
1183: /* Here we are assuming that process 0 always has everything */
1184: static PetscErrorCode DMPlexDistributeLabels(DM dm, PetscSF migrationSF, DM dmParallel)
1185: {
1186: DM_Plex *mesh = (DM_Plex*) dm->data;
1187: MPI_Comm comm;
1188: DMLabel depthLabel;
1189: PetscMPIInt rank;
1190: PetscInt depth, d, numLabels, numLocalLabels, l;
1191: PetscBool hasLabels = PETSC_FALSE, lsendDepth, sendDepth;
1192: PetscObjectState depthState = -1;
1193: PetscErrorCode ierr;
1198: PetscLogEventBegin(DMPLEX_DistributeLabels,dm,0,0,0);
1199: PetscObjectGetComm((PetscObject)dm, &comm);
1200: MPI_Comm_rank(comm, &rank);
1202: /* If the user has changed the depth label, communicate it instead */
1203: DMPlexGetDepth(dm, &depth);
1204: DMPlexGetDepthLabel(dm, &depthLabel);
1205: if (depthLabel) {DMLabelGetState(depthLabel, &depthState);}
1206: lsendDepth = mesh->depthState != depthState ? PETSC_TRUE : PETSC_FALSE;
1207: MPIU_Allreduce(&lsendDepth, &sendDepth, 1, MPIU_BOOL, MPI_LOR, comm);
1208: if (sendDepth) {
1209: DMRemoveLabel(dmParallel, "depth", &depthLabel);
1210: DMLabelDestroy(&depthLabel);
1211: }
1212: /* Everyone must have either the same number of labels, or none */
1213: DMGetNumLabels(dm, &numLocalLabels);
1214: numLabels = numLocalLabels;
1215: MPI_Bcast(&numLabels, 1, MPIU_INT, 0, comm);
1216: if (numLabels == numLocalLabels) hasLabels = PETSC_TRUE;
1217: for (l = numLabels-1; l >= 0; --l) {
1218: DMLabel label = NULL, labelNew = NULL;
1219: PetscBool isDepth, lisOutput = PETSC_TRUE, isOutput;
1221: if (hasLabels) {DMGetLabelByNum(dm, l, &label);}
1222: /* Skip "depth" because it is recreated */
1223: if (hasLabels) {PetscStrcmp(label->name, "depth", &isDepth);}
1224: MPI_Bcast(&isDepth, 1, MPIU_BOOL, 0, comm);
1225: if (isDepth && !sendDepth) continue;
1226: DMLabelDistribute(label, migrationSF, &labelNew);
1227: if (isDepth) {
1228: /* Put in any missing strata which can occur if users are managing the depth label themselves */
1229: PetscInt gdepth;
1231: MPIU_Allreduce(&depth, &gdepth, 1, MPIU_INT, MPI_MAX, comm);
1232: if ((depth >= 0) && (gdepth != depth)) SETERRQ2(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Inconsistent Plex depth %d != %d", depth, gdepth);
1233: for (d = 0; d <= gdepth; ++d) {
1234: PetscBool has;
1236: DMLabelHasStratum(labelNew, d, &has);
1237: if (!has) {DMLabelAddStratum(labelNew, d);}
1238: }
1239: }
1240: DMAddLabel(dmParallel, labelNew);
1241: /* Put the output flag in the new label */
1242: if (hasLabels) {DMGetLabelOutput(dm, label->name, &lisOutput);}
1243: MPIU_Allreduce(&lisOutput, &isOutput, 1, MPIU_BOOL, MPI_LAND, comm);
1244: DMSetLabelOutput(dmParallel, labelNew->name, isOutput);
1245: }
1246: PetscLogEventEnd(DMPLEX_DistributeLabels,dm,0,0,0);
1247: return(0);
1248: }
1250: static PetscErrorCode DMPlexDistributeSetupHybrid(DM dm, PetscSF migrationSF, ISLocalToGlobalMapping renumbering, DM dmParallel)
1251: {
1252: DM_Plex *mesh = (DM_Plex*) dm->data;
1253: DM_Plex *pmesh = (DM_Plex*) (dmParallel)->data;
1254: PetscBool *isHybrid, *isHybridParallel;
1255: PetscInt dim, depth, d;
1256: PetscInt pStart, pEnd, pStartP, pEndP;
1257: PetscErrorCode ierr;
1263: DMGetDimension(dm, &dim);
1264: DMPlexGetDepth(dm, &depth);
1265: DMPlexGetChart(dm,&pStart,&pEnd);
1266: DMPlexGetChart(dmParallel,&pStartP,&pEndP);
1267: PetscCalloc2(pEnd-pStart,&isHybrid,pEndP-pStartP,&isHybridParallel);
1268: for (d = 0; d <= depth; d++) {
1269: PetscInt hybridMax = (depth == 1 && d == 1) ? mesh->hybridPointMax[dim] : mesh->hybridPointMax[d];
