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: static PetscErrorCode PetscViewerParseVersion_Private(PetscViewer, const char[], DMPlexStorageVersion *);
8: static PetscErrorCode PetscViewerCheckVersion_Private(PetscViewer, DMPlexStorageVersion);
9: static PetscErrorCode PetscViewerAttachVersion_Private(PetscViewer, const char[], DMPlexStorageVersion);
10: static PetscErrorCode PetscViewerGetAttachedVersion_Private(PetscViewer, const char[], DMPlexStorageVersion *);
12: PETSC_SINGLE_LIBRARY_INTERN PetscErrorCode VecView_MPI(Vec, PetscViewer);
14: static PetscErrorCode PetscViewerPrintVersion_Private(PetscViewer viewer, DMPlexStorageVersion version, char str[], size_t len)
15: {
16: PetscFunctionBegin;
17: PetscCall(PetscViewerCheckVersion_Private(viewer, version));
18: PetscCall(PetscSNPrintf(str, len, "%d.%d.%d", version->major, version->minor, version->subminor));
19: PetscFunctionReturn(PETSC_SUCCESS);
20: }
22: static PetscErrorCode PetscViewerParseVersion_Private(PetscViewer viewer, const char str[], DMPlexStorageVersion *version)
23: {
24: PetscToken t;
25: const char *ts;
26: PetscInt i;
27: PetscInt ti[3];
28: DMPlexStorageVersion v;
30: PetscFunctionBegin;
31: PetscCall(PetscTokenCreate(str, '.', &t));
32: for (i = 0; i < 3; i++) {
33: PetscCall(PetscTokenFind(t, &ts));
34: PetscCheck(ts, PetscObjectComm((PetscObject)viewer), PETSC_ERR_ARG_WRONG, "Malformed version string %s", str);
35: PetscCall(PetscOptionsStringToInt(ts, &ti[i]));
36: }
37: PetscCall(PetscTokenFind(t, &ts));
38: PetscCheck(!ts, PetscObjectComm((PetscObject)viewer), PETSC_ERR_ARG_WRONG, "Malformed version string %s", str);
39: PetscCall(PetscTokenDestroy(&t));
40: PetscCall(PetscNew(&v));
41: v->major = (int)ti[0];
42: v->minor = (int)ti[1];
43: v->subminor = (int)ti[2];
44: PetscCall(PetscViewerCheckVersion_Private(viewer, v));
45: *version = v;
46: PetscFunctionReturn(PETSC_SUCCESS);
47: }
49: static PetscErrorCode PetscViewerAttachVersion_Private(PetscViewer viewer, const char key[], DMPlexStorageVersion v)
50: {
51: PetscFunctionBegin;
52: PetscCall(PetscObjectContainerCompose((PetscObject)viewer, key, v, PetscCtxDestroyDefault));
53: PetscFunctionReturn(PETSC_SUCCESS);
54: }
56: static PetscErrorCode PetscViewerGetAttachedVersion_Private(PetscViewer viewer, const char key[], DMPlexStorageVersion *v)
57: {
58: PetscContainer cont;
60: PetscFunctionBegin;
61: PetscCall(PetscObjectQuery((PetscObject)viewer, key, (PetscObject *)&cont));
62: *v = NULL;
63: if (cont) PetscCall(PetscContainerGetPointer(cont, v));
64: PetscFunctionReturn(PETSC_SUCCESS);
65: }
67: /*
68: Version log:
69: 1.0.0 legacy version (default if no "dmplex_storage_version" attribute found in file)
70: 1.1.0 legacy version, but output VIZ by default
71: 2.0.0 introduce versioning and multiple topologies
72: 2.1.0 introduce distributions
73: 3.0.0 new checkpointing format in Firedrake paper
74: 3.1.0 new format with IS compression
75: */
76: static PetscErrorCode PetscViewerCheckVersion_Private(PetscViewer viewer, DMPlexStorageVersion version)
77: {
78: PetscBool valid = PETSC_FALSE;
80: PetscFunctionBegin;
81: switch (version->major) {
82: case 1:
83: switch (version->minor) {
84: case 0:
85: switch (version->subminor) {
86: case 0:
87: valid = PETSC_TRUE;
88: break;
89: }
90: break;
91: case 1:
92: switch (version->subminor) {
93: case 0:
94: valid = PETSC_TRUE;
95: break;
96: }
97: break;
98: }
99: break;
100: case 2:
101: switch (version->minor) {
102: case 0:
103: switch (version->subminor) {
104: case 0:
105: valid = PETSC_TRUE;
106: break;
107: }
108: break;
109: case 1:
110: switch (version->subminor) {
111: case 0:
112: valid = PETSC_TRUE;
113: break;
114: }
115: break;
116: }
117: break;
118: case 3:
119: switch (version->minor) {
120: case 0:
121: switch (version->subminor) {
122: case 0:
123: valid = PETSC_TRUE;
124: break;
125: }
126: break;
127: case 1:
128: switch (version->subminor) {
129: case 0:
130: valid = PETSC_TRUE;
131: break;
132: }
133: break;
134: }
135: break;
136: }
137: PetscCheck(valid, PetscObjectComm((PetscObject)viewer), PETSC_ERR_SUP, "DMPlexStorageVersion %d.%d.%d not supported", version->major, version->minor, version->subminor);
138: PetscFunctionReturn(PETSC_SUCCESS);
139: }
141: static inline PetscBool DMPlexStorageVersionEQ(DMPlexStorageVersion version, int major, int minor, int subminor)
142: {
143: return (PetscBool)(version->major == major && version->minor == minor && version->subminor == subminor);
144: }
146: static inline PetscBool DMPlexStorageVersionGE(DMPlexStorageVersion version, int major, int minor, int subminor)
147: {
148: return (PetscBool)((version->major == major && version->minor == minor && version->subminor >= subminor) || (version->major == major && version->minor > minor) || version->major > major);
149: }
151: /*@C
152: PetscViewerHDF5SetDMPlexStorageVersionWriting - Set the storage version for writing
154: Logically collective
156: Input Parameters:
157: + viewer - The `PetscViewer`
158: - version - The storage format version
160: Level: advanced
162: Note:
163: The version has major, minor, and subminor integers. Parallel operations are only available for version 3.0.0.
165: .seealso: [](ch_dmbase), `DM`, `PetscViewerHDF5GetDMPlexStorageVersionWriting()`, `PetscViewerHDF5GetDMPlexStorageVersionReading()`, `PetscViewerHDF5SetDMPlexStorageVersionReading()`
166: @*/
167: PetscErrorCode PetscViewerHDF5SetDMPlexStorageVersionWriting(PetscViewer viewer, DMPlexStorageVersion version)
168: {
169: const char ATTR_NAME[] = "dmplex_storage_version";
170: DMPlexStorageVersion viewerVersion;
171: PetscBool fileHasVersion;
172: char fileVersion[16], versionStr[16], viewerVersionStr[16];
174: PetscFunctionBegin;
176: PetscAssertPointer(version, 2);
177: PetscCall(PetscViewerPrintVersion_Private(viewer, version, versionStr, 16));
178: PetscCall(PetscViewerGetAttachedVersion_Private(viewer, DMPLEX_STORAGE_VERSION_WRITING_KEY, &viewerVersion));
179: if (viewerVersion) {
180: PetscBool flg;
182: PetscCall(PetscViewerPrintVersion_Private(viewer, viewerVersion, viewerVersionStr, 16));
183: PetscCall(PetscStrcmp(versionStr, viewerVersionStr, &flg));
184: 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);
185: }
187: PetscCall(PetscViewerHDF5HasAttribute(viewer, NULL, ATTR_NAME, &fileHasVersion));
188: if (fileHasVersion) {
189: PetscBool flg;
190: char *tmp;
192: PetscCall(PetscViewerHDF5ReadAttribute(viewer, "/", ATTR_NAME, PETSC_STRING, NULL, &tmp));
193: PetscCall(PetscStrncpy(fileVersion, tmp, sizeof(fileVersion)));
194: PetscCall(PetscFree(tmp));
195: PetscCall(PetscStrcmp(fileVersion, versionStr, &flg));
196: 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);
197: } else {
198: PetscCall(PetscViewerHDF5WriteAttribute(viewer, "/", ATTR_NAME, PETSC_STRING, versionStr));
199: }
200: PetscCall(PetscNew(&viewerVersion));
201: viewerVersion->major = version->major;
202: viewerVersion->minor = version->minor;
203: viewerVersion->subminor = version->subminor;
204: PetscCall(PetscViewerAttachVersion_Private(viewer, DMPLEX_STORAGE_VERSION_WRITING_KEY, viewerVersion));
205: PetscFunctionReturn(PETSC_SUCCESS);
206: }
208: /*@C
209: PetscViewerHDF5GetDMPlexStorageVersionWriting - Get the storage version for writing
211: Logically collective
213: Input Parameter:
214: . viewer - The `PetscViewer`
216: Output Parameter:
217: . version - The storage format version
219: Options Database Keys:
220: . -dm_plex_view_hdf5_storage_version num - Overrides the storage format version
222: Level: advanced
224: Note:
225: The version has major, minor, and subminor integers. Parallel operations are only available for version 3.0.0.
227: .seealso: [](ch_dmbase), `DM`, `PetscViewerHDF5SetDMPlexStorageVersionWriting()`, `PetscViewerHDF5GetDMPlexStorageVersionReading()`, `PetscViewerHDF5SetDMPlexStorageVersionReading()`
228: @*/
229: PetscErrorCode PetscViewerHDF5GetDMPlexStorageVersionWriting(PetscViewer viewer, DMPlexStorageVersion *version)
230: {
231: const char ATTR_NAME[] = "dmplex_storage_version";
232: PetscBool fileHasVersion;
233: char optVersion[16], fileVersion[16];
235: PetscFunctionBegin;
237: PetscAssertPointer(version, 2);
238: PetscCall(PetscViewerGetAttachedVersion_Private(viewer, DMPLEX_STORAGE_VERSION_WRITING_KEY, version));
239: if (*version) PetscFunctionReturn(PETSC_SUCCESS);
241: PetscCall(PetscStrncpy(fileVersion, DMPLEX_STORAGE_VERSION_STABLE, sizeof(fileVersion)));
242: PetscCall(PetscViewerHDF5HasAttribute(viewer, NULL, ATTR_NAME, &fileHasVersion));
243: if (fileHasVersion) {
244: char *tmp;
246: PetscCall(PetscViewerHDF5ReadAttribute(viewer, "/", ATTR_NAME, PETSC_STRING, NULL, &tmp));
247: PetscCall(PetscStrncpy(fileVersion, tmp, sizeof(fileVersion)));
248: PetscCall(PetscFree(tmp));
249: }
250: PetscCall(PetscStrncpy(optVersion, fileVersion, sizeof(optVersion)));
251: PetscObjectOptionsBegin((PetscObject)viewer);
252: PetscCall(PetscOptionsString("-dm_plex_view_hdf5_storage_version", "DMPlex HDF5 viewer storage version", NULL, optVersion, optVersion, sizeof(optVersion), NULL));
253: PetscOptionsEnd();
254: if (!fileHasVersion) {
255: PetscCall(PetscViewerHDF5WriteAttribute(viewer, "/", ATTR_NAME, PETSC_STRING, optVersion));
256: } else {
257: PetscBool flg;
259: PetscCall(PetscStrcmp(fileVersion, optVersion, &flg));
260: 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);
261: }
262: PetscCall(PetscViewerHDF5WriteAttribute(viewer, NULL, "petsc_version_git", PETSC_STRING, PETSC_VERSION_GIT));
263: PetscCall(PetscViewerParseVersion_Private(viewer, optVersion, version));
264: PetscCall(PetscViewerAttachVersion_Private(viewer, DMPLEX_STORAGE_VERSION_WRITING_KEY, *version));
265: PetscFunctionReturn(PETSC_SUCCESS);
266: }
268: /*@C
269: PetscViewerHDF5SetDMPlexStorageVersionReading - Set the storage version for reading
271: Logically collective
273: Input Parameters:
274: + viewer - The `PetscViewer`
275: - version - The storage format version
277: Level: advanced
279: Note:
280: The version has major, minor, and subminor integers. Parallel operations are only available for version 3.0.0.
282: .seealso: [](ch_dmbase), `DM`, `PetscViewerHDF5GetDMPlexStorageVersionReading()`, `PetscViewerHDF5GetDMPlexStorageVersionWriting()`, `PetscViewerHDF5SetDMPlexStorageVersionWriting()`
283: @*/
284: PetscErrorCode PetscViewerHDF5SetDMPlexStorageVersionReading(PetscViewer viewer, DMPlexStorageVersion version)
285: {
286: const char ATTR_NAME[] = "dmplex_storage_version";
287: DMPlexStorageVersion viewerVersion;
288: PetscBool fileHasVersion;
289: char versionStr[16], viewerVersionStr[16];
291: PetscFunctionBegin;
293: PetscAssertPointer(version, 2);
294: PetscCall(PetscViewerPrintVersion_Private(viewer, version, versionStr, 16));
295: PetscCall(PetscViewerGetAttachedVersion_Private(viewer, DMPLEX_STORAGE_VERSION_READING_KEY, &viewerVersion));
296: if (viewerVersion) {
297: PetscBool flg;
299: PetscCall(PetscViewerPrintVersion_Private(viewer, viewerVersion, viewerVersionStr, 16));
300: PetscCall(PetscStrcmp(versionStr, viewerVersionStr, &flg));
301: 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);
302: }
304: PetscCall(PetscViewerHDF5HasAttribute(viewer, NULL, ATTR_NAME, &fileHasVersion));
305: if (fileHasVersion) {
306: char *fileVersion;
307: PetscBool flg;
309: PetscCall(PetscViewerHDF5ReadAttribute(viewer, "/", ATTR_NAME, PETSC_STRING, NULL, &fileVersion));
310: PetscCall(PetscStrcmp(fileVersion, versionStr, &flg));
311: 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);
312: PetscCall(PetscFree(fileVersion));
313: }
314: PetscCall(PetscNew(&viewerVersion));
315: viewerVersion->major = version->major;
316: viewerVersion->minor = version->minor;
317: viewerVersion->subminor = version->subminor;
318: PetscCall(PetscViewerAttachVersion_Private(viewer, DMPLEX_STORAGE_VERSION_READING_KEY, viewerVersion));
319: PetscFunctionReturn(PETSC_SUCCESS);
320: }
322: /*@C
323: PetscViewerHDF5GetDMPlexStorageVersionReading - Get the storage version for reading
325: Logically collective
327: Input Parameter:
328: . viewer - The `PetscViewer`
330: Output Parameter:
331: . version - The storage format version
333: Options Database Keys:
334: . -dm_plex_view_hdf5_storage_version num - Overrides the storage format version
336: Level: advanced
338: Note:
339: The version has major, minor, and subminor integers. Parallel operations are only available for version 3.0.0.
341: .seealso: [](ch_dmbase), `DM`, `PetscViewerHDF5SetDMPlexStorageVersionReading()`, `PetscViewerHDF5GetDMPlexStorageVersionWriting()`, `PetscViewerHDF5SetDMPlexStorageVersionWriting()`
342: @*/
343: PetscErrorCode PetscViewerHDF5GetDMPlexStorageVersionReading(PetscViewer viewer, DMPlexStorageVersion *version)
344: {
345: const char ATTR_NAME[] = "dmplex_storage_version";
346: char *defaultVersion;
347: char *versionString;
349: PetscFunctionBegin;
351: PetscAssertPointer(version, 2);
352: PetscCall(PetscViewerGetAttachedVersion_Private(viewer, DMPLEX_STORAGE_VERSION_READING_KEY, version));
353: if (*version) PetscFunctionReturn(PETSC_SUCCESS);
355: //TODO string HDF5 attribute handling is terrible and should be redesigned
356: PetscCall(PetscStrallocpy(DMPLEX_STORAGE_VERSION_FIRST, &defaultVersion));
357: PetscCall(PetscViewerHDF5ReadAttribute(viewer, "/", ATTR_NAME, PETSC_STRING, &defaultVersion, &versionString));
358: PetscCall(PetscViewerParseVersion_Private(viewer, versionString, version));
359: PetscCall(PetscViewerAttachVersion_Private(viewer, DMPLEX_STORAGE_VERSION_READING_KEY, *version));
360: PetscCall(PetscFree(versionString));
361: PetscCall(PetscFree(defaultVersion));
362: PetscFunctionReturn(PETSC_SUCCESS);
363: }
365: static PetscErrorCode DMPlexGetHDF5Name_Private(DM dm, const char *name[])
366: {
367: PetscFunctionBegin;
368: if (((PetscObject)dm)->name) PetscCall(PetscObjectGetName((PetscObject)dm, name));
369: else *name = "plex";
370: PetscFunctionReturn(PETSC_SUCCESS);
371: }
373: PetscErrorCode DMSequenceGetLength_HDF5_Internal(DM dm, const char seqname[], PetscInt *seqlen, PetscViewer viewer)
374: {
375: hid_t file, group, dset, dspace;
376: hsize_t rdim, *dims;
377: const char *groupname;
378: PetscBool has;
380: PetscFunctionBegin;
381: PetscCall(PetscViewerHDF5GetGroup(viewer, NULL, &groupname));
382: PetscCall(PetscViewerHDF5HasDataset(viewer, seqname, &has));
383: PetscCheck(has, PetscObjectComm((PetscObject)viewer), PETSC_ERR_FILE_UNEXPECTED, "Object (dataset) \"%s\" not stored in group %s", seqname, groupname);
385: PetscCall(PetscViewerHDF5OpenGroup(viewer, NULL, &file, &group));
386: PetscCallHDF5Return(dset, H5Dopen2, (group, seqname, H5P_DEFAULT));
387: PetscCallHDF5Return(dspace, H5Dget_space, (dset));
388: PetscCallHDF5ReturnNoCheck(rdim, H5Sget_simple_extent_dims, (dspace, NULL, NULL));
389: PetscCall(PetscMalloc1(rdim, &dims));
390: PetscCallHDF5ReturnNoCheck(rdim, H5Sget_simple_extent_dims, (dspace, dims, NULL));
391: *seqlen = (PetscInt)dims[0];
392: PetscCall(PetscFree(dims));
393: PetscCallHDF5(H5Dclose, (dset));
394: PetscCallHDF5(H5Gclose, (group));
395: PetscFunctionReturn(PETSC_SUCCESS);
396: }
398: static PetscErrorCode DMSequenceView_HDF5(DM dm, const char seqname[], PetscInt seqnum, PetscScalar value, PetscViewer viewer)
399: {
400: Vec stamp;
401: PetscMPIInt rank;
403: PetscFunctionBegin;
404: if (seqnum < 0) PetscFunctionReturn(PETSC_SUCCESS);
405: PetscCallMPI(MPI_Comm_rank(PetscObjectComm((PetscObject)viewer), &rank));
406: PetscCall(VecCreateMPI(PetscObjectComm((PetscObject)viewer), rank ? 0 : 1, 1, &stamp));
407: PetscCall(VecSetBlockSize(stamp, 1));
408: PetscCall(PetscObjectSetName((PetscObject)stamp, seqname));
409: if (rank == 0) {
410: PetscReal timeScale;
411: PetscBool istime;
413: PetscCall(PetscStrncmp(seqname, "time", 5, &istime));
414: if (istime) {
415: PetscCall(DMPlexGetScale(dm, PETSC_UNIT_TIME, &timeScale));
416: value *= timeScale;
417: }
418: PetscCall(VecSetValue(stamp, 0, value, INSERT_VALUES));
419: }
420: PetscCall(VecAssemblyBegin(stamp));
421: PetscCall(VecAssemblyEnd(stamp));
422: PetscCall(PetscViewerHDF5PushGroup(viewer, "/"));
423: PetscCall(PetscViewerHDF5PushTimestepping(viewer));
424: PetscCall(PetscViewerHDF5SetTimestep(viewer, seqnum)); /* seqnum < 0 jumps out above */
425: PetscCall(VecView(stamp, viewer));
426: PetscCall(PetscViewerHDF5PopTimestepping(viewer));
427: PetscCall(PetscViewerHDF5PopGroup(viewer));
428: PetscCall(VecDestroy(&stamp));
429: PetscFunctionReturn(PETSC_SUCCESS);
430: }
432: PetscErrorCode DMSequenceLoad_HDF5_Internal(DM dm, const char seqname[], PetscInt seqnum, PetscScalar *value, PetscViewer viewer)
433: {
434: Vec stamp;
435: PetscMPIInt rank;
437: PetscFunctionBegin;
438: if (seqnum < 0) PetscFunctionReturn(PETSC_SUCCESS);
439: PetscCallMPI(MPI_Comm_rank(PetscObjectComm((PetscObject)viewer), &rank));
440: PetscCall(VecCreateMPI(PetscObjectComm((PetscObject)viewer), rank ? 0 : 1, 1, &stamp));
441: PetscCall(VecSetBlockSize(stamp, 1));
442: PetscCall(PetscObjectSetName((PetscObject)stamp, seqname));
443: PetscCall(PetscViewerHDF5PushGroup(viewer, "/"));
444: PetscCall(PetscViewerHDF5PushTimestepping(viewer));
445: PetscCall(PetscViewerHDF5SetTimestep(viewer, seqnum)); /* seqnum < 0 jumps out above */
446: PetscCall(VecLoad(stamp, viewer));
447: PetscCall(PetscViewerHDF5PopTimestepping(viewer));
448: PetscCall(PetscViewerHDF5PopGroup(viewer));
449: if (rank == 0) {
450: const PetscScalar *a;
451: PetscReal timeScale;
452: PetscBool istime;
454: PetscCall(VecGetArrayRead(stamp, &a));
455: *value = a[0];
456: PetscCall(VecRestoreArrayRead(stamp, &a));
457: PetscCall(PetscStrncmp(seqname, "time", 5, &istime));
458: if (istime) {
459: PetscCall(DMPlexGetScale(dm, PETSC_UNIT_TIME, &timeScale));
460: *value /= timeScale;
461: }
462: }
463: PetscCall(VecDestroy(&stamp));
464: PetscFunctionReturn(PETSC_SUCCESS);
465: }
467: static PetscErrorCode DMPlexCreateCutVertexLabel_Private(DM dm, DMLabel cutLabel, DMLabel *cutVertexLabel)
468: {
469: IS cutcells = NULL;
470: const PetscInt *cutc;
471: PetscInt cellHeight, vStart, vEnd, cStart, cEnd, c;
473: PetscFunctionBegin;
474: if (!cutLabel) PetscFunctionReturn(PETSC_SUCCESS);
475: PetscCall(DMPlexGetVTKCellHeight(dm, &cellHeight));
476: PetscCall(DMPlexGetHeightStratum(dm, cellHeight, &cStart, &cEnd));
477: PetscCall(DMPlexGetDepthStratum(dm, 0, &vStart, &vEnd));
478: /* Label vertices that should be duplicated */
479: PetscCall(DMLabelCreate(PETSC_COMM_SELF, "Cut Vertices", cutVertexLabel));
480: PetscCall(DMLabelGetStratumIS(cutLabel, 2, &cutcells));
481: if (cutcells) {
482: PetscInt n;
484: PetscCall(ISGetIndices(cutcells, &cutc));
485: PetscCall(ISGetLocalSize(cutcells, &n));
486: for (c = 0; c < n; ++c) {
487: if ((cutc[c] >= cStart) && (cutc[c] < cEnd)) {
488: PetscInt *closure = NULL;
489: PetscInt closureSize, cl, value;
491: PetscCall(DMPlexGetTransitiveClosure(dm, cutc[c], PETSC_TRUE, &closureSize, &closure));
492: for (cl = 0; cl < closureSize * 2; cl += 2) {
493: if ((closure[cl] >= vStart) && (closure[cl] < vEnd)) {
494: PetscCall(DMLabelGetValue(cutLabel, closure[cl], &value));
495: if (value == 1) PetscCall(DMLabelSetValue(*cutVertexLabel, closure[cl], 1));
496: }
497: }
498: PetscCall(DMPlexRestoreTransitiveClosure(dm, cutc[c], PETSC_TRUE, &closureSize, &closure));
499: }
500: }
501: PetscCall(ISRestoreIndices(cutcells, &cutc));
502: }
503: PetscCall(ISDestroy(&cutcells));
504: PetscFunctionReturn(PETSC_SUCCESS);
505: }
507: PetscErrorCode VecView_Plex_Local_HDF5_Internal(Vec v, PetscViewer viewer)
508: {
509: DMPlexStorageVersion version;
510: DM dm;
511: DM dmBC;
512: PetscSection section, sectionGlobal;
513: Vec gv;
514: const char *name;
515: PetscViewerFormat format;
516: PetscInt seqnum;
517: PetscReal seqval;
518: PetscBool isseq;
520: PetscFunctionBegin;
521: PetscCall(PetscViewerHDF5GetDMPlexStorageVersionWriting(viewer, &version));
522: PetscCall(PetscObjectTypeCompare((PetscObject)v, VECSEQ, &isseq));
523: PetscCall(VecGetDM(v, &dm));
524: PetscCall(DMGetLocalSection(dm, §ion));
525: PetscCall(DMGetOutputSequenceNumber(dm, &seqnum, &seqval));
526: PetscCall(DMSequenceView_HDF5(dm, "time", seqnum, (PetscScalar)seqval, viewer));
527: if (seqnum >= 0) {
528: PetscCall(PetscViewerHDF5PushTimestepping(viewer));
529: PetscCall(PetscViewerHDF5SetTimestep(viewer, seqnum));
530: }
531: PetscCall(PetscViewerGetFormat(viewer, &format));
532: PetscCall(DMGetOutputDM(dm, &dmBC));
533: PetscCall(DMGetGlobalSection(dmBC, §ionGlobal));
534: PetscCall(DMGetGlobalVector(dmBC, &gv));
535: PetscCall(PetscObjectGetName((PetscObject)v, &name));
536: PetscCall(PetscObjectSetName((PetscObject)gv, name));
537: PetscCall(DMLocalToGlobalBegin(dmBC, v, INSERT_VALUES, gv));
538: PetscCall(DMLocalToGlobalEnd(dmBC, v, INSERT_VALUES, gv));
539: PetscCall(PetscObjectTypeCompare((PetscObject)gv, VECSEQ, &isseq));
540: if (format == PETSC_VIEWER_HDF5_VIZ) {
541: /* Output visualization representation */
542: PetscInt numFields, f;
543: DMLabel cutLabel, cutVertexLabel = NULL;
545: PetscCall(PetscSectionGetNumFields(section, &numFields));
546: PetscCall(DMGetLabel(dm, "periodic_cut", &cutLabel));
547: for (f = 0; f < numFields; ++f) {
548: Vec subv;
549: IS is;
550: const char *fname, *fgroup, *componentName, *fname_def = "unnamed";
551: char subname[PETSC_MAX_PATH_LEN];
552: PetscInt Nc, Nt = 1;
553: PetscInt *pStart, *pEnd;
554: PetscViewerVTKFieldType *ft;
556: if (DMPlexStorageVersionEQ(version, 1, 1, 0)) PetscCall(DMPlexGetFieldTypes_Internal(dm, section, f, &Nt, &pStart, &pEnd, &ft));
557: else {
558: PetscCall(PetscMalloc3(Nt, &pStart, Nt, &pEnd, Nt, &ft));
559: PetscCall(DMPlexGetFieldType_Internal(dm, section, f, &pStart[0], &pEnd[0], &ft[0]));
560: }
561: for (PetscInt t = 0; t < Nt; ++t) {
562: size_t lname;
564: if (ft[t] == PETSC_VTK_INVALID) continue;
565: fgroup = (ft[t] == PETSC_VTK_POINT_VECTOR_FIELD) || (ft[t] == PETSC_VTK_POINT_FIELD) ? "/vertex_fields" : "/cell_fields";
566: PetscCall(PetscSectionGetFieldName(section, f, &fname));
567: if (!fname) fname = fname_def;
569: if (!t) {
570: PetscCall(PetscViewerHDF5PushGroup(viewer, fgroup));
571: } else {
572: char group[PETSC_MAX_PATH_LEN];
574: PetscCall(PetscSNPrintf(group, PETSC_MAX_PATH_LEN, "%s_%" PetscInt_FMT, fgroup, t));
575: PetscCall(PetscViewerHDF5PushGroup(viewer, group));
576: }
578: if (cutLabel) {
579: const PetscScalar *ga;
580: PetscScalar *suba;
581: PetscInt gstart, subSize = 0, extSize = 0, subOff = 0, newOff = 0;
583: PetscCall(DMPlexCreateCutVertexLabel_Private(dm, cutLabel, &cutVertexLabel));
584: PetscCall(PetscSectionGetFieldComponents(section, f, &Nc));
585: for (PetscInt p = pStart[t]; p < pEnd[t]; ++p) {
586: PetscInt gdof, fdof = 0, val;
588: PetscCall(PetscSectionGetDof(sectionGlobal, p, &gdof));
589: if (gdof > 0) PetscCall(PetscSectionGetFieldDof(section, p, f, &fdof));
590: subSize += fdof;
591: PetscCall(DMLabelGetValue(cutVertexLabel, p, &val));
592: if (val == 1) extSize += fdof;
593: }
594: PetscCall(VecCreate(PetscObjectComm((PetscObject)gv), &subv));
595: PetscCall(VecSetSizes(subv, subSize + extSize, PETSC_DETERMINE));
596: PetscCall(VecSetBlockSize(subv, Nc));
597: PetscCall(VecSetType(subv, VECSTANDARD));
598: PetscCall(VecGetOwnershipRange(gv, &gstart, NULL));
599: PetscCall(VecGetArrayRead(gv, &ga));
600: PetscCall(VecGetArray(subv, &suba));
601: for (PetscInt p = pStart[t]; p < pEnd[t]; ++p) {
602: PetscInt gdof, goff, val;
604: PetscCall(PetscSectionGetDof(sectionGlobal, p, &gdof));
605: if (gdof > 0) {
606: PetscInt fdof, fc, f2, poff = 0;
608: PetscCall(PetscSectionGetOffset(sectionGlobal, p, &goff));
609: /* Can get rid of this loop by storing field information in the global section */
610: for (f2 = 0; f2 < f; ++f2) {
611: PetscCall(PetscSectionGetFieldDof(section, p, f2, &fdof));
612: poff += fdof;
613: }
614: PetscCall(PetscSectionGetFieldDof(section, p, f, &fdof));
615: for (fc = 0; fc < fdof; ++fc, ++subOff) suba[subOff] = ga[goff + poff + fc - gstart];
616: PetscCall(DMLabelGetValue(cutVertexLabel, p, &val));
617: if (val == 1) {
618: for (fc = 0; fc < fdof; ++fc, ++newOff) suba[subSize + newOff] = ga[goff + poff + fc - gstart];
619: }
620: }
621: }
622: PetscCall(VecRestoreArrayRead(gv, &ga));
623: PetscCall(VecRestoreArray(subv, &suba));
624: PetscCall(DMLabelDestroy(&cutVertexLabel));
625: } else {
626: PetscCall(PetscSectionGetField_Internal(section, sectionGlobal, gv, f, pStart[t], pEnd[t], &is, &subv));
627: }
628: PetscCall(PetscStrlen(name, &lname));
629: if (lname) {
630: PetscCall(PetscStrncpy(subname, name, sizeof(subname)));
631: PetscCall(PetscStrlcat(subname, "_", sizeof(subname)));
632: }
633: PetscCall(PetscStrlcat(subname, fname, sizeof(subname)));
634: PetscCall(PetscObjectSetName((PetscObject)subv, subname));
635: if (isseq) PetscCall(VecView_Seq(subv, viewer));
636: else PetscCall(VecView_MPI(subv, viewer));
637: if (ft[t] == PETSC_VTK_POINT_VECTOR_FIELD || ft[t] == PETSC_VTK_CELL_VECTOR_FIELD) {
638: PetscCall(PetscViewerHDF5WriteObjectAttribute(viewer, (PetscObject)subv, "vector_field_type", PETSC_STRING, "vector"));
639: } else {
640: PetscCall(PetscViewerHDF5WriteObjectAttribute(viewer, (PetscObject)subv, "vector_field_type", PETSC_STRING, "scalar"));
641: }
643: /* Output the component names in the field if available */
644: PetscCall(PetscSectionGetFieldComponents(section, f, &Nc));
645: for (PetscInt c = 0; c < Nc; ++c) {
646: char componentNameLabel[PETSC_MAX_PATH_LEN];
647: PetscCall(PetscSectionGetComponentName(section, f, c, &componentName));
648: PetscCall(PetscSNPrintf(componentNameLabel, sizeof(componentNameLabel), "componentName%" PetscInt_FMT, c));
649: PetscCall(PetscViewerHDF5WriteObjectAttribute(viewer, (PetscObject)subv, componentNameLabel, PETSC_STRING, componentName));
650: }
652: if (cutLabel) PetscCall(VecDestroy(&subv));
653: else PetscCall(PetscSectionRestoreField_Internal(section, sectionGlobal, gv, f, pStart[t], pEnd[t], &is, &subv));
654: PetscCall(PetscViewerHDF5PopGroup(viewer));
655: }
656: if (!DMPlexStorageVersionEQ(version, 1, 1, 0)) PetscCall(PetscFree3(pStart, pEnd, ft));
657: }
658: } else {
659: /* Output full vector */
660: PetscCall(PetscViewerHDF5PushGroup(viewer, "/fields"));
661: if (isseq) PetscCall(VecView_Seq(gv, viewer));
662: else PetscCall(VecView_MPI(gv, viewer));
663: PetscCall(PetscViewerHDF5PopGroup(viewer));
664: }
665: if (seqnum >= 0) PetscCall(PetscViewerHDF5PopTimestepping(viewer));
666: PetscCall(DMRestoreGlobalVector(dmBC, &gv));
667: PetscFunctionReturn(PETSC_SUCCESS);
668: }
670: PetscErrorCode VecView_Plex_HDF5_Internal(Vec v, PetscViewer viewer)
671: {
672: DMPlexStorageVersion version;
673: DM dm;
674: Vec locv;
675: PetscObject isZero;
676: const char *name;
677: PetscReal time;
679: PetscFunctionBegin;
680: PetscCall(PetscViewerHDF5GetDMPlexStorageVersionWriting(viewer, &version));
681: PetscCall(PetscInfo(v, "Writing Vec %s storage version %d.%d.%d\n", v->hdr.name, version->major, version->minor, version->subminor));
683: PetscCall(VecGetDM(v, &dm));
684: PetscCall(DMGetLocalVector(dm, &locv));
685: PetscCall(PetscObjectGetName((PetscObject)v, &name));
686: PetscCall(PetscObjectSetName((PetscObject)locv, name));
687: PetscCall(PetscObjectQuery((PetscObject)v, "__Vec_bc_zero__", &isZero));
688: PetscCall(PetscObjectCompose((PetscObject)locv, "__Vec_bc_zero__", isZero));
689: PetscCall(DMGlobalToLocalBegin(dm, v, INSERT_VALUES, locv));
690: PetscCall(DMGlobalToLocalEnd(dm, v, INSERT_VALUES, locv));
691: PetscCall(DMGetOutputSequenceNumber(dm, NULL, &time));
692: PetscCall(DMPlexInsertBoundaryValues(dm, PETSC_TRUE, locv, time, NULL, NULL, NULL));
693: PetscCall(VecView_Plex_Local_HDF5_Internal(locv, viewer));
694: if (DMPlexStorageVersionEQ(version, 1, 1, 0)) {
695: PetscCall(PetscViewerHDF5PushGroup(viewer, "/fields"));
696: PetscCall(PetscViewerPushFormat(viewer, PETSC_VIEWER_HDF5_VIZ));
697: PetscCall(VecView_Plex_Local_HDF5_Internal(locv, viewer));
698: PetscCall(PetscViewerPopFormat(viewer));
699: PetscCall(PetscViewerHDF5PopGroup(viewer));
700: }
701: PetscCall(PetscObjectCompose((PetscObject)locv, "__Vec_bc_zero__", NULL));
702: PetscCall(DMRestoreLocalVector(dm, &locv));
703: PetscFunctionReturn(PETSC_SUCCESS);
704: }
706: PetscErrorCode VecView_Plex_HDF5_Native_Internal(Vec v, PetscViewer viewer)
707: {
708: PetscBool isseq;
710: PetscFunctionBegin;
711: PetscCall(PetscObjectTypeCompare((PetscObject)v, VECSEQ, &isseq));
712: PetscCall(PetscViewerHDF5PushGroup(viewer, "/fields"));
713: if (isseq) PetscCall(VecView_Seq(v, viewer));
714: else PetscCall(VecView_MPI(v, viewer));
715: PetscCall(PetscViewerHDF5PopGroup(viewer));
716: PetscFunctionReturn(PETSC_SUCCESS);
717: }
719: PetscErrorCode VecLoad_Plex_HDF5_Internal(Vec v, PetscViewer viewer)
720: {
721: DM dm;
722: Vec locv;
723: const char *name;
724: PetscInt seqnum;
726: PetscFunctionBegin;
727: PetscCall(VecGetDM(v, &dm));
728: PetscCall(DMGetLocalVector(dm, &locv));
729: PetscCall(PetscObjectGetName((PetscObject)v, &name));
730: PetscCall(PetscObjectSetName((PetscObject)locv, name));
731: PetscCall(DMGetOutputSequenceNumber(dm, &seqnum, NULL));
732: PetscCall(PetscViewerHDF5PushGroup(viewer, "/fields"));
733: if (seqnum >= 0) {
734: PetscCall(PetscViewerHDF5PushTimestepping(viewer));
735: PetscCall(PetscViewerHDF5SetTimestep(viewer, seqnum));
736: }
737: PetscCall(VecLoad_Plex_Local(locv, viewer));
738: if (seqnum >= 0) PetscCall(PetscViewerHDF5PopTimestepping(viewer));
739: PetscCall(PetscViewerHDF5PopGroup(viewer));
740: PetscCall(DMLocalToGlobalBegin(dm, locv, INSERT_VALUES, v));
741: PetscCall(DMLocalToGlobalEnd(dm, locv, INSERT_VALUES, v));
742: PetscCall(DMRestoreLocalVector(dm, &locv));
743: PetscFunctionReturn(PETSC_SUCCESS);
744: }
746: PetscErrorCode VecLoad_Plex_HDF5_Native_Internal(Vec v, PetscViewer viewer)
747: {
748: DM dm;
749: PetscInt seqnum;
751: PetscFunctionBegin;
752: PetscCall(VecGetDM(v, &dm));
753: PetscCall(DMGetOutputSequenceNumber(dm, &seqnum, NULL));
754: PetscCall(PetscViewerHDF5PushGroup(viewer, "/fields"));
755: if (seqnum >= 0) {
756: PetscCall(PetscViewerHDF5PushTimestepping(viewer));
757: PetscCall(PetscViewerHDF5SetTimestep(viewer, seqnum));
758: }
759: PetscCall(VecLoad_Default(v, viewer));
760: if (seqnum >= 0) PetscCall(PetscViewerHDF5PopTimestepping(viewer));
761: PetscCall(PetscViewerHDF5PopGroup(viewer));
762: PetscFunctionReturn(PETSC_SUCCESS);
763: }
765: static PetscErrorCode DMPlexDistributionView_HDF5_Private(DM dm, IS globalPointNumbers, PetscViewer viewer)
766: {
767: DMPlexStorageVersion version;
768: MPI_Comm comm;
769: PetscMPIInt size, rank;
770: PetscInt size_petsc_int;
771: const char *topologydm_name, *distribution_name;
772: const PetscInt *gpoint;
773: PetscInt pStart, pEnd, p;
774: PetscSF pointSF;
775: PetscInt nroots, nleaves;
776: const PetscInt *ilocal;
777: const PetscSFNode *iremote;
778: IS chartSizesIS, ownersIS, gpointsIS;
779: PetscInt *chartSize, *owners, *gpoints;
780: PetscBool ocompress;
782: PetscFunctionBegin;
783: PetscCall(PetscViewerHDF5GetDMPlexStorageVersionWriting(viewer, &version));
784: PetscCall(PetscObjectGetComm((PetscObject)dm, &comm));
785: PetscCallMPI(MPI_Comm_size(comm, &size));
786: PetscCallMPI(MPI_Comm_rank(comm, &rank));
787: PetscCall(DMPlexGetHDF5Name_Private(dm, &topologydm_name));
788: PetscCall(DMPlexDistributionGetName(dm, &distribution_name));
789: if (!distribution_name) PetscFunctionReturn(PETSC_SUCCESS);
790: PetscCall(PetscLogEventBegin(DMPLEX_DistributionView, viewer, 0, 0, 0));
791: size_petsc_int = (PetscInt)size;
792: PetscCall(PetscViewerHDF5WriteAttribute(viewer, NULL, "comm_size", PETSC_INT, (void *)&size_petsc_int));
793: PetscCall(ISGetIndices(globalPointNumbers, &gpoint));
794: PetscCall(DMPlexGetChart(dm, &pStart, &pEnd));
795: PetscCall(PetscMalloc1(1, &chartSize));
796: *chartSize = pEnd - pStart;
797: PetscCall(PetscMalloc1(*chartSize, &owners));
798: PetscCall(PetscMalloc1(*chartSize, &gpoints));
799: PetscCall(DMGetPointSF(dm, &pointSF));
800: PetscCall(PetscSFGetGraph(pointSF, &nroots, &nleaves, &ilocal, &iremote));
801: for (p = pStart; p < pEnd; ++p) {
802: PetscInt gp = gpoint[p - pStart];
804: owners[p - pStart] = rank;
805: gpoints[p - pStart] = (gp < 0 ? -(gp + 1) : gp);
806: }
807: for (p = 0; p < nleaves; ++p) {
808: PetscInt ilocalp = (ilocal ? ilocal[p] : p);
810: owners[ilocalp] = iremote[p].rank;
811: }
812: PetscCall(ISCreateGeneral(comm, 1, chartSize, PETSC_OWN_POINTER, &chartSizesIS));
813: PetscCall(ISCreateGeneral(comm, *chartSize, owners, PETSC_OWN_POINTER, &ownersIS));
814: PetscCall(ISCreateGeneral(comm, *chartSize, gpoints, PETSC_OWN_POINTER, &gpointsIS));
815: if (DMPlexStorageVersionGE(version, 3, 1, 0)) {
816: PetscCall(PetscViewerHDF5GetCompress(viewer, &ocompress));
817: PetscCall(PetscViewerHDF5SetCompress(viewer, PETSC_TRUE));
818: }
819: PetscCall(PetscObjectSetName((PetscObject)chartSizesIS, "chart_sizes"));
820: PetscCall(PetscObjectSetName((PetscObject)ownersIS, "owners"));
821: PetscCall(PetscObjectSetName((PetscObject)gpointsIS, "global_point_numbers"));
822: PetscCall(ISView(chartSizesIS, viewer));
823: PetscCall(ISView(ownersIS, viewer));
824: PetscCall(ISView(gpointsIS, viewer));
825: PetscCall(ISDestroy(&chartSizesIS));
826: PetscCall(ISDestroy(&ownersIS));
827: PetscCall(ISDestroy(&gpointsIS));
828: PetscCall(ISRestoreIndices(globalPointNumbers, &gpoint));
829: if (DMPlexStorageVersionGE(version, 3, 1, 0)) PetscCall(PetscViewerHDF5SetCompress(viewer, ocompress));
830: PetscCall(PetscLogEventEnd(DMPLEX_DistributionView, viewer, 0, 0, 0));
831: PetscFunctionReturn(PETSC_SUCCESS);
832: }
834: 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[])
835: {
836: DMPlexStorageVersion version;
837: IS coneSizesIS, conesIS, orientationsIS;
838: PetscInt *coneSizes, *cones, *orientations;
839: const PetscInt *gpoint;
840: PetscInt nPoints = 0, conesSize = 0;
841: PetscInt p, c, s;
842: PetscBool ocompress;
843: MPI_Comm comm;
845: PetscFunctionBegin;
846: PetscCall(PetscViewerHDF5GetDMPlexStorageVersionWriting(viewer, &version));
847: PetscCall(PetscObjectGetComm((PetscObject)dm, &comm));
848: PetscCall(ISGetIndices(globalPointNumbers, &gpoint));
849: for (p = pStart; p < pEnd; ++p) {
850: if (gpoint[p] >= 0) {
851: PetscInt coneSize;
853: PetscCall(DMPlexGetConeSize(dm, p, &coneSize));
854: nPoints += 1;
855: conesSize += coneSize;
856: }
857: }
858: PetscCall(PetscMalloc1(nPoints, &coneSizes));
859: PetscCall(PetscMalloc1(conesSize, &cones));
860: PetscCall(PetscMalloc1(conesSize, &orientations));
861: for (p = pStart, c = 0, s = 0; p < pEnd; ++p) {
862: if (gpoint[p] >= 0) {
863: const PetscInt *cone, *ornt;
864: PetscInt coneSize, cp;
866: PetscCall(DMPlexGetConeSize(dm, p, &coneSize));
867: PetscCall(DMPlexGetCone(dm, p, &cone));
868: PetscCall(DMPlexGetConeOrientation(dm, p, &ornt));
869: coneSizes[s] = coneSize;
870: for (cp = 0; cp < coneSize; ++cp, ++c) {
871: cones[c] = gpoint[cone[cp]] < 0 ? -(gpoint[cone[cp]] + 1) : gpoint[cone[cp]];
872: orientations[c] = ornt[cp];
873: }
874: ++s;
875: }
876: }
877: PetscCheck(s == nPoints, PETSC_COMM_SELF, PETSC_ERR_LIB, "Total number of points %" PetscInt_FMT " != %" PetscInt_FMT, s, nPoints);
878: PetscCheck(c == conesSize, PETSC_COMM_SELF, PETSC_ERR_LIB, "Total number of cone points %" PetscInt_FMT " != %" PetscInt_FMT, c, conesSize);
879: PetscCall(ISCreateGeneral(comm, nPoints, coneSizes, PETSC_OWN_POINTER, &coneSizesIS));
880: PetscCall(ISCreateGeneral(comm, conesSize, cones, PETSC_OWN_POINTER, &conesIS));
881: PetscCall(ISCreateGeneral(comm, conesSize, orientations, PETSC_OWN_POINTER, &orientationsIS));
882: PetscCall(PetscObjectSetName((PetscObject)coneSizesIS, coneSizesName));
883: PetscCall(PetscObjectSetName((PetscObject)conesIS, conesName));
884: PetscCall(PetscObjectSetName((PetscObject)orientationsIS, orientationsName));
885: if (DMPlexStorageVersionGE(version, 3, 1, 0)) {
886: PetscCall(PetscViewerHDF5GetCompress(viewer, &ocompress));
887: PetscCall(PetscViewerHDF5SetCompress(viewer, PETSC_TRUE));
888: }
889: PetscCall(ISView(coneSizesIS, viewer));
890: PetscCall(ISView(conesIS, viewer));
891: PetscCall(ISView(orientationsIS, viewer));
892: PetscCall(ISDestroy(&coneSizesIS));
893: PetscCall(ISDestroy(&conesIS));
894: PetscCall(ISDestroy(&orientationsIS));
895: if (pointsName) {
896: IS pointsIS;
897: PetscInt *points;
899: PetscCall(PetscMalloc1(nPoints, &points));
900: for (p = pStart, c = 0, s = 0; p < pEnd; ++p) {
901: if (gpoint[p] >= 0) {
902: points[s] = gpoint[p];
903: ++s;
904: }
905: }
906: PetscCall(ISCreateGeneral(comm, nPoints, points, PETSC_OWN_POINTER, &pointsIS));
907: PetscCall(PetscObjectSetName((PetscObject)pointsIS, pointsName));
908: PetscCall(ISView(pointsIS, viewer));
909: PetscCall(ISDestroy(&pointsIS));
910: }
911: PetscCall(ISRestoreIndices(globalPointNumbers, &gpoint));
912: if (DMPlexStorageVersionGE(version, 3, 1, 0)) PetscCall(PetscViewerHDF5SetCompress(viewer, ocompress));
913: PetscFunctionReturn(PETSC_SUCCESS);
914: }
916: static PetscErrorCode DMPlexTopologyView_HDF5_Legacy_Private(DM dm, IS globalPointNumbers, PetscViewer viewer)
917: {
918: const char *pointsName, *coneSizesName, *conesName, *orientationsName;
919: PetscInt pStart, pEnd, dim;
921: PetscFunctionBegin;
922: pointsName = "order";
923: coneSizesName = "cones";
924: conesName = "cells";
925: orientationsName = "orientation";
926: PetscCall(DMPlexGetChart(dm, &pStart, &pEnd));
927: PetscCall(DMPlexTopologyView_HDF5_Inner_Private(dm, globalPointNumbers, viewer, pStart, pEnd, pointsName, coneSizesName, conesName, orientationsName));
928: PetscCall(DMGetDimension(dm, &dim));
929: PetscCall(PetscViewerHDF5WriteAttribute(viewer, conesName, "cell_dim", PETSC_INT, (void *)&dim));
930: PetscFunctionReturn(PETSC_SUCCESS);
931: }
933: //TODO get this numbering right away without needing this function
934: /* Renumber global point numbers so that they are 0-based per stratum */
935: static PetscErrorCode RenumberGlobalPointNumbersPerStratum_Private(DM dm, IS globalPointNumbers, IS *newGlobalPointNumbers, IS *strataPermutation)
936: {
937: PetscInt d, depth, p, n;
938: PetscInt *offsets;
939: const PetscInt *gpn;
940: PetscInt *ngpn;
941: MPI_Comm comm;
943: PetscFunctionBegin;
944: PetscCall(PetscObjectGetComm((PetscObject)dm, &comm));
945: PetscCall(ISGetLocalSize(globalPointNumbers, &n));
946: PetscCall(ISGetIndices(globalPointNumbers, &gpn));
947: PetscCall(PetscMalloc1(n, &ngpn));
948: PetscCall(DMPlexGetDepth(dm, &depth));
949: PetscCall(PetscMalloc1(depth + 1, &offsets));
950: for (d = 0; d <= depth; d++) {
951: PetscInt pStart, pEnd;
953: PetscCall(DMPlexGetDepthStratum(dm, d, &pStart, &pEnd));
954: offsets[d] = PETSC_INT_MAX;
955: for (p = pStart; p < pEnd; p++) {
956: if (gpn[p] >= 0 && gpn[p] < offsets[d]) offsets[d] = gpn[p];
957: }
958: }
959: PetscCallMPI(MPIU_Allreduce(MPI_IN_PLACE, offsets, depth + 1, MPIU_INT, MPI_MIN, comm));
960: for (d = 0; d <= depth; d++) {
961: PetscInt pStart, pEnd;
963: PetscCall(DMPlexGetDepthStratum(dm, d, &pStart, &pEnd));
964: for (p = pStart; p < pEnd; p++) ngpn[p] = gpn[p] - PetscSign(gpn[p]) * offsets[d];
965: }
966: PetscCall(ISRestoreIndices(globalPointNumbers, &gpn));
967: PetscCall(ISCreateGeneral(PetscObjectComm((PetscObject)globalPointNumbers), n, ngpn, PETSC_OWN_POINTER, newGlobalPointNumbers));
968: {
969: PetscInt *perm;
971: PetscCall(PetscMalloc1(depth + 1, &perm));
972: for (d = 0; d <= depth; d++) perm[d] = d;
973: PetscCall(PetscSortIntWithPermutation(depth + 1, offsets, perm));
974: PetscCall(ISCreateGeneral(PETSC_COMM_SELF, depth + 1, perm, PETSC_OWN_POINTER, strataPermutation));
975: }
976: PetscCall(PetscFree(offsets));
977: PetscFunctionReturn(PETSC_SUCCESS);
978: }
980: static PetscErrorCode DMPlexTopologyView_HDF5_Private(DM dm, IS globalPointNumbers, PetscViewer viewer)
981: {
982: IS globalPointNumbers0, strataPermutation;
983: const char *coneSizesName, *conesName, *orientationsName;
984: PetscInt depth, d;
985: MPI_Comm comm;
987: PetscFunctionBegin;
988: coneSizesName = "cone_sizes";
989: conesName = "cones";
990: orientationsName = "orientations";
991: PetscCall(PetscObjectGetComm((PetscObject)dm, &comm));
992: PetscCall(DMPlexGetDepth(dm, &depth));
993: {
994: PetscInt dim;
996: PetscCall(DMGetDimension(dm, &dim));
997: PetscCall(PetscViewerHDF5WriteAttribute(viewer, NULL, "cell_dim", PETSC_INT, &dim));
998: PetscCall(PetscViewerHDF5WriteAttribute(viewer, NULL, "depth", PETSC_INT, &depth));
999: }
1001: PetscCall(RenumberGlobalPointNumbersPerStratum_Private(dm, globalPointNumbers, &globalPointNumbers0, &strataPermutation));
1002: /* TODO dirty trick to save serial IS using the same parallel viewer */
1003: {
1004: IS spOnComm;
1005: PetscInt n = 0, N;
1006: const PetscInt *idx = NULL;
1007: const PetscInt *old;
1008: PetscMPIInt rank;
1010: PetscCallMPI(MPI_Comm_rank(comm, &rank));
1011: PetscCall(ISGetLocalSize(strataPermutation, &N));
1012: PetscCall(ISGetIndices(strataPermutation, &old));
1013: if (!rank) {
1014: n = N;
1015: idx = old;
1016: }
1017: PetscCall(ISCreateGeneral(comm, n, idx, PETSC_COPY_VALUES, &spOnComm));
1018: PetscCall(ISRestoreIndices(strataPermutation, &old));
1019: PetscCall(ISDestroy(&strataPermutation));
1020: strataPermutation = spOnComm;
1021: }
1022: PetscCall(PetscObjectSetName((PetscObject)strataPermutation, "permutation"));
1023: PetscCall(ISView(strataPermutation, viewer));
1024: PetscCall(PetscViewerHDF5PushGroup(viewer, "strata"));
1025: for (d = 0; d <= depth; d++) {
1026: PetscInt pStart, pEnd;
1027: char group[128];
1029: PetscCall(PetscSNPrintf(group, sizeof(group), "%" PetscInt_FMT, d));
1030: PetscCall(PetscViewerHDF5PushGroup(viewer, group));
1031: PetscCall(DMPlexGetDepthStratum(dm, d, &pStart, &pEnd));
1032: PetscCall(DMPlexTopologyView_HDF5_Inner_Private(dm, globalPointNumbers0, viewer, pStart, pEnd, NULL, coneSizesName, conesName, orientationsName));
1033: PetscCall(PetscViewerHDF5PopGroup(viewer));
1034: }
1035: PetscCall(PetscViewerHDF5PopGroup(viewer)); /* strata */
1036: PetscCall(ISDestroy(&globalPointNumbers0));
1037: PetscCall(ISDestroy(&strataPermutation));
1038: PetscFunctionReturn(PETSC_SUCCESS);
1039: }
1041: PetscErrorCode DMPlexTopologyView_HDF5_Internal(DM dm, IS globalPointNumbers, PetscViewer viewer)
1042: {
1043: DMPlexStorageVersion version;
1044: const char *topologydm_name;
1045: char group[PETSC_MAX_PATH_LEN];
1047: PetscFunctionBegin;
1048: PetscCall(PetscViewerHDF5GetDMPlexStorageVersionWriting(viewer, &version));
1049: PetscCall(PetscInfo(dm, "Writing DM %s storage version %d.%d.%d\n", dm->hdr.name, version->major, version->minor, version->subminor));
1050: PetscCall(DMPlexGetHDF5Name_Private(dm, &topologydm_name));
1051: if (DMPlexStorageVersionGE(version, 2, 0, 0)) {
1052: PetscCall(PetscSNPrintf(group, sizeof(group), "topologies/%s", topologydm_name));
1053: } else {
1054: PetscCall(PetscStrncpy(group, "/", sizeof(group)));
1055: }
1056: PetscCall(PetscViewerHDF5PushGroup(viewer, group));
1058: PetscCall(PetscViewerHDF5PushGroup(viewer, "topology"));
1059: if (version->major < 3) {
1060: PetscCall(DMPlexTopologyView_HDF5_Legacy_Private(dm, globalPointNumbers, viewer));
1061: } else {
1062: /* since DMPlexStorageVersion 3.0.0 */
1063: PetscCall(DMPlexTopologyView_HDF5_Private(dm, globalPointNumbers, viewer));
1064: }
1065: PetscCall(PetscViewerHDF5PopGroup(viewer)); /* "topology" */
1067: if (DMPlexStorageVersionGE(version, 2, 1, 0)) {
1068: const char *distribution_name;
1070: PetscCall(DMPlexDistributionGetName(dm, &distribution_name));
1071: PetscCall(PetscViewerHDF5PushGroup(viewer, "distributions"));
1072: PetscCall(PetscViewerHDF5WriteGroup(viewer, NULL));
1073: PetscCall(PetscViewerHDF5PushGroup(viewer, distribution_name));
1074: PetscCall(DMPlexDistributionView_HDF5_Private(dm, globalPointNumbers, viewer));
1075: PetscCall(PetscViewerHDF5PopGroup(viewer)); /* distribution_name */
1076: PetscCall(PetscViewerHDF5PopGroup(viewer)); /* "distributions" */
1077: }
1079: PetscCall(PetscViewerHDF5PopGroup(viewer));
1080: PetscFunctionReturn(PETSC_SUCCESS);
1081: }
1083: static PetscErrorCode CreateConesIS_Private(DM dm, PetscInt cStart, PetscInt cEnd, IS globalCellNumbers, PetscInt *numCorners, IS *cellIS)
1084: {
1085: PetscSF sfPoint;
1086: DMLabel cutLabel, cutVertexLabel = NULL;
1087: IS globalVertexNumbers, cutvertices = NULL;
1088: const PetscInt *gcell, *gvertex, *cutverts = NULL;
1089: PetscInt *vertices;
1090: PetscInt conesSize = 0;
1091: PetscInt dim, numCornersLocal = 0, cell, vStart, vEnd, vExtra = 0, v;
1093: PetscFunctionBegin;
1094: *numCorners = 0;
1095: PetscCall(DMGetDimension(dm, &dim));
1096: PetscCall(DMPlexGetDepthStratum(dm, 0, &vStart, &vEnd));
1097: PetscCall(ISGetIndices(globalCellNumbers, &gcell));
1099: for (cell = cStart; cell < cEnd; ++cell) {
1100: PetscInt *closure = NULL;
1101: PetscInt closureSize, v, Nc = 0;
1103: if (gcell[cell] < 0) continue;
1104: PetscCall(DMPlexGetTransitiveClosure(dm, cell, PETSC_TRUE, &closureSize, &closure));
1105: for (v = 0; v < closureSize * 2; v += 2) {
1106: if ((closure[v] >= vStart) && (closure[v] < vEnd)) ++Nc;
1107: }
1108: PetscCall(DMPlexRestoreTransitiveClosure(dm, cell, PETSC_TRUE, &closureSize, &closure));
1109: conesSize += Nc;
1110: if (!numCornersLocal) numCornersLocal = Nc;
1111: else if (numCornersLocal != Nc) numCornersLocal = 1;
1112: }
1113: PetscCallMPI(MPIU_Allreduce(&numCornersLocal, numCorners, 1, MPIU_INT, MPI_MAX, PetscObjectComm((PetscObject)dm)));
1114: PetscCheck(!numCornersLocal || !(numCornersLocal != *numCorners || *numCorners == 0), PETSC_COMM_SELF, PETSC_ERR_SUP, "Visualization topology currently only supports identical cell shapes");
1115: /* Handle periodic cuts by identifying vertices which should be duplicated */
1116: PetscCall(DMGetLabel(dm, "periodic_cut", &cutLabel));
1117: PetscCall(DMPlexCreateCutVertexLabel_Private(dm, cutLabel, &cutVertexLabel));
1118: if (cutVertexLabel) PetscCall(DMLabelGetStratumIS(cutVertexLabel, 1, &cutvertices));
1119: if (cutvertices) {
1120: PetscCall(ISGetIndices(cutvertices, &cutverts));
1121: PetscCall(ISGetLocalSize(cutvertices, &vExtra));
1122: }
1123: PetscCall(DMGetPointSF(dm, &sfPoint));
1124: if (cutLabel) {
1125: const PetscInt *ilocal;
1126: const PetscSFNode *iremote;
1127: PetscInt nroots, nleaves;
1129: PetscCall(PetscSFGetGraph(sfPoint, &nroots, &nleaves, &ilocal, &iremote));
1130: if (nleaves < 0) {
1131: PetscCall(PetscObjectReference((PetscObject)sfPoint));
1132: } else {
1133: PetscCall(PetscSFCreate(PetscObjectComm((PetscObject)sfPoint), &sfPoint));
1134: PetscCall(PetscSFSetGraph(sfPoint, nroots + vExtra, nleaves, (PetscInt *)ilocal, PETSC_COPY_VALUES, (PetscSFNode *)iremote, PETSC_COPY_VALUES));
1135: }
1136: } else {
1137: PetscCall(PetscObjectReference((PetscObject)sfPoint));
1138: }
1139: /* Number all vertices */
1140: PetscCall(DMPlexCreateNumbering_Plex(dm, vStart, vEnd + vExtra, 0, NULL, sfPoint, &globalVertexNumbers));
1141: PetscCall(PetscSFDestroy(&sfPoint));
1142: /* Create cones */
1143: PetscCall(ISGetIndices(globalVertexNumbers, &gvertex));
1144: PetscCall(PetscMalloc1(conesSize, &vertices));
1145: for (cell = cStart, v = 0; cell < cEnd; ++cell) {
1146: PetscInt *closure = NULL;
1147: PetscInt closureSize, Nc = 0, p, value = -1;
1148: PetscBool replace;
1150: if (gcell[cell] < 0) continue;
1151: if (cutLabel) PetscCall(DMLabelGetValue(cutLabel, cell, &value));
1152: replace = (value == 2) ? PETSC_TRUE : PETSC_FALSE;
1153: PetscCall(DMPlexGetTransitiveClosure(dm, cell, PETSC_TRUE, &closureSize, &closure));
1154: for (p = 0; p < closureSize * 2; p += 2) {
1155: if ((closure[p] >= vStart) && (closure[p] < vEnd)) closure[Nc++] = closure[p];
1156: }
1157: PetscCall(DMPlexReorderCell(dm, cell, closure));
1158: for (p = 0; p < Nc; ++p) {
1159: PetscInt nv, gv = gvertex[closure[p] - vStart];
1161: if (replace) {
1162: PetscCall(PetscFindInt(closure[p], vExtra, cutverts, &nv));
1163: if (nv >= 0) gv = gvertex[vEnd - vStart + nv];
1164: }
1165: vertices[v++] = gv < 0 ? -(gv + 1) : gv;
1166: }
1167: PetscCall(DMPlexRestoreTransitiveClosure(dm, cell, PETSC_TRUE, &closureSize, &closure));
1168: }
1169: PetscCall(ISRestoreIndices(globalVertexNumbers, &gvertex));
1170: PetscCall(ISDestroy(&globalVertexNumbers));
1171: PetscCall(ISRestoreIndices(globalCellNumbers, &gcell));
1172: if (cutvertices) PetscCall(ISRestoreIndices(cutvertices, &cutverts));
1173: PetscCall(ISDestroy(&cutvertices));
1174: PetscCall(DMLabelDestroy(&cutVertexLabel));
1175: PetscCheck(v == conesSize, PETSC_COMM_SELF, PETSC_ERR_LIB, "Total number of cell vertices %" PetscInt_FMT " != %" PetscInt_FMT, v, conesSize);
1176: PetscCall(ISCreateGeneral(PetscObjectComm((PetscObject)dm), conesSize, vertices, PETSC_OWN_POINTER, cellIS));
1177: PetscCall(PetscLayoutSetBlockSize((*cellIS)->map, *numCorners));
1178: PetscCall(PetscObjectSetName((PetscObject)*cellIS, "cells"));
1179: PetscFunctionReturn(PETSC_SUCCESS);
1180: }
1182: static PetscErrorCode DMPlexTopologyView_HDF5_XDMF_Private(DM dm, IS globalCellNumbers, PetscViewer viewer)
1183: {
1184: DM cdm;
1185: DMLabel depthLabel, ctLabel;
1186: IS cellIS;
1187: PetscInt dim, depth, cellHeight, c, n = 0;
1189: PetscFunctionBegin;
1190: PetscCall(PetscViewerHDF5PushGroup(viewer, "/viz"));
1191: PetscCall(PetscViewerHDF5WriteGroup(viewer, NULL));
1193: PetscCall(PetscViewerHDF5PopGroup(viewer));
1194: PetscCall(DMGetDimension(dm, &dim));
1195: PetscCall(DMPlexGetDepth(dm, &depth));
1196: PetscCall(DMGetCoordinateDM(dm, &cdm));
1197: PetscCall(DMPlexGetVTKCellHeight(dm, &cellHeight));
1198: PetscCall(DMPlexGetDepthLabel(dm, &depthLabel));
1199: PetscCall(DMPlexGetCellTypeLabel(dm, &ctLabel));
1200: for (c = 0; c < DM_NUM_POLYTOPES; ++c) {
1201: const DMPolytopeType ict = (DMPolytopeType)c;
1202: PetscInt pStart, pEnd, dep, numCorners;
1203: PetscBool output = PETSC_FALSE, doOutput;
1205: if (ict == DM_POLYTOPE_FV_GHOST) continue;
1206: PetscCall(DMLabelGetStratumBounds(ctLabel, ict, &pStart, &pEnd));
1207: if (pStart >= 0) {
1208: PetscCall(DMLabelGetValue(depthLabel, pStart, &dep));
1209: if (dep == depth - cellHeight) output = PETSC_TRUE;
1210: }
1211: PetscCallMPI(MPIU_Allreduce(&output, &doOutput, 1, MPI_C_BOOL, MPI_LOR, PetscObjectComm((PetscObject)dm)));
1212: if (!doOutput) continue;
1213: PetscCall(CreateConesIS_Private(dm, pStart, pEnd, globalCellNumbers, &numCorners, &cellIS));
1214: if (!n) {
1215: PetscCall(PetscViewerHDF5PushGroup(viewer, "/viz/topology"));
1216: } else {
1217: char group[PETSC_MAX_PATH_LEN];
1219: PetscCall(PetscSNPrintf(group, PETSC_MAX_PATH_LEN, "/viz/topology_%" PetscInt_FMT, n));
1220: PetscCall(PetscViewerHDF5PushGroup(viewer, group));
1221: }
1222: PetscCall(ISView(cellIS, viewer));
1223: PetscCall(PetscViewerHDF5WriteObjectAttribute(viewer, (PetscObject)cellIS, "cell_corners", PETSC_INT, (void *)&numCorners));
1224: PetscCall(PetscViewerHDF5WriteObjectAttribute(viewer, (PetscObject)cellIS, "cell_dim", PETSC_INT, (void *)&dim));
1225: PetscCall(ISDestroy(&cellIS));
1226: PetscCall(PetscViewerHDF5PopGroup(viewer));
1227: ++n;
1228: }
1229: PetscFunctionReturn(PETSC_SUCCESS);
1230: }
1232: static PetscErrorCode DMPlexCoordinatesView_HDF5_Legacy_Private(DM dm, PetscViewer viewer)
1233: {
1234: DM cdm;
1235: Vec coordinates, newcoords;
1236: PetscReal lengthScale;
1237: PetscInt m, M, bs;
1239: PetscFunctionBegin;
1240: PetscCall(DMPlexGetScale(dm, PETSC_UNIT_LENGTH, &lengthScale));
1241: PetscCall(DMGetCoordinateDM(dm, &cdm));
1242: PetscCall(DMGetCoordinates(dm, &coordinates));
1243: PetscCall(VecCreate(PetscObjectComm((PetscObject)coordinates), &newcoords));
1244: PetscCall(PetscObjectSetName((PetscObject)newcoords, "vertices"));
1245: PetscCall(VecGetSize(coordinates, &M));
1246: PetscCall(VecGetLocalSize(coordinates, &m));
1247: PetscCall(VecSetSizes(newcoords, m, M));
1248: PetscCall(VecGetBlockSize(coordinates, &bs));
1249: PetscCall(VecSetBlockSize(newcoords, bs));
1250: PetscCall(VecSetType(newcoords, VECSTANDARD));
1251: PetscCall(VecCopy(coordinates, newcoords));
1252: PetscCall(VecScale(newcoords, lengthScale));
1253: /* Did not use DMGetGlobalVector() in order to bypass default group assignment */
1254: PetscCall(PetscViewerHDF5PushGroup(viewer, "/geometry"));
1255: PetscCall(PetscViewerPushFormat(viewer, PETSC_VIEWER_NATIVE));
1256: PetscCall(VecView(newcoords, viewer));
1257: PetscCall(PetscViewerPopFormat(viewer));
1258: PetscCall(PetscViewerHDF5PopGroup(viewer));
1259: PetscCall(VecDestroy(&newcoords));
1260: PetscFunctionReturn(PETSC_SUCCESS);
1261: }
1263: PetscErrorCode DMPlexCoordinatesView_HDF5_Internal(DM dm, PetscViewer viewer)
1264: {
1265: DM cdm;
1266: Vec coords, newcoords;
1267: PetscInt m, M, bs;
1268: PetscReal lengthScale;
1269: PetscBool viewSection = PETSC_TRUE, ocompress;
1270: const char *topologydm_name, *coordinatedm_name, *coordinates_name;
1271: PetscViewerFormat format;
1272: DMPlexStorageVersion version;
1274: PetscFunctionBegin;
1275: PetscCall(PetscViewerGetFormat(viewer, &format));
1276: PetscCall(PetscViewerHDF5GetDMPlexStorageVersionWriting(viewer, &version));
1277: if (!DMPlexStorageVersionGE(version, 2, 0, 0) || format == PETSC_VIEWER_HDF5_XDMF || format == PETSC_VIEWER_HDF5_VIZ) {
1278: PetscCall(DMPlexCoordinatesView_HDF5_Legacy_Private(dm, viewer));
1279: PetscFunctionReturn(PETSC_SUCCESS);
1280: }
1281: /* since 2.0.0 */
1282: if (DMPlexStorageVersionGE(version, 3, 1, 0)) {
1283: PetscCall(PetscViewerHDF5GetCompress(viewer, &ocompress));
1284: PetscCall(PetscViewerHDF5SetCompress(viewer, PETSC_TRUE));
1285: }
1286: PetscCall(PetscOptionsGetBool(NULL, dm->hdr.prefix, "-dm_plex_view_coordinate_section", &viewSection, NULL));
1287: PetscCall(DMGetCoordinateDM(dm, &cdm));
1288: PetscCall(DMGetCoordinates(dm, &coords));
1289: PetscCall(PetscObjectGetName((PetscObject)cdm, &coordinatedm_name));
1290: PetscCall(PetscObjectGetName((PetscObject)coords, &coordinates_name));
1291: PetscCall(DMPlexGetHDF5Name_Private(dm, &topologydm_name));
1292: PetscCall(PetscViewerHDF5PushGroup(viewer, "topologies"));
1293: PetscCall(PetscViewerHDF5PushGroup(viewer, topologydm_name));
1294: PetscCall(PetscViewerHDF5WriteAttribute(viewer, NULL, "coordinateDMName", PETSC_STRING, coordinatedm_name));
1295: PetscCall(PetscViewerHDF5WriteAttribute(viewer, NULL, "coordinatesName", PETSC_STRING, coordinates_name));
1296: PetscCall(PetscViewerHDF5PopGroup(viewer));
1297: PetscCall(PetscViewerHDF5PopGroup(viewer));
1298: if (viewSection) PetscCall(DMPlexSectionView(dm, viewer, cdm));
1299: PetscCall(VecCreate(PetscObjectComm((PetscObject)coords), &newcoords));
1300: PetscCall(PetscObjectSetName((PetscObject)newcoords, coordinates_name));
1301: PetscCall(VecGetSize(coords, &M));
1302: PetscCall(VecGetLocalSize(coords, &m));
1303: PetscCall(VecSetSizes(newcoords, m, M));
1304: PetscCall(VecGetBlockSize(coords, &bs));
1305: PetscCall(VecSetBlockSize(newcoords, bs));
1306: PetscCall(VecSetType(newcoords, VECSTANDARD));
1307: PetscCall(VecCopy(coords, newcoords));
1308: PetscCall(DMPlexGetScale(dm, PETSC_UNIT_LENGTH, &lengthScale));
1309: PetscCall(VecScale(newcoords, lengthScale));
1310: PetscCall(PetscViewerPushFormat(viewer, PETSC_VIEWER_NATIVE));
1311: PetscCall(DMPlexGlobalVectorView(dm, viewer, cdm, newcoords));
1312: PetscCall(PetscViewerPopFormat(viewer));
1313: PetscCall(VecDestroy(&newcoords));
1314: if (DMPlexStorageVersionGE(version, 3, 1, 0)) PetscCall(PetscViewerHDF5SetCompress(viewer, ocompress));
1315: PetscFunctionReturn(PETSC_SUCCESS);
1316: }
1318: static PetscErrorCode DMPlexCoordinatesView_HDF5_XDMF_Private(DM dm, PetscViewer viewer)
1319: {
1320: DM cdm;
1321: Vec coordinatesLocal, newcoords;
1322: PetscSection cSection, cGlobalSection;
1323: PetscScalar *coords, *ncoords;
1324: DMLabel cutLabel, cutVertexLabel = NULL;
1325: const PetscReal *L;
1326: PetscReal lengthScale;
1327: PetscInt vStart, vEnd, v, bs, N, coordSize, dof, off, d;
1328: PetscBool localized, embedded;
1330: PetscFunctionBegin;
1331: PetscCall(DMPlexGetDepthStratum(dm, 0, &vStart, &vEnd));
1332: PetscCall(DMPlexGetScale(dm, PETSC_UNIT_LENGTH, &lengthScale));
1333: PetscCall(DMGetCoordinatesLocal(dm, &coordinatesLocal));
1334: PetscCall(VecGetBlockSize(coordinatesLocal, &bs));
1335: PetscCall(DMGetCoordinatesLocalized(dm, &localized));
1336: if (localized == PETSC_FALSE) PetscFunctionReturn(PETSC_SUCCESS);
1337: PetscCall(DMGetPeriodicity(dm, NULL, NULL, &L));
1338: PetscCall(DMGetCoordinateDM(dm, &cdm));
1339: PetscCall(DMGetLocalSection(cdm, &cSection));
1340: PetscCall(DMGetGlobalSection(cdm, &cGlobalSection));
1341: PetscCall(DMGetLabel(dm, "periodic_cut", &cutLabel));
1342: N = 0;
1344: PetscCall(DMPlexCreateCutVertexLabel_Private(dm, cutLabel, &cutVertexLabel));
1345: PetscCall(VecCreate(PetscObjectComm((PetscObject)dm), &newcoords));
1346: PetscCall(PetscSectionGetDof(cSection, vStart, &dof));
1347: PetscCall(PetscPrintf(PETSC_COMM_SELF, "DOF: %" PetscInt_FMT "\n", dof));
1348: embedded = (PetscBool)(L && dof == 2 && !cutLabel);
1349: if (cutVertexLabel) {
1350: PetscCall(DMLabelGetStratumSize(cutVertexLabel, 1, &v));
1351: N += dof * v;
1352: }
1353: for (v = vStart; v < vEnd; ++v) {
1354: PetscCall(PetscSectionGetDof(cGlobalSection, v, &dof));
1355: if (dof < 0) continue;
1356: if (embedded) N += dof + 1;
1357: else N += dof;
1358: }
1359: if (embedded) PetscCall(VecSetBlockSize(newcoords, bs + 1));
1360: else PetscCall(VecSetBlockSize(newcoords, bs));
1361: PetscCall(VecSetSizes(newcoords, N, PETSC_DETERMINE));
1362: PetscCall(VecSetType(newcoords, VECSTANDARD));
1363: PetscCall(VecGetArray(coordinatesLocal, &coords));
1364: PetscCall(VecGetArray(newcoords, &ncoords));
1365: coordSize = 0;
1366: for (v = vStart; v < vEnd; ++v) {
1367: PetscCall(PetscSectionGetDof(cGlobalSection, v, &dof));
1368: PetscCall(PetscSectionGetOffset(cSection, v, &off));
1369: if (dof < 0) continue;
1370: if (embedded) {
1371: if (L && (L[0] > 0.0) && (L[1] > 0.0)) {
1372: PetscReal theta, phi, r, R;
1373: /* XY-periodic */
1374: /* Suppose its an y-z circle, then
1375: \hat r = (0, cos(th), sin(th)) \hat x = (1, 0, 0)
1376: and the circle in that plane is
1377: \hat r cos(phi) + \hat x sin(phi) */
1378: theta = 2.0 * PETSC_PI * PetscRealPart(coords[off + 1]) / L[1];
1379: phi = 2.0 * PETSC_PI * PetscRealPart(coords[off + 0]) / L[0];
1380: r = L[0] / (2.0 * PETSC_PI * 2.0 * L[1]);
1381: R = L[1] / (2.0 * PETSC_PI);
1382: ncoords[coordSize++] = PetscSinReal(phi) * r;
1383: ncoords[coordSize++] = -PetscCosReal(theta) * (R + r * PetscCosReal(phi));
1384: ncoords[coordSize++] = PetscSinReal(theta) * (R + r * PetscCosReal(phi));
1385: } else if (L && (L[0] > 0.0)) {
1386: /* X-periodic */
1387: ncoords[coordSize++] = -PetscCosReal(2.0 * PETSC_PI * PetscRealPart(coords[off + 0]) / L[0]) * (L[0] / (2.0 * PETSC_PI));
1388: ncoords[coordSize++] = coords[off + 1];
1389: ncoords[coordSize++] = PetscSinReal(2.0 * PETSC_PI * PetscRealPart(coords[off + 0]) / L[0]) * (L[0] / (2.0 * PETSC_PI));
1390: } else if (L && (L[1] > 0.0)) {
1391: /* Y-periodic */
1392: ncoords[coordSize++] = coords[off + 0];
1393: ncoords[coordSize++] = PetscSinReal(2.0 * PETSC_PI * PetscRealPart(coords[off + 1]) / L[1]) * (L[1] / (2.0 * PETSC_PI));
1394: ncoords[coordSize++] = -PetscCosReal(2.0 * PETSC_PI * PetscRealPart(coords[off + 1]) / L[1]) * (L[1] / (2.0 * PETSC_PI));
1395: #if 0
1396: } else if ((bd[0] == DM_BOUNDARY_TWIST)) {
1397: PetscReal phi, r, R;
1398: /* Mobius strip */
1399: /* Suppose its an x-z circle, then
1400: \hat r = (-cos(phi), 0, sin(phi)) \hat y = (0, 1, 0)
1401: and in that plane we rotate by pi as we go around the circle
1402: \hat r cos(phi/2) + \hat y sin(phi/2) */
1403: phi = 2.0*PETSC_PI*PetscRealPart(coords[off+0])/L[0];
1404: R = L[0];
1405: r = PetscRealPart(coords[off+1]) - L[1]/2.0;
1406: ncoords[coordSize++] = -PetscCosReal(phi) * (R + r * PetscCosReal(phi/2.0));
1407: ncoords[coordSize++] = PetscSinReal(phi/2.0) * r;
1408: ncoords[coordSize++] = PetscSinReal(phi) * (R + r * PetscCosReal(phi/2.0));
1409: #endif
1410: } else SETERRQ(PetscObjectComm((PetscObject)dm), PETSC_ERR_SUP, "Cannot handle periodicity in this domain");
1411: } else {
1412: for (d = 0; d < dof; ++d, ++coordSize) ncoords[coordSize] = coords[off + d];
1413: }
1414: }
1415: if (cutVertexLabel) {
1416: IS vertices;
1417: const PetscInt *verts;
1418: PetscInt n;
1420: PetscCall(DMLabelGetStratumIS(cutVertexLabel, 1, &vertices));
1421: if (vertices) {
1422: PetscCall(ISGetIndices(vertices, &verts));
1423: PetscCall(ISGetLocalSize(vertices, &n));
1424: for (v = 0; v < n; ++v) {
1425: PetscCall(PetscSectionGetDof(cSection, verts[v], &dof));
1426: PetscCall(PetscSectionGetOffset(cSection, verts[v], &off));
1427: for (d = 0; d < dof; ++d) ncoords[coordSize++] = coords[off + d] + ((L[d] > 0.) ? L[d] : 0.0);
1428: }
1429: PetscCall(ISRestoreIndices(vertices, &verts));
1430: PetscCall(ISDestroy(&vertices));
1431: }
1432: }
1433: PetscCheck(coordSize == N, PETSC_COMM_SELF, PETSC_ERR_PLIB, "Mismatched sizes: %" PetscInt_FMT " != %" PetscInt_FMT, coordSize, N);
1434: PetscCall(DMLabelDestroy(&cutVertexLabel));
1435: PetscCall(VecRestoreArray(coordinatesLocal, &coords));
1436: PetscCall(VecRestoreArray(newcoords, &ncoords));
1437: PetscCall(PetscObjectSetName((PetscObject)newcoords, "vertices"));
1438: PetscCall(VecScale(newcoords, lengthScale));
1439: PetscCall(PetscViewerHDF5PushGroup(viewer, "/viz"));
1440: PetscCall(PetscViewerHDF5WriteGroup(viewer, NULL));
1441: PetscCall(PetscViewerHDF5PopGroup(viewer));
1442: PetscCall(PetscViewerHDF5PushGroup(viewer, "/viz/geometry"));
1443: PetscCall(VecView(newcoords, viewer));
1444: PetscCall(PetscViewerHDF5PopGroup(viewer));
1445: PetscCall(VecDestroy(&newcoords));
1446: PetscFunctionReturn(PETSC_SUCCESS);
1447: }
1449: PetscErrorCode DMPlexLabelsView_HDF5_Internal(DM dm, IS globalPointNumbers, PetscViewer viewer)
1450: {
1451: const char *topologydm_name;
1452: const PetscInt *gpoint;
1453: PetscInt numLabels;
1454: PetscBool omitCelltypes = PETSC_FALSE, ocompress;
1455: DMPlexStorageVersion version;
1456: char group[PETSC_MAX_PATH_LEN];
1458: PetscFunctionBegin;
1459: PetscCall(PetscOptionsGetBool(NULL, dm->hdr.prefix, "-dm_plex_omit_celltypes", &omitCelltypes, NULL));
1460: PetscCall(PetscViewerHDF5GetDMPlexStorageVersionWriting(viewer, &version));
1461: if (DMPlexStorageVersionGE(version, 3, 1, 0)) {
1462: PetscCall(PetscViewerHDF5GetCompress(viewer, &ocompress));
1463: PetscCall(PetscViewerHDF5SetCompress(viewer, PETSC_TRUE));
1464: }
1465: PetscCall(ISGetIndices(globalPointNumbers, &gpoint));
1466: PetscCall(DMPlexGetHDF5Name_Private(dm, &topologydm_name));
1467: if (DMPlexStorageVersionGE(version, 2, 0, 0)) {
1468: PetscCall(PetscSNPrintf(group, sizeof(group), "topologies/%s/labels", topologydm_name));
1469: } else {
1470: PetscCall(PetscStrncpy(group, "/labels", sizeof(group)));
1471: }
1472: PetscCall(PetscViewerHDF5PushGroup(viewer, group));
1473: PetscCall(DMGetNumLabels(dm, &numLabels));
1474: for (PetscInt l = 0; l < numLabels; ++l) {
1475: DMLabel label;
1476: const char *name;
1477: IS valueIS, pvalueIS, globalValueIS;
1478: const PetscInt *values;
1479: PetscInt numValues, v;
1480: PetscBool isDepth, isCelltype, output;
1482: PetscCall(DMGetLabelByNum(dm, l, &label));
1483: PetscCall(PetscObjectGetName((PetscObject)label, &name));
1484: PetscCall(DMGetLabelOutput(dm, name, &output));
1485: PetscCall(PetscStrncmp(name, "depth", 10, &isDepth));
1486: PetscCall(PetscStrncmp(name, "celltype", 10, &isCelltype));
1487: // TODO Should only filter out celltype if it can be calculated
1488: if (isDepth || (isCelltype && omitCelltypes) || !output) continue;
1489: PetscCall(PetscViewerHDF5PushGroup(viewer, name));
1490: PetscCall(DMLabelGetValueIS(label, &valueIS));
1491: /* Must copy to a new IS on the global comm */
1492: PetscCall(ISGetLocalSize(valueIS, &numValues));
1493: PetscCall(ISGetIndices(valueIS, &values));
1494: PetscCall(ISCreateGeneral(PetscObjectComm((PetscObject)dm), numValues, values, PETSC_COPY_VALUES, &pvalueIS));
1495: PetscCall(ISRestoreIndices(valueIS, &values));
1496: PetscCall(ISAllGather(pvalueIS, &globalValueIS));
1497: PetscCall(ISDestroy(&pvalueIS));
1498: PetscCall(ISSortRemoveDups(globalValueIS));
1499: PetscCall(ISGetLocalSize(globalValueIS, &numValues));
1500: PetscCall(ISGetIndices(globalValueIS, &values));
1501: for (v = 0; v < numValues; ++v) {
1502: IS stratumIS, globalStratumIS;
1503: const PetscInt *spoints = NULL;
1504: PetscInt *gspoints, n = 0, gn, p;
1505: const char *iname = "indices";
1506: char group[PETSC_MAX_PATH_LEN];
1508: PetscCall(PetscSNPrintf(group, sizeof(group), "%" PetscInt_FMT, values[v]));
1509: PetscCall(PetscViewerHDF5PushGroup(viewer, group));
1510: PetscCall(DMLabelGetStratumIS(label, values[v], &stratumIS));
1512: if (stratumIS) PetscCall(ISGetLocalSize(stratumIS, &n));
1513: if (stratumIS) PetscCall(ISGetIndices(stratumIS, &spoints));
1514: for (gn = 0, p = 0; p < n; ++p)
1515: if (gpoint[spoints[p]] >= 0) ++gn;
1516: PetscCall(PetscMalloc1(gn, &gspoints));
1517: for (gn = 0, p = 0; p < n; ++p)
1518: if (gpoint[spoints[p]] >= 0) gspoints[gn++] = gpoint[spoints[p]];
1519: if (stratumIS) PetscCall(ISRestoreIndices(stratumIS, &spoints));
1520: PetscCall(ISCreateGeneral(PetscObjectComm((PetscObject)dm), gn, gspoints, PETSC_OWN_POINTER, &globalStratumIS));
1521: PetscCall(PetscObjectSetName((PetscObject)globalStratumIS, iname));
1522: PetscCall(ISView(globalStratumIS, viewer));
1523: PetscCall(ISDestroy(&globalStratumIS));
1524: PetscCall(ISDestroy(&stratumIS));
1525: PetscCall(PetscViewerHDF5PopGroup(viewer));
1526: }
1527: PetscCall(ISRestoreIndices(globalValueIS, &values));
1528: PetscCall(ISDestroy(&globalValueIS));
1529: PetscCall(ISDestroy(&valueIS));
1530: PetscCall(PetscViewerHDF5PopGroup(viewer));
1531: }
1532: PetscCall(ISRestoreIndices(globalPointNumbers, &gpoint));
1533: PetscCall(PetscViewerHDF5PopGroup(viewer));
1534: if (DMPlexStorageVersionGE(version, 3, 1, 0)) PetscCall(PetscViewerHDF5SetCompress(viewer, ocompress));
1535: PetscFunctionReturn(PETSC_SUCCESS);
1536: }
1538: /* We only write cells and vertices. Does this screw up parallel reading? */
1539: PetscErrorCode DMPlexView_HDF5_Internal(DM dm, PetscViewer viewer)
1540: {
1541: IS globalPointNumbers;
1542: PetscViewerFormat format;
1543: PetscBool viz_geom = PETSC_FALSE, xdmf_topo = PETSC_FALSE, petsc_topo = PETSC_FALSE, view_rank = PETSC_FALSE;
1545: PetscFunctionBegin;
1546: PetscCall(DMPlexCreatePointNumbering(dm, &globalPointNumbers));
1547: PetscCall(DMPlexCoordinatesView_HDF5_Internal(dm, viewer));
1549: PetscCall(PetscViewerGetFormat(viewer, &format));
1550: switch (format) {
1551: case PETSC_VIEWER_HDF5_VIZ:
1552: viz_geom = PETSC_TRUE;
1553: xdmf_topo = PETSC_TRUE;
1554: view_rank = PETSC_TRUE;
1555: break;
1556: case PETSC_VIEWER_HDF5_XDMF:
1557: xdmf_topo = PETSC_TRUE;
1558: break;
1559: case PETSC_VIEWER_HDF5_PETSC:
1560: petsc_topo = PETSC_TRUE;
1561: break;
1562: case PETSC_VIEWER_DEFAULT:
1563: case PETSC_VIEWER_NATIVE:
1564: viz_geom = PETSC_TRUE;
1565: xdmf_topo = PETSC_TRUE;
1566: petsc_topo = PETSC_TRUE;
1567: break;
1568: default:
1569: SETERRQ(PetscObjectComm((PetscObject)dm), PETSC_ERR_SUP, "PetscViewerFormat %s not supported for HDF5 output.", PetscViewerFormats[format]);
1570: }
1572: if (viz_geom) PetscCall(DMPlexCoordinatesView_HDF5_XDMF_Private(dm, viewer));
1573: if (xdmf_topo) PetscCall(DMPlexTopologyView_HDF5_XDMF_Private(dm, globalPointNumbers, viewer));
1574: if (petsc_topo) {
1575: PetscBool viewLabels = PETSC_TRUE;
1577: PetscCall(DMPlexTopologyView_HDF5_Internal(dm, globalPointNumbers, viewer));
1578: PetscCall(PetscOptionsGetBool(NULL, dm->hdr.prefix, "-dm_plex_view_labels", &viewLabels, NULL));
1579: if (viewLabels) PetscCall(DMPlexLabelsView_HDF5_Internal(dm, globalPointNumbers, viewer));
1580: }
1581: if (view_rank) {
1582: Vec v;
1584: PetscCall(DMPlexCreateRankField(dm, &v));
1585: PetscCall(VecView(v, viewer));
1586: PetscCall(VecDestroy(&v));
1587: }
1588: PetscCall(ISDestroy(&globalPointNumbers));
1589: PetscFunctionReturn(PETSC_SUCCESS);
1590: }
1592: PetscErrorCode DMPlexSectionView_HDF5_Internal(DM dm, PetscViewer viewer, DM sectiondm)
1593: {
1594: DMPlexStorageVersion version;
1595: MPI_Comm comm;
1596: const char *topologydm_name;
1597: const char *sectiondm_name;
1598: PetscSection gsection;
1599: PetscBool ocompress;
1601: PetscFunctionBegin;
1602: PetscCall(PetscViewerHDF5GetDMPlexStorageVersionWriting(viewer, &version));
1603: if (DMPlexStorageVersionGE(version, 3, 1, 0)) {
1604: PetscCall(PetscViewerHDF5GetCompress(viewer, &ocompress));
1605: PetscCall(PetscViewerHDF5SetCompress(viewer, PETSC_TRUE));
1606: }
1607: PetscCall(PetscObjectGetComm((PetscObject)sectiondm, &comm));
1608: PetscCall(DMPlexGetHDF5Name_Private(dm, &topologydm_name));
1609: PetscCall(PetscObjectGetName((PetscObject)sectiondm, §iondm_name));
1610: PetscCall(PetscViewerHDF5PushGroup(viewer, "topologies"));
1611: PetscCall(PetscViewerHDF5PushGroup(viewer, topologydm_name));
1612: PetscCall(PetscViewerHDF5PushGroup(viewer, "dms"));
1613: PetscCall(PetscViewerHDF5PushGroup(viewer, sectiondm_name));
1614: PetscCall(DMGetGlobalSection(sectiondm, &gsection));
1615: /* Save raw section */
1616: PetscCall(PetscSectionView(gsection, viewer));
1617: /* Save plex wrapper */
1618: {
1619: PetscInt pStart, pEnd, p, n;
1620: IS globalPointNumbers;
1621: const PetscInt *gpoints;
1622: IS orderIS;
1623: PetscInt *order;
1625: PetscCall(PetscSectionGetChart(gsection, &pStart, &pEnd));
1626: PetscCall(DMPlexCreatePointNumbering(dm, &globalPointNumbers));
1627: PetscCall(ISGetIndices(globalPointNumbers, &gpoints));
1628: for (p = pStart, n = 0; p < pEnd; ++p)
1629: if (gpoints[p] >= 0) n++;
1630: /* "order" is an array of global point numbers.
1631: When loading, it is used with topology/order array
1632: to match section points with plex topology points. */
1633: PetscCall(PetscMalloc1(n, &order));
1634: for (p = pStart, n = 0; p < pEnd; ++p)
1635: if (gpoints[p] >= 0) order[n++] = gpoints[p];
1636: PetscCall(ISRestoreIndices(globalPointNumbers, &gpoints));
1637: PetscCall(ISDestroy(&globalPointNumbers));
1638: PetscCall(ISCreateGeneral(comm, n, order, PETSC_OWN_POINTER, &orderIS));
1639: PetscCall(PetscObjectSetName((PetscObject)orderIS, "order"));
1640: PetscCall(ISView(orderIS, viewer));
1641: PetscCall(ISDestroy(&orderIS));
1642: }
1643: PetscCall(PetscViewerHDF5PopGroup(viewer));
1644: PetscCall(PetscViewerHDF5PopGroup(viewer));
1645: PetscCall(PetscViewerHDF5PopGroup(viewer));
1646: PetscCall(PetscViewerHDF5PopGroup(viewer));
1647: if (DMPlexStorageVersionGE(version, 3, 1, 0)) PetscCall(PetscViewerHDF5SetCompress(viewer, ocompress));
1648: PetscFunctionReturn(PETSC_SUCCESS);
1649: }
1651: PetscErrorCode DMPlexGlobalVectorView_HDF5_Internal(DM dm, PetscViewer viewer, DM sectiondm, Vec vec)
1652: {
1653: const char *topologydm_name;
1654: const char *sectiondm_name;
1655: const char *vec_name;
1656: PetscInt bs;
1658: PetscFunctionBegin;
1659: /* Check consistency */
1660: {
1661: PetscSF pointsf, pointsf1;
1663: PetscCall(DMGetPointSF(dm, &pointsf));
1664: PetscCall(DMGetPointSF(sectiondm, &pointsf1));
1665: PetscCheck(pointsf1 == pointsf, PETSC_COMM_SELF, PETSC_ERR_PLIB, "Mismatching point SFs for dm and sectiondm");
1666: }
1667: PetscCall(DMPlexGetHDF5Name_Private(dm, &topologydm_name));
1668: PetscCall(PetscObjectGetName((PetscObject)sectiondm, §iondm_name));
1669: PetscCall(PetscObjectGetName((PetscObject)vec, &vec_name));
1670: PetscCall(PetscViewerHDF5PushGroup(viewer, "topologies"));
1671: PetscCall(PetscViewerHDF5PushGroup(viewer, topologydm_name));
1672: PetscCall(PetscViewerHDF5PushGroup(viewer, "dms"));
1673: PetscCall(PetscViewerHDF5PushGroup(viewer, sectiondm_name));
1674: PetscCall(PetscViewerHDF5PushGroup(viewer, "vecs"));
1675: PetscCall(PetscViewerHDF5PushGroup(viewer, vec_name));
1676: PetscCall(VecGetBlockSize(vec, &bs));
1677: PetscCall(PetscViewerHDF5WriteAttribute(viewer, NULL, "blockSize", PETSC_INT, (void *)&bs));
1678: PetscCall(VecSetBlockSize(vec, 1));
1679: /* VecView(vec, viewer) would call (*vec->opt->view)(vec, viewer), but, */
1680: /* if vec was created with DMGet{Global, Local}Vector(), vec->opt->view */
1681: /* is set to VecView_Plex, which would save vec in a predefined location. */
1682: /* To save vec in where we want, we create a new Vec (temp) with */
1683: /* VecCreate(), wrap the vec data in temp, and call VecView(temp, viewer). */
1684: {
1685: Vec temp;
1686: const PetscScalar *array;
1687: PetscLayout map;
1689: PetscCall(VecCreate(PetscObjectComm((PetscObject)vec), &temp));
1690: PetscCall(PetscObjectSetName((PetscObject)temp, vec_name));
1691: PetscCall(VecGetLayout(vec, &map));
1692: PetscCall(VecSetLayout(temp, map));
1693: PetscCall(VecSetUp(temp));
1694: PetscCall(VecGetArrayRead(vec, &array));
1695: PetscCall(VecPlaceArray(temp, array));
1696: PetscCall(VecView(temp, viewer));
1697: PetscCall(VecResetArray(temp));
1698: PetscCall(VecRestoreArrayRead(vec, