Actual source code: plexhdf5.c
1: #include <petsc/private/dmpleximpl.h>
2: #include <petsc/private/isimpl.h>
3: #include <petsc/private/vecimpl.h>
4: #include <petsc/private/viewerhdf5impl.h>
5: #include <petsclayouthdf5.h>
7: /* Logging support */
8: PetscLogEvent DMPLEX_DistributionView, DMPLEX_DistributionLoad;
10: static PetscErrorCode PetscViewerParseVersion_Private(PetscViewer, const char[], DMPlexStorageVersion *);
11: static PetscErrorCode PetscViewerCheckVersion_Private(PetscViewer, DMPlexStorageVersion);
12: static PetscErrorCode PetscViewerAttachVersion_Private(PetscViewer, const char[], DMPlexStorageVersion);
13: static PetscErrorCode PetscViewerGetAttachedVersion_Private(PetscViewer, const char[], DMPlexStorageVersion *);
15: PETSC_EXTERN PetscErrorCode VecView_MPI(Vec, PetscViewer);
17: static PetscErrorCode PetscViewerPrintVersion_Private(PetscViewer viewer, DMPlexStorageVersion version, char str[], size_t len)
18: {
19: PetscFunctionBegin;
20: PetscCall(PetscViewerCheckVersion_Private(viewer, version));
21: PetscCall(PetscSNPrintf(str, len, "%d.%d.%d", version->major, version->minor, version->subminor));
22: PetscFunctionReturn(PETSC_SUCCESS);
23: }
25: static PetscErrorCode PetscViewerParseVersion_Private(PetscViewer viewer, const char str[], DMPlexStorageVersion *version)
26: {
27: PetscToken t;
28: char *ts;
29: PetscInt i;
30: PetscInt ti[3];
31: DMPlexStorageVersion v;
33: PetscFunctionBegin;
34: PetscCall(PetscTokenCreate(str, '.', &t));
35: for (i = 0; i < 3; i++) {
36: PetscCall(PetscTokenFind(t, &ts));
37: PetscCheck(ts, PetscObjectComm((PetscObject)viewer), PETSC_ERR_ARG_WRONG, "Malformed version string %s", str);
38: PetscCall(PetscOptionsStringToInt(ts, &ti[i]));
39: }
40: PetscCall(PetscTokenFind(t, &ts));
41: PetscCheck(!ts, PetscObjectComm((PetscObject)viewer), PETSC_ERR_ARG_WRONG, "Malformed version string %s", str);
42: PetscCall(PetscTokenDestroy(&t));
43: PetscCall(PetscNew(&v));
44: v->major = (int)ti[0];
45: v->minor = (int)ti[1];
46: v->subminor = (int)ti[2];
47: PetscCall(PetscViewerCheckVersion_Private(viewer, v));
48: *version = v;
49: PetscFunctionReturn(PETSC_SUCCESS);
50: }
52: static PetscErrorCode PetscViewerAttachVersion_Private(PetscViewer viewer, const char key[], DMPlexStorageVersion v)
53: {
54: PetscFunctionBegin;
55: PetscCall(PetscObjectContainerCompose((PetscObject)viewer, key, v, PetscContainerUserDestroyDefault));
56: PetscFunctionReturn(PETSC_SUCCESS);
57: }
59: static PetscErrorCode PetscViewerGetAttachedVersion_Private(PetscViewer viewer, const char key[], DMPlexStorageVersion *v)
60: {
61: PetscContainer cont;
63: PetscFunctionBegin;
64: PetscCall(PetscObjectQuery((PetscObject)viewer, key, (PetscObject *)&cont));
65: *v = NULL;
66: if (cont) PetscCall(PetscContainerGetPointer(cont, (void **)v));
67: PetscFunctionReturn(PETSC_SUCCESS);
68: }
70: /*
71: Version log:
72: 1.0.0 legacy version (default if no "dmplex_storage_version" attribute found in file)
73: 1.1.0 legacy version, but output VIZ by default
74: 2.0.0 introduce versioning and multiple topologies
75: 2.1.0 introduce distributions
76: 3.0.0 new checkpointing format in Firedrake paper
77: 3.1.0 new format with IS compression
78: */
79: static PetscErrorCode PetscViewerCheckVersion_Private(PetscViewer viewer, DMPlexStorageVersion version)
80: {
81: PetscBool valid = PETSC_FALSE;
83: PetscFunctionBegin;
84: switch (version->major) {
85: case 1:
86: switch (version->minor) {
87: case 0:
88: switch (version->subminor) {
89: case 0:
90: valid = PETSC_TRUE;
91: break;
92: }
93: break;
94: case 1:
95: switch (version->subminor) {
96: case 0:
97: valid = PETSC_TRUE;
98: break;
99: }
100: break;
101: }
102: break;
103: case 2:
104: switch (version->minor) {
105: case 0:
106: switch (version->subminor) {
107: case 0:
108: valid = PETSC_TRUE;
109: break;
110: }
111: break;
112: case 1:
113: switch (version->subminor) {
114: case 0:
115: valid = PETSC_TRUE;
116: break;
117: }
118: break;
119: }
120: break;
121: case 3:
122: switch (version->minor) {
123: case 0:
124: switch (version->subminor) {
125: case 0:
126: valid = PETSC_TRUE;
127: break;
128: }
129: break;
130: case 1:
131: switch (version->subminor) {
132: case 0:
133: valid = PETSC_TRUE;
134: break;
135: }
136: break;
137: }
138: break;
139: }
140: PetscCheck(valid, PetscObjectComm((PetscObject)viewer), PETSC_ERR_SUP, "DMPlexStorageVersion %d.%d.%d not supported", version->major, version->minor, version->subminor);
141: PetscFunctionReturn(PETSC_SUCCESS);
142: }
144: static inline PetscBool DMPlexStorageVersionEQ(DMPlexStorageVersion version, int major, int minor, int subminor)
145: {
146: return (PetscBool)(version->major == major && version->minor == minor && version->subminor == subminor);
147: }
149: static inline PetscBool DMPlexStorageVersionGE(DMPlexStorageVersion version, int major, int minor, int subminor)
150: {
151: return (PetscBool)((version->major == major && version->minor == minor && version->subminor >= subminor) || (version->major == major && version->minor > minor) || (version->major > major));
152: }
154: /*@C
155: PetscViewerHDF5SetDMPlexStorageVersionWriting - Set the storage version for writing
157: Logically collective
159: Input Parameters:
160: + viewer - The `PetscViewer`
161: - version - The storage format version
163: Level: advanced
165: Note:
166: The version has major, minor, and subminor integers. Parallel operations are only available for version 3.0.0.
168: .seealso: [](ch_dmbase), `DM`, `PetscViewerHDF5GetDMPlexStorageVersionWriting()`, `PetscViewerHDF5GetDMPlexStorageVersionReading()`, `PetscViewerHDF5SetDMPlexStorageVersionReading()`
169: @*/
170: PetscErrorCode PetscViewerHDF5SetDMPlexStorageVersionWriting(PetscViewer viewer, DMPlexStorageVersion version)
171: {
172: const char ATTR_NAME[] = "dmplex_storage_version";
173: DMPlexStorageVersion viewerVersion;
174: PetscBool fileHasVersion;
175: char fileVersion[16], versionStr[16], viewerVersionStr[16];
177: PetscFunctionBegin;
179: PetscAssertPointer(version, 2);
180: PetscCall(PetscViewerPrintVersion_Private(viewer, version, versionStr, 16));
181: PetscCall(PetscViewerGetAttachedVersion_Private(viewer, DMPLEX_STORAGE_VERSION_WRITING_KEY, &viewerVersion));
182: if (viewerVersion) {
183: PetscBool flg;
185: PetscCall(PetscViewerPrintVersion_Private(viewer, viewerVersion, viewerVersionStr, 16));
186: PetscCall(PetscStrcmp(versionStr, viewerVersionStr, &flg));
187: PetscCheck(flg, PetscObjectComm((PetscObject)viewer), PETSC_ERR_FILE_UNEXPECTED, "User requested DMPlex storage version %s but viewer already has version %s - cannot mix versions", versionStr, viewerVersionStr);
188: }
190: PetscCall(PetscViewerHDF5HasAttribute(viewer, NULL, ATTR_NAME, &fileHasVersion));
191: if (fileHasVersion) {
192: PetscBool flg;
193: char *tmp;
195: PetscCall(PetscViewerHDF5ReadAttribute(viewer, "/", ATTR_NAME, PETSC_STRING, NULL, &tmp));
196: PetscCall(PetscStrncpy(fileVersion, tmp, sizeof(fileVersion)));
197: PetscCall(PetscFree(tmp));
198: PetscCall(PetscStrcmp(fileVersion, versionStr, &flg));
199: PetscCheck(flg, PetscObjectComm((PetscObject)viewer), PETSC_ERR_FILE_UNEXPECTED, "User requested DMPlex storage version %s but file already has version %s - cannot mix versions", versionStr, fileVersion);
200: } else {
201: PetscCall(PetscViewerHDF5WriteAttribute(viewer, "/", ATTR_NAME, PETSC_STRING, versionStr));
202: }
203: PetscCall(PetscNew(&viewerVersion));
204: viewerVersion->major = version->major;
205: viewerVersion->minor = version->minor;
206: viewerVersion->subminor = version->subminor;
207: PetscCall(PetscViewerAttachVersion_Private(viewer, DMPLEX_STORAGE_VERSION_WRITING_KEY, viewerVersion));
208: PetscFunctionReturn(PETSC_SUCCESS);
209: }
211: /*@C
212: PetscViewerHDF5GetDMPlexStorageVersionWriting - Get the storage version for writing
214: Logically collective
216: Input Parameter:
217: . viewer - The `PetscViewer`
219: Output Parameter:
220: . version - The storage format version
222: Options Database Keys:
223: . -dm_plex_view_hdf5_storage_version <num> - Overrides the storage format version
225: Level: advanced
227: Note:
228: The version has major, minor, and subminor integers. Parallel operations are only available for version 3.0.0.
230: .seealso: [](ch_dmbase), `DM`, `PetscViewerHDF5SetDMPlexStorageVersionWriting()`, `PetscViewerHDF5GetDMPlexStorageVersionReading()`, `PetscViewerHDF5SetDMPlexStorageVersionReading()`
231: @*/
232: PetscErrorCode PetscViewerHDF5GetDMPlexStorageVersionWriting(PetscViewer viewer, DMPlexStorageVersion *version)
233: {
234: const char ATTR_NAME[] = "dmplex_storage_version";
235: PetscBool fileHasVersion;
236: char optVersion[16], fileVersion[16];
238: PetscFunctionBegin;
240: PetscAssertPointer(version, 2);
241: PetscCall(PetscViewerGetAttachedVersion_Private(viewer, DMPLEX_STORAGE_VERSION_WRITING_KEY, version));
242: if (*version) PetscFunctionReturn(PETSC_SUCCESS);
244: PetscCall(PetscStrncpy(fileVersion, DMPLEX_STORAGE_VERSION_STABLE, sizeof(fileVersion)));
245: PetscCall(PetscViewerHDF5HasAttribute(viewer, NULL, ATTR_NAME, &fileHasVersion));
246: if (fileHasVersion) {
247: char *tmp;
249: PetscCall(PetscViewerHDF5ReadAttribute(viewer, "/", ATTR_NAME, PETSC_STRING, NULL, &tmp));
250: PetscCall(PetscStrncpy(fileVersion, tmp, sizeof(fileVersion)));
251: PetscCall(PetscFree(tmp));
252: }
253: PetscCall(PetscStrncpy(optVersion, fileVersion, sizeof(optVersion)));
254: PetscObjectOptionsBegin((PetscObject)viewer);
255: PetscCall(PetscOptionsString("-dm_plex_view_hdf5_storage_version", "DMPlex HDF5 viewer storage version", NULL, optVersion, optVersion, sizeof(optVersion), NULL));
256: PetscOptionsEnd();
257: if (!fileHasVersion) {
258: PetscCall(PetscViewerHDF5WriteAttribute(viewer, "/", ATTR_NAME, PETSC_STRING, optVersion));
259: } else {
260: PetscBool flg;
262: PetscCall(PetscStrcmp(fileVersion, optVersion, &flg));
263: PetscCheck(flg, PetscObjectComm((PetscObject)viewer), PETSC_ERR_FILE_UNEXPECTED, "User requested DMPlex storage version %s but file already has version %s - cannot mix versions", optVersion, fileVersion);
264: }
265: PetscCall(PetscViewerHDF5WriteAttribute(viewer, NULL, "petsc_version_git", PETSC_STRING, PETSC_VERSION_GIT));
266: PetscCall(PetscViewerParseVersion_Private(viewer, optVersion, version));
267: PetscCall(PetscViewerAttachVersion_Private(viewer, DMPLEX_STORAGE_VERSION_WRITING_KEY, *version));
268: PetscFunctionReturn(PETSC_SUCCESS);
269: }
271: /*@C
272: PetscViewerHDF5SetDMPlexStorageVersionReading - Set the storage version for reading
274: Logically collective
276: Input Parameters:
277: + viewer - The `PetscViewer`
278: - version - The storage format version
280: Level: advanced
282: Note:
283: The version has major, minor, and subminor integers. Parallel operations are only available for version 3.0.0.
285: .seealso: [](ch_dmbase), `DM`, `PetscViewerHDF5GetDMPlexStorageVersionReading()`, `PetscViewerHDF5GetDMPlexStorageVersionWriting()`, `PetscViewerHDF5SetDMPlexStorageVersionWriting()`
286: @*/
287: PetscErrorCode PetscViewerHDF5SetDMPlexStorageVersionReading(PetscViewer viewer, DMPlexStorageVersion version)
288: {
289: const char ATTR_NAME[] = "dmplex_storage_version";
290: DMPlexStorageVersion viewerVersion;
291: PetscBool fileHasVersion;
292: char versionStr[16], viewerVersionStr[16];
294: PetscFunctionBegin;
296: PetscAssertPointer(version, 2);
297: PetscCall(PetscViewerPrintVersion_Private(viewer, version, versionStr, 16));
298: PetscCall(PetscViewerGetAttachedVersion_Private(viewer, DMPLEX_STORAGE_VERSION_READING_KEY, &viewerVersion));
299: if (viewerVersion) {
300: PetscBool flg;
302: PetscCall(PetscViewerPrintVersion_Private(viewer, viewerVersion, viewerVersionStr, 16));
303: PetscCall(PetscStrcmp(versionStr, viewerVersionStr, &flg));
304: PetscCheck(flg, PetscObjectComm((PetscObject)viewer), PETSC_ERR_FILE_UNEXPECTED, "User requested DMPlex storage version %s but viewer already has version %s - cannot mix versions", versionStr, viewerVersionStr);
305: }
307: PetscCall(PetscViewerHDF5HasAttribute(viewer, NULL, ATTR_NAME, &fileHasVersion));
308: if (fileHasVersion) {
309: char *fileVersion;
310: PetscBool flg;
312: PetscCall(PetscViewerHDF5ReadAttribute(viewer, "/", ATTR_NAME, PETSC_STRING, NULL, &fileVersion));
313: PetscCall(PetscStrcmp(fileVersion, versionStr, &flg));
314: PetscCheck(flg, PetscObjectComm((PetscObject)viewer), PETSC_ERR_FILE_UNEXPECTED, "User requested DMPlex storage version %s but file already has version %s - cannot mix versions", versionStr, fileVersion);
315: PetscCall(PetscFree(fileVersion));
316: }
317: PetscCall(PetscNew(&viewerVersion));
318: viewerVersion->major = version->major;
319: viewerVersion->minor = version->minor;
320: viewerVersion->subminor = version->subminor;
321: PetscCall(PetscViewerAttachVersion_Private(viewer, DMPLEX_STORAGE_VERSION_READING_KEY, viewerVersion));
322: PetscFunctionReturn(PETSC_SUCCESS);
323: }
325: /*@C
326: PetscViewerHDF5GetDMPlexStorageVersionReading - Get the storage version for reading
328: Logically collective
330: Input Parameter:
331: . viewer - The `PetscViewer`
333: Output Parameter:
334: . version - The storage format version
336: Options Database Keys:
337: . -dm_plex_view_hdf5_storage_version <num> - Overrides the storage format version
339: Level: advanced
341: Note:
342: The version has major, minor, and subminor integers. Parallel operations are only available for version 3.0.0.
344: .seealso: [](ch_dmbase), `DM`, `PetscViewerHDF5SetDMPlexStorageVersionReading()`, `PetscViewerHDF5GetDMPlexStorageVersionWriting()`, `PetscViewerHDF5SetDMPlexStorageVersionWriting()`
345: @*/
346: PetscErrorCode PetscViewerHDF5GetDMPlexStorageVersionReading(PetscViewer viewer, DMPlexStorageVersion *version)
347: {
348: const char ATTR_NAME[] = "dmplex_storage_version";
349: char *defaultVersion;
350: char *versionString;
352: PetscFunctionBegin;
354: PetscAssertPointer(version, 2);
355: PetscCall(PetscViewerGetAttachedVersion_Private(viewer, DMPLEX_STORAGE_VERSION_READING_KEY, version));
356: if (*version) PetscFunctionReturn(PETSC_SUCCESS);
358: //TODO string HDF5 attribute handling is terrible and should be redesigned
359: PetscCall(PetscStrallocpy(DMPLEX_STORAGE_VERSION_FIRST, &defaultVersion));
360: PetscCall(PetscViewerHDF5ReadAttribute(viewer, "/", ATTR_NAME, PETSC_STRING, &defaultVersion, &versionString));
361: PetscCall(PetscViewerParseVersion_Private(viewer, versionString, version));
362: PetscCall(PetscViewerAttachVersion_Private(viewer, DMPLEX_STORAGE_VERSION_READING_KEY, *version));
363: PetscCall(PetscFree(versionString));
364: PetscCall(PetscFree(defaultVersion));
365: PetscFunctionReturn(PETSC_SUCCESS);
366: }
368: static PetscErrorCode DMPlexGetHDF5Name_Private(DM dm, const char *name[])
369: {
370: PetscFunctionBegin;
371: if (((PetscObject)dm)->name) {
372: PetscCall(PetscObjectGetName((PetscObject)dm, name));
373: } else {
374: *name = "plex";
375: }
376: PetscFunctionReturn(PETSC_SUCCESS);
377: }
379: PetscErrorCode DMSequenceGetLength_HDF5_Internal(DM dm, const char seqname[], PetscInt *seqlen, PetscViewer viewer)
380: {
381: hid_t file, group, dset, dspace;
382: hsize_t rdim, *dims;
383: char *groupname;
384: PetscBool has;
386: PetscFunctionBegin;
387: PetscCall(PetscViewerHDF5GetGroup(viewer, NULL, &groupname));
388: PetscCall(PetscViewerHDF5HasDataset(viewer, seqname, &has));
389: PetscCheck(has, PetscObjectComm((PetscObject)viewer), PETSC_ERR_FILE_UNEXPECTED, "Object (dataset) \"%s\" not stored in group %s", seqname, groupname);
391: PetscCall(PetscViewerHDF5OpenGroup(viewer, NULL, &file, &group));
392: PetscCallHDF5Return(dset, H5Dopen2, (group, seqname, H5P_DEFAULT));
393: PetscCallHDF5Return(dspace, H5Dget_space, (dset));
394: PetscCallHDF5ReturnNoCheck(rdim, H5Sget_simple_extent_dims, (dspace, NULL, NULL));
395: PetscCall(PetscMalloc1(rdim, &dims));
396: PetscCallHDF5ReturnNoCheck(rdim, H5Sget_simple_extent_dims, (dspace, dims, NULL));
397: *seqlen = (PetscInt)dims[0];
398: PetscCall(PetscFree(dims));
399: PetscCallHDF5(H5Dclose, (dset));
400: PetscCallHDF5(H5Gclose, (group));
401: PetscFunctionReturn(PETSC_SUCCESS);
402: }
404: static PetscErrorCode DMSequenceView_HDF5(DM dm, const char seqname[], PetscInt seqnum, PetscScalar value, PetscViewer viewer)
405: {
406: Vec stamp;
407: PetscMPIInt rank;
409: PetscFunctionBegin;
410: if (seqnum < 0) PetscFunctionReturn(PETSC_SUCCESS);
411: PetscCallMPI(MPI_Comm_rank(PetscObjectComm((PetscObject)viewer), &rank));
412: PetscCall(VecCreateMPI(PetscObjectComm((PetscObject)viewer), rank ? 0 : 1, 1, &stamp));
413: PetscCall(VecSetBlockSize(stamp, 1));
414: PetscCall(PetscObjectSetName((PetscObject)stamp, seqname));
415: if (rank == 0) {
416: PetscReal timeScale;
417: PetscBool istime;
419: PetscCall(PetscStrncmp(seqname, "time", 5, &istime));
420: if (istime) {
421: PetscCall(DMPlexGetScale(dm, PETSC_UNIT_TIME, &timeScale));
422: value *= timeScale;
423: }
424: PetscCall(VecSetValue(stamp, 0, value, INSERT_VALUES));
425: }
426: PetscCall(VecAssemblyBegin(stamp));
427: PetscCall(VecAssemblyEnd(stamp));
428: PetscCall(PetscViewerHDF5PushGroup(viewer, "/"));
429: PetscCall(PetscViewerHDF5PushTimestepping(viewer));
430: PetscCall(PetscViewerHDF5SetTimestep(viewer, seqnum)); /* seqnum < 0 jumps out above */
431: PetscCall(VecView(stamp, viewer));
432: PetscCall(PetscViewerHDF5PopTimestepping(viewer));
433: PetscCall(PetscViewerHDF5PopGroup(viewer));
434: PetscCall(VecDestroy(&stamp));
435: PetscFunctionReturn(PETSC_SUCCESS);
436: }
438: PetscErrorCode DMSequenceLoad_HDF5_Internal(DM dm, const char seqname[], PetscInt seqnum, PetscScalar *value, PetscViewer viewer)
439: {
440: Vec stamp;
441: PetscMPIInt rank;
443: PetscFunctionBegin;
444: if (seqnum < 0) PetscFunctionReturn(PETSC_SUCCESS);
445: PetscCallMPI(MPI_Comm_rank(PetscObjectComm((PetscObject)viewer), &rank));
446: PetscCall(VecCreateMPI(PetscObjectComm((PetscObject)viewer), rank ? 0 : 1, 1, &stamp));
447: PetscCall(VecSetBlockSize(stamp, 1));
448: PetscCall(PetscObjectSetName((PetscObject)stamp, seqname));
449: PetscCall(PetscViewerHDF5PushGroup(viewer, "/"));
450: PetscCall(PetscViewerHDF5PushTimestepping(viewer));
451: PetscCall(PetscViewerHDF5SetTimestep(viewer, seqnum)); /* seqnum < 0 jumps out above */
452: PetscCall(VecLoad(stamp, viewer));
453: PetscCall(PetscViewerHDF5PopTimestepping(viewer));
454: PetscCall(PetscViewerHDF5PopGroup(viewer));
455: if (rank == 0) {
456: const PetscScalar *a;
457: PetscReal timeScale;
458: PetscBool istime;
460: PetscCall(VecGetArrayRead(stamp, &a));
461: *value = a[0];
462: PetscCall(VecRestoreArrayRead(stamp, &a));
463: PetscCall(PetscStrncmp(seqname, "time", 5, &istime));
464: if (istime) {
465: PetscCall(DMPlexGetScale(dm, PETSC_UNIT_TIME, &timeScale));
466: *value /= timeScale;
467: }
468: }
469: PetscCall(VecDestroy(&stamp));
470: PetscFunctionReturn(PETSC_SUCCESS);
471: }
473: static PetscErrorCode DMPlexCreateCutVertexLabel_Private(DM dm, DMLabel cutLabel, DMLabel *cutVertexLabel)
474: {
475: IS cutcells = NULL;
476: const PetscInt *cutc;
477: PetscInt cellHeight, vStart, vEnd, cStart, cEnd, c;
479: PetscFunctionBegin;
480: if (!cutLabel) PetscFunctionReturn(PETSC_SUCCESS);
481: PetscCall(DMPlexGetVTKCellHeight(dm, &cellHeight));
482: PetscCall(DMPlexGetHeightStratum(dm, cellHeight, &cStart, &cEnd));
483: PetscCall(DMPlexGetDepthStratum(dm, 0, &vStart, &vEnd));
484: /* Label vertices that should be duplicated */
485: PetscCall(DMLabelCreate(PETSC_COMM_SELF, "Cut Vertices", cutVertexLabel));
486: PetscCall(DMLabelGetStratumIS(cutLabel, 2, &cutcells));
487: if (cutcells) {
488: PetscInt n;
490: PetscCall(ISGetIndices(cutcells, &cutc));
491: PetscCall(ISGetLocalSize(cutcells, &n));
492: for (c = 0; c < n; ++c) {
493: if ((cutc[c] >= cStart) && (cutc[c] < cEnd)) {
494: PetscInt *closure = NULL;
495: PetscInt closureSize, cl, value;
497: PetscCall(DMPlexGetTransitiveClosure(dm, cutc[c], PETSC_TRUE, &closureSize, &closure));
498: for (cl = 0; cl < closureSize * 2; cl += 2) {
499: if ((closure[cl] >= vStart) && (closure[cl] < vEnd)) {
500: PetscCall(DMLabelGetValue(cutLabel, closure[cl], &value));
501: if (value == 1) PetscCall(DMLabelSetValue(*cutVertexLabel, closure[cl], 1));
502: }
503: }
504: PetscCall(DMPlexRestoreTransitiveClosure(dm, cutc[c], PETSC_TRUE, &closureSize, &closure));
505: }
506: }
507: PetscCall(ISRestoreIndices(cutcells, &cutc));
508: }
509: PetscCall(ISDestroy(&cutcells));
510: PetscFunctionReturn(PETSC_SUCCESS);
511: }
513: PetscErrorCode VecView_Plex_Local_HDF5_Internal(Vec v, PetscViewer viewer)
514: {
515: DM dm;
516: DM dmBC;
517: PetscSection section, sectionGlobal;
518: Vec gv;
519: const char *name;
520: PetscViewerFormat format;
521: PetscInt seqnum;
522: PetscReal seqval;
523: PetscBool isseq;
525: PetscFunctionBegin;
526: PetscCall(PetscObjectTypeCompare((PetscObject)v, VECSEQ, &isseq));
527: PetscCall(VecGetDM(v, &dm));
528: PetscCall(DMGetLocalSection(dm, §ion));
529: PetscCall(DMGetOutputSequenceNumber(dm, &seqnum, &seqval));
530: PetscCall(DMSequenceView_HDF5(dm, "time", seqnum, (PetscScalar)seqval, viewer));
531: if (seqnum >= 0) {
532: PetscCall(PetscViewerHDF5PushTimestepping(viewer));
533: PetscCall(PetscViewerHDF5SetTimestep(viewer, seqnum));
534: }
535: PetscCall(PetscViewerGetFormat(viewer, &format));
536: PetscCall(DMGetOutputDM(dm, &dmBC));
537: PetscCall(DMGetGlobalSection(dmBC, §ionGlobal));
538: PetscCall(DMGetGlobalVector(dmBC, &gv));
539: PetscCall(PetscObjectGetName((PetscObject)v, &name));
540: PetscCall(PetscObjectSetName((PetscObject)gv, name));
541: PetscCall(DMLocalToGlobalBegin(dmBC, v, INSERT_VALUES, gv));
542: PetscCall(DMLocalToGlobalEnd(dmBC, v, INSERT_VALUES, gv));
543: PetscCall(PetscObjectTypeCompare((PetscObject)gv, VECSEQ, &isseq));
544: if (format == PETSC_VIEWER_HDF5_VIZ) {
545: /* Output visualization representation */
546: PetscInt numFields, f;
547: DMLabel cutLabel, cutVertexLabel = NULL;
549: PetscCall(PetscSectionGetNumFields(section, &numFields));
550: PetscCall(DMGetLabel(dm, "periodic_cut", &cutLabel));
551: for (f = 0; f < numFields; ++f) {
552: Vec subv;
553: IS is;
554: const char *fname, *fgroup, *componentName, *fname_def = "unnamed";
555: char subname[PETSC_MAX_PATH_LEN];
556: PetscInt Nc, c;
557: PetscInt pStart, pEnd;
558: PetscViewerVTKFieldType ft;
560: PetscCall(DMPlexGetFieldType_Internal(dm, section, f, &pStart, &pEnd, &ft));
561: if (ft == PETSC_VTK_INVALID) continue;
562: fgroup = (ft == PETSC_VTK_POINT_VECTOR_FIELD) || (ft == PETSC_VTK_POINT_FIELD) ? "/vertex_fields" : "/cell_fields";
563: PetscCall(PetscSectionGetFieldName(section, f, &fname));
564: if (!fname) fname = fname_def;
566: PetscCall(PetscViewerHDF5PushGroup(viewer, fgroup));
568: if (cutLabel) {
569: const PetscScalar *ga;
570: PetscScalar *suba;
571: PetscInt gstart, subSize = 0, extSize = 0, subOff = 0, newOff = 0, p;
573: PetscCall(DMPlexCreateCutVertexLabel_Private(dm, cutLabel, &cutVertexLabel));
574: PetscCall(PetscSectionGetFieldComponents(section, f, &Nc));
575: for (p = pStart; p < pEnd; ++p) {
576: PetscInt gdof, fdof = 0, val;
578: PetscCall(PetscSectionGetDof(sectionGlobal, p, &gdof));
579: if (gdof > 0) PetscCall(PetscSectionGetFieldDof(section, p, f, &fdof));
580: subSize += fdof;
581: PetscCall(DMLabelGetValue(cutVertexLabel, p, &val));
582: if (val == 1) extSize += fdof;
583: }
584: PetscCall(VecCreate(PetscObjectComm((PetscObject)gv), &subv));
585: PetscCall(VecSetSizes(subv, subSize + extSize, PETSC_DETERMINE));
586: PetscCall(VecSetBlockSize(subv, Nc));
587: PetscCall(VecSetType(subv, VECSTANDARD));
588: PetscCall(VecGetOwnershipRange(gv, &gstart, NULL));
589: PetscCall(VecGetArrayRead(gv, &ga));
590: PetscCall(VecGetArray(subv, &suba));
591: for (p = pStart; p < pEnd; ++p) {
592: PetscInt gdof, goff, val;
594: PetscCall(PetscSectionGetDof(sectionGlobal, p, &gdof));
595: if (gdof > 0) {
596: PetscInt fdof, fc, f2, poff = 0;
598: PetscCall(PetscSectionGetOffset(sectionGlobal, p, &goff));
599: /* Can get rid of this loop by storing field information in the global section */
600: for (f2 = 0; f2 < f; ++f2) {
601: PetscCall(PetscSectionGetFieldDof(section, p, f2, &fdof));
602: poff += fdof;
603: }
604: PetscCall(PetscSectionGetFieldDof(section, p, f, &fdof));
605: for (fc = 0; fc < fdof; ++fc, ++subOff) suba[subOff] = ga[goff + poff + fc - gstart];
606: PetscCall(DMLabelGetValue(cutVertexLabel, p, &val));
607: if (val == 1) {
608: for (fc = 0; fc < fdof; ++fc, ++newOff) suba[subSize + newOff] = ga[goff + poff + fc - gstart];
609: }
610: }
611: }
612: PetscCall(VecRestoreArrayRead(gv, &ga));
613: PetscCall(VecRestoreArray(subv, &suba));
614: PetscCall(DMLabelDestroy(&cutVertexLabel));
615: } else {
616: PetscCall(PetscSectionGetField_Internal(section, sectionGlobal, gv, f, pStart, pEnd, &is, &subv));
617: }
618: PetscCall(PetscStrncpy(subname, name, sizeof(subname)));
619: PetscCall(PetscStrlcat(subname, "_", sizeof(subname)));
620: PetscCall(PetscStrlcat(subname, fname, sizeof(subname)));
621: PetscCall(PetscObjectSetName((PetscObject)subv, subname));
622: if (isseq) PetscCall(VecView_Seq(subv, viewer));
623: else PetscCall(VecView_MPI(subv, viewer));
624: if (ft == PETSC_VTK_POINT_VECTOR_FIELD || ft == PETSC_VTK_CELL_VECTOR_FIELD) {
625: PetscCall(PetscViewerHDF5WriteObjectAttribute(viewer, (PetscObject)subv, "vector_field_type", PETSC_STRING, "vector"));
626: } else {
627: PetscCall(PetscViewerHDF5WriteObjectAttribute(viewer, (PetscObject)subv, "vector_field_type", PETSC_STRING, "scalar"));
628: }
630: /* Output the component names in the field if available */
631: PetscCall(PetscSectionGetFieldComponents(section, f, &Nc));
632: for (c = 0; c < Nc; ++c) {
633: char componentNameLabel[PETSC_MAX_PATH_LEN];
634: PetscCall(PetscSectionGetComponentName(section, f, c, &componentName));
635: PetscCall(PetscSNPrintf(componentNameLabel, sizeof(componentNameLabel), "componentName%" PetscInt_FMT, c));
636: PetscCall(PetscViewerHDF5WriteObjectAttribute(viewer, (PetscObject)subv, componentNameLabel, PETSC_STRING, componentName));
637: }
639: if (cutLabel) PetscCall(VecDestroy(&subv));
640: else PetscCall(PetscSectionRestoreField_Internal(section, sectionGlobal, gv, f, pStart, pEnd, &is, &subv));
641: PetscCall(PetscViewerHDF5PopGroup(viewer));
642: }
643: } else {
644: /* Output full vector */
645: PetscCall(PetscViewerHDF5PushGroup(viewer, "/fields"));
646: if (isseq) PetscCall(VecView_Seq(gv, viewer));
647: else PetscCall(VecView_MPI(gv, viewer));
648: PetscCall(PetscViewerHDF5PopGroup(viewer));
649: }
650: if (seqnum >= 0) PetscCall(PetscViewerHDF5PopTimestepping(viewer));
651: PetscCall(DMRestoreGlobalVector(dmBC, &gv));
652: PetscFunctionReturn(PETSC_SUCCESS);
653: }
655: PetscErrorCode VecView_Plex_HDF5_Internal(Vec v, PetscViewer viewer)
656: {
657: DMPlexStorageVersion version;
658: DM dm;
659: Vec locv;
660: PetscObject isZero;
661: const char *name;
662: PetscReal time;
664: PetscFunctionBegin;
665: PetscCall(PetscViewerHDF5GetDMPlexStorageVersionWriting(viewer, &version));
666: PetscCall(PetscInfo(v, "Writing Vec %s storage version %d.%d.%d\n", v->hdr.name, version->major, version->minor, version->subminor));
668: PetscCall(VecGetDM(v, &dm));
669: PetscCall(DMGetLocalVector(dm, &locv));
670: PetscCall(PetscObjectGetName((PetscObject)v, &name));
671: PetscCall(PetscObjectSetName((PetscObject)locv, name));
672: PetscCall(PetscObjectQuery((PetscObject)v, "__Vec_bc_zero__", &isZero));
673: PetscCall(PetscObjectCompose((PetscObject)locv, "__Vec_bc_zero__", isZero));
674: PetscCall(DMGlobalToLocalBegin(dm, v, INSERT_VALUES, locv));
675: PetscCall(DMGlobalToLocalEnd(dm, v, INSERT_VALUES, locv));
676: PetscCall(DMGetOutputSequenceNumber(dm, NULL, &time));
677: PetscCall(DMPlexInsertBoundaryValues(dm, PETSC_TRUE, locv, time, NULL, NULL, NULL));
678: PetscCall(VecView_Plex_Local_HDF5_Internal(locv, viewer));
679: if (DMPlexStorageVersionEQ(version, 1, 1, 0)) {
680: PetscCall(PetscViewerHDF5PushGroup(viewer, "/fields"));
681: PetscCall(PetscViewerPushFormat(viewer, PETSC_VIEWER_HDF5_VIZ));
682: PetscCall(VecView_Plex_Local_HDF5_Internal(locv, viewer));
683: PetscCall(PetscViewerPopFormat(viewer));
684: PetscCall(PetscViewerHDF5PopGroup(viewer));
685: }
686: PetscCall(PetscObjectCompose((PetscObject)locv, "__Vec_bc_zero__", NULL));
687: PetscCall(DMRestoreLocalVector(dm, &locv));
688: PetscFunctionReturn(PETSC_SUCCESS);
689: }
691: PetscErrorCode VecView_Plex_HDF5_Native_Internal(Vec v, PetscViewer viewer)
692: {
693: PetscBool isseq;
695: PetscFunctionBegin;
696: PetscCall(PetscObjectTypeCompare((PetscObject)v, VECSEQ, &isseq));
697: PetscCall(PetscViewerHDF5PushGroup(viewer, "/fields"));
698: if (isseq) PetscCall(VecView_Seq(v, viewer));
699: else PetscCall(VecView_MPI(v, viewer));
700: PetscCall(PetscViewerHDF5PopGroup(viewer));
701: PetscFunctionReturn(PETSC_SUCCESS);
702: }
704: PetscErrorCode VecLoad_Plex_HDF5_Internal(Vec v, PetscViewer viewer)
705: {
706: DM dm;
707: Vec locv;
708: const char *name;
709: PetscInt seqnum;
711: PetscFunctionBegin;
712: PetscCall(VecGetDM(v, &dm));
713: PetscCall(DMGetLocalVector(dm, &locv));
714: PetscCall(PetscObjectGetName((PetscObject)v, &name));
715: PetscCall(PetscObjectSetName((PetscObject)locv, name));
716: PetscCall(DMGetOutputSequenceNumber(dm, &seqnum, NULL));
717: PetscCall(PetscViewerHDF5PushGroup(viewer, "/fields"));
718: if (seqnum >= 0) {
719: PetscCall(PetscViewerHDF5PushTimestepping(viewer));
720: PetscCall(PetscViewerHDF5SetTimestep(viewer, seqnum));
721: }
722: PetscCall(VecLoad_Plex_Local(locv, viewer));
723: if (seqnum >= 0) PetscCall(PetscViewerHDF5PopTimestepping(viewer));
724: PetscCall(PetscViewerHDF5PopGroup(viewer));
725: PetscCall(DMLocalToGlobalBegin(dm, locv, INSERT_VALUES, v));
726: PetscCall(DMLocalToGlobalEnd(dm, locv, INSERT_VALUES, v));
727: PetscCall(DMRestoreLocalVector(dm, &locv));
728: PetscFunctionReturn(PETSC_SUCCESS);
729: }
731: PetscErrorCode VecLoad_Plex_HDF5_Native_Internal(Vec v, PetscViewer viewer)
732: {
733: DM dm;
734: PetscInt seqnum;
736: PetscFunctionBegin;
737: PetscCall(VecGetDM(v, &dm));
738: PetscCall(DMGetOutputSequenceNumber(dm, &seqnum, NULL));
739: PetscCall(PetscViewerHDF5PushGroup(viewer, "/fields"));
740: if (seqnum >= 0) {
741: PetscCall(PetscViewerHDF5PushTimestepping(viewer));
742: PetscCall(PetscViewerHDF5SetTimestep(viewer, seqnum));
743: }
744: PetscCall(VecLoad_Default(v, viewer));
745: if (seqnum >= 0) PetscCall(PetscViewerHDF5PopTimestepping(viewer));
746: PetscCall(PetscViewerHDF5PopGroup(viewer));
747: PetscFunctionReturn(PETSC_SUCCESS);
748: }
750: static PetscErrorCode DMPlexDistributionView_HDF5_Private(DM dm, IS globalPointNumbers, PetscViewer viewer)
751: {
752: MPI_Comm comm;
753: PetscMPIInt size, rank;
754: PetscInt size_petsc_int;
755: const char *topologydm_name, *distribution_name;
756: const PetscInt *gpoint;
757: PetscInt pStart, pEnd, p;
758: PetscSF pointSF;
759: PetscInt nroots, nleaves;
760: const PetscInt *ilocal;
761: const PetscSFNode *iremote;
762: IS chartSizesIS, ownersIS, gpointsIS;
763: PetscInt *chartSize, *owners, *gpoints;
765: PetscFunctionBegin;
766: PetscCall(PetscObjectGetComm((PetscObject)dm, &comm));
767: PetscCallMPI(MPI_Comm_size(comm, &size));
768: PetscCallMPI(MPI_Comm_rank(comm, &rank));
769: PetscCall(DMPlexGetHDF5Name_Private(dm, &topologydm_name));
770: PetscCall(DMPlexDistributionGetName(dm, &distribution_name));
771: if (!distribution_name) PetscFunctionReturn(PETSC_SUCCESS);
772: PetscCall(PetscLogEventBegin(DMPLEX_DistributionView, viewer, 0, 0, 0));
773: size_petsc_int = (PetscInt)size;
774: PetscCall(PetscViewerHDF5WriteAttribute(viewer, NULL, "comm_size", PETSC_INT, (void *)&size_petsc_int));
775: PetscCall(ISGetIndices(globalPointNumbers, &gpoint));
776: PetscCall(DMPlexGetChart(dm, &pStart, &pEnd));
777: PetscCall(PetscMalloc1(1, &chartSize));
778: *chartSize = pEnd - pStart;
779: PetscCall(PetscMalloc1(*chartSize, &owners));
780: PetscCall(PetscMalloc1(*chartSize, &gpoints));
781: PetscCall(DMGetPointSF(dm, &pointSF));
782: PetscCall(PetscSFGetGraph(pointSF, &nroots, &nleaves, &ilocal, &iremote));
783: for (p = pStart; p < pEnd; ++p) {
784: PetscInt gp = gpoint[p - pStart];
786: owners[p - pStart] = rank;
787: gpoints[p - pStart] = (gp < 0 ? -(gp + 1) : gp);
788: }
789: for (p = 0; p < nleaves; ++p) {
790: PetscInt ilocalp = (ilocal ? ilocal[p] : p);
792: owners[ilocalp] = iremote[p].rank;
793: }
794: PetscCall(ISCreateGeneral(comm, 1, chartSize, PETSC_OWN_POINTER, &chartSizesIS));
795: PetscCall(ISCreateGeneral(comm, *chartSize, owners, PETSC_OWN_POINTER, &ownersIS));
796: PetscCall(ISCreateGeneral(comm, *chartSize, gpoints, PETSC_OWN_POINTER, &gpointsIS));
797: PetscCall(PetscObjectSetName((PetscObject)chartSizesIS, "chart_sizes"));
798: PetscCall(PetscObjectSetName((PetscObject)ownersIS, "owners"));
799: PetscCall(PetscObjectSetName((PetscObject)gpointsIS, "global_point_numbers"));
800: PetscCall(ISView(chartSizesIS, viewer));
801: PetscCall(ISView(ownersIS, viewer));
802: PetscCall(ISView(gpointsIS, viewer));
803: PetscCall(ISDestroy(&chartSizesIS));
804: PetscCall(ISDestroy(&ownersIS));
805: PetscCall(ISDestroy(&gpointsIS));
806: PetscCall(ISRestoreIndices(globalPointNumbers, &gpoint));
807: PetscCall(PetscLogEventEnd(DMPLEX_DistributionView, viewer, 0, 0, 0));
808: PetscFunctionReturn(PETSC_SUCCESS);
809: }
811: static PetscErrorCode DMPlexTopologyView_HDF5_Inner_Private(DM dm, IS globalPointNumbers, PetscViewer viewer, PetscInt pStart, PetscInt pEnd, const char pointsName[], const char coneSizesName[], const char conesName[], const char orientationsName[])
812: {
813: IS coneSizesIS, conesIS, orientationsIS;
814: PetscInt *coneSizes, *cones, *orientations;
815: const PetscInt *gpoint;
816: PetscInt nPoints = 0, conesSize = 0;
817: PetscInt p, c, s;
818: MPI_Comm comm;
820: PetscFunctionBegin;
821: PetscCall(PetscObjectGetComm((PetscObject)dm, &comm));
822: PetscCall(ISGetIndices(globalPointNumbers, &gpoint));
823: for (p = pStart; p < pEnd; ++p) {
824: if (gpoint[p] >= 0) {
825: PetscInt coneSize;
827: PetscCall(DMPlexGetConeSize(dm, p, &coneSize));
828: nPoints += 1;
829: conesSize += coneSize;
830: }
831: }
832: PetscCall(PetscMalloc1(nPoints, &coneSizes));
833: PetscCall(PetscMalloc1(conesSize, &cones));
834: PetscCall(PetscMalloc1(conesSize, &orientations));
835: for (p = pStart, c = 0, s = 0; p < pEnd; ++p) {
836: if (gpoint[p] >= 0) {
837: const PetscInt *cone, *ornt;
838: PetscInt coneSize, cp;
840: PetscCall(DMPlexGetConeSize(dm, p, &coneSize));
841: PetscCall(DMPlexGetCone(dm, p, &cone));
842: PetscCall(DMPlexGetConeOrientation(dm, p, &ornt));
843: coneSizes[s] = coneSize;
844: for (cp = 0; cp < coneSize; ++cp, ++c) {
845: cones[c] = gpoint[cone[cp]] < 0 ? -(gpoint[cone[cp]] + 1) : gpoint[cone[cp]];
846: orientations[c] = ornt[cp];
847: }
848: ++s;
849: }
850: }
851: PetscCheck(s == nPoints, PETSC_COMM_SELF, PETSC_ERR_LIB, "Total number of points %" PetscInt_FMT " != %" PetscInt_FMT, s, nPoints);
852: PetscCheck(c == conesSize, PETSC_COMM_SELF, PETSC_ERR_LIB, "Total number of cone points %" PetscInt_FMT " != %" PetscInt_FMT, c, conesSize);
853: PetscCall(ISCreateGeneral(comm, nPoints, coneSizes, PETSC_OWN_POINTER, &coneSizesIS));
854: PetscCall(ISCreateGeneral(comm, conesSize, cones, PETSC_OWN_POINTER, &conesIS));
855: PetscCall(ISCreateGeneral(comm, conesSize, orientations, PETSC_OWN_POINTER, &orientationsIS));
856: PetscCall(PetscObjectSetName((PetscObject)coneSizesIS, coneSizesName));
857: PetscCall(PetscObjectSetName((PetscObject)conesIS, conesName));
858: PetscCall(PetscObjectSetName((PetscObject)orientationsIS, orientationsName));
859: PetscCall(ISView(coneSizesIS, viewer));
860: PetscCall(ISView(conesIS, viewer));
861: PetscCall(ISView(orientationsIS, viewer));
862: PetscCall(ISDestroy(&coneSizesIS));
863: PetscCall(ISDestroy(&conesIS));
864: PetscCall(ISDestroy(&orientationsIS));
865: if (pointsName) {
866: IS pointsIS;
867: PetscInt *points;
869: PetscCall(PetscMalloc1(nPoints, &points));
870: for (p = pStart, c = 0, s = 0; p < pEnd; ++p) {
871: if (gpoint[p] >= 0) {
872: points[s] = gpoint[p];
873: ++s;
874: }
875: }
876: PetscCall(ISCreateGeneral(comm, nPoints, points, PETSC_OWN_POINTER, &pointsIS));
877: PetscCall(PetscObjectSetName((PetscObject)pointsIS, pointsName));
878: PetscCall(ISView(pointsIS, viewer));
879: PetscCall(ISDestroy(&pointsIS));
880: }
881: PetscCall(ISRestoreIndices(globalPointNumbers, &gpoint));
882: PetscFunctionReturn(PETSC_SUCCESS);
883: }
885: static PetscErrorCode DMPlexTopologyView_HDF5_Legacy_Private(DM dm, IS globalPointNumbers, PetscViewer viewer)
886: {
887: const char *pointsName, *coneSizesName, *conesName, *orientationsName;
888: PetscInt pStart, pEnd, dim;
890: PetscFunctionBegin;
891: pointsName = "order";
892: coneSizesName = "cones";
893: conesName = "cells";
894: orientationsName = "orientation";
895: PetscCall(DMPlexGetChart(dm, &pStart, &pEnd));
896: PetscCall(DMPlexTopologyView_HDF5_Inner_Private(dm, globalPointNumbers, viewer, pStart, pEnd, pointsName, coneSizesName, conesName, orientationsName));
897: PetscCall(DMGetDimension(dm, &dim));
898: PetscCall(PetscViewerHDF5WriteAttribute(viewer, conesName, "cell_dim", PETSC_INT, (void *)&dim));
899: PetscFunctionReturn(PETSC_SUCCESS);
900: }
902: //TODO get this numbering right away without needing this function
903: /* Renumber global point numbers so that they are 0-based per stratum */
904: static PetscErrorCode RenumberGlobalPointNumbersPerStratum_Private(DM dm, IS globalPointNumbers, IS *newGlobalPointNumbers, IS *strataPermutation)
905: {
906: PetscInt d, depth, p, n;
907: PetscInt *offsets;
908: const PetscInt *gpn;
909: PetscInt *ngpn;
910: MPI_Comm comm;
912: PetscFunctionBegin;
913: PetscCall(PetscObjectGetComm((PetscObject)dm, &comm));
914: PetscCall(ISGetLocalSize(globalPointNumbers, &n));
915: PetscCall(ISGetIndices(globalPointNumbers, &gpn));
916: PetscCall(PetscMalloc1(n, &ngpn));
917: PetscCall(DMPlexGetDepth(dm, &depth));
918: PetscCall(PetscMalloc1(depth + 1, &offsets));
919: for (d = 0; d <= depth; d++) {
920: PetscInt pStart, pEnd;
922: PetscCall(DMPlexGetDepthStratum(dm, d, &pStart, &pEnd));
923: offsets[d] = PETSC_INT_MAX;
924: for (p = pStart; p < pEnd; p++) {
925: if (gpn[p] >= 0 && gpn[p] < offsets[d]) offsets[d] = gpn[p];
926: }
927: }
928: PetscCallMPI(MPIU_Allreduce(MPI_IN_PLACE, offsets, depth + 1, MPIU_INT, MPI_MIN, comm));
929: for (d = 0; d <= depth; d++) {
930: PetscInt pStart, pEnd;
932: PetscCall(DMPlexGetDepthStratum(dm, d, &pStart, &pEnd));
933: for (p = pStart; p < pEnd; p++) ngpn[p] = gpn[p] - PetscSign(gpn[p]) * offsets[d];
934: }
935: PetscCall(ISRestoreIndices(globalPointNumbers, &gpn));
936: PetscCall(ISCreateGeneral(PetscObjectComm((PetscObject)globalPointNumbers), n, ngpn, PETSC_OWN_POINTER, newGlobalPointNumbers));
937: {
938: PetscInt *perm;
940: PetscCall(PetscMalloc1(depth + 1, &perm));
941: for (d = 0; d <= depth; d++) perm[d] = d;
942: PetscCall(PetscSortIntWithPermutation(depth + 1, offsets, perm));
943: PetscCall(ISCreateGeneral(PETSC_COMM_SELF, depth + 1, perm, PETSC_OWN_POINTER, strataPermutation));
944: }
945: PetscCall(PetscFree(offsets));
946: PetscFunctionReturn(PETSC_SUCCESS);
947: }
949: static PetscErrorCode DMPlexTopologyView_HDF5_Private(DM dm, IS globalPointNumbers, PetscViewer viewer)
950: {
951: IS globalPointNumbers0, strataPermutation;
952: const char *coneSizesName, *conesName, *orientationsName;
953: PetscInt depth, d;
954: MPI_Comm comm;
956: PetscFunctionBegin;
957: coneSizesName = "cone_sizes";
958: conesName = "cones";
959: orientationsName = "orientations";
960: PetscCall(PetscObjectGetComm((PetscObject)dm, &comm));
961: PetscCall(DMPlexGetDepth(dm, &depth));
962: {
963: PetscInt dim;
965: PetscCall(DMGetDimension(dm, &dim));
966: PetscCall(PetscViewerHDF5WriteAttribute(viewer, NULL, "cell_dim", PETSC_INT, &dim));
967: PetscCall(PetscViewerHDF5WriteAttribute(viewer, NULL, "depth", PETSC_INT, &depth));
968: }
970: PetscCall(RenumberGlobalPointNumbersPerStratum_Private(dm, globalPointNumbers, &globalPointNumbers0, &strataPermutation));
971: /* TODO dirty trick to save serial IS using the same parallel viewer */
972: {
973: IS spOnComm;
974: PetscInt n = 0, N;
975: const PetscInt *idx = NULL;
976: const PetscInt *old;
977: PetscMPIInt rank;
979: PetscCallMPI(MPI_Comm_rank(comm, &rank));
980: PetscCall(ISGetLocalSize(strataPermutation, &N));
981: PetscCall(ISGetIndices(strataPermutation, &old));
982: if (!rank) {
983: n = N;
984: idx = old;
985: }
986: PetscCall(ISCreateGeneral(comm, n, idx, PETSC_COPY_VALUES, &spOnComm));
987: PetscCall(ISRestoreIndices(strataPermutation, &old));
988: PetscCall(ISDestroy(&strataPermutation));
989: strataPermutation = spOnComm;
990: }
991: PetscCall(PetscObjectSetName((PetscObject)strataPermutation, "permutation"));
992: PetscCall(ISView(strataPermutation, viewer));
993: PetscCall(PetscViewerHDF5PushGroup(viewer, "strata"));
994: for (d = 0; d <= depth; d++) {
995: PetscInt pStart, pEnd;
996: char group[128];
998: PetscCall(PetscSNPrintf(group, sizeof(group), "%" PetscInt_FMT, d));
999: PetscCall(PetscViewerHDF5PushGroup(viewer, group));
1000: PetscCall(DMPlexGetDepthStratum(dm, d, &pStart, &pEnd));
1001: PetscCall(DMPlexTopologyView_HDF5_Inner_Private(dm, globalPointNumbers0, viewer, pStart, pEnd, NULL, coneSizesName, conesName, orientationsName));
1002: PetscCall(PetscViewerHDF5PopGroup(viewer));
1003: }
1004: PetscCall(PetscViewerHDF5PopGroup(viewer)); /* strata */
1005: PetscCall(ISDestroy(&globalPointNumbers0));
1006: PetscCall(ISDestroy(&strataPermutation));
1007: PetscFunctionReturn(PETSC_SUCCESS);
1008: }
1010: PetscErrorCode DMPlexTopologyView_HDF5_Internal(DM dm, IS globalPointNumbers, PetscViewer viewer)
1011: {
1012: DMPlexStorageVersion version;
1013: const char *topologydm_name;
1014: char group[PETSC_MAX_PATH_LEN];
1016: PetscFunctionBegin;
1017: PetscCall(PetscViewerHDF5GetDMPlexStorageVersionWriting(viewer, &version));
1018: PetscCall(PetscInfo(dm, "Writing DM %s storage version %d.%d.%d\n", dm->hdr.name, version->major, version->minor, version->subminor));
1019: PetscCall(DMPlexGetHDF5Name_Private(dm, &topologydm_name));
1020: if (DMPlexStorageVersionGE(version, 2, 0, 0)) {
1021: PetscCall(PetscSNPrintf(group, sizeof(group), "topologies/%s", topologydm_name));
1022: } else {
1023: PetscCall(PetscStrncpy(group, "/", sizeof(group)));
1024: }
1025: PetscCall(PetscViewerHDF5PushGroup(viewer, group));
1027: PetscCall(PetscViewerHDF5PushGroup(viewer, "topology"));
1028: if (version->major < 3) {
1029: PetscCall(DMPlexTopologyView_HDF5_Legacy_Private(dm, globalPointNumbers, viewer));
1030: } else {
1031: /* since DMPlexStorageVersion 3.0.0 */
1032: PetscCall(DMPlexTopologyView_HDF5_Private(dm, globalPointNumbers, viewer));
1033: }
1034: PetscCall(PetscViewerHDF5PopGroup(viewer)); /* "topology" */
1036: if (DMPlexStorageVersionGE(version, 2, 1, 0)) {
1037: const char *distribution_name;
1039: PetscCall(DMPlexDistributionGetName(dm, &distribution_name));
1040: PetscCall(PetscViewerHDF5PushGroup(viewer, "distributions"));
1041: PetscCall(PetscViewerHDF5WriteGroup(viewer, NULL));
1042: PetscCall(PetscViewerHDF5PushGroup(viewer, distribution_name));
1043: PetscCall(DMPlexDistributionView_HDF5_Private(dm, globalPointNumbers, viewer));
1044: PetscCall(PetscViewerHDF5PopGroup(viewer)); /* distribution_name */
1045: PetscCall(PetscViewerHDF5PopGroup(viewer)); /* "distributions" */
1046: }
1048: PetscCall(PetscViewerHDF5PopGroup(viewer));
1049: PetscFunctionReturn(PETSC_SUCCESS);
1050: }
1052: static PetscErrorCode CreateConesIS_Private(DM dm, PetscInt cStart, PetscInt cEnd, IS globalCellNumbers, PetscInt *numCorners, IS *cellIS)
1053: {
1054: PetscSF sfPoint;
1055: DMLabel cutLabel, cutVertexLabel = NULL;
1056: IS globalVertexNumbers, cutvertices = NULL;
1057: const PetscInt *gcell, *gvertex, *cutverts = NULL;
1058: PetscInt *vertices;
1059: PetscInt conesSize = 0;
1060: PetscInt dim, numCornersLocal = 0, cell, vStart, vEnd, vExtra = 0, v;
1062: PetscFunctionBegin;
1063: *numCorners = 0;
1064: PetscCall(DMGetDimension(dm, &dim));
1065: PetscCall(DMPlexGetDepthStratum(dm, 0, &vStart, &vEnd));
1066: PetscCall(ISGetIndices(globalCellNumbers, &gcell));
1068: for (cell = cStart; cell < cEnd; ++cell) {
1069: PetscInt *closure = NULL;
1070: PetscInt closureSize, v, Nc = 0;
1072: if (gcell[cell] < 0) continue;
1073: PetscCall(DMPlexGetTransitiveClosure(dm, cell, PETSC_TRUE, &closureSize, &closure));
1074: for (v = 0; v < closureSize * 2; v += 2) {
1075: if ((closure[v] >= vStart) && (closure[v] < vEnd)) ++Nc;
1076: }
1077: PetscCall(DMPlexRestoreTransitiveClosure(dm, cell, PETSC_TRUE, &closureSize, &closure));
1078: conesSize += Nc;
1079: if (!numCornersLocal) numCornersLocal = Nc;
1080: else if (numCornersLocal != Nc) numCornersLocal = 1;
1081: }
1082: PetscCallMPI(MPIU_Allreduce(&numCornersLocal, numCorners, 1, MPIU_INT, MPI_MAX, PetscObjectComm((PetscObject)dm)));
1083: PetscCheck(!numCornersLocal || !(numCornersLocal != *numCorners || *numCorners == 0), PETSC_COMM_SELF, PETSC_ERR_SUP, "Visualization topology currently only supports identical cell shapes");
1084: /* Handle periodic cuts by identifying vertices which should be duplicated */
1085: PetscCall(DMGetLabel(dm, "periodic_cut", &cutLabel));
1086: PetscCall(DMPlexCreateCutVertexLabel_Private(dm, cutLabel, &cutVertexLabel));
1087: if (cutVertexLabel) PetscCall(DMLabelGetStratumIS(cutVertexLabel, 1, &cutvertices));
1088: if (cutvertices) {
1089: PetscCall(ISGetIndices(cutvertices, &cutverts));
1090: PetscCall(ISGetLocalSize(cutvertices, &vExtra));
1091: }
1092: PetscCall(DMGetPointSF(dm, &sfPoint));
1093: if (cutLabel) {
1094: const PetscInt *ilocal;
1095: const PetscSFNode *iremote;
1096: PetscInt nroots, nleaves;
1098: PetscCall(PetscSFGetGraph(sfPoint, &nroots, &nleaves, &ilocal, &iremote));
1099: if (nleaves < 0) {
1100: PetscCall(PetscObjectReference((PetscObject)sfPoint));
1101: } else {
1102: PetscCall(PetscSFCreate(PetscObjectComm((PetscObject)sfPoint), &sfPoint));
1103: PetscCall(PetscSFSetGraph(sfPoint, nroots + vExtra, nleaves, (PetscInt *)ilocal, PETSC_COPY_VALUES, (PetscSFNode *)iremote, PETSC_COPY_VALUES));
1104: }
1105: } else {
1106: PetscCall(PetscObjectReference((PetscObject)sfPoint));
1107: }
1108: /* Number all vertices */
1109: PetscCall(DMPlexCreateNumbering_Plex(dm, vStart, vEnd + vExtra, 0, NULL, sfPoint, &globalVertexNumbers));
1110: PetscCall(PetscSFDestroy(&sfPoint));
1111: /* Create cones */
1112: PetscCall(ISGetIndices(globalVertexNumbers, &gvertex));
1113: PetscCall(PetscMalloc1(conesSize, &vertices));
1114: for (cell = cStart, v = 0; cell < cEnd; ++cell) {
1115: PetscInt *closure = NULL;
1116: PetscInt closureSize, Nc = 0, p, value = -1;
1117: PetscBool replace;
1119: if (gcell[cell] < 0) continue;
1120: if (cutLabel) PetscCall(DMLabelGetValue(cutLabel, cell, &value));
1121: replace = (value == 2) ? PETSC_TRUE : PETSC_FALSE;
1122: PetscCall(DMPlexGetTransitiveClosure(dm, cell, PETSC_TRUE, &closureSize, &closure));
1123: for (p = 0; p < closureSize * 2; p += 2) {
1124: if ((closure[p] >= vStart) && (closure[p] < vEnd)) closure[Nc++] = closure[p];
1125: }
1126: PetscCall(DMPlexReorderCell(dm, cell, closure));
1127: for (p = 0; p < Nc; ++p) {
1128: PetscInt nv, gv = gvertex[closure[p] - vStart];
1130: if (replace) {
1131: PetscCall(PetscFindInt(closure[p], vExtra, cutverts, &nv));
1132: if (nv >= 0) gv = gvertex[vEnd - vStart + nv];
1133: }
1134: vertices[v++] = gv < 0 ? -(gv + 1) : gv;
1135: }
1136: PetscCall(DMPlexRestoreTransitiveClosure(dm, cell, PETSC_TRUE, &closureSize, &closure));
1137: }
1138: PetscCall(ISRestoreIndices(globalVertexNumbers, &gvertex));
1139: PetscCall(ISDestroy(&globalVertexNumbers));
1140: PetscCall(ISRestoreIndices(globalCellNumbers, &gcell));
1141: if (cutvertices) PetscCall(ISRestoreIndices(cutvertices, &cutverts));
1142: PetscCall(ISDestroy(&cutvertices));
1143: PetscCall(DMLabelDestroy(&cutVertexLabel));
1144: PetscCheck(v == conesSize, PETSC_COMM_SELF, PETSC_ERR_LIB, "Total number of cell vertices %" PetscInt_FMT " != %" PetscInt_FMT, v, conesSize);
1145: PetscCall(ISCreateGeneral(PetscObjectComm((PetscObject)dm), conesSize, vertices, PETSC_OWN_POINTER, cellIS));
1146: PetscCall(PetscLayoutSetBlockSize((*cellIS)->map, *numCorners));
1147: PetscCall(PetscObjectSetName((PetscObject)*cellIS, "cells"));
1148: PetscFunctionReturn(PETSC_SUCCESS);
1149: }
1151: static PetscErrorCode DMPlexTopologyView_HDF5_XDMF_Private(DM dm, IS globalCellNumbers, PetscViewer viewer)
1152: {
1153: DM cdm;
1154: DMLabel depthLabel, ctLabel;
1155: IS cellIS;
1156: PetscInt dim, depth, cellHeight, c, n = 0;
1158: PetscFunctionBegin;
1159: PetscCall(PetscViewerHDF5PushGroup(viewer, "/viz"));
1160: PetscCall(PetscViewerHDF5WriteGroup(viewer, NULL));
1162: PetscCall(PetscViewerHDF5PopGroup(viewer));
1163: PetscCall(DMGetDimension(dm, &dim));
1164: PetscCall(DMPlexGetDepth(dm, &depth));
1165: PetscCall(DMGetCoordinateDM(dm, &cdm));
1166: PetscCall(DMPlexGetVTKCellHeight(dm, &cellHeight));
1167: PetscCall(DMPlexGetDepthLabel(dm, &depthLabel));
1168: PetscCall(DMPlexGetCellTypeLabel(dm, &ctLabel));
1169: for (c = 0; c < DM_NUM_POLYTOPES; ++c) {
1170: const DMPolytopeType ict = (DMPolytopeType)c;
1171: PetscInt pStart, pEnd, dep, numCorners;
1172: PetscBool output = PETSC_FALSE, doOutput;
1174: if (ict == DM_POLYTOPE_FV_GHOST) continue;
1175: PetscCall(DMLabelGetStratumBounds(ctLabel, ict, &pStart, &pEnd));
1176: if (pStart >= 0) {
1177: PetscCall(DMLabelGetValue(depthLabel, pStart, &dep));
1178: if (dep == depth - cellHeight) output = PETSC_TRUE;
1179: }
1180: PetscCallMPI(MPIU_Allreduce(&output, &doOutput, 1, MPIU_BOOL, MPI_LOR, PetscObjectComm((PetscObject)dm)));
1181: if (!doOutput) continue;
1182: PetscCall(CreateConesIS_Private(dm, pStart, pEnd, globalCellNumbers, &numCorners, &cellIS));
1183: if (!n) {
1184: PetscCall(PetscViewerHDF5PushGroup(viewer, "/viz/topology"));
1185: } else {
1186: char group[PETSC_MAX_PATH_LEN];
1188: PetscCall(PetscSNPrintf(group, PETSC_MAX_PATH_LEN, "/viz/topology_%" PetscInt_FMT, n));
1189: PetscCall(PetscViewerHDF5PushGroup(viewer, group));
1190: }
1191: PetscCall(ISView(cellIS, viewer));
1192: PetscCall(PetscViewerHDF5WriteObjectAttribute(viewer, (PetscObject)cellIS, "cell_corners", PETSC_INT, (void *)&numCorners));
1193: PetscCall(PetscViewerHDF5WriteObjectAttribute(viewer, (PetscObject)cellIS, "cell_dim", PETSC_INT, (void *)&dim));
1194: PetscCall(ISDestroy(&cellIS));
1195: PetscCall(PetscViewerHDF5PopGroup(viewer));
1196: ++n;
1197: }
1198: PetscFunctionReturn(PETSC_SUCCESS);
1199: }
1201: static PetscErrorCode DMPlexCoordinatesView_HDF5_Legacy_Private(DM dm, PetscViewer viewer)
1202: {
1203: DM cdm;
1204: Vec coordinates, newcoords;
1205: PetscReal lengthScale;
1206: PetscInt m, M, bs;
1208: PetscFunctionBegin;
1209: PetscCall(DMPlexGetScale(dm, PETSC_UNIT_LENGTH, &lengthScale));
1210: PetscCall(DMGetCoordinateDM(dm, &cdm));
1211: PetscCall(DMGetCoordinates(dm, &coordinates));
1212: PetscCall(VecCreate(PetscObjectComm((PetscObject)coordinates), &newcoords));
1213: PetscCall(PetscObjectSetName((PetscObject)newcoords, "vertices"));
1214: PetscCall(VecGetSize(coordinates, &M));
1215: PetscCall(VecGetLocalSize(coordinates, &m));
1216: PetscCall(VecSetSizes(newcoords, m, M));
1217: PetscCall(VecGetBlockSize(coordinates, &bs));
1218: PetscCall(VecSetBlockSize(newcoords, bs));
1219: PetscCall(VecSetType(newcoords, VECSTANDARD));
1220: PetscCall(VecCopy(coordinates, newcoords));
1221: PetscCall(VecScale(newcoords, lengthScale));
1222: /* Did not use DMGetGlobalVector() in order to bypass default group assignment */
1223: PetscCall(PetscViewerHDF5PushGroup(viewer, "/geometry"));
1224: PetscCall(PetscViewerPushFormat(viewer, PETSC_VIEWER_NATIVE));
1225: PetscCall(VecView(newcoords, viewer));
1226: PetscCall(PetscViewerPopFormat(viewer));
1227: PetscCall(PetscViewerHDF5PopGroup(viewer));
1228: PetscCall(VecDestroy(&newcoords));
1229: PetscFunctionReturn(PETSC_SUCCESS);
1230: }
1232: PetscErrorCode DMPlexCoordinatesView_HDF5_Internal(DM dm, PetscViewer viewer)
1233: {
1234: DM cdm;
1235: Vec coords, newcoords;
1236: PetscInt m, M, bs;
1237: PetscReal lengthScale;
1238: PetscBool viewSection = PETSC_TRUE;
1239: const char *topologydm_name, *coordinatedm_name, *coordinates_name;
1241: PetscFunctionBegin;
1242: {
1243: PetscViewerFormat format;
1244: DMPlexStorageVersion version;
1246: PetscCall(PetscViewerGetFormat(viewer, &format));
1247: PetscCall(PetscViewerHDF5GetDMPlexStorageVersionWriting(viewer, &version));
1248: if (!DMPlexStorageVersionGE(version, 2, 0, 0) || format == PETSC_VIEWER_HDF5_XDMF || format == PETSC_VIEWER_HDF5_VIZ) {
1249: PetscCall(DMPlexCoordinatesView_HDF5_Legacy_Private(dm, viewer));
1250: PetscFunctionReturn(PETSC_SUCCESS);
1251: }
1252: }
1253: /* since 2.0.0 */
1254: PetscCall(PetscOptionsGetBool(NULL, dm->hdr.prefix, "-dm_plex_view_coordinate_section", &viewSection, NULL));
1255: PetscCall(DMGetCoordinateDM(dm, &cdm));
1256: PetscCall(DMGetCoordinates(dm, &coords));
1257: PetscCall(PetscObjectGetName((PetscObject)cdm, &coordinatedm_name));
1258: PetscCall(PetscObjectGetName((PetscObject)coords, &coordinates_name));
1259: PetscCall(DMPlexGetHDF5Name_Private(dm, &topologydm_name));
1260: PetscCall(PetscViewerHDF5PushGroup(viewer, "topologies"));
1261: PetscCall(PetscViewerHDF5PushGroup(viewer, topologydm_name));
1262: PetscCall(PetscViewerHDF5WriteAttribute(viewer, NULL, "coordinateDMName", PETSC_STRING, coordinatedm_name));
1263: PetscCall(PetscViewerHDF5WriteAttribute(viewer, NULL, "coordinatesName", PETSC_STRING, coordinates_name));
1264: PetscCall(PetscViewerHDF5PopGroup(viewer));
1265: PetscCall(PetscViewerHDF5PopGroup(viewer));
1266: if (viewSection) PetscCall(DMPlexSectionView(dm, viewer, cdm));
1267: PetscCall(VecCreate(PetscObjectComm((PetscObject)coords), &newcoords));
1268: PetscCall(PetscObjectSetName((PetscObject)newcoords, coordinates_name));
1269: PetscCall(VecGetSize(coords, &M));
1270: PetscCall(VecGetLocalSize(coords, &m));
1271: PetscCall(VecSetSizes(newcoords, m, M));
1272: PetscCall(VecGetBlockSize(coords, &bs));
1273: PetscCall(VecSetBlockSize(newcoords, bs));
1274: PetscCall(VecSetType(newcoords, VECSTANDARD));
1275: PetscCall(VecCopy(coords, newcoords));
1276: PetscCall(DMPlexGetScale(dm, PETSC_UNIT_LENGTH, &lengthScale));
1277: PetscCall(VecScale(newcoords, lengthScale));
1278: PetscCall(PetscViewerPushFormat(viewer, PETSC_VIEWER_NATIVE));
1279: PetscCall(DMPlexGlobalVectorView(dm, viewer, cdm, newcoords));
1280: PetscCall(PetscViewerPopFormat(viewer));
1281: PetscCall(VecDestroy(&newcoords));
1282: PetscFunctionReturn(PETSC_SUCCESS);
1283: }
1285: static PetscErrorCode DMPlexCoordinatesView_HDF5_XDMF_Private(DM dm, PetscViewer viewer)
1286: {
1287: DM cdm;
1288: Vec coordinatesLocal, newcoords;
1289: PetscSection cSection, cGlobalSection;
1290: PetscScalar *coords, *ncoords;
1291: DMLabel cutLabel, cutVertexLabel = NULL;
1292: const PetscReal *L;
1293: PetscReal lengthScale;
1294: PetscInt vStart, vEnd, v, bs, N, coordSize, dof, off, d;
1295: PetscBool localized, embedded;
1297: PetscFunctionBegin;
1298: PetscCall(DMPlexGetDepthStratum(dm, 0, &vStart, &vEnd));
1299: PetscCall(DMPlexGetScale(dm, PETSC_UNIT_LENGTH, &lengthScale));
1300: PetscCall(DMGetCoordinatesLocal(dm, &coordinatesLocal));
1301: PetscCall(VecGetBlockSize(coordinatesLocal, &bs));
1302: PetscCall(DMGetCoordinatesLocalized(dm, &localized));
1303: if (localized == PETSC_FALSE) PetscFunctionReturn(PETSC_SUCCESS);
1304: PetscCall(DMGetPeriodicity(dm, NULL, NULL, &L));
1305: PetscCall(DMGetCoordinateDM(dm, &cdm));
1306: PetscCall(DMGetLocalSection(cdm, &cSection));
1307: PetscCall(DMGetGlobalSection(cdm, &cGlobalSection));
1308: PetscCall(DMGetLabel(dm, "periodic_cut", &cutLabel));
1309: N = 0;
1311: PetscCall(DMPlexCreateCutVertexLabel_Private(dm, cutLabel, &cutVertexLabel));
1312: PetscCall(VecCreate(PetscObjectComm((PetscObject)dm), &newcoords));
1313: PetscCall(PetscSectionGetDof(cSection, vStart, &dof));
1314: PetscCall(PetscPrintf(PETSC_COMM_SELF, "DOF: %" PetscInt_FMT "\n", dof));
1315: embedded = (PetscBool)(L && dof == 2 && !cutLabel);
1316: if (cutVertexLabel) {
1317: PetscCall(DMLabelGetStratumSize(cutVertexLabel, 1, &v));
1318: N += dof * v;
1319: }
1320: for (v = vStart; v < vEnd; ++v) {
1321: PetscCall(PetscSectionGetDof(cGlobalSection, v, &dof));
1322: if (dof < 0) continue;
1323: if (embedded) N += dof + 1;
1324: else N += dof;
1325: }
1326: if (embedded) PetscCall(VecSetBlockSize(newcoords, bs + 1));
1327: else PetscCall(VecSetBlockSize(newcoords, bs));
1328: PetscCall(VecSetSizes(newcoords, N, PETSC_DETERMINE));
1329: PetscCall(VecSetType(newcoords, VECSTANDARD));
1330: PetscCall(VecGetArray(coordinatesLocal, &coords));
1331: PetscCall(VecGetArray(newcoords, &ncoords));
1332: coordSize = 0;
1333: for (v = vStart; v < vEnd; ++v) {
1334: PetscCall(PetscSectionGetDof(cGlobalSection, v, &dof));
1335: PetscCall(PetscSectionGetOffset(cSection, v, &off));
1336: if (dof < 0) continue;
1337: if (embedded) {
1338: if (L && (L[0] > 0.0) && (L[1] > 0.0)) {
1339: PetscReal theta, phi, r, R;
1340: /* XY-periodic */
1341: /* Suppose its an y-z circle, then
1342: \hat r = (0, cos(th), sin(th)) \hat x = (1, 0, 0)
1343: and the circle in that plane is
1344: \hat r cos(phi) + \hat x sin(phi) */
1345: theta = 2.0 * PETSC_PI * PetscRealPart(coords[off + 1]) / L[1];
1346: phi = 2.0 * PETSC_PI * PetscRealPart(coords[off + 0]) / L[0];
1347: r = L[0] / (2.0 * PETSC_PI * 2.0 * L[1]);
1348: R = L[1] / (2.0 * PETSC_PI);
1349: ncoords[coordSize++] = PetscSinReal(phi) * r;
1350: ncoords[coordSize++] = -PetscCosReal(theta) * (R + r * PetscCosReal(phi));
1351: ncoords[coordSize++] = PetscSinReal(theta) * (R + r * PetscCosReal(phi));
1352: } else if (L && (L[0] > 0.0)) {
1353: /* X-periodic */
1354: ncoords[coordSize++] = -PetscCosReal(2.0 * PETSC_PI * PetscRealPart(coords[off + 0]) / L[0]) * (L[0] / (2.0 * PETSC_PI));
1355: ncoords[coordSize++] = coords[off + 1];
1356: ncoords[coordSize++] = PetscSinReal(2.0 * PETSC_PI * PetscRealPart(coords[off + 0]) / L[0]) * (L[0] / (2.0 * PETSC_PI));
1357: } else if (L && (L[1] > 0.0)) {
1358: /* Y-periodic */
1359: ncoords[coordSize++] = coords[off + 0];
1360: ncoords[coordSize++] = PetscSinReal(2.0 * PETSC_PI * PetscRealPart(coords[off + 1]) / L[1]) * (L[1] / (2.0 * PETSC_PI));
1361: ncoords[coordSize++] = -PetscCosReal(2.0 * PETSC_PI * PetscRealPart(coords[off + 1]) / L[1]) * (L[1] / (2.0 * PETSC_PI));
1362: #if 0
1363: } else if ((bd[0] == DM_BOUNDARY_TWIST)) {
1364: PetscReal phi, r, R;
1365: /* Mobius strip */
1366: /* Suppose its an x-z circle, then
1367: \hat r = (-cos(phi), 0, sin(phi)) \hat y = (0, 1, 0)
1368: and in that plane we rotate by pi as we go around the circle
1369: \hat r cos(phi/2) + \hat y sin(phi/2) */
1370: phi = 2.0*PETSC_PI*PetscRealPart(coords[off+0])/L[0];
1371: R = L[0];
1372: r = PetscRealPart(coords[off+1]) - L[1]/2.0;
1373: ncoords[coordSize++] = -PetscCosReal(phi) * (R + r * PetscCosReal(phi/2.0));
1374: ncoords[coordSize++] = PetscSinReal(phi/2.0) * r;
1375: ncoords[coordSize++] = PetscSinReal(phi) * (R + r * PetscCosReal(phi/2.0));
1376: #endif
1377: } else SETERRQ(PetscObjectComm((PetscObject)dm), PETSC_ERR_SUP, "Cannot handle periodicity in this domain");
1378: } else {
1379: for (d = 0; d < dof; ++d, ++coordSize) ncoords[coordSize] = coords[off + d];
1380: }
1381: }
1382: if (cutVertexLabel) {
1383: IS vertices;
1384: const PetscInt *verts;
1385: PetscInt n;
1387: PetscCall(DMLabelGetStratumIS(cutVertexLabel, 1, &vertices));
1388: if (vertices) {
1389: PetscCall(ISGetIndices(vertices, &verts));
1390: PetscCall(ISGetLocalSize(vertices, &n));
1391: for (v = 0; v < n; ++v) {
1392: PetscCall(PetscSectionGetDof(cSection, verts[v], &dof));
1393: PetscCall(PetscSectionGetOffset(cSection, verts[v], &off));
1394: for (d = 0; d < dof; ++d) ncoords[coordSize++] = coords[off + d] + ((L[d] > 0.) ? L[d] : 0.0);
1395: }
1396: PetscCall(ISRestoreIndices(vertices, &verts));
1397: PetscCall(ISDestroy(&vertices));
1398: }
1399: }
1400: PetscCheck(coordSize == N, PETSC_COMM_SELF, PETSC_ERR_PLIB, "Mismatched sizes: %" PetscInt_FMT " != %" PetscInt_FMT, coordSize, N);
1401: PetscCall(DMLabelDestroy(&cutVertexLabel));
1402: PetscCall(VecRestoreArray(coordinatesLocal, &coords));
1403: PetscCall(VecRestoreArray(newcoords, &ncoords));
1404: PetscCall(PetscObjectSetName((PetscObject)newcoords, "vertices"));
1405: PetscCall(VecScale(newcoords, lengthScale));
1406: PetscCall(PetscViewerHDF5PushGroup(viewer, "/viz"));
1407: PetscCall(PetscViewerHDF5WriteGroup(viewer, NULL));
1408: PetscCall(PetscViewerHDF5PopGroup(viewer));
1409: PetscCall(PetscViewerHDF5PushGroup(viewer, "/viz/geometry"));
1410: PetscCall(VecView(newcoords, viewer));
1411: PetscCall(PetscViewerHDF5PopGroup(viewer));
1412: PetscCall(VecDestroy(&newcoords));
1413: PetscFunctionReturn(PETSC_SUCCESS);
1414: }
1416: PetscErrorCode DMPlexLabelsView_HDF5_Internal(DM dm, IS globalPointNumbers, PetscViewer viewer)
1417: {
1418: const char *topologydm_name;
1419: const PetscInt *gpoint;
1420: PetscInt numLabels;
1421: PetscBool omitCelltypes = PETSC_FALSE;
1422: DMPlexStorageVersion version;
1423: char group[PETSC_MAX_PATH_LEN];
1425: PetscFunctionBegin;
1426: PetscCall(PetscOptionsGetBool(NULL, dm->hdr.prefix, "-dm_plex_omit_celltypes", &omitCelltypes, NULL));
1427: PetscCall(PetscViewerHDF5GetDMPlexStorageVersionWriting(viewer, &version));
1428: PetscCall(ISGetIndices(globalPointNumbers, &gpoint));
1429: PetscCall(DMPlexGetHDF5Name_Private(dm, &topologydm_name));
1430: if (DMPlexStorageVersionGE(version, 2, 0, 0)) {
1431: PetscCall(PetscSNPrintf(group, sizeof(group), "topologies/%s/labels", topologydm_name));
1432: } else {
1433: PetscCall(PetscStrncpy(group, "/labels", sizeof(group)));
1434: }
1435: PetscCall(PetscViewerHDF5PushGroup(viewer, group));
1436: PetscCall(DMGetNumLabels(dm, &numLabels));
1437: for (PetscInt l = 0; l < numLabels; ++l) {
1438: DMLabel label;
1439: const char *name;
1440: IS valueIS, pvalueIS, globalValueIS;
1441: const PetscInt *values;
1442: PetscInt numValues, v;
1443: PetscBool isDepth, isCelltype, output;
1445: PetscCall(DMGetLabelByNum(dm, l, &label));
1446: PetscCall(PetscObjectGetName((PetscObject)label, &name));
1447: PetscCall(DMGetLabelOutput(dm, name, &output));
1448: PetscCall(PetscStrncmp(name, "depth", 10, &isDepth));
1449: PetscCall(PetscStrncmp(name, "celltype", 10, &isCelltype));
1450: // TODO Should only filter out celltype if it can be calculated
1451: if (isDepth || (isCelltype && omitCelltypes) || !output) continue;
1452: PetscCall(PetscViewerHDF5PushGroup(viewer, name));
1453: PetscCall(DMLabelGetValueIS(label, &valueIS));
1454: /* Must copy to a new IS on the global comm */
1455: PetscCall(ISGetLocalSize(valueIS, &numValues));
1456: PetscCall(ISGetIndices(valueIS, &values));
1457: PetscCall(ISCreateGeneral(PetscObjectComm((PetscObject)dm), numValues, values, PETSC_COPY_VALUES, &pvalueIS));
1458: PetscCall(ISRestoreIndices(valueIS, &values));
1459: PetscCall(ISAllGather(pvalueIS, &globalValueIS));
1460: PetscCall(ISDestroy(&pvalueIS));
1461: PetscCall(ISSortRemoveDups(globalValueIS));
1462: PetscCall(ISGetLocalSize(globalValueIS, &numValues));
1463: PetscCall(ISGetIndices(globalValueIS, &values));
1464: for (v = 0; v < numValues; ++v) {
1465: IS stratumIS, globalStratumIS;
1466: const PetscInt *spoints = NULL;
1467: PetscInt *gspoints, n = 0, gn, p;
1468: const char *iname = "indices";
1469: char group[PETSC_MAX_PATH_LEN];
1471: PetscCall(PetscSNPrintf(group, sizeof(group), "%" PetscInt_FMT, values[v]));
1472: PetscCall(PetscViewerHDF5PushGroup(viewer, group));
1473: PetscCall(DMLabelGetStratumIS(label, values[v], &stratumIS));
1475: if (stratumIS) PetscCall(ISGetLocalSize(stratumIS, &n));
1476: if (stratumIS) PetscCall(ISGetIndices(stratumIS, &spoints));
1477: for (gn = 0, p = 0; p < n; ++p)
1478: if (gpoint[spoints[p]] >= 0) ++gn;
1479: PetscCall(PetscMalloc1(gn, &gspoints));
1480: for (gn = 0, p = 0; p < n; ++p)
1481: if (gpoint[spoints[p]] >= 0) gspoints[gn++] = gpoint[spoints[p]];
1482: if (stratumIS) PetscCall(ISRestoreIndices(stratumIS, &spoints));
1483: PetscCall(ISCreateGeneral(PetscObjectComm((PetscObject)dm), gn, gspoints, PETSC_OWN_POINTER, &globalStratumIS));
1484: PetscCall(PetscObjectSetName((PetscObject)globalStratumIS, iname));
1486: PetscCall(ISView(globalStratumIS, viewer));
1487: PetscCall(ISDestroy(&globalStratumIS));
1488: PetscCall(ISDestroy(&stratumIS));
1489: PetscCall(PetscViewerHDF5PopGroup(viewer));
1490: }
1491: PetscCall(ISRestoreIndices(globalValueIS, &values));
1492: PetscCall(ISDestroy(&globalValueIS));
1493: PetscCall(ISDestroy(&valueIS));
1494: PetscCall(PetscViewerHDF5PopGroup(viewer));
1495: }
1496: PetscCall(ISRestoreIndices(globalPointNumbers, &gpoint));
1497: PetscCall(PetscViewerHDF5PopGroup(viewer));
1498: PetscFunctionReturn(PETSC_SUCCESS);
1499: }
1501: /* We only write cells and vertices. Does this screw up parallel reading? */
1502: PetscErrorCode DMPlexView_HDF5_Internal(DM dm, PetscViewer viewer)
1503: {
1504: IS globalPointNumbers;
1505: PetscViewerFormat format;
1506: PetscBool viz_geom = PETSC_FALSE, xdmf_topo = PETSC_FALSE, petsc_topo = PETSC_FALSE;
1508: PetscFunctionBegin;
1509: PetscCall(DMPlexCreatePointNumbering(dm, &globalPointNumbers));
1510: PetscCall(DMPlexCoordinatesView_HDF5_Internal(dm, viewer));
1512: PetscCall(PetscViewerGetFormat(viewer, &format));
1513: switch (format) {
1514: case PETSC_VIEWER_HDF5_VIZ:
1515: viz_geom = PETSC_TRUE;
1516: xdmf_topo = PETSC_TRUE;
1517: break;
1518: case PETSC_VIEWER_HDF5_XDMF:
1519: xdmf_topo = PETSC_TRUE;
1520: break;
1521: case PETSC_VIEWER_HDF5_PETSC:
1522: petsc_topo = PETSC_TRUE;
1523: break;
1524: case PETSC_VIEWER_DEFAULT:
1525: case PETSC_VIEWER_NATIVE:
1526: viz_geom = PETSC_TRUE;
1527: xdmf_topo = PETSC_TRUE;
1528: petsc_topo = PETSC_TRUE;
1529: break;
1530: default:
1531: SETERRQ(PetscObjectComm((PetscObject)dm), PETSC_ERR_SUP, "PetscViewerFormat %s not supported for HDF5 output.", PetscViewerFormats[format]);
1532: }
1534: if (viz_geom) PetscCall(DMPlexCoordinatesView_HDF5_XDMF_Private(dm, viewer));
1535: if (xdmf_topo) PetscCall(DMPlexTopologyView_HDF5_XDMF_Private(dm, globalPointNumbers, viewer));
1536: if (petsc_topo) {
1537: PetscBool viewLabels = PETSC_TRUE;
1539: PetscCall(DMPlexTopologyView_HDF5_Internal(dm, globalPointNumbers, viewer));
1540: PetscCall(PetscOptionsGetBool(NULL, dm->hdr.prefix, "-dm_plex_view_labels", &viewLabels, NULL));
1541: if (viewLabels) PetscCall(DMPlexLabelsView_HDF5_Internal(dm, globalPointNumbers, viewer));
1542: }
1544: PetscCall(ISDestroy(&globalPointNumbers));
1545: PetscFunctionReturn(PETSC_SUCCESS);
1546: }
1548: PetscErrorCode DMPlexSectionView_HDF5_Internal(DM dm, PetscViewer viewer, DM sectiondm)
1549: {
1550: MPI_Comm comm;
1551: const char *topologydm_name;
1552: const char *sectiondm_name;
1553: PetscSection gsection;
1555: PetscFunctionBegin;
1556: PetscCall(PetscObjectGetComm((PetscObject)sectiondm, &comm));
1557: PetscCall(DMPlexGetHDF5Name_Private(dm, &topologydm_name));
1558: PetscCall(PetscObjectGetName((PetscObject)sectiondm, §iondm_name));
1559: PetscCall(PetscViewerHDF5PushGroup(viewer, "topologies"));
1560: PetscCall(PetscViewerHDF5PushGroup(viewer, topologydm_name));
1561: PetscCall(PetscViewerHDF5PushGroup(viewer, "dms"));
1562: PetscCall(PetscViewerHDF5PushGroup(viewer, sectiondm_name));
1563: PetscCall(DMGetGlobalSection(sectiondm, &gsection));
1564: /* Save raw section */
1565: PetscCall(PetscSectionView(gsection, viewer));
1566: /* Save plex wrapper */
1567: {
1568: PetscInt pStart, pEnd, p, n;
1569: IS globalPointNumbers;
1570: const PetscInt *gpoints;
1571: IS orderIS;
1572: PetscInt *order;
1574: PetscCall(PetscSectionGetChart(gsection, &pStart, &pEnd));
1575: PetscCall(DMPlexCreatePointNumbering(dm, &globalPointNumbers));
1576: PetscCall(ISGetIndices(globalPointNumbers, &gpoints));
1577: for (p = pStart, n = 0; p < pEnd; ++p)
1578: if (gpoints[p] >= 0) n++;
1579: /* "order" is an array of global point numbers.
1580: When loading, it is used with topology/order array
1581: to match section points with plex topology points. */
1582: PetscCall(PetscMalloc1(n, &order));
1583: for (p = pStart, n = 0; p < pEnd; ++p)
1584: if (gpoints[p] >= 0) order[n++] = gpoints[p];
1585: PetscCall(ISRestoreIndices(globalPointNumbers, &gpoints));
1586: PetscCall(ISDestroy(&globalPointNumbers));
1587: PetscCall(ISCreateGeneral(comm, n, order, PETSC_OWN_POINTER, &orderIS));
1588: PetscCall(PetscObjectSetName((PetscObject)orderIS, "order"));
1589: PetscCall(ISView(orderIS, viewer));
1590: PetscCall(ISDestroy(&orderIS));
1591: }
1592: PetscCall(PetscViewerHDF5PopGroup(viewer));
1593: PetscCall(PetscViewerHDF5PopGroup(viewer));
1594: PetscCall(PetscViewerHDF5PopGroup(viewer));
1595: PetscCall(PetscViewerHDF5PopGroup(viewer));
1596: PetscFunctionReturn(PETSC_SUCCESS);
1597: }
1599: PetscErrorCode DMPlexGlobalVectorView_HDF5_Internal(DM dm, PetscViewer viewer, DM sectiondm, Vec vec)
1600: {
1601: const char *topologydm_name;
1602: const char *sectiondm_name;
1603: const char *vec_name;
1604: PetscInt bs;
1606: PetscFunctionBegin;
1607: /* Check consistency */
1608: {
1609: PetscSF pointsf, pointsf1;
1611: PetscCall(DMGetPointSF(dm, &pointsf));
1612: PetscCall(DMGetPointSF(sectiondm, &pointsf1));
1613: PetscCheck(pointsf1 == pointsf, PETSC_COMM_SELF, PETSC_ERR_PLIB, "Mismatching point SFs for dm and sectiondm");
1614: }
1615: PetscCall(DMPlexGetHDF5Name_Private(dm, &topologydm_name));
1616: PetscCall(PetscObjectGetName((PetscObject)sectiondm, §iondm_name));
1617: PetscCall(PetscObjectGetName((PetscObject)vec, &vec_name));
1618: PetscCall(PetscViewerHDF5PushGroup(viewer, "topologies"));
1619: PetscCall(PetscViewerHDF5PushGroup(viewer, topologydm_name));
1620: PetscCall(PetscViewerHDF5PushGroup(viewer, "dms"));
1621: PetscCall(PetscViewerHDF5PushGroup(viewer, sectiondm_name));
1622: PetscCall(PetscViewerHDF5PushGroup(viewer, "vecs"));
1623: PetscCall(PetscViewerHDF5PushGroup(viewer, vec_name));
1624: PetscCall(VecGetBlockSize(vec, &bs));
1625: PetscCall(PetscViewerHDF5WriteAttribute(viewer, NULL, "blockSize", PETSC_INT, (void *)&bs));
1626: PetscCall(VecSetBlockSize(vec, 1));
1627: /* VecView(vec, viewer) would call (*vec->opt->view)(vec, viewer), but, */
1628: /* if vec was created with DMGet{Global, Local}Vector(), vec->opt->view */
1629: /* is set to VecView_Plex, which would save vec in a predefined location. */
1630: /* To save vec in where we want, we create a new Vec (temp) with */
1631: /* VecCreate(), wrap the vec data in temp, and call VecView(temp, viewer). */
1632: {
1633: Vec temp;
1634: const PetscScalar *array;
1635: PetscLayout map;
1637: PetscCall(VecCreate(PetscObjectComm((PetscObject)vec), &temp));
1638: PetscCall(PetscObjectSetName((PetscObject)temp, vec_name));
1639: PetscCall(VecGetLayout(vec, &map));
1640: PetscCall(VecSetLayout(temp, map));
1641: PetscCall(VecSetUp(temp));
1642: PetscCall(VecGetArrayRead(vec, &array));
1643: PetscCall(VecPlaceArray(temp, array));
1644: PetscCall(VecView(temp, viewer));
1645: PetscCall(VecResetArray(temp));
1646: PetscCall(VecRestoreArrayRead(vec, &array));
1647: PetscCall(VecDestroy(&temp));
1648: }
1649: PetscCall(VecSetBlockSize(vec, bs));
1650: PetscCall(PetscViewerHDF5PopGroup(viewer));
1651: PetscCall(PetscViewerHDF5PopGroup(viewer));
1652: PetscCall(PetscViewerHDF5PopGroup(viewer));
1653: PetscCall(PetscViewerHDF5PopGroup(viewer));
1654: PetscCall(PetscViewerHDF5PopGroup(viewer));
1655: PetscCall(PetscViewerHDF5PopGroup(viewer));
1656: PetscFunctionReturn(PETSC_SUCCESS);
1657: }
1659: PetscErrorCode DMPlexLocalVectorView_HDF5_Internal(DM dm, PetscViewer viewer, DM sectiondm, Vec vec)
1660: {
1661: MPI_Comm comm;
1662: const char *topologydm_name;
1663: const char *sectiondm_name;
1664: const char *vec_name;
1665: PetscSection section;
1666: PetscBool includesConstraints;
1667: Vec gvec;
1668: PetscInt m, bs;
1670: PetscFunctionBegin;
1671: PetscCall(PetscObjectGetComm((PetscObject)dm, &comm));
1672: /* Check consistency */
1673: {
1674: PetscSF pointsf, pointsf1;
1676: PetscCall(DMGetPointSF(dm, &pointsf));
1677: PetscCall(DMGetPointSF(sectiondm, &pointsf1));
1678: PetscCheck(pointsf1 == pointsf, PETSC_COMM_SELF, PETSC_ERR_PLIB, "Mismatching point SFs for dm and sectiondm");
1679: }
1680: PetscCall(DMPlexGetHDF5Name_Private(dm, &topologydm_name));
1681: PetscCall(PetscObjectGetName((PetscObject)sectiondm, §iondm_name));
1682: PetscCall(PetscObjectGetName((PetscObject)vec, &vec_name));
1683: PetscCall(PetscViewerHDF5PushGroup(viewer, "topologies"));
1684: PetscCall(PetscViewerHDF5PushGroup(viewer, topologydm_name));
1685: PetscCall(PetscViewerHDF5PushGroup(viewer, "dms"));
1686: PetscCall(PetscViewerHDF5PushGroup(viewer, sectiondm_name));
1687: PetscCall(PetscViewerHDF5PushGroup(viewer, "vecs"));
1688: PetscCall(PetscViewerHDF5PushGroup(viewer, vec_name));
1689: PetscCall(VecGetBlockSize(vec, &bs));
1690: PetscCall(PetscViewerHDF5WriteAttribute(viewer, NULL, "blockSize", PETSC_INT, (void *)&bs));
1691: PetscCall(VecCreate(comm, &gvec));
1692: PetscCall(PetscObjectSetName((PetscObject)gvec, vec_name));
1693: PetscCall(DMGetGlobalSection(sectiondm, §ion));
1694: PetscCall(PetscSectionGetIncludesConstraints(section, &includesConstraints));
1695: if (includesConstraints) PetscCall(PetscSectionGetStorageSize(section, &m));
1696: else PetscCall(PetscSectionGetConstrainedStorageSize(section, &m));
1697: PetscCall(VecSetSizes(gvec, m, PETSC_DECIDE));
1698: PetscCall(VecSetUp(gvec));
1699: PetscCall(DMLocalToGlobalBegin(sectiondm, vec, INSERT_VALUES, gvec));
1700: PetscCall(DMLocalToGlobalEnd(sectiondm, vec, INSERT_VALUES, gvec));
1701: PetscCall(VecView(gvec, viewer));
1702: PetscCall(VecDestroy(&gvec));
1703: PetscCall(PetscViewerHDF5PopGroup(viewer));
1704: PetscCall(PetscViewerHDF5PopGroup(viewer));
1705: PetscCall(PetscViewerHDF5PopGroup(viewer));
1706: PetscCall(PetscViewerHDF5PopGroup(viewer));
1707: PetscCall(PetscViewerHDF5PopGroup(viewer));
1708: PetscCall(PetscViewerHDF5PopGroup(viewer));
1709: PetscFunctionReturn(PETSC_SUCCESS);
1710: }
1712: struct _n_LoadLabelsCtx {
1713: MPI_Comm comm;
1714: PetscMPIInt rank;
1715: DM dm;
1716: PetscViewer viewer;
1717: DMLabel label;
1718: PetscSF sfXC;
1719: PetscLayout layoutX;
1720: };
1721: typedef struct _n_LoadLabelsCtx *LoadLabelsCtx;
1723: static PetscErrorCode LoadLabelsCtxCreate(DM dm, PetscViewer viewer, PetscSF sfXC, LoadLabelsCtx *ctx)
1724: {
1725: PetscFunctionBegin;
1726: PetscCall(PetscNew(ctx));
1727: PetscCall(PetscObjectReference((PetscObject)((*ctx)->dm = dm)));
1728: PetscCall(PetscObjectReference((PetscObject)((*ctx)->viewer = viewer)));
1729: PetscCall(PetscObjectGetComm((PetscObject)dm, &(*ctx)->comm));
1730: PetscCallMPI(MPI_Comm_rank((*ctx)->comm, &(*ctx)->rank));
1731: (*ctx)->sfXC = sfXC;
1732: if (sfXC) {
1733: PetscInt nX;
1735: PetscCall(PetscObjectReference((PetscObject)sfXC));
1736: PetscCall(PetscSFGetGraph(sfXC, &nX, NULL, NULL, NULL));
1737: PetscCall(PetscLayoutCreateFromSizes((*ctx)->comm, nX, PETSC_DECIDE, 1, &(*ctx)->layoutX));
1738: }
1739: PetscFunctionReturn(PETSC_SUCCESS);
1740: }
1742: static PetscErrorCode LoadLabelsCtxDestroy(LoadLabelsCtx *ctx)
1743: {
1744: PetscFunctionBegin;
1745: if (!*ctx) PetscFunctionReturn(PETSC_SUCCESS);
1746: PetscCall(DMDestroy(&(*ctx)->dm));
1747: PetscCall(PetscViewerDestroy(&(*ctx)->viewer));
1748: PetscCall(PetscSFDestroy(&(*ctx)->sfXC));
1749: PetscCall(PetscLayoutDestroy(&(*ctx)->layoutX));
1750: PetscCall(PetscFree(*ctx));
1751: PetscFunctionReturn(PETSC_SUCCESS);
1752: }
1754: /*
1755: A: on-disk points
1756: X: global points [0, NX)
1757: C: distributed plex points
1758: */
1759: static herr_t ReadLabelStratumHDF5_Distribute_Private(IS stratumIS, LoadLabelsCtx ctx, IS *newStratumIS)
1760: {
1761: MPI_Comm comm = ctx->comm;
1762: PetscSF sfXC = ctx->sfXC;
1763: PetscLayout layoutX = ctx->layoutX;
1764: PetscSF sfXA;
1765: const PetscInt *A_points;
1766: PetscInt nX, nC;
1767: PetscInt n;
1769: PetscFunctionBegin;
1770: PetscCall(PetscSFGetGraph(sfXC, &nX, &nC, NULL, NULL));
1771: PetscCall(ISGetLocalSize(stratumIS, &n));
1772: PetscCall(ISGetIndices(stratumIS, &A_points));
1773: PetscCall(PetscSFCreate(comm, &sfXA));
1774: PetscCall(PetscSFSetGraphLayout(sfXA, layoutX, n, NULL, PETSC_USE_POINTER, A_points));
1775: PetscCall(ISCreate(comm, newStratumIS));
1776: PetscCall(ISSetType(*newStratumIS, ISGENERAL));
1777: {
1778: PetscInt i;
1779: PetscBool *A_mask, *X_mask, *C_mask;
1781: PetscCall(PetscCalloc3(n, &A_mask, nX, &X_mask, nC, &C_mask));
1782: for (i = 0; i < n; i++) A_mask[i] = PETSC_TRUE;
1783: PetscCall(PetscSFReduceBegin(sfXA, MPIU_BOOL, A_mask, X_mask, MPI_REPLACE));
1784: PetscCall(PetscSFReduceEnd(sfXA, MPIU_BOOL, A_mask, X_mask, MPI_REPLACE));
1785: PetscCall(PetscSFBcastBegin(sfXC, MPIU_BOOL, X_mask, C_mask, MPI_LOR));
1786: PetscCall(PetscSFBcastEnd(sfXC, MPIU_BOOL, X_mask, C_mask, MPI_LOR));
1787: PetscCall(ISGeneralSetIndicesFromMask(*newStratumIS, 0, nC, C_mask));
1788: PetscCall(PetscFree3(A_mask, X_mask, C_mask));
1789: }
1790: PetscCall(PetscSFDestroy(&sfXA));
1791: PetscCall(ISRestoreIndices(stratumIS, &A_points));
1792: PetscFunctionReturn(PETSC_SUCCESS);
1793: }
1795: static herr_t ReadLabelStratumHDF5_Static(hid_t g_id, const char *vname, const H5L_info_t *info, void *op_data)
1796: {
1797: LoadLabelsCtx ctx = (LoadLabelsCtx)op_data;
1798: PetscViewer viewer = ctx->viewer;
1799: DMLabel label = ctx->label;
1800: MPI_Comm comm = ctx->comm;
1801: IS stratumIS;
1802: const PetscInt *ind;
1803: PetscInt value, N, i;
1805: PetscCall(PetscOptionsStringToInt(vname, &value));
1806: PetscCall(ISCreate(comm, &stratumIS));
1807: PetscCall(PetscObjectSetName((PetscObject)stratumIS, "indices"));
1808: PetscCall(PetscViewerHDF5PushGroup(viewer, vname)); /* labels/<lname>/<vname> */
1810: if (!ctx->sfXC) {
1811: /* Force serial load */
1812: PetscCall(PetscViewerHDF5ReadSizes(viewer, "indices", NULL, &N));
1813: PetscCall(PetscLayoutSetLocalSize(stratumIS->map, !ctx->rank ? N : 0));
1814: PetscCall(PetscLayoutSetSize(stratumIS->map, N));
1815: }
1816: PetscCall(ISLoad(stratumIS, viewer));
1818: if (ctx->sfXC) {
1819: IS newStratumIS;
1821: PetscCallHDF5(ReadLabelStratumHDF5_Distribute_Private, (stratumIS, ctx, &newStratumIS));
1822: PetscCall(ISDestroy(&stratumIS));
1823: stratumIS = newStratumIS;
1824: }
1826: PetscCall(PetscViewerHDF5PopGroup(viewer));
1827: PetscCall(ISGetLocalSize(stratumIS, &N));
1828: PetscCall(ISGetIndices(stratumIS, &ind));
1829: for (i = 0; i < N; ++i) PetscCall(DMLabelSetValue(label, ind[i], value));
1830: PetscCall(ISRestoreIndices(stratumIS, &ind));
1831: PetscCall(ISDestroy(&stratumIS));
1832: return 0;
1833: }
1835: /* TODO: Fix this code, it is returning PETSc error codes when it should be translating them to herr_t codes */
1836: static herr_t ReadLabelHDF5_Static(hid_t g_id, const char *lname, const H5L_info_t *info, void *op_data)
1837: {
1838: LoadLabelsCtx ctx = (LoadLabelsCtx)op_data;
1839: DM dm = ctx->dm;
1840: hsize_t idx = 0;
1841: PetscErrorCode ierr;
1842: PetscBool flg;
1843: herr_t err;
1845: PetscCall(DMHasLabel(dm, lname, &flg));
1846: if (flg) PetscCall(DMRemoveLabel(dm, lname, NULL));
1847: ierr = DMCreateLabel(dm, lname);
1848: if (ierr) return (herr_t)ierr;
1849: ierr = DMGetLabel(dm, lname, &ctx->label);
1850: if (ierr) return (herr_t)ierr;
1851: ierr = PetscViewerHDF5PushGroup(ctx->viewer, lname);
1852: if (ierr) return (herr_t)ierr;
1853: /* Iterate over the label's strata */
1854: PetscCallHDF5Return(err, H5Literate_by_name, (g_id, lname, H5_INDEX_NAME, H5_ITER_NATIVE, &idx, ReadLabelStratumHDF5_Static, op_data, 0));
1855: ierr = PetscViewerHDF5PopGroup(ctx->viewer);
1856: if (ierr) return (herr_t)ierr;
1857: return err;
1858: }
1860: PetscErrorCode DMPlexLabelsLoad_HDF5_Internal(DM dm, PetscViewer viewer, PetscSF sfXC)
1861: {
1862: const char *topologydm_name;
1863: LoadLabelsCtx ctx;
1864: hsize_t idx = 0;
1865: char group[PETSC_MAX_PATH_LEN];
1866: DMPlexStorageVersion version;
1867: PetscBool distributed, hasGroup;
1869: PetscFunctionBegin;
1870: PetscCall(DMPlexIsDistributed(dm, &distributed));
1871: if (distributed) PetscCheck(sfXC, PetscObjectComm((PetscObject)dm), PETSC_ERR_ARG_NULL, "PetscSF must be given for parallel load");
1872: PetscCall(LoadLabelsCtxCreate(dm, viewer, sfXC, &ctx));
1873: PetscCall(DMPlexGetHDF5Name_Private(dm, &topologydm_name));
1874: PetscCall(PetscViewerHDF5GetDMPlexStorageVersionReading(viewer, &version));
1875: if (DMPlexStorageVersionGE(version, 2, 0, 0)) {
1876: PetscCall(PetscSNPrintf(group, sizeof(group), "topologies/%s/labels", topologydm_name));
1877: } else {
1878: PetscCall(PetscStrncpy(group, "labels", sizeof(group)));
1879: }
1880: PetscCall(PetscViewerHDF5PushGroup(viewer, group));
1881: PetscCall(PetscViewerHDF5HasGroup(viewer, NULL, &hasGroup));
1882: if (hasGroup) {
1883: hid_t fileId, groupId;
1885: PetscCall(PetscViewerHDF5OpenGroup(viewer, NULL, &fileId, &groupId));
1886: /* Iterate over labels */
1887: PetscCallHDF5(H5Literate, (groupId, H5_INDEX_NAME, H5_ITER_NATIVE, &idx, ReadLabelHDF5_Static, ctx));
1888: PetscCallHDF5(H5Gclose, (groupId));
1889: }
1890: PetscCall(PetscViewerHDF5PopGroup(viewer));
1891: PetscCall(LoadLabelsCtxDestroy(&ctx));
1892: PetscFunctionReturn(PETSC_SUCCESS);
1893: }
1895: static PetscErrorCode DMPlexDistributionLoad_HDF5_Private(DM dm, PetscViewer viewer, PetscSF sf, PetscSF *distsf, DM *distdm)
1896: {
1897: MPI_Comm comm;
1898: PetscMPIInt size, rank;
1899: PetscInt dist_size;
1900: const char *distribution_name;
1901: PetscInt p, lsize;
1902: IS chartSizesIS, ownersIS, gpointsIS;
1903: const PetscInt *chartSize, *owners, *gpoints;
1904: PetscLayout layout;
1905: PetscBool has;
1907: PetscFunctionBegin;
1908: *distsf = NULL;
1909: *distdm = NULL;
1910: PetscCall(PetscObjectGetComm((PetscObject)dm, &comm));
1911: PetscCallMPI(MPI_Comm_size(comm, &size));
1912: PetscCallMPI(MPI_Comm_rank(comm, &rank));
1913: PetscCall(DMPlexDistributionGetName(dm, &distribution_name));
1914: if (!distribution_name) PetscFunctionReturn(PETSC_SUCCESS);
1915: PetscCall(PetscLogEventBegin(DMPLEX_DistributionLoad, viewer, 0, 0, 0));
1916: PetscCall(PetscViewerHDF5HasGroup(viewer, NULL, &has));
1917: if (!has) {
1918: char *full_group;
1920: PetscCall(PetscViewerHDF5GetGroup(viewer, NULL, &full_group));
1921: PetscCheck(has, PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Distribution %s cannot be found: HDF5 group %s not found in file", distribution_name, full_group);
1922: }
1923: PetscCall(PetscViewerHDF5ReadAttribute(viewer, NULL, "comm_size", PETSC_INT, NULL, (void *)&dist_size));
1924: PetscCheck(dist_size == (PetscInt)size, PETSC_COMM_SELF, PETSC_ERR_ARG_SIZ, "Mismatching comm sizes: comm size of this session (%d) != comm size used for %s (%" PetscInt_FMT ")", size, distribution_name, dist_size);
1925: PetscCall(ISCreate(comm, &chartSizesIS));
1926: PetscCall(PetscObjectSetName((PetscObject)chartSizesIS, "chart_sizes"));
1927: PetscCall(ISCreate(comm, &ownersIS));
1928: PetscCall(PetscObjectSetName((PetscObject)ownersIS, "owners"));
1929: PetscCall(ISCreate(comm, &gpointsIS));
1930: PetscCall(PetscObjectSetName((PetscObject)gpointsIS, "global_point_numbers"));
1931: PetscCall(PetscLayoutSetLocalSize(chartSizesIS->map, 1));
1932: PetscCall(ISLoad(chartSizesIS, viewer));
1933: PetscCall(ISGetIndices(chartSizesIS, &chartSize));
1934: PetscCall(PetscLayoutSetLocalSize(ownersIS->map, *chartSize));
1935: PetscCall(PetscLayoutSetLocalSize(gpointsIS->map, *chartSize));
1936: PetscCall(ISLoad(ownersIS, viewer));
1937: PetscCall(ISLoad(gpointsIS, viewer));
1938: PetscCall(ISGetIndices(ownersIS, &owners));
1939: PetscCall(ISGetIndices(gpointsIS, &gpoints));
1940: PetscCall(PetscSFCreate(comm, distsf));
1941: PetscCall(PetscSFSetFromOptions(*distsf));
1942: PetscCall(PetscLayoutCreate(comm, &layout));
1943: PetscCall(PetscSFGetGraph(sf, &lsize, NULL, NULL, NULL));
1944: PetscCall(PetscLayoutSetLocalSize(layout, lsize));
1945: PetscCall(PetscLayoutSetBlockSize(layout, 1));
1946: PetscCall(PetscLayoutSetUp(layout));
1947: PetscCall(PetscSFSetGraphLayout(*distsf, layout, *chartSize, NULL, PETSC_OWN_POINTER, gpoints));
1948: PetscCall(PetscLayoutDestroy(&layout));
1949: /* Migrate DM */
1950: {
1951: PetscInt pStart, pEnd;
1952: PetscSFNode *buffer0, *buffer1, *buffer2;
1954: PetscCall(DMPlexGetChart(dm, &pStart, &pEnd));
1955: PetscCall(PetscMalloc2(pEnd - pStart, &buffer0, lsize, &buffer1));
1956: PetscCall(PetscMalloc1(*chartSize, &buffer2));
1957: {
1958: PetscSF workPointSF;
1959: PetscInt workNroots, workNleaves;
1960: const PetscInt *workIlocal;
1961: const PetscSFNode *workIremote;
1963: for (p = pStart; p < pEnd; ++p) {
1964: buffer0[p - pStart].rank = rank;
1965: buffer0[p - pStart].index = p - pStart;
1966: }
1967: PetscCall(DMGetPointSF(dm, &workPointSF));
1968: PetscCall(PetscSFGetGraph(workPointSF, &workNroots, &workNleaves, &workIlocal, &workIremote));
1969: for (p = 0; p < workNleaves; ++p) {
1970: PetscInt workIlocalp = (workIlocal ? workIlocal[p] : p);
1972: buffer0[workIlocalp].rank = -1;
1973: }
1974: }
1975: for (p = 0; p < lsize; ++p) buffer1[p].rank = -1;
1976: for (p = 0; p < *chartSize; ++p) buffer2[p].rank = -1;
1977: PetscCall(PetscSFReduceBegin(sf, MPIU_SF_NODE, buffer0, buffer1, MPI_MAXLOC));
1978: PetscCall(PetscSFReduceEnd(sf, MPIU_SF_NODE, buffer0, buffer1, MPI_MAXLOC));
1979: PetscCall(PetscSFBcastBegin(*distsf, MPIU_SF_NODE, buffer1, buffer2, MPI_REPLACE));
1980: PetscCall(PetscSFBcastEnd(*distsf, MPIU_SF_NODE, buffer1, buffer2, MPI_REPLACE));
1981: if (PetscDefined(USE_DEBUG)) {
1982: for (p = 0; p < *chartSize; ++p) {
1983: PetscCheck(buffer2[p].rank >= 0, PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Found negative root rank %" PetscInt_FMT " at local point %" PetscInt_FMT " on rank %d when making migrationSF", buffer2[p].rank, p, rank);
1984: }
1985: }
1986: PetscCall(PetscFree2(buffer0, buffer1));
1987: PetscCall(DMCreate(comm, distdm));
1988: PetscCall(DMSetType(*distdm, DMPLEX));
1989: PetscCall(PetscObjectSetName((PetscObject)*distdm, ((PetscObject)dm)->name));
1990: PetscCall(DMPlexDistributionSetName(*distdm, distribution_name));
1991: {
1992: PetscSF migrationSF;
1994: PetscCall(PetscSFCreate(comm, &migrationSF));
1995: PetscCall(PetscSFSetFromOptions(migrationSF));
1996: PetscCall(PetscSFSetGraph(migrationSF, pEnd - pStart, *chartSize, NULL, PETSC_OWN_POINTER, buffer2, PETSC_OWN_POINTER));
1997: PetscCall(PetscSFSetUp(migrationSF));
1998: PetscCall(DMPlexMigrate(dm, migrationSF, *distdm));
1999: PetscCall(PetscSFDestroy(&migrationSF));
2000: }
2001: }
2002: /* Set pointSF */
2003: {
2004: PetscSF pointSF;
2005: PetscInt *ilocal, nleaves, q;
2006: PetscSFNode *iremote, *buffer0, *buffer1;
2008: PetscCall(PetscMalloc2(*chartSize, &buffer0, lsize, &buffer1));
2009: for (p = 0, nleaves = 0; p < *chartSize; ++p) {
2010: if (owners[p] == rank) {
2011: buffer0[p].rank = rank;
2012: } else {
2013: buffer0[p].rank = -1;
2014: nleaves++;
2015: }
2016: buffer0[p].index = p;
2017: }
2018: for (p = 0; p < lsize; ++p) buffer1[p].rank = -1;
2019: PetscCall(PetscSFReduceBegin(*distsf, MPIU_SF_NODE, buffer0, buffer1, MPI_MAXLOC));
2020: PetscCall(PetscSFReduceEnd(*distsf, MPIU_SF_NODE, buffer0, buffer1, MPI_MAXLOC));
2021: for (p = 0; p < *chartSize; ++p) buffer0[p].rank = -1;
2022: PetscCall(PetscSFBcastBegin(*distsf, MPIU_SF_NODE, buffer1, buffer0, MPI_REPLACE));
2023: PetscCall(PetscSFBcastEnd(*distsf, MPIU_SF_NODE, buffer1, buffer0, MPI_REPLACE));
2024: if (PetscDefined(USE_DEBUG)) {
2025: for (p = 0; p < *chartSize; ++p) PetscCheck(buffer0[p].rank >= 0, PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Found negative root rank %" PetscInt_FMT " at local point %" PetscInt_FMT " on rank %d when making pointSF", buffer0[p].rank, p, rank);
2026: }
2027: PetscCall(PetscMalloc1(nleaves, &ilocal));
2028: PetscCall(PetscMalloc1(nleaves, &iremote));
2029: for (p = 0, q = 0; p < *chartSize; ++p) {
2030: if (buffer0[p].rank != rank) {
2031: ilocal[q] = p;
2032: iremote[q].rank = buffer0[p].rank;
2033: iremote[q].index = buffer0[p].index;
2034: q++;
2035: }
2036: }
2037: PetscCheck(q == nleaves, PETSC_COMM_SELF, PETSC_ERR_PLIB, "Mismatching leaf sizes: %" PetscInt_FMT " != %" PetscInt_FMT, q, nleaves);
2038: PetscCall(PetscFree2(buffer0, buffer1));
2039: PetscCall(PetscSFCreate(comm, &pointSF));
2040: PetscCall(PetscSFSetFromOptions(pointSF));
2041: PetscCall(PetscSFSetGraph(pointSF, *chartSize, nleaves, ilocal, PETSC_OWN_POINTER, iremote, PETSC_OWN_POINTER));
2042: PetscCall(DMSetPointSF(*distdm, pointSF));
2043: {
2044: DM cdm;
2046: PetscCall(DMGetCoordinateDM(*distdm, &cdm));
2047: PetscCall(DMSetPointSF(cdm, pointSF));
2048: }
2049: PetscCall(PetscSFDestroy(&pointSF));
2050: }
2051: PetscCall(ISRestoreIndices(chartSizesIS, &chartSize));
2052: PetscCall(ISRestoreIndices(ownersIS, &owners));
2053: PetscCall(ISRestoreIndices(gpointsIS, &gpoints));
2054: PetscCall(ISDestroy(&chartSizesIS));
2055: PetscCall(ISDestroy(&ownersIS));
2056: PetscCall(ISDestroy(&gpointsIS));
2057: /* Record that overlap has been manually created. */
2058: /* This is to pass `DMPlexCheckPointSF()`, which checks that */
2059: /* pointSF does not contain cells in the leaves if overlap = 0. */
2060: PetscCall(DMPlexSetOverlap_Plex(*distdm, NULL, DMPLEX_OVERLAP_MANUAL));
2061: PetscCall(DMPlexDistributeSetDefault(*distdm, PETSC_FALSE));
2062: PetscCall(DMPlexReorderSetDefault(*distdm, DM_REORDER_DEFAULT_FALSE));
2063: PetscCall(PetscLogEventEnd(DMPLEX_DistributionLoad, viewer, 0, 0, 0));
2064: PetscFunctionReturn(PETSC_SUCCESS);
2065: }
2067: // Serial load of topology
2068: static PetscErrorCode DMPlexTopologyLoad_HDF5_Legacy_Private(DM dm, PetscViewer viewer, PetscSF *sf)
2069: {
2070: MPI_Comm comm;
2071: const char *pointsName, *coneSizesName, *conesName, *orientationsName;
2072: IS pointsIS, coneSizesIS, conesIS, orientationsIS;
2073: const PetscInt *points, *coneSizes, *cones, *orientations;
2074: PetscInt *cone, *ornt;
2075: PetscInt dim, N, Np, pEnd, p, q, maxConeSize = 0, c;
2076: PetscMPIInt size, rank;
2078: PetscFunctionBegin;
2079: pointsName = "order";
2080: coneSizesName = "cones";
2081: conesName = "cells";
2082: orientationsName = "orientation";
2083: PetscCall(PetscObjectGetComm((PetscObject)dm, &comm));
2084: PetscCallMPI(MPI_Comm_size(comm, &size));
2085: PetscCallMPI(MPI_Comm_rank(comm, &rank));
2086: PetscCall(ISCreate(comm, &pointsIS));
2087: PetscCall(PetscObjectSetName((PetscObject)pointsIS, pointsName));
2088: PetscCall(ISCreate(comm, &coneSizesIS));
2089: PetscCall(PetscObjectSetName((PetscObject)coneSizesIS, coneSizesName));
2090: PetscCall(ISCreate(comm, &conesIS));
2091: PetscCall(PetscObjectSetName((PetscObject)conesIS, conesName));
2092: PetscCall(ISCreate(comm, &orientationsIS));
2093: PetscCall(PetscObjectSetName((PetscObject)orientationsIS, orientationsName));
2094: PetscCall(PetscViewerHDF5ReadObjectAttribute(viewer, (PetscObject)conesIS, "cell_dim", PETSC_INT, NULL, &dim));
2095: PetscCall(DMSetDimension(dm, dim));
2096: {
2097: /* Force serial load */
2098: PetscCall(PetscInfo(dm, "Loading DM %s in serial\n", dm->hdr.name));
2099: PetscCall(PetscViewerHDF5ReadSizes(viewer, pointsName, NULL, &Np));
2100: PetscCall(PetscLayoutSetLocalSize(pointsIS->map, rank == 0 ? Np : 0));
2101: PetscCall(PetscLayoutSetSize(pointsIS->map, Np));
2102: pEnd = rank == 0 ? Np : 0;
2103: PetscCall(PetscViewerHDF5ReadSizes(viewer, coneSizesName, NULL, &Np));
2104: PetscCall(PetscLayoutSetLocalSize(coneSizesIS->map, rank == 0 ? Np : 0));
2105: PetscCall(PetscLayoutSetSize(coneSizesIS->map, Np));
2106: PetscCall(PetscViewerHDF5ReadSizes(viewer, conesName, NULL, &N));
2107: PetscCall(PetscLayoutSetLocalSize(conesIS->map, rank == 0 ? N : 0));
2108: PetscCall(PetscLayoutSetSize(conesIS->map, N));
2109: PetscCall(PetscViewerHDF5ReadSizes(viewer, orientationsName, NULL, &N));
2110: PetscCall(PetscLayoutSetLocalSize(orientationsIS->map, rank == 0 ? N : 0));
2111: PetscCall(PetscLayoutSetSize(orientationsIS->map, N));
2112: }
2113: PetscCall(ISLoad(pointsIS, viewer));
2114: PetscCall(ISLoad(coneSizesIS, viewer));
2115: PetscCall(ISLoad(conesIS, viewer));
2116: PetscCall(ISLoad(orientationsIS, viewer));
2117: /* Create Plex */
2118: PetscCall(DMPlexSetChart(dm, 0, pEnd));
2119: PetscCall(ISGetIndices(pointsIS, &points));
2120: PetscCall(ISGetIndices(coneSizesIS, &coneSizes));
2121: for (p = 0; p < pEnd; ++p) {
2122: PetscCall(DMPlexSetConeSize(dm, points[p], coneSizes[p]));
2123: maxConeSize = PetscMax(maxConeSize, coneSizes[p]);
2124: }
2125: PetscCall(DMSetUp(dm));
2126: PetscCall(ISGetIndices(conesIS, &cones));
2127: PetscCall(ISGetIndices(orientationsIS, &orientations));
2128: PetscCall(PetscMalloc2(maxConeSize, &cone, maxConeSize, &ornt));
2129: for (p = 0, q = 0; p < pEnd; ++p) {
2130: for (c = 0; c < coneSizes[p]; ++c, ++q) {
2131: cone[c] = cones[q];
2132: ornt[c] = orientations[q];
2133: }
2134: PetscCall(DMPlexSetCone(dm, points[p], cone));
2135: PetscCall(DMPlexSetConeOrientation(dm, points[p], ornt));
2136: }
2137: PetscCall(PetscFree2(cone, ornt));
2138: /* Create global section migration SF */
2139: if (sf) {
2140: PetscLayout layout;
2141: PetscInt *globalIndices;
2143: PetscCall(PetscMalloc1(pEnd, &globalIndices));
2144: /* plex point == globalPointNumber in this case */
2145: for (p = 0; p < pEnd; ++p) globalIndices[p] = p;
2146: PetscCall(PetscLayoutCreate(comm, &layout));
2147: PetscCall(PetscLayoutSetSize(layout, Np));
2148: PetscCall(PetscLayoutSetBlockSize(layout, 1));
2149: PetscCall(PetscLayoutSetUp(layout));
2150: PetscCall(PetscSFCreate(comm, sf));
2151: PetscCall(PetscSFSetFromOptions(*sf));
2152: PetscCall(PetscSFSetGraphLayout(*sf, layout, pEnd, NULL, PETSC_OWN_POINTER, globalIndices));
2153: PetscCall(PetscLayoutDestroy(&layout));
2154: PetscCall(PetscFree(globalIndices));
2155: }
2156: /* Clean-up */
2157: PetscCall(ISRestoreIndices(pointsIS, &points));
2158: PetscCall(ISRestoreIndices(coneSizesIS, &coneSizes));
2159: PetscCall(ISRestoreIndices(conesIS, &cones));
2160: PetscCall(ISRestoreIndices(orientationsIS, &orientations));
2161: PetscCall(ISDestroy(&pointsIS));
2162: PetscCall(ISDestroy(&coneSizesIS));
2163: PetscCall(ISDestroy(&conesIS));
2164: PetscCall(ISDestroy(&orientationsIS));
2165: /* Fill in the rest of the topology structure */
2166: PetscCall(DMPlexSymmetrize(dm));
2167: PetscCall(DMPlexStratify(dm));
2168: PetscFunctionReturn(PETSC_SUCCESS);
2169: }
2171: /* Representation of two DMPlex strata in 0-based global numbering */
2172: struct _n_PlexLayer {
2173: PetscInt d;
2174: IS conesIS, orientationsIS;
2175: PetscSection coneSizesSection;
2176: PetscLayout vertexLayout;
2177: PetscSF overlapSF, l2gSF; //TODO maybe confusing names (in DMPlex in general)
2178: PetscInt offset, conesOffset, leafOffset;
2179: };
2180: typedef struct _n_PlexLayer *PlexLayer;
2182: static PetscErrorCode PlexLayerDestroy(PlexLayer *layer)
2183: {
2184: PetscFunctionBegin;
2185: if (!*layer) PetscFunctionReturn(PETSC_SUCCESS);
2186: PetscCall(PetscSectionDestroy(&(*layer)->coneSizesSection));
2187: PetscCall(ISDestroy(&(*layer)->conesIS));
2188: PetscCall(ISDestroy(&(*layer)->orientationsIS));
2189: PetscCall(PetscSFDestroy(&(*layer)->overlapSF));
2190: PetscCall(PetscSFDestroy(&(*layer)->l2gSF));
2191: PetscCall(PetscLayoutDestroy(&(*layer)->vertexLayout));
2192: PetscCall(PetscFree(*layer));
2193: PetscFunctionReturn(PETSC_SUCCESS);
2194: }
2196: static PetscErrorCode PlexLayerCreate_Private(PlexLayer *layer)
2197: {
2198: PetscFunctionBegin;
2199: PetscCall(PetscNew(layer));
2200: (*layer)->d = -1;
2201: (*layer)->offset = -1;
2202: (*layer)->conesOffset = -1;
2203: (*layer)->leafOffset = -1;
2204: PetscFunctionReturn(PETSC_SUCCESS);
2205: }
2207: // Parallel load of a depth stratum
2208: static PetscErrorCode PlexLayerLoad_Private(PlexLayer layer, PetscViewer viewer, PetscInt d, PetscLayout pointsLayout)
2209: {
2210: char path[128];
2211: MPI_Comm comm;
2212: const char *coneSizesName, *conesName, *orientationsName;
2213: IS coneSizesIS, conesIS, orientationsIS;
2214: PetscSection coneSizesSection;
2215: PetscLayout vertexLayout = NULL;
2216: PetscInt s;
2218: PetscFunctionBegin;
2219: coneSizesName = "cone_sizes";
2220: conesName = "cones";
2221: orientationsName = "orientations";
2222: PetscCall(PetscObjectGetComm((PetscObject)viewer, &comm));
2224: /* query size of next lower depth stratum (next lower dimension) */
2225: if (d > 0) {
2226: PetscInt NVertices;
2228: PetscCall(PetscSNPrintf(path, sizeof(path), "%" PetscInt_FMT "/%s", d - 1, coneSizesName));
2229: PetscCall(PetscViewerHDF5ReadSizes(viewer, path, NULL, &NVertices));
2230: PetscCall(PetscLayoutCreate(comm, &vertexLayout));
2231: PetscCall(PetscLayoutSetSize(vertexLayout, NVertices));
2232: PetscCall(PetscLayoutSetUp(vertexLayout));
2233: }
2235: PetscCall(PetscSNPrintf(path, sizeof(path), "%" PetscInt_FMT, d));
2236: PetscCall(PetscViewerHDF5PushGroup(viewer, path));
2238: /* create coneSizesSection from stored IS coneSizes */
2239: {
2240: const PetscInt *coneSizes;
2242: PetscCall(ISCreate(comm, &coneSizesIS));
2243: PetscCall(PetscObjectSetName((PetscObject)coneSizesIS, coneSizesName));
2244: if (pointsLayout) PetscCall(ISSetLayout(coneSizesIS, pointsLayout));
2245: PetscCall(ISLoad(coneSizesIS, viewer));
2246: if (!pointsLayout) PetscCall(ISGetLayout(coneSizesIS, &pointsLayout));
2247: PetscCall(ISGetIndices(coneSizesIS, &coneSizes));
2248: PetscCall(PetscSectionCreate(comm, &coneSizesSection));
2249: //TODO different start ?
2250: PetscCall(PetscSectionSetChart(coneSizesSection, 0, pointsLayout->n));
2251: for (s = 0; s < pointsLayout->n; ++s) PetscCall(PetscSectionSetDof(coneSizesSection, s, coneSizes[s]));
2252: PetscCall(PetscSectionSetUp(coneSizesSection));
2253: PetscCall(ISRestoreIndices(coneSizesIS, &coneSizes));
2254: {
2255: PetscLayout tmp = NULL;
2257: /* We need to keep the layout until the end of function */
2258: PetscCall(PetscLayoutReference((PetscLayout)pointsLayout, &tmp));
2259: }
2260: PetscCall(ISDestroy(&coneSizesIS));
2261: }
2263: /* use value layout of coneSizesSection as layout of cones and orientations */
2264: {
2265: PetscLayout conesLayout;
2267: PetscCall(PetscSectionGetValueLayout(comm, coneSizesSection, &conesLayout));
2268: PetscCall(ISCreate(comm, &conesIS));
2269: PetscCall(ISCreate(comm, &orientationsIS));
2270: PetscCall(PetscObjectSetName((PetscObject)conesIS, conesName));
2271: PetscCall(PetscObjectSetName((PetscObject)orientationsIS, orientationsName));
2272: PetscCall(PetscLayoutDuplicate(conesLayout, &conesIS->map));
2273: PetscCall(PetscLayoutDuplicate(conesLayout, &orientationsIS->map));
2274: PetscCall(ISLoad(conesIS, viewer));
2275: PetscCall(ISLoad(orientationsIS, viewer));
2276: PetscCall(PetscLayoutDestroy(&conesLayout));
2277: }
2279: /* check assertion that layout of points is the same as point layout of coneSizesSection */
2280: {
2281: PetscLayout pointsLayout0;
2282: PetscBool flg;
2284: PetscCall(PetscSectionGetPointLayout(comm, coneSizesSection, &pointsLayout0));
2285: PetscCall(PetscLayoutCompare(pointsLayout, pointsLayout0, &flg));
2286: PetscCheck(flg, comm, PETSC_ERR_PLIB, "points layout != coneSizesSection point layout");
2287: PetscCall(PetscLayoutDestroy(&pointsLayout0));
2288: }
2289: PetscCall(PetscViewerHDF5PopGroup(viewer));
2290: PetscCall(PetscLayoutDestroy(&pointsLayout));
2292: layer->d = d;
2293: layer->conesIS = conesIS;
2294: layer->coneSizesSection = coneSizesSection;
2295: layer->orientationsIS = orientationsIS;
2296: layer->vertexLayout = vertexLayout;
2297: PetscFunctionReturn(PETSC_SUCCESS);
2298: }
2300: static PetscErrorCode PlexLayerDistribute_Private(PlexLayer layer, PetscSF cellLocalToGlobalSF)
2301: {
2302: IS newConesIS, newOrientationsIS;
2303: PetscSection newConeSizesSection;
2304: MPI_Comm comm;
2306: PetscFunctionBegin;
2307: PetscCall(PetscObjectGetComm((PetscObject)cellLocalToGlobalSF, &comm));
2308: PetscCall(PetscSectionCreate(comm, &newConeSizesSection));
2309: //TODO rename to something like ISDistribute() with optional PetscSection argument
2310: PetscCall(DMPlexDistributeFieldIS(NULL, cellLocalToGlobalSF, layer->coneSizesSection, layer->conesIS, newConeSizesSection, &newConesIS));
2311: PetscCall(DMPlexDistributeFieldIS(NULL, cellLocalToGlobalSF, layer->coneSizesSection, layer->orientationsIS, newConeSizesSection, &newOrientationsIS));
2313: PetscCall(PetscObjectSetName((PetscObject)newConeSizesSection, ((PetscObject)layer->coneSizesSection)->name));
2314: PetscCall(PetscObjectSetName((PetscObject)newConesIS, ((PetscObject)layer->conesIS)->name));
2315: PetscCall(PetscObjectSetName((PetscObject)newOrientationsIS, ((PetscObject)layer->orientationsIS)->name));
2316: PetscCall(PetscSectionDestroy(&layer->coneSizesSection));
2317: PetscCall(ISDestroy(&layer->conesIS));
2318: PetscCall(ISDestroy(&layer->orientationsIS));
2319: layer->coneSizesSection = newConeSizesSection;
2320: layer->conesIS = newConesIS;
2321: layer->orientationsIS = newOrientationsIS;
2322: PetscFunctionReturn(PETSC_SUCCESS);
2323: }
2325: //TODO share code with DMPlexBuildFromCellListParallel()
2326: #include <petsc/private/hashseti.h>
2327: static PetscErrorCode PlexLayerCreateSFs_Private(PlexLayer layer, PetscSF *vertexOverlapSF, PetscSF *sfXC)
2328: {
2329: PetscLayout vertexLayout = layer->vertexLayout;
2330: PetscSection coneSection = layer->coneSizesSection;
2331: IS cellVertexData = layer->conesIS;
2332: IS coneOrientations = layer->orientationsIS;
2333: PetscSF vl2gSF, vOverlapSF;
2334: PetscInt *verticesAdj;
2335: PetscInt i, n, numVerticesAdj;
2336: const PetscInt *cvd, *co = NULL;
2337: MPI_Comm comm;
2339: PetscFunctionBegin;
2340: PetscCall(PetscObjectGetComm((PetscObject)coneSection, &comm));
2341: PetscCall(PetscSectionGetStorageSize(coneSection, &n));
2342: {
2343: PetscInt n0;
2345: PetscCall(ISGetLocalSize(cellVertexData, &n0));
2346: PetscCheck(n == n0, PETSC_COMM_SELF, PETSC_ERR_ARG_SIZ, "Local size of IS cellVertexData = %" PetscInt_FMT " != %" PetscInt_FMT " = storage size of PetscSection coneSection", n0, n);
2347: PetscCall(ISGetIndices(cellVertexData, &cvd));
2348: }
2349: if (coneOrientations) {
2350: PetscInt n0;
2352: PetscCall(ISGetLocalSize(coneOrientations, &n0));
2353: PetscCheck(n == n0, PETSC_COMM_SELF, PETSC_ERR_ARG_SIZ, "Local size of IS coneOrientations = %" PetscInt_FMT " != %" PetscInt_FMT " = storage size of PetscSection coneSection", n0, n);
2354: PetscCall(ISGetIndices(coneOrientations, &co));
2355: }
2356: /* Get/check global number of vertices */
2357: {
2358: PetscInt NVerticesInCells = PETSC_INT_MIN;
2360: /* NVerticesInCells = max(cellVertexData) + 1 */
2361: for (i = 0; i < n; i++)
2362: if (cvd[i] > NVerticesInCells) NVerticesInCells = cvd[i];
2363: ++NVerticesInCells;
2364: PetscCallMPI(MPIU_Allreduce(MPI_IN_PLACE, &NVerticesInCells, 1, MPIU_INT, MPI_MAX, comm));
2366: if (vertexLayout->n == PETSC_DECIDE && vertexLayout->N == PETSC_DECIDE) vertexLayout->N = NVerticesInCells;
2367: else
2368: PetscCheck(vertexLayout->N == PETSC_DECIDE || vertexLayout->N >= NVerticesInCells, comm, PETSC_ERR_ARG_SIZ, "Specified global number of vertices %" PetscInt_FMT " must be greater than or equal to the number of unique vertices in the cell-vertex dataset %" PetscInt_FMT,
2369: vertexLayout->N, NVerticesInCells);
2370: PetscCall(PetscLayoutSetUp(vertexLayout));
2371: }
2372: /* Find locally unique vertices in cellVertexData */
2373: {
2374: PetscHSetI vhash;
2375: PetscInt off = 0;
2377: PetscCall(PetscHSetICreate(&vhash));
2378: for (i = 0; i < n; ++i) PetscCall(PetscHSetIAdd(vhash, cvd[i]));
2379: PetscCall(PetscHSetIGetSize(vhash, &numVerticesAdj));
2380: PetscCall(PetscMalloc1(numVerticesAdj, &verticesAdj));
2381: PetscCall(PetscHSetIGetElems(vhash, &off, verticesAdj));
2382: PetscAssert(off == numVerticesAdj, PETSC_COMM_SELF, PETSC_ERR_PLIB, "Assertion failed: off == numVerticesAdj (%" PetscInt_FMT " != %" PetscInt_FMT ")", off, numVerticesAdj);
2383: PetscCall(PetscHSetIDestroy(&vhash));
2384: }
2385: /* We must sort vertices to preserve numbering */
2386: PetscCall(PetscSortInt(numVerticesAdj, verticesAdj));
2387: /* Connect locally unique vertices with star forest */
2388: PetscCall(PetscSFCreateByMatchingIndices(vertexLayout, numVerticesAdj, verticesAdj, NULL, 0, numVerticesAdj, verticesAdj, NULL, 0, &vl2gSF, &vOverlapSF));
2389: PetscCall(PetscObjectSetName((PetscObject)vOverlapSF, "overlapSF"));
2390: PetscCall(PetscObjectSetName((PetscObject)vl2gSF, "localToGlobalSF"));
2392: PetscCall(PetscFree(verticesAdj));
2393: *vertexOverlapSF = vOverlapSF;
2394: *sfXC = vl2gSF;
2395: PetscFunctionReturn(PETSC_SUCCESS);
2396: }
2398: static PetscErrorCode PlexLayerCreateCellSFs_Private(PlexLayer layer, PetscSF *cellOverlapSF, PetscSF *cellLocalToGlobalSF)
2399: {
2400: PetscSection coneSection = layer->coneSizesSection;
2401: PetscInt nCells;
2402: MPI_Comm comm;
2404: PetscFunctionBegin;
2405: PetscCall(PetscObjectGetComm((PetscObject)coneSection, &comm));
2406: {
2407: PetscInt cStart;
2409: PetscCall(PetscSectionGetChart(coneSection, &cStart, &nCells));
2410: PetscCheck(cStart == 0, comm, PETSC_ERR_ARG_OUTOFRANGE, "coneSection must start at 0");
2411: }
2412: /* Create overlapSF as empty SF with the right number of roots */
2413: PetscCall(PetscSFCreate(comm, cellOverlapSF));
2414: PetscCall(PetscSFSetGraph(*cellOverlapSF, nCells, 0, NULL, PETSC_USE_POINTER, NULL, PETSC_USE_POINTER));
2415: PetscCall(PetscSFSetUp(*cellOverlapSF));
2416: /* Create localToGlobalSF as identity mapping */
2417: {
2418: PetscLayout map;
2420: PetscCall(PetscLayoutCreateFromSizes(comm, nCells, PETSC_DECIDE, 1, &map));
2421: PetscCall(PetscSFCreateFromLayouts(map, map, cellLocalToGlobalSF));
2422: PetscCall(PetscSFSetUp(*cellLocalToGlobalSF));
2423: PetscCall(PetscLayoutDestroy(&map));
2424: }
2425: PetscFunctionReturn(PETSC_SUCCESS);
2426: }
2428: static PetscErrorCode DMPlexTopologyBuildFromLayers_Private(DM dm, PetscInt depth, PlexLayer *layers, IS strataPermutation)
2429: {
2430: const PetscInt *permArr;
2431: PetscInt d, nPoints;
2432: MPI_Comm comm;
2434: PetscFunctionBegin;
2435: PetscCall(PetscObjectGetComm((PetscObject)dm, &comm));
2436: PetscCall(ISGetIndices(strataPermutation, &permArr));
2438: /* Count points, strata offsets and cones offsets (taking strataPermutation into account) */
2439: {
2440: PetscInt stratumOffset = 0;
2441: PetscInt conesOffset = 0;
2443: for (d = 0; d <= depth; d++) {
2444: const PetscInt e = permArr[d];
2445: const PlexLayer l = layers[e];
2446: PetscInt lo, n, size;
2448: PetscCall(PetscSectionGetChart(l->coneSizesSection, &lo, &n));
2449: PetscCall(PetscSectionGetStorageSize(l->coneSizesSection, &size));
2450: PetscCheck(lo == 0, comm, PETSC_ERR_PLIB, "starting point should be 0 in coneSizesSection %" PetscInt_FMT, d);
2451: l->offset = stratumOffset;
2452: l->conesOffset = conesOffset;
2453: stratumOffset += n;
2454: conesOffset += size;
2455: }
2456: nPoints = stratumOffset;
2457: }
2459: /* Set interval for all plex points */
2460: //TODO we should store starting point of plex
2461: PetscCall(DMPlexSetChart(dm, 0, nPoints));
2463: /* Set up plex coneSection from layer coneSections */
2464: {
2465: PetscSection coneSection;
2467: PetscCall(DMPlexGetConeSection(dm, &coneSection));
2468: for (d = 0; d <= depth; d++) {
2469: const PlexLayer l = layers[d];
2470: PetscInt n, q;
2472: PetscCall(PetscSectionGetChart(l->coneSizesSection, NULL, &n));
2473: for (q = 0; q < n; q++) {
2474: const PetscInt p = l->offset + q;
2475: PetscInt coneSize;
2477: PetscCall(PetscSectionGetDof(l->coneSizesSection, q, &coneSize));
2478: PetscCall(PetscSectionSetDof(coneSection, p, coneSize));
2479: }
2480: }
2481: }
2482: //TODO this is terrible, DMSetUp_Plex() should be DMPlexSetUpSections() or so
2483: PetscCall(DMSetUp(dm));
2485: /* Renumber cones points from layer-global numbering to plex-local numbering */
2486: {
2487: PetscInt *cones, *ornts;
2489: PetscCall(DMPlexGetCones(dm, &cones));
2490: PetscCall(DMPlexGetConeOrientations(dm, &ornts));
2491: for (d = 1; d <= depth; d++) {
2492: const PlexLayer l = layers[d];
2493: PetscInt i, lConesSize;
2494: PetscInt *lCones;
2495: const PetscInt *lOrnts;
2496: PetscInt *pCones = &cones[l->conesOffset];
2497: PetscInt *pOrnts = &ornts[l->conesOffset];
2499: PetscCall(PetscSectionGetStorageSize(l->coneSizesSection, &lConesSize));
2500: /* Get cones in local plex numbering */
2501: {
2502: ISLocalToGlobalMapping l2g;
2503: PetscLayout vertexLayout = l->vertexLayout;
2504: PetscSF vertexSF = layers[d - 1]->l2gSF; /* vertices of this layer are cells of previous layer */
2505: const PetscInt *gCones;
2506: PetscInt lConesSize0;
2508: PetscCall(ISGetLocalSize(l->conesIS, &lConesSize0));
2509: PetscCheck(lConesSize0 == lConesSize, comm, PETSC_ERR_PLIB, "layer %" PetscInt_FMT " size(conesIS) = %" PetscInt_FMT " != %" PetscInt_FMT " = storageSize(coneSizesSection)", d, lConesSize0, lConesSize);
2510: PetscCall(ISGetLocalSize(l->orientationsIS, &lConesSize0));
2511: PetscCheck(lConesSize0 == lConesSize, comm, PETSC_ERR_PLIB, "layer %" PetscInt_FMT " size(orientationsIS) = %" PetscInt_FMT " != %" PetscInt_FMT " = storageSize(coneSizesSection)", d, lConesSize0, lConesSize);
2513: PetscCall(PetscMalloc1(lConesSize, &lCones));
2514: PetscCall(ISGetIndices(l->conesIS, &gCones));
2515: PetscCall(ISLocalToGlobalMappingCreateSF(vertexSF, vertexLayout->rstart, &l2g));
2516: PetscCall(ISGlobalToLocalMappingApply(l2g, IS_GTOLM_MASK, lConesSize, gCones, &lConesSize0, lCones));
2517: PetscCheck(lConesSize0 == lConesSize, comm, PETSC_ERR_PLIB, "global to local does not cover all indices (%" PetscInt_FMT " of %" PetscInt_FMT ")", lConesSize0, lConesSize);
2518: PetscCall(ISLocalToGlobalMappingDestroy(&l2g));
2519: PetscCall(ISRestoreIndices(l->conesIS, &gCones));
2520: }
2521: PetscCall(ISGetIndices(l->orientationsIS, &lOrnts));
2522: /* Set cones, need to add stratum offset */
2523: for (i = 0; i < lConesSize; i++) {
2524: pCones[i] = lCones[i] + layers[d - 1]->offset; /* cone points of current layer are points of previous layer */
2525: pOrnts[i] = lOrnts[i];
2526: }
2527: PetscCall(PetscFree(lCones));
2528: PetscCall(ISRestoreIndices(l->orientationsIS, &lOrnts));
2529: }
2530: }
2531: PetscCall(DMPlexSymmetrize(dm));
2532: PetscCall(DMPlexStratify(dm));
2533: PetscCall(ISRestoreIndices(strataPermutation, &permArr));
2534: PetscFunctionReturn(PETSC_SUCCESS);
2535: }
2537: static PetscErrorCode PlexLayerConcatenateSFs_Private(MPI_Comm comm, PetscInt depth, PlexLayer layers[], IS strataPermutation, PetscSF *overlapSF, PetscSF *l2gSF)
2538: {
2539: PetscInt d;
2540: PetscSF *osfs, *lsfs;
2541: PetscInt *leafOffsets;
2542: const PetscInt *permArr;
2544: PetscFunctionBegin;
2545: PetscCall(ISGetIndices(strataPermutation, &permArr));
2546: PetscCall(PetscCalloc3(depth + 1, &osfs, depth + 1, &lsfs, depth + 1, &leafOffsets));
2547: for (d = 0; d <= depth; d++) {
2548: const PetscInt e = permArr[d];
2550: PetscAssert(e == layers[e]->d, PETSC_COMM_SELF, PETSC_ERR_PLIB, "assertion: e == layers[e]->d");
2551: osfs[d] = layers[e]->overlapSF;
2552: lsfs[d] = layers[e]->l2gSF;
2553: leafOffsets[d] = layers[e]->offset;
2554: }
2555: PetscCall(PetscSFConcatenate(comm, depth + 1, osfs, PETSCSF_CONCATENATE_ROOTMODE_LOCAL, leafOffsets, overlapSF));
2556: PetscCall(PetscSFConcatenate(comm, depth + 1, lsfs, PETSCSF_CONCATENATE_ROOTMODE_GLOBAL, leafOffsets, l2gSF));
2557: PetscCall(PetscFree3(osfs, lsfs, leafOffsets));
2558: PetscCall(ISRestoreIndices(strataPermutation, &permArr));
2559: PetscFunctionReturn(PETSC_SUCCESS);
2560: }
2562: // Parallel load of topology
2563: static PetscErrorCode DMPlexTopologyLoad_HDF5_Private(DM dm, PetscViewer viewer, PetscSF *sfXC)
2564: {
2565: PlexLayer *layers;
2566: IS strataPermutation;
2567: PetscLayout pointsLayout;
2568: PetscInt depth;
2569: PetscInt d;
2570: MPI_Comm comm;
2572: PetscFunctionBegin;
2573: {
2574: PetscInt dim;
2576: PetscCall(PetscViewerHDF5ReadAttribute(viewer, NULL, "depth", PETSC_INT, NULL, &depth));
2577: PetscCall(PetscViewerHDF5ReadAttribute(viewer, NULL, "cell_dim", PETSC_INT, NULL, &dim));
2578: PetscCall(DMSetDimension(dm, dim));
2579: }
2580: PetscCall(PetscObjectGetComm((PetscObject)dm, &comm));
2582: PetscCall(PetscInfo(dm, "Loading DM %s in parallel\n", dm->hdr.name));
2583: {
2584: IS spOnComm;
2586: PetscCall(ISCreate(comm, &spOnComm));
2587: PetscCall(PetscObjectSetName((PetscObject)spOnComm, "permutation"));
2588: PetscCall(ISLoad(spOnComm, viewer));
2589: /* have the same serial IS on every rank */
2590: PetscCall(ISAllGather(spOnComm, &strataPermutation));
2591: PetscCall(PetscObjectSetName((PetscObject)strataPermutation, ((PetscObject)spOnComm)->name));
2592: PetscCall(ISDestroy(&spOnComm));
2593: }
2595: /* Create layers, load raw data for each layer */
2596: PetscCall(PetscViewerHDF5PushGroup(viewer, "strata"));
2597: PetscCall(PetscMalloc1(depth + 1, &layers));
2598: for (d = depth, pointsLayout = NULL; d >= 0; pointsLayout = layers[d]->vertexLayout, d--) {
2599: PetscCall(PlexLayerCreate_Private(&layers[d]));
2600: PetscCall(PlexLayerLoad_Private(layers[d], viewer, d, pointsLayout));
2601: }
2602: PetscCall(PetscViewerHDF5PopGroup(viewer)); /* strata */
2604: for (d = depth; d >= 0; d--) {
2605: /* Redistribute cells and vertices for each applicable layer */
2606: if (d < depth) PetscCall(PlexLayerDistribute_Private(layers[d], layers[d]->l2gSF));
2607: /* Create vertex overlap SF and vertex localToGlobal SF for each applicable layer */
2608: if (d > 0) PetscCall(PlexLayerCreateSFs_Private(layers[d], &layers[d - 1]->overlapSF, &layers[d - 1]->l2gSF));
2609: }
2610: /* Build trivial SFs for the cell layer as well */
2611: PetscCall(PlexLayerCreateCellSFs_Private(layers[depth], &layers[depth]->overlapSF, &layers[depth]->l2gSF));
2613: /* Build DMPlex topology from the layers */
2614: PetscCall(DMPlexTopologyBuildFromLayers_Private(dm, depth, layers, strataPermutation));
2616: /* Build overall point SF alias overlap SF */
2617: {
2618: PetscSF overlapSF;
2620: PetscCall(PlexLayerConcatenateSFs_Private(comm, depth, layers, strataPermutation, &overlapSF, sfXC));
2621: PetscCall(DMSetPointSF(dm, overlapSF));
2622: PetscCall(PetscSFDestroy(&overlapSF));
2623: }
2625: for (d = depth; d >= 0; d--) PetscCall(PlexLayerDestroy(&layers[d]));
2626: PetscCall(PetscFree(layers));
2627: PetscCall(ISDestroy(&strataPermutation));
2628: PetscFunctionReturn(PETSC_SUCCESS);
2629: }
2631: PetscErrorCode DMPlexTopologyLoad_HDF5_Internal(DM dm, PetscViewer viewer, PetscSF *sfXC)
2632: {
2633: DMPlexStorageVersion version;
2634: const char *topologydm_name;
2635: char group[PETSC_MAX_PATH_LEN];
2636: PetscSF sfwork = NULL;
2638: PetscFunctionBegin;
2639: PetscCall(DMPlexGetHDF5Name_Private(dm, &topologydm_name));
2640: PetscCall(PetscViewerHDF5GetDMPlexStorageVersionReading(viewer, &version));
2641: if (DMPlexStorageVersionGE(version, 2, 0, 0)) {
2642: PetscCall(PetscSNPrintf(group, sizeof(group), "topologies/%s", topologydm_name));
2643: } else {
2644: PetscCall(PetscStrncpy(group, "/", sizeof(group)));
2645: }
2646: PetscCall(PetscViewerHDF5PushGroup(viewer, group));
2648: PetscCall(PetscViewerHDF5PushGroup(viewer, "topology"));
2649: if (version->major < 3) {
2650: PetscCall(DMPlexTopologyLoad_HDF5_Legacy_Private(dm, viewer, &sfwork));
2651: } else {
2652: /* since DMPlexStorageVersion 3.0.0 */
2653: PetscCall(DMPlexTopologyLoad_HDF5_Private(dm, viewer, &sfwork));
2654: }
2655: PetscCall(PetscViewerHDF5PopGroup(viewer)); /* "topology" */
2657: if (DMPlexStorageVersionGE(version, 2, 0, 0)) {
2658: DM distdm;
2659: PetscSF distsf;
2660: const char *distribution_name;
2661: PetscBool exists;
2663: PetscCall(DMPlexDistributionGetName(dm, &distribution_name));
2664: /* this group is guaranteed to be present since DMPlexStorageVersion 2.1.0 */
2665: PetscCall(PetscViewerHDF5PushGroup(viewer, "distributions"));
2666: PetscCall(PetscViewerHDF5HasGroup(viewer, NULL, &exists));
2667: if (exists) {
2668: PetscCall(PetscViewerHDF5PushGroup(viewer, distribution_name));
2669: PetscCall(DMPlexDistributionLoad_HDF5_Private(dm, viewer, sfwork, &distsf, &distdm));
2670: if (distdm) {
2671: PetscCall(DMPlexReplace_Internal(dm, &distdm));
2672: PetscCall(PetscSFDestroy(&sfwork));
2673: sfwork = distsf;
2674: }
2675: PetscCall(PetscViewerHDF5PopGroup(viewer)); /* distribution_name */
2676: }
2677: PetscCall(PetscViewerHDF5PopGroup(viewer)); /* "distributions" */
2678: }
2679: if (sfXC) {
2680: *sfXC = sfwork;
2681: } else {
2682: PetscCall(PetscSFDestroy(&sfwork));
2683: }
2685: PetscCall(PetscViewerHDF5PopGroup(viewer));
2686: PetscFunctionReturn(PETSC_SUCCESS);
2687: }
2689: /* If the file is old, it not only has different path to the coordinates, but */
2690: /* does not contain coordinateDMs, so must fall back to the old implementation. */
2691: static PetscErrorCode DMPlexCoordinatesLoad_HDF5_Legacy_Private(DM dm, PetscViewer viewer)
2692: {
2693: PetscSection coordSection;
2694: Vec coordinates;
2695: PetscReal lengthScale;
2696: PetscInt spatialDim, N, numVertices, vStart, vEnd, v;
2697: PetscMPIInt rank;
2699: PetscFunctionBegin;
2700: PetscCallMPI(MPI_Comm_rank(PetscObjectComm((PetscObject)dm), &rank));
2701: /* Read geometry */
2702: PetscCall(PetscViewerHDF5PushGroup(viewer, "/geometry"));
2703: PetscCall(VecCreate(PetscObjectComm((PetscObject)dm), &coordinates));
2704: PetscCall(PetscObjectSetName((PetscObject)coordinates, "vertices"));
2705: {
2706: /* Force serial load */
2707: PetscCall(PetscViewerHDF5ReadSizes(viewer, "vertices", &spatialDim, &N));
2708: PetscCall(VecSetSizes(coordinates, rank == 0 ? N : 0, N));
2709: PetscCall(VecSetBlockSize(coordinates, spatialDim));
2710: }
2711: PetscCall(VecLoad(coordinates, viewer));
2712: PetscCall(PetscViewerHDF5PopGroup(viewer));
2713: PetscCall(DMPlexGetScale(dm, PETSC_UNIT_LENGTH, &lengthScale));
2714: PetscCall(VecScale(coordinates, 1.0 / lengthScale));
2715: PetscCall(VecGetLocalSize(coordinates, &numVertices));
2716: PetscCall(VecGetBlockSize(coordinates, &spatialDim));
2717: numVertices /= spatialDim;
2718: /* Create coordinates */
2719: PetscCall(DMPlexGetDepthStratum(dm, 0, &vStart, &vEnd));
2720: PetscCheck(numVertices == vEnd - vStart, PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Number of coordinates loaded %" PetscInt_FMT " does not match number of vertices %" PetscInt_FMT, numVertices, vEnd - vStart);
2721: PetscCall(DMGetCoordinateSection(dm, &coordSection));
2722: PetscCall(PetscSectionSetNumFields(coordSection, 1));
2723: PetscCall(PetscSectionSetFieldComponents(coordSection, 0, spatialDim));
2724: PetscCall(PetscSectionSetChart(coordSection, vStart, vEnd));
2725: for (v = vStart; v < vEnd; ++v) {
2726: PetscCall(PetscSectionSetDof(coordSection, v, spatialDim));
2727: PetscCall(PetscSectionSetFieldDof(coordSection, v, 0, spatialDim));
2728: }
2729: PetscCall(PetscSectionSetUp(coordSection));
2730: PetscCall(DMSetCoordinates(dm, coordinates));
2731: PetscCall(VecDestroy(&coordinates));
2732: PetscFunctionReturn(PETSC_SUCCESS);
2733: }
2735: PetscErrorCode DMPlexCoordinatesLoad_HDF5_Internal(DM dm, PetscViewer viewer, PetscSF sfXC)
2736: {
2737: DMPlexStorageVersion version;
2738: DM cdm;
2739: Vec coords;
2740: PetscInt blockSize;
2741: PetscReal lengthScale;
2742: PetscSF lsf;
2743: const char *topologydm_name;
2744: char *coordinatedm_name, *coordinates_name;
2746: PetscFunctionBegin;
2747: PetscCall(PetscViewerHDF5GetDMPlexStorageVersionReading(viewer, &version));
2748: if (!DMPlexStorageVersionGE(version, 2, 0, 0)) {
2749: PetscCall(DMPlexCoordinatesLoad_HDF5_Legacy_Private(dm, viewer));
2750: PetscFunctionReturn(PETSC_SUCCESS);
2751: }
2752: /* else: since DMPlexStorageVersion 2.0.0 */
2753: PetscCheck(sfXC, PetscObjectComm((PetscObject)dm), PETSC_ERR_ARG_NULL, "PetscSF must be given for parallel load");
2754: PetscCall(DMPlexGetHDF5Name_Private(dm, &topologydm_name));
2755: PetscCall(PetscViewerHDF5PushGroup(viewer, "topologies"));
2756: PetscCall(PetscViewerHDF5PushGroup(viewer, topologydm_name));
2757: PetscCall(PetscViewerHDF5ReadAttribute(viewer, NULL, "coordinateDMName", PETSC_STRING, NULL, &coordinatedm_name));
2758: PetscCall(PetscViewerHDF5ReadAttribute(viewer, NULL, "coordinatesName", PETSC_STRING, NULL, &coordinates_name));
2759: PetscCall(PetscViewerHDF5PopGroup(viewer));
2760: PetscCall(PetscViewerHDF5PopGroup(viewer));
2761: PetscCall(DMGetCoordinateDM(dm, &cdm));
2762: PetscCall(PetscObjectSetName((PetscObject)cdm, coordinatedm_name));
2763: PetscCall(PetscFree(coordinatedm_name));
2764: /* lsf: on-disk data -> in-memory local vector associated with cdm's local section */
2765: PetscCall(DMPlexSectionLoad(dm, viewer, cdm, sfXC, NULL, &lsf));
2766: PetscCall(DMCreateLocalVector(cdm, &coords));
2767: PetscCall(PetscObjectSetName((PetscObject)coords, coordinates_name));
2768: PetscCall(PetscFree(coordinates_name));
2769: PetscCall(PetscViewerPushFormat(viewer, PETSC_VIEWER_NATIVE));
2770: PetscCall(DMPlexLocalVectorLoad(dm, viewer, cdm, lsf, coords));
2771: PetscCall(PetscViewerPopFormat(viewer));
2772: PetscCall(DMPlexGetScale(dm, PETSC_UNIT_LENGTH, &lengthScale));
2773: PetscCall(VecScale(coords, 1.0 / lengthScale));
2774: PetscCall(DMSetCoordinatesLocal(dm, coords));
2775: PetscCall(VecGetBlockSize(coords, &blockSize));
2776: PetscCall(DMSetCoordinateDim(dm, blockSize));
2777: PetscCall(VecDestroy(&coords));
2778: PetscCall(PetscSFDestroy(&lsf));
2779: PetscFunctionReturn(PETSC_SUCCESS);
2780: }
2782: PetscErrorCode DMPlexLoad_HDF5_Internal(DM dm, PetscViewer viewer)
2783: {
2784: DMPlexStorageVersion version;
2786: PetscFunctionBegin;
2787: PetscCall(PetscViewerHDF5GetDMPlexStorageVersionReading(viewer, &version));
2788: PetscCall(PetscInfo(dm, "Loading DM %s storage version %d.%d.%d\n", dm->hdr.name, version->major, version->minor, version->subminor));
2789: if (!DMPlexStorageVersionGE(version, 2, 0, 0)) {
2790: PetscCall(DMPlexTopologyLoad_HDF5_Internal(dm, viewer, NULL));
2791: PetscCall(DMPlexLabelsLoad_HDF5_Internal(dm, viewer, NULL));
2792: PetscCall(DMPlexCoordinatesLoad_HDF5_Legacy_Private(dm, viewer));
2793: } else {
2794: PetscSF sfXC;
2796: /* since DMPlexStorageVersion 2.0.0 */
2797: PetscCall(DMPlexTopologyLoad_HDF5_Internal(dm, viewer, &sfXC));
2798: PetscCall(DMPlexLabelsLoad_HDF5_Internal(dm, viewer, sfXC));
2799: PetscCall(DMPlexCoordinatesLoad_HDF5_Internal(dm, viewer, sfXC));
2800: PetscCall(PetscSFDestroy(&sfXC));
2801: }
2802: PetscFunctionReturn(PETSC_SUCCESS);
2803: }
2805: static PetscErrorCode DMPlexSectionLoad_HDF5_Internal_CreateDataSF(PetscSection rootSection, PetscLayout layout, PetscInt globalOffsets[], PetscSection leafSection, PetscSF *sectionSF)
2806: {
2807: MPI_Comm comm;
2808: PetscInt pStart, pEnd, p, m;
2809: PetscInt *goffs, *ilocal;
2810: PetscBool rootIncludeConstraints, leafIncludeConstraints;
2812: PetscFunctionBegin;
2813: PetscCall(PetscObjectGetComm((PetscObject)leafSection, &comm));
2814: PetscCall(PetscSectionGetChart(leafSection, &pStart, &pEnd));
2815: PetscCall(PetscSectionGetIncludesConstraints(rootSection, &rootIncludeConstraints));
2816: PetscCall(PetscSectionGetIncludesConstraints(leafSection, &leafIncludeConstraints));
2817: if (rootIncludeConstraints && leafIncludeConstraints) PetscCall(PetscSectionGetStorageSize(leafSection, &m));
2818: else PetscCall(PetscSectionGetConstrainedStorageSize(leafSection, &m));
2819: PetscCall(PetscMalloc1(m, &ilocal));
2820: PetscCall(PetscMalloc1(m, &goffs));
2821: /* Currently, PetscSFDistributeSection() returns globalOffsets[] only */
2822: /* for the top-level section (not for each field), so one must have */
2823: /* rootSection->pointMajor == PETSC_TRUE. */
2824: PetscCheck(rootSection->pointMajor, PETSC_COMM_SELF, PETSC_ERR_SUP, "No support for field major ordering");
2825: /* Currently, we also assume that leafSection->pointMajor == PETSC_TRUE. */
2826: PetscCheck(leafSection->pointMajor, PETSC_COMM_SELF, PETSC_ERR_SUP, "No support for field major ordering");
2827: for (p = pStart, m = 0; p < pEnd; ++p) {
2828: PetscInt dof, cdof, i, j, off, goff;
2829: const PetscInt *cinds;
2831: PetscCall(PetscSectionGetDof(leafSection, p, &dof));
2832: if (dof < 0) continue;
2833: goff = globalOffsets[p - pStart];
2834: PetscCall(PetscSectionGetOffset(leafSection, p, &off));
2835: PetscCall(PetscSectionGetConstraintDof(leafSection, p, &cdof));
2836: PetscCall(PetscSectionGetConstraintIndices(leafSection, p, &cinds));
2837: for (i = 0, j = 0; i < dof; ++i) {
2838: PetscBool constrained = (PetscBool)(j < cdof && i == cinds[j]);
2840: if (!constrained || (leafIncludeConstraints && rootIncludeConstraints)) {
2841: ilocal[m] = off++;
2842: goffs[m++] = goff++;
2843: } else if (leafIncludeConstraints && !rootIncludeConstraints) ++off;
2844: else if (!leafIncludeConstraints && rootIncludeConstraints) ++goff;
2845: if (constrained) ++j;
2846: }
2847: }
2848: PetscCall(PetscSFCreate(comm, sectionSF));
2849: PetscCall(PetscSFSetFromOptions(*sectionSF));
2850: PetscCall(PetscSFSetGraphLayout(*sectionSF, layout, m, ilocal, PETSC_OWN_POINTER, goffs));
2851: PetscCall(PetscFree(goffs));
2852: PetscFunctionReturn(PETSC_SUCCESS);
2853: }
2855: PetscErrorCode DMPlexSectionLoad_HDF5_Internal(DM dm, PetscViewer viewer, DM sectiondm, PetscSF sfXB, PetscSF *gsf, PetscSF *lsf)
2856: {
2857: MPI_Comm comm;
2858: PetscMPIInt size, rank;
2859: const char *topologydm_name;
2860: const char *sectiondm_name;
2861: PetscSection sectionA, sectionB;
2862: PetscBool has;
2863: PetscInt nX, n, i;
2864: PetscSF sfAB;
2866: PetscFunctionBegin;
2867: PetscCall(PetscObjectGetComm((PetscObject)dm, &comm));
2868: PetscCallMPI(MPI_Comm_size(comm, &size));
2869: PetscCallMPI(MPI_Comm_rank(comm, &rank));
2870: PetscCall(DMPlexGetHDF5Name_Private(dm, &topologydm_name));
2871: PetscCall(PetscObjectGetName((PetscObject)sectiondm, §iondm_name));
2872: PetscCall(PetscViewerHDF5PushGroup(viewer, "topologies"));
2873: PetscCall(PetscViewerHDF5PushGroup(viewer, topologydm_name));
2874: PetscCall(PetscViewerHDF5PushGroup(viewer, "dms"));
2875: PetscCall(PetscViewerHDF5PushGroup(viewer, sectiondm_name));
2876: /* A: on-disk points */
2877: /* X: list of global point numbers, [0, NX) */
2878: /* B: plex points */
2879: /* Load raw section (sectionA) */
2880: PetscCall(PetscSectionCreate(comm, §ionA));
2881: PetscCall(PetscViewerHDF5HasGroup(viewer, "section", &has));
2882: if (has) PetscCall(PetscSectionLoad(sectionA, viewer));
2883: else {
2884: // TODO If section is missing, create the default affine section with dim dofs on each vertex. Use PetscSplitOwnership() to split vertices.
2885: // How do I know the total number of vertices?
2886: PetscInt dim, Nf = 1, Nv, nv = PETSC_DECIDE;
2888: PetscCall(DMGetDimension(dm, &dim));
2889: PetscCall(DMPlexGetDepthStratumGlobalSize(dm, 0, &Nv));
2890: PetscCall(PetscSectionSetNumFields(sectionA, Nf));
2891: PetscCall(PetscSectionSetFieldName(sectionA, 0, "Cartesian"));
2892: PetscCall(PetscSectionSetFieldComponents(sectionA, 0, dim));
2893: for (PetscInt c = 0; c < dim; ++c) {
2894: char axis = 'X' + (char)c;
2896: PetscCall(PetscSectionSetComponentName(sectionA, 0, c, &axis));
2897: }
2898: PetscCall(PetscSplitOwnership(comm, &nv, &Nv));
2899: PetscCall(PetscSectionSetChart(sectionA, 0, nv));
2900: for (PetscInt p = 0; p < nv; ++p) {
2901: PetscCall(PetscSectionSetDof(sectionA, p, dim));
2902: PetscCall(PetscSectionSetFieldDof(sectionA, p, 0, dim));
2903: }
2904: PetscCall(PetscSectionSetUp(sectionA));
2905: }
2906: PetscCall(PetscSectionGetChart(sectionA, NULL, &n));
2907: /* Create sfAB: A -> B */
2908: #if defined(PETSC_USE_DEBUG)
2909: {
2910: PetscInt N, N1;
2912: PetscCall(PetscViewerHDF5ReadSizes(viewer, "order", NULL, &N1));
2913: PetscCallMPI(MPIU_Allreduce(&n, &N, 1, MPIU_INT, MPI_SUM, comm));
2914: PetscCheck(N1 == N, comm, PETSC_ERR_ARG_SIZ, "Mismatching sizes: on-disk order array size (%" PetscInt_FMT ") != number of loaded section points (%" PetscInt_FMT ")", N1, N);
2915: }
2916: #endif
2917: {
2918: IS orderIS;
2919: const PetscInt *gpoints;
2920: PetscSF sfXA, sfAX;
2921: PetscLayout layout;
2922: PetscSFNode *owners, *buffer;
2923: PetscInt nleaves;
2924: PetscInt *ilocal;
2925: PetscSFNode *iremote;
2927: /* Create sfAX: A -> X */
2928: PetscCall(ISCreate(comm, &orderIS));
2929: PetscCall(PetscObjectSetName((PetscObject)orderIS, "order"));
2930: PetscCall(PetscLayoutSetLocalSize(orderIS->map, n));
2931: PetscCall(ISLoad(orderIS, viewer));
2932: PetscCall(PetscLayoutCreate(comm, &layout));
2933: PetscCall(PetscSFGetGraph(sfXB, &nX, NULL, NULL, NULL));
2934: PetscCall(PetscLayoutSetLocalSize(layout, nX));
2935: PetscCall(PetscLayoutSetBlockSize(layout, 1));
2936: PetscCall(PetscLayoutSetUp(layout));
2937: PetscCall(PetscSFCreate(comm, &sfXA));
2938: PetscCall(ISGetIndices(orderIS, &gpoints));
2939: PetscCall(PetscSFSetGraphLayout(sfXA, layout, n, NULL, PETSC_OWN_POINTER, gpoints));
2940: PetscCall(ISRestoreIndices(orderIS, &gpoints));
2941: PetscCall(ISDestroy(&orderIS));
2942: PetscCall(PetscLayoutDestroy(&layout));
2943: PetscCall(PetscMalloc1(n, &owners));
2944: PetscCall(PetscMalloc1(nX, &buffer));
2945: for (i = 0; i < n; ++i) {
2946: owners[i].rank = rank;
2947: owners[i].index = i;
2948: }
2949: for (i = 0; i < nX; ++i) {
2950: buffer[i].rank = -1;
2951: buffer[i].index = -1;
2952: }
2953: PetscCall(PetscSFReduceBegin(sfXA, MPIU_SF_NODE, owners, buffer, MPI_MAXLOC));
2954: PetscCall(PetscSFReduceEnd(sfXA, MPIU_SF_NODE, owners, buffer, MPI_MAXLOC));
2955: PetscCall(PetscSFDestroy(&sfXA));
2956: PetscCall(PetscFree(owners));
2957: for (i = 0, nleaves = 0; i < nX; ++i)
2958: if (buffer[i].rank >= 0) nleaves++;
2959: PetscCall(PetscMalloc1(nleaves, &ilocal));
2960: PetscCall(PetscMalloc1(nleaves, &iremote));
2961: for (i = 0, nleaves = 0; i < nX; ++i) {
2962: if (buffer[i].rank >= 0) {
2963: ilocal[nleaves] = i;
2964: iremote[nleaves].rank = buffer[i].rank;
2965: iremote[nleaves].index = buffer[i].index;
2966: nleaves++;
2967: }
2968: }
2969: PetscCall(PetscFree(buffer));
2970: PetscCall(PetscSFCreate(comm, &sfAX));
2971: PetscCall(PetscSFSetFromOptions(sfAX));
2972: PetscCall(PetscSFSetGraph(sfAX, n, nleaves, ilocal, PETSC_OWN_POINTER, iremote, PETSC_OWN_POINTER));
2973: PetscCall(PetscSFCompose(sfAX, sfXB, &sfAB));
2974: PetscCall(PetscSFDestroy(&sfAX));
2975: }
2976: PetscCall(PetscViewerHDF5PopGroup(viewer));
2977: PetscCall(PetscViewerHDF5PopGroup(viewer));
2978: PetscCall(PetscViewerHDF5PopGroup(viewer));
2979: PetscCall(PetscViewerHDF5PopGroup(viewer));
2980: /* Create plex section (sectionB) */
2981: PetscCall(DMGetLocalSection(sectiondm, §ionB));
2982: if (lsf || gsf) {
2983: PetscLayout layout;
2984: PetscInt M, m;
2985: PetscInt *offsetsA;
2986: PetscBool includesConstraintsA;
2988: PetscCall(PetscSFDistributeSection(sfAB, sectionA, &offsetsA, sectionB));
2989: PetscCall(PetscSectionGetIncludesConstraints(sectionA, &includesConstraintsA));
2990: if (includesConstraintsA) PetscCall(PetscSectionGetStorageSize(sectionA, &m));
2991: else PetscCall(PetscSectionGetConstrainedStorageSize(sectionA, &m));
2992: PetscCallMPI(MPIU_Allreduce(&m, &M, 1, MPIU_INT, MPI_SUM, comm));
2993: PetscCall(PetscLayoutCreate(comm, &layout));
2994: PetscCall(PetscLayoutSetSize(layout, M));
2995: PetscCall(PetscLayoutSetUp(layout));
2996: if (lsf) {
2997: PetscSF lsfABdata;
2999: PetscCall(DMPlexSectionLoad_HDF5_Internal_CreateDataSF(sectionA, layout, offsetsA, sectionB, &lsfABdata));
3000: *lsf = lsfABdata;
3001: }
3002: if (gsf) {
3003: PetscSection gsectionB, gsectionB1;
3004: PetscBool includesConstraintsB;
3005: PetscSF gsfABdata, pointsf;
3007: PetscCall(DMGetGlobalSection(sectiondm, &gsectionB1));
3008: PetscCall(PetscSectionGetIncludesConstraints(gsectionB1, &includesConstraintsB));
3009: PetscCall(DMGetPointSF(sectiondm, &pointsf));
3010: PetscCall(PetscSectionCreateGlobalSection(sectionB, pointsf, PETSC_TRUE, includesConstraintsB, PETSC_TRUE, &gsectionB));
3011: PetscCall(DMPlexSectionLoad_HDF5_Internal_CreateDataSF(sectionA, layout, offsetsA, gsectionB, &gsfABdata));
3012: PetscCall(PetscSectionDestroy(&gsectionB));
3013: *gsf = gsfABdata;
3014: }
3015: PetscCall(PetscLayoutDestroy(&layout));
3016: PetscCall(PetscFree(offsetsA));
3017: } else {
3018: PetscCall(PetscSFDistributeSection(sfAB, sectionA, NULL, sectionB));
3019: }
3020: PetscCall(PetscSFDestroy(&sfAB));
3021: PetscCall(PetscSectionDestroy(§ionA));
3022: PetscFunctionReturn(PETSC_SUCCESS);
3023: }
3025: PetscErrorCode DMPlexVecLoad_HDF5_Internal(DM dm, PetscViewer viewer, DM sectiondm, PetscSF sf, Vec vec)
3026: {
3027: MPI_Comm comm;
3028: const char *topologydm_name;
3029: const char *sectiondm_name;
3030: const char *vec_name;
3031: Vec vecA;
3032: PetscInt mA, m, bs;
3033: const PetscInt *ilocal;
3034: const PetscScalar *src;
3035: PetscScalar *dest;
3037: PetscFunctionBegin;
3038: PetscCall(PetscObjectGetComm((PetscObject)dm, &comm));
3039: PetscCall(DMPlexGetHDF5Name_Private(dm, &topologydm_name));
3040: PetscCall(PetscObjectGetName((PetscObject)sectiondm, §iondm_name));
3041: PetscCall(PetscObjectGetName((PetscObject)vec, &vec_name));
3042: PetscCall(PetscViewerHDF5PushGroup(viewer, "topologies"));
3043: PetscCall(PetscViewerHDF5PushGroup(viewer, topologydm_name));
3044: PetscCall(PetscViewerHDF5PushGroup(viewer, "dms"));
3045: PetscCall(PetscViewerHDF5PushGroup(viewer, sectiondm_name));
3046: PetscCall(PetscViewerHDF5PushGroup(viewer, "vecs"));
3047: PetscCall(PetscViewerHDF5PushGroup(viewer, vec_name));
3048: PetscCall(VecCreate(comm, &vecA));
3049: PetscCall(PetscObjectSetName((PetscObject)vecA, vec_name));
3050: PetscCall(PetscSFGetGraph(sf, &mA, &m, &ilocal, NULL));
3051: /* Check consistency */
3052: {
3053: PetscSF pointsf, pointsf1;
3054: PetscInt m1, i, j;
3056: PetscCall(DMGetPointSF(dm, &pointsf));
3057: PetscCall(DMGetPointSF(sectiondm, &pointsf1));
3058: PetscCheck(pointsf1 == pointsf, PETSC_COMM_SELF, PETSC_ERR_PLIB, "Mismatching point SFs for dm and sectiondm");
3059: #if defined(PETSC_USE_DEBUG)
3060: {
3061: PetscInt MA, MA1;
3063: PetscCallMPI(MPIU_Allreduce(&mA, &MA, 1, MPIU_INT, MPI_SUM, comm));
3064: PetscCall(PetscViewerHDF5ReadSizes(viewer, vec_name, NULL, &MA1));
3065: PetscCheck(MA1 == MA, PETSC_COMM_SELF, PETSC_ERR_PLIB, "Total SF root size (%" PetscInt_FMT ") != On-disk vector data size (%" PetscInt_FMT ")", MA, MA1);
3066: }
3067: #endif
3068: PetscCall(VecGetLocalSize(vec, &m1));
3069: PetscCheck(m1 >= m, PETSC_COMM_SELF, PETSC_ERR_PLIB, "Target vector size (%" PetscInt_FMT ") < SF leaf size (%" PetscInt_FMT ")", m1, m);
3070: for (i = 0; i < m; ++i) {
3071: j = ilocal ? ilocal[i] : i;
3072: PetscCheck(j >= 0 && j < m1, PETSC_COMM_SELF, PETSC_ERR_PLIB, "Leaf's %" PetscInt_FMT "-th index, %" PetscInt_FMT ", not in [%" PetscInt_FMT ", %" PetscInt_FMT ")", i, j, (PetscInt)0, m1);
3073: }
3074: }
3075: PetscCall(VecSetSizes(vecA, mA, PETSC_DECIDE));
3076: PetscCall(VecLoad(vecA, viewer));
3077: PetscCall(VecGetArrayRead(vecA, &src));
3078: PetscCall(VecGetArray(vec, &dest));
3079: PetscCall(PetscSFBcastBegin(sf, MPIU_SCALAR, src, dest, MPI_REPLACE));
3080: PetscCall(PetscSFBcastEnd(sf, MPIU_SCALAR, src, dest, MPI_REPLACE));
3081: PetscCall(VecRestoreArray(vec, &dest));
3082: PetscCall(VecRestoreArrayRead(vecA, &src));
3083: PetscCall(VecDestroy(&vecA));
3084: PetscCall(PetscViewerHDF5ReadAttribute(viewer, NULL, "blockSize", PETSC_INT, NULL, (void *)&bs));
3085: PetscCall(VecSetBlockSize(vec, bs));
3086: PetscCall(PetscViewerHDF5PopGroup(viewer));
3087: PetscCall(PetscViewerHDF5PopGroup(viewer));
3088: PetscCall(PetscViewerHDF5PopGroup(viewer));
3089: PetscCall(PetscViewerHDF5PopGroup(viewer));
3090: PetscCall(PetscViewerHDF5PopGroup(viewer));
3091: PetscCall(PetscViewerHDF5PopGroup(viewer));
3092: PetscFunctionReturn(PETSC_SUCCESS);
3093: }