1271: if (hybridMax >= 0) {
1272: PetscInt sStart, sEnd, p;
1274: DMPlexGetDepthStratum(dm,d,&sStart,&sEnd);
1275: for (p = hybridMax; p < sEnd; p++) isHybrid[p-pStart] = PETSC_TRUE;
1276: }
1277: }
1278: PetscSFBcastBegin(migrationSF,MPIU_BOOL,isHybrid,isHybridParallel);
1279: PetscSFBcastEnd(migrationSF,MPIU_BOOL,isHybrid,isHybridParallel);
1280: for (d = 0; d <= dim; d++) pmesh->hybridPointMax[d] = -1;
1281: for (d = 0; d <= depth; d++) {
1282: PetscInt sStart, sEnd, p, dd;
1284: DMPlexGetDepthStratum(dmParallel,d,&sStart,&sEnd);
1285: dd = (depth == 1 && d == 1) ? dim : d;
1286: for (p = sStart; p < sEnd; p++) {
1287: if (isHybridParallel[p-pStartP]) {
1288: pmesh->hybridPointMax[dd] = p;
1289: break;
1290: }
1291: }
1292: }
1293: PetscFree2(isHybrid,isHybridParallel);
1294: return(0);
1295: }
1297: static PetscErrorCode DMPlexDistributeSetupTree(DM dm, PetscSF migrationSF, ISLocalToGlobalMapping original, ISLocalToGlobalMapping renumbering, DM dmParallel)
1298: {
1299: DM_Plex *mesh = (DM_Plex*) dm->data;
1300: DM_Plex *pmesh = (DM_Plex*) (dmParallel)->data;
1301: MPI_Comm comm;
1302: DM refTree;
1303: PetscSection origParentSection, newParentSection;
1304: PetscInt *origParents, *origChildIDs;
1305: PetscBool flg;
1306: PetscErrorCode ierr;
1311: PetscObjectGetComm((PetscObject)dm, &comm);
1313: /* Set up tree */
1314: DMPlexGetReferenceTree(dm,&refTree);
1315: DMPlexSetReferenceTree(dmParallel,refTree);
1316: DMPlexGetTree(dm,&origParentSection,&origParents,&origChildIDs,NULL,NULL);
1317: if (origParentSection) {
1318: PetscInt pStart, pEnd;
1319: PetscInt *newParents, *newChildIDs, *globParents;
1320: PetscInt *remoteOffsetsParents, newParentSize;
1321: PetscSF parentSF;
1323: DMPlexGetChart(dmParallel, &pStart, &pEnd);
1324: PetscSectionCreate(PetscObjectComm((PetscObject)dmParallel),&newParentSection);
1325: PetscSectionSetChart(newParentSection,pStart,pEnd);
1326: PetscSFDistributeSection(migrationSF, origParentSection, &remoteOffsetsParents, newParentSection);
1327: PetscSFCreateSectionSF(migrationSF, origParentSection, remoteOffsetsParents, newParentSection, &parentSF);
1328: PetscFree(remoteOffsetsParents);
1329: PetscSectionGetStorageSize(newParentSection,&newParentSize);
1330: PetscMalloc2(newParentSize,&newParents,newParentSize,&newChildIDs);
1331: if (original) {
1332: PetscInt numParents;
1334: PetscSectionGetStorageSize(origParentSection,&numParents);
1335: PetscMalloc1(numParents,&globParents);
1336: ISLocalToGlobalMappingApplyBlock(original, numParents, origParents, globParents);
1337: }
1338: else {
1339: globParents = origParents;
1340: }
1341: PetscSFBcastBegin(parentSF, MPIU_INT, globParents, newParents);
1342: PetscSFBcastEnd(parentSF, MPIU_INT, globParents, newParents);
1343: if (original) {
1344: PetscFree(globParents);
1345: }
1346: PetscSFBcastBegin(parentSF, MPIU_INT, origChildIDs, newChildIDs);
1347: PetscSFBcastEnd(parentSF, MPIU_INT, origChildIDs, newChildIDs);
1348: ISGlobalToLocalMappingApplyBlock(renumbering,IS_GTOLM_MASK, newParentSize, newParents, NULL, newParents);
1349: #if PETSC_USE_DEBUG
1350: {
1351: PetscInt p;
1352: PetscBool valid = PETSC_TRUE;
1353: for (p = 0; p < newParentSize; ++p) {
1354: if (newParents[p] < 0) {valid = PETSC_FALSE; PetscPrintf(PETSC_COMM_SELF, "Point %d not in overlap SF\n", p);}
1355: }
1356: if (!valid) SETERRQ(PETSC_COMM_SELF, PETSC_ERR_ARG_OUTOFRANGE, "Invalid global to local map");
1357: }
1358: #endif
1359: PetscOptionsHasName(((PetscObject) dm)->options,((PetscObject) dm)->prefix, "-parents_view", &flg);
1360: if (flg) {
1361: PetscPrintf(comm, "Serial Parent Section: \n");
1362: PetscSectionView(origParentSection, PETSC_VIEWER_STDOUT_WORLD);
1363: PetscPrintf(comm, "Parallel Parent Section: \n");
1364: PetscSectionView(newParentSection, PETSC_VIEWER_STDOUT_WORLD);
1365: PetscSFView(parentSF, NULL);
1366: }
1367: DMPlexSetTree(dmParallel,newParentSection,newParents,newChildIDs);
1368: PetscSectionDestroy(&newParentSection);
1369: PetscFree2(newParents,newChildIDs);
1370: PetscSFDestroy(&parentSF);
1371: }
1372: pmesh->useAnchors = mesh->useAnchors;
1373: return(0);
1374: }
1376: PETSC_UNUSED static PetscErrorCode DMPlexDistributeSF(DM dm, PetscSF migrationSF, DM dmParallel)
1377: {
1378: PetscMPIInt rank, size;
1379: MPI_Comm comm;
1380: PetscErrorCode ierr;
1386: /* Create point SF for parallel mesh */
1387: PetscLogEventBegin(DMPLEX_DistributeSF,dm,0,0,0);
1388: PetscObjectGetComm((PetscObject)dm, &comm);
1389: MPI_Comm_rank(comm, &rank);
1390: MPI_Comm_size(comm, &size);
1391: {
1392: const PetscInt *leaves;
1393: PetscSFNode *remotePoints, *rowners, *lowners;
1394: PetscInt numRoots, numLeaves, numGhostPoints = 0, p, gp, *ghostPoints;
1395: PetscInt pStart, pEnd;
1397: DMPlexGetChart(dmParallel, &pStart, &pEnd);
1398: PetscSFGetGraph(migrationSF, &numRoots, &numLeaves, &leaves, NULL);
1399: PetscMalloc2(numRoots,&rowners,numLeaves,&lowners);
1400: for (p=0; p<numRoots; p++) {
1401: rowners[p].rank = -1;
1402: rowners[p].index = -1;
1403: }
1404: PetscSFBcastBegin(migrationSF, MPIU_2INT, rowners, lowners);
1405: PetscSFBcastEnd(migrationSF, MPIU_2INT, rowners, lowners);
1406: for (p = 0; p < numLeaves; ++p) {
1407: if (lowners[p].rank < 0 || lowners[p].rank == rank) { /* Either put in a bid or we know we own it */
1408: lowners[p].rank = rank;
1409: lowners[p].index = leaves ? leaves[p] : p;
1410: } else if (lowners[p].rank >= 0) { /* Point already claimed so flag so that MAXLOC does not listen to us */
1411: lowners[p].rank = -2;
1412: lowners[p].index = -2;
1413: }
1414: }
1415: for (p=0; p<numRoots; p++) { /* Root must not participate in the rediction, flag so that MAXLOC does not use */
1416: rowners[p].rank = -3;
1417: rowners[p].index = -3;
1418: }
1419: PetscSFReduceBegin(migrationSF, MPIU_2INT, lowners, rowners, MPI_MAXLOC);
1420: PetscSFReduceEnd(migrationSF, MPIU_2INT, lowners, rowners, MPI_MAXLOC);
1421: PetscSFBcastBegin(migrationSF, MPIU_2INT, rowners, lowners);
1422: PetscSFBcastEnd(migrationSF, MPIU_2INT, rowners, lowners);
1423: for (p = 0; p < numLeaves; ++p) {
1424: if (lowners[p].rank < 0 || lowners[p].index < 0) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_PLIB,"Cell partition corrupt: point not claimed");
1425: if (lowners[p].rank != rank) ++numGhostPoints;
1426: }
1427: PetscMalloc1(numGhostPoints, &ghostPoints);
1428: PetscMalloc1(numGhostPoints, &remotePoints);
1429: for (p = 0, gp = 0; p < numLeaves; ++p) {
1430: if (lowners[p].rank != rank) {
1431: ghostPoints[gp] = leaves ? leaves[p] : p;
1432: remotePoints[gp].rank = lowners[p].rank;
1433: remotePoints[gp].index = lowners[p].index;
1434: ++gp;
1435: }
1436: }
1437: PetscFree2(rowners,lowners);
1438: PetscSFSetGraph((dmParallel)->sf, pEnd - pStart, numGhostPoints, ghostPoints, PETSC_OWN_POINTER, remotePoints, PETSC_OWN_POINTER);
1439: PetscSFSetFromOptions((dmParallel)->sf);
1440: }
1441: {
1442: PetscBool useCone, useClosure, useAnchors;
1444: DMPlexGetAdjacencyUseCone(dm, &useCone);
1445: DMPlexGetAdjacencyUseClosure(dm, &useClosure);
1446: DMPlexGetAdjacencyUseAnchors(dm, &useAnchors);
1447: DMPlexSetAdjacencyUseCone(dmParallel, useCone);
1448: DMPlexSetAdjacencyUseClosure(dmParallel, useClosure);
1449: DMPlexSetAdjacencyUseAnchors(dmParallel, useAnchors);
1450: }
1451: PetscLogEventEnd(DMPLEX_DistributeSF,dm,0,0,0);
1452: return(0);
1453: }
1455: /*@C
1456: DMPlexDerivePointSF - Build a point SF from an SF describing a point migration
1458: Input Parameter:
1459: + dm - The source DMPlex object
1460: . migrationSF - The star forest that describes the parallel point remapping
1461: . ownership - Flag causing a vote to determine point ownership
1463: Output Parameter:
1464: - pointSF - The star forest describing the point overlap in the remapped DM
1466: Level: developer
1468: .seealso: DMPlexDistribute(), DMPlexDistributeOverlap()
1469: @*/
1470: PetscErrorCode DMPlexCreatePointSF(DM dm, PetscSF migrationSF, PetscBool ownership, PetscSF *pointSF)
1471: {
1472: PetscMPIInt rank;
1473: PetscInt p, nroots, nleaves, idx, npointLeaves;
1474: PetscInt *pointLocal;
1475: const PetscInt *leaves;
1476: const PetscSFNode *roots;
1477: PetscSFNode *rootNodes, *leafNodes, *pointRemote;
1478: PetscErrorCode ierr;
1482: MPI_Comm_rank(PetscObjectComm((PetscObject) dm), &rank);
1484: PetscSFGetGraph(migrationSF, &nroots, &nleaves, &leaves, &roots);
1485: PetscMalloc2(nroots, &rootNodes, nleaves, &leafNodes);
1486: if (ownership) {
1487: /* Point ownership vote: Process with highest rank ownes shared points */
1488: for (p = 0; p < nleaves; ++p) {
1489: /* Either put in a bid or we know we own it */
1490: leafNodes[p].rank = rank;
1491: leafNodes[p].index = p;
1492: }
1493: for (p = 0; p < nroots; p++) {
1494: /* Root must not participate in the reduction, flag so that MAXLOC does not use */
1495: rootNodes[p].rank = -3;
1496: rootNodes[p].index = -3;
1497: }
1498: PetscSFReduceBegin(migrationSF, MPIU_2INT, leafNodes, rootNodes, MPI_MAXLOC);
1499: PetscSFReduceEnd(migrationSF, MPIU_2INT, leafNodes, rootNodes, MPI_MAXLOC);
1500: } else {
1501: for (p = 0; p < nroots; p++) {
1502: rootNodes[p].index = -1;
1503: rootNodes[p].rank = rank;
1504: };
1505: for (p = 0; p < nleaves; p++) {
1506: /* Write new local id into old location */
1507: if (roots[p].rank == rank) {
1508: rootNodes[roots[p].index].index = leaves ? leaves[p] : p;
1509: }
1510: }
1511: }
1512: PetscSFBcastBegin(migrationSF, MPIU_2INT, rootNodes, leafNodes);
1513: PetscSFBcastEnd(migrationSF, MPIU_2INT, rootNodes, leafNodes);
1515: for (npointLeaves = 0, p = 0; p < nleaves; p++) {if (leafNodes[p].rank != rank) npointLeaves++;}
1516: PetscMalloc1(npointLeaves, &pointLocal);
1517: PetscMalloc1(npointLeaves, &pointRemote);
1518: for (idx = 0, p = 0; p < nleaves; p++) {
1519: if (leafNodes[p].rank != rank) {
1520: pointLocal[idx] = p;
1521: pointRemote[idx] = leafNodes[p];
1522: idx++;
1523: }
1524: }
1525: PetscSFCreate(PetscObjectComm((PetscObject) dm), pointSF);
1526: PetscSFSetFromOptions(*pointSF);
1527: PetscSFSetGraph(*pointSF, nleaves, npointLeaves, pointLocal, PETSC_OWN_POINTER, pointRemote, PETSC_OWN_POINTER);
1528: PetscFree2(rootNodes, leafNodes);
1529: return(0);
1530: }
1532: /*@C
1533: DMPlexMigrate - Migrates internal DM data over the supplied star forest
1535: Input Parameter:
1536: + dm - The source DMPlex object
1537: . sf - The star forest communication context describing the migration pattern
1539: Output Parameter:
1540: - targetDM - The target DMPlex object
1542: Level: intermediate
1544: .seealso: DMPlexDistribute(), DMPlexDistributeOverlap()
1545: @*/
1546: PetscErrorCode DMPlexMigrate(DM dm, PetscSF sf, DM targetDM)
1547: {
1548: MPI_Comm comm;
1549: PetscInt dim, nroots;
1550: PetscSF sfPoint;
1551: ISLocalToGlobalMapping ltogMigration;
1552: ISLocalToGlobalMapping ltogOriginal = NULL;
1553: PetscBool flg;
1554: PetscErrorCode ierr;
1558: PetscLogEventBegin(DMPLEX_Migrate, dm, 0, 0, 0);
1559: PetscObjectGetComm((PetscObject) dm, &comm);
1560: DMGetDimension(dm, &dim);
1561: DMSetDimension(targetDM, dim);
1563: /* Check for a one-to-all distribution pattern */
1564: DMGetPointSF(dm, &sfPoint);
1565: PetscSFGetGraph(sfPoint, &nroots, NULL, NULL, NULL);
1566: if (nroots >= 0) {
1567: IS isOriginal;
1568: PetscInt n, size, nleaves;
1569: PetscInt *numbering_orig, *numbering_new;
1570: /* Get the original point numbering */
1571: DMPlexCreatePointNumbering(dm, &isOriginal);
1572: ISLocalToGlobalMappingCreateIS(isOriginal, <ogOriginal);
1573: ISLocalToGlobalMappingGetSize(ltogOriginal, &size);
1574: ISLocalToGlobalMappingGetBlockIndices(ltogOriginal, (const PetscInt**)&numbering_orig);
1575: /* Convert to positive global numbers */
1576: for (n=0; n<size; n++) {if (numbering_orig[n] < 0) numbering_orig[n] = -(numbering_orig[n]+1);}
1577: /* Derive the new local-to-global mapping from the old one */
1578: PetscSFGetGraph(sf, NULL, &nleaves, NULL, NULL);
1579: PetscMalloc1(nleaves, &numbering_new);
1580: PetscSFBcastBegin(sf, MPIU_INT, (PetscInt *) numbering_orig, numbering_new);
1581: PetscSFBcastEnd(sf, MPIU_INT, (PetscInt *) numbering_orig, numbering_new);
1582: ISLocalToGlobalMappingCreate(comm, 1, nleaves, (const PetscInt*) numbering_new, PETSC_OWN_POINTER, <ogMigration);
1583: ISLocalToGlobalMappingRestoreIndices(ltogOriginal, (const PetscInt**)&numbering_orig);
1584: ISDestroy(&isOriginal);
1585: } else {
1586: /* One-to-all distribution pattern: We can derive LToG from SF */
1587: ISLocalToGlobalMappingCreateSF(sf, 0, <ogMigration);
1588: }
1589: PetscOptionsHasName(((PetscObject) dm)->options,((PetscObject) dm)->prefix, "-partition_view", &flg);
1590: if (flg) {
1591: PetscPrintf(comm, "Point renumbering for DM migration:\n");
1592: ISLocalToGlobalMappingView(ltogMigration, NULL);
1593: }
1594: /* Migrate DM data to target DM */
1595: DMPlexDistributeCones(dm, sf, ltogOriginal, ltogMigration, targetDM);
1596: DMPlexDistributeLabels(dm, sf, targetDM);
1597: DMPlexDistributeCoordinates(dm, sf, targetDM);
1598: DMPlexDistributeSetupHybrid(dm, sf, ltogMigration, targetDM);
1599: DMPlexDistributeSetupTree(dm, sf, ltogOriginal, ltogMigration, targetDM);
1600: ISLocalToGlobalMappingDestroy(<ogOriginal);
1601: ISLocalToGlobalMappingDestroy(<ogMigration);
1602: PetscLogEventEnd(DMPLEX_Migrate, dm, 0, 0, 0);
1603: return(0);
1604: }
1606: /*@C
1607: DMPlexDistribute - Distributes the mesh and any associated sections.
1609: Not Collective
1611: Input Parameter:
1612: + dm - The original DMPlex object
1613: - overlap - The overlap of partitions, 0 is the default
1615: Output Parameter:
1616: + sf - The PetscSF used for point distribution
1617: - parallelMesh - The distributed DMPlex object, or NULL
1619: Note: If the mesh was not distributed, the return value is NULL.
1621: The user can control the definition of adjacency for the mesh using DMPlexSetAdjacencyUseCone() and
1622: DMPlexSetAdjacencyUseClosure(). They should choose the combination appropriate for the function
1623: representation on the mesh.
1625: Level: intermediate
1627: .keywords: mesh, elements
1628: .seealso: DMPlexCreate(), DMPlexDistributeByFace(), DMPlexSetAdjacencyUseCone(), DMPlexSetAdjacencyUseClosure()
1629: @*/
1630: PetscErrorCode DMPlexDistribute(DM dm, PetscInt overlap, PetscSF *sf, DM *dmParallel)
1631: {
1632: MPI_Comm comm;
1633: PetscPartitioner partitioner;
1634: IS cellPart;
1635: PetscSection cellPartSection;
1636: DM dmCoord;
1637: DMLabel lblPartition, lblMigration;
1638: PetscSF sfProcess, sfMigration, sfStratified, sfPoint;
1639: PetscBool flg;
1640: PetscMPIInt rank, size, p;
1641: PetscErrorCode ierr;
1648: PetscLogEventBegin(DMPLEX_Distribute,dm,0,0,0);
1649: PetscObjectGetComm((PetscObject)dm,&comm);
1650: MPI_Comm_rank(comm, &rank);
1651: MPI_Comm_size(comm, &size);
1653: if (sf) *sf = NULL;
1654: *dmParallel = NULL;
1655: if (size == 1) {
1656: PetscLogEventEnd(DMPLEX_Distribute,dm,0,0,0);
1657: return(0);
1658: }
1660: /* Create cell partition */
1661: PetscLogEventBegin(PETSCPARTITIONER_Partition,dm,0,0,0);
1662: PetscSectionCreate(comm, &cellPartSection);
1663: DMPlexGetPartitioner(dm, &partitioner);
1664: PetscPartitionerPartition(partitioner, dm, cellPartSection, &cellPart);
1665: {
1666: /* Convert partition to DMLabel */
1667: PetscInt proc, pStart, pEnd, npoints, poffset;
1668: const PetscInt *points;
1669: DMLabelCreate("Point Partition", &lblPartition);
1670: ISGetIndices(cellPart, &points);
1671: PetscSectionGetChart(cellPartSection, &pStart, &pEnd);
1672: for (proc = pStart; proc < pEnd; proc++) {
1673: PetscSectionGetDof(cellPartSection, proc, &npoints);
1674: PetscSectionGetOffset(cellPartSection, proc, &poffset);
1675: for (p = poffset; p < poffset+npoints; p++) {
1676: DMLabelSetValue(lblPartition, points[p], proc);
1677: }
1678: }
1679: ISRestoreIndices(cellPart, &points);
1680: }
1681: DMPlexPartitionLabelClosure(dm, lblPartition);
1682: {
1683: /* Build a global process SF */
1684: PetscSFNode *remoteProc;
1685: PetscMalloc1(size, &remoteProc);
1686: for (p = 0; p < size; ++p) {
1687: remoteProc[p].rank = p;
1688: remoteProc[p].index = rank;
1689: }
1690: PetscSFCreate(comm, &sfProcess);
1691: PetscObjectSetName((PetscObject) sfProcess, "Process SF");
1692: PetscSFSetGraph(sfProcess, size, size, NULL, PETSC_OWN_POINTER, remoteProc, PETSC_OWN_POINTER);
1693: }
1694: DMLabelCreate("Point migration", &lblMigration);
1695: DMPlexPartitionLabelInvert(dm, lblPartition, sfProcess, lblMigration);
1696: DMPlexPartitionLabelCreateSF(dm, lblMigration, &sfMigration);
1697: /* Stratify the SF in case we are migrating an already parallel plex */
1698: DMPlexStratifyMigrationSF(dm, sfMigration, &sfStratified);
1699: PetscSFDestroy(&sfMigration);
1700: sfMigration = sfStratified;
1701: PetscLogEventEnd(PETSCPARTITIONER_Partition,dm,0,0,0);
1702: PetscOptionsHasName(((PetscObject) dm)->options,((PetscObject) dm)->prefix, "-partition_view", &flg);
1703: if (flg) {
1704: DMLabelView(lblPartition, PETSC_VIEWER_STDOUT_WORLD);
1705: PetscSFView(sfMigration, PETSC_VIEWER_STDOUT_WORLD);
1706: }
1708: /* Create non-overlapping parallel DM and migrate internal data */
1709: DMPlexCreate(comm, dmParallel);
1710: PetscObjectSetName((PetscObject) *dmParallel, "Parallel Mesh");
1711: DMPlexMigrate(dm, sfMigration, *dmParallel);
1713: /* Build the point SF without overlap */
1714: DMPlexCreatePointSF(*dmParallel, sfMigration, PETSC_TRUE, &sfPoint);
1715: DMSetPointSF(*dmParallel, sfPoint);
1716: DMGetCoordinateDM(*dmParallel, &dmCoord);
1717: if (dmCoord) {DMSetPointSF(dmCoord, sfPoint);}
1718: if (flg) {PetscSFView(sfPoint, PETSC_VIEWER_STDOUT_WORLD);}
1720: if (overlap > 0) {
1721: DM dmOverlap;
1722: PetscInt nroots, nleaves;
1723: PetscSFNode *newRemote;
1724: const PetscSFNode *oldRemote;
1725: PetscSF sfOverlap, sfOverlapPoint;
1726: /* Add the partition overlap to the distributed DM */
1727: DMPlexDistributeOverlap(*dmParallel, overlap, &sfOverlap, &dmOverlap);
1728: DMDestroy(dmParallel);
1729: *dmParallel = dmOverlap;
1730: if (flg) {
1731: PetscPrintf(comm, "Overlap Migration SF:\n");
1732: PetscSFView(sfOverlap, NULL);
1733: }
1735: /* Re-map the migration SF to establish the full migration pattern */
1736: PetscSFGetGraph(sfMigration, &nroots, NULL, NULL, &oldRemote);
1737: PetscSFGetGraph(sfOverlap, NULL, &nleaves, NULL, NULL);
1738: PetscMalloc1(nleaves, &newRemote);
1739: PetscSFBcastBegin(sfOverlap, MPIU_2INT, oldRemote, newRemote);
1740: PetscSFBcastEnd(sfOverlap, MPIU_2INT, oldRemote, newRemote);
1741: PetscSFCreate(comm, &sfOverlapPoint);
1742: PetscSFSetGraph(sfOverlapPoint, nroots, nleaves, NULL, PETSC_OWN_POINTER, newRemote, PETSC_OWN_POINTER);
1743: PetscSFDestroy(&sfOverlap);
1744: PetscSFDestroy(&sfMigration);
1745: sfMigration = sfOverlapPoint;
1746: }
1747: /* Cleanup Partition */
1748: PetscSFDestroy(&sfProcess);
1749: DMLabelDestroy(&lblPartition);
1750: DMLabelDestroy(&lblMigration);
1751: PetscSectionDestroy(&cellPartSection);
1752: ISDestroy(&cellPart);
1753: /* Copy BC */
1754: DMCopyBoundary(dm, *dmParallel);
1755: /* Create sfNatural */
1756: if (dm->useNatural) {
1757: PetscSection section;
1759: DMGetDefaultSection(dm, §ion);
1760: DMPlexCreateGlobalToNaturalSF(*dmParallel, section, sfMigration, &(*dmParallel)->sfNatural);
1761: DMSetUseNatural(*dmParallel, PETSC_TRUE);
1762: }
1763: /* Cleanup */
1764: if (sf) {*sf = sfMigration;}
1765: else {PetscSFDestroy(&sfMigration);}
1766: PetscSFDestroy(&sfPoint);
1767: PetscLogEventEnd(DMPLEX_Distribute,dm,0,0,0);
1768: return(0);
1769: }
1771: /*@C
1772: DMPlexDistributeOverlap - Add partition overlap to a distributed non-overlapping DM.
1774: Not Collective
1776: Input Parameter:
1777: + dm - The non-overlapping distrbuted DMPlex object
1778: - overlap - The overlap of partitions, 0 is the default
1780: Output Parameter:
1781: + sf - The PetscSF used for point distribution
1782: - dmOverlap - The overlapping distributed DMPlex object, or NULL
1784: Note: If the mesh was not distributed, the return value is NULL.
1786: The user can control the definition of adjacency for the mesh using DMPlexGetAdjacencyUseCone() and
1787: DMPlexSetAdjacencyUseClosure(). They should choose the combination appropriate for the function
1788: representation on the mesh.
1790: Level: intermediate
1792: .keywords: mesh, elements
1793: .seealso: DMPlexCreate(), DMPlexDistributeByFace(), DMPlexSetAdjacencyUseCone(), DMPlexSetAdjacencyUseClosure()
1794: @*/
1795: PetscErrorCode DMPlexDistributeOverlap(DM dm, PetscInt overlap, PetscSF *sf, DM *dmOverlap)
1796: {
1797: MPI_Comm comm;
1798: PetscMPIInt size, rank;
1799: PetscSection rootSection, leafSection;
1800: IS rootrank, leafrank;
1801: DM dmCoord;
1802: DMLabel lblOverlap;
1803: PetscSF sfOverlap, sfStratified, sfPoint;
1804: PetscErrorCode ierr;
1811: PetscObjectGetComm((PetscObject)dm,&comm);
1812: MPI_Comm_size(comm, &size);
1813: MPI_Comm_rank(comm, &rank);
1814: if (size == 1) {*dmOverlap = NULL; return(0);}
1815: PetscLogEventBegin(DMPLEX_DistributeOverlap, dm, 0, 0, 0);
1817: /* Compute point overlap with neighbouring processes on the distributed DM */
1818: PetscLogEventBegin(PETSCPARTITIONER_Partition,dm,0,0,0);
1819: PetscSectionCreate(comm, &rootSection);
1820: PetscSectionCreate(comm, &leafSection);
1821: DMPlexDistributeOwnership(dm, rootSection, &rootrank, leafSection, &leafrank);
1822: DMPlexCreateOverlap(dm, overlap, rootSection, rootrank, leafSection, leafrank, &lblOverlap);
1823: /* Convert overlap label to stratified migration SF */
1824: DMPlexPartitionLabelCreateSF(dm, lblOverlap, &sfOverlap);
1825: DMPlexStratifyMigrationSF(dm, sfOverlap, &sfStratified);
1826: PetscSFDestroy(&sfOverlap);
1827: sfOverlap = sfStratified;
1828: PetscObjectSetName((PetscObject) sfOverlap, "Overlap SF");
1829: PetscSFSetFromOptions(sfOverlap);
1831: PetscSectionDestroy(&rootSection);
1832: PetscSectionDestroy(&leafSection);
1833: ISDestroy(&rootrank);
1834: ISDestroy(&leafrank);
1835: PetscLogEventEnd(PETSCPARTITIONER_Partition,dm,0,0,0);
1837: /* Build the overlapping DM */
1838: DMPlexCreate(comm, dmOverlap);
1839: PetscObjectSetName((PetscObject) *dmOverlap, "Parallel Mesh");
1840: DMPlexMigrate(dm, sfOverlap, *dmOverlap);
1841: /* Build the new point SF */
1842: DMPlexCreatePointSF(*dmOverlap, sfOverlap, PETSC_FALSE, &sfPoint);
1843: DMSetPointSF(*dmOverlap, sfPoint);
1844: DMGetCoordinateDM(*dmOverlap, &dmCoord);
1845: if (dmCoord) {DMSetPointSF(dmCoord, sfPoint);}
1846: PetscSFDestroy(&sfPoint);
1847: /* Cleanup overlap partition */
1848: DMLabelDestroy(&lblOverlap);
1849: if (sf) *sf = sfOverlap;
1850: else {PetscSFDestroy(&sfOverlap);}
1851: PetscLogEventEnd(DMPLEX_DistributeOverlap, dm, 0, 0, 0);
1852: return(0);
1853: }
1855: /*@C
1856: DMPlexGetGatherDM - Get a copy of the DMPlex that gathers all points on the
1857: root process of the original's communicator.
1859: Input Parameters:
1860: . dm - the original DMPlex object
1862: Output Parameters:
1863: . gatherMesh - the gathered DM object, or NULL
1865: Level: intermediate
1867: .keywords: mesh
1868: .seealso: DMPlexDistribute(), DMPlexGetRedundantDM()
1869: @*/
1870: PetscErrorCode DMPlexGetGatherDM(DM dm, DM * gatherMesh)
1871: {
1872: MPI_Comm comm;
1873: PetscMPIInt size;
1874: PetscPartitioner oldPart, gatherPart;
1879: comm = PetscObjectComm((PetscObject)dm);
1880: MPI_Comm_size(comm,&size);
1881: *gatherMesh = NULL;
1882: if (size == 1) return(0);
1883: DMPlexGetPartitioner(dm,&oldPart);
1884: PetscObjectReference((PetscObject)oldPart);
1885: PetscPartitionerCreate(comm,&gatherPart);
1886: PetscPartitionerSetType(gatherPart,PETSCPARTITIONERGATHER);
1887: DMPlexSetPartitioner(dm,gatherPart);
1888: DMPlexDistribute(dm,0,NULL,gatherMesh);
1889: DMPlexSetPartitioner(dm,oldPart);
1890: PetscPartitionerDestroy(&gatherPart);
1891: PetscPartitionerDestroy(&oldPart);
1892: return(0);
1893: }
1895: /*@C
1896: DMPlexGetRedundantDM - Get a copy of the DMPlex that is completely copied on each process.
1898: Input Parameters:
1899: . dm - the original DMPlex object
1901: Output Parameters:
1902: . redundantMesh - the redundant DM object, or NULL
1904: Level: intermediate
1906: .keywords: mesh
1907: .seealso: DMPlexDistribute(), DMPlexGetGatherDM()
1908: @*/
1909: PetscErrorCode DMPlexGetRedundantDM(DM dm, DM * redundantMesh)
1910: {
1911: MPI_Comm comm;
1912: PetscMPIInt size, rank;
1913: PetscInt pStart, pEnd, p;
1914: PetscInt numPoints = -1;
1915: PetscSF migrationSF, sfPoint;
1916: DM gatherDM, dmCoord;
1917: PetscSFNode *points;
1922: comm = PetscObjectComm((PetscObject)dm);
1923: MPI_Comm_size(comm,&size);
1924: *redundantMesh = NULL;
1925: if (size == 1) {
1926: PetscObjectReference((PetscObject) dm);
1927: *redundantMesh = dm;
1928: return(0);
1929: }
1930: DMPlexGetGatherDM(dm,&gatherDM);
1931: if (!gatherDM) return(0);
1932: MPI_Comm_rank(comm,&rank);
1933: DMPlexGetChart(gatherDM,&pStart,&pEnd);
1934: numPoints = pEnd - pStart;
1935: MPI_Bcast(&numPoints,1,MPIU_INT,0,comm);
1936: PetscMalloc1(numPoints,&points);
1937: PetscSFCreate(comm,&migrationSF);
1938: for (p = 0; p < numPoints; p++) {
1939: points[p].index = p;
1940: points[p].rank = 0;
1941: }
1942: PetscSFSetGraph(migrationSF,pEnd-pStart,numPoints,NULL,PETSC_OWN_POINTER,points,PETSC_OWN_POINTER);
1943: DMPlexCreate(comm, redundantMesh);
1944: PetscObjectSetName((PetscObject) *redundantMesh, "Redundant Mesh");
1945: DMPlexMigrate(gatherDM, migrationSF, *redundantMesh);
1946: DMPlexCreatePointSF(*redundantMesh, migrationSF, PETSC_FALSE, &sfPoint);
1947: DMSetPointSF(*redundantMesh, sfPoint);
1948: DMGetCoordinateDM(*redundantMesh, &dmCoord);
1949: if (dmCoord) {DMSetPointSF(dmCoord, sfPoint);}
1950: PetscSFDestroy(&sfPoint);
1951: PetscSFDestroy(&migrationSF);
1952: DMDestroy(&gatherDM);
1953: return(0);
1954: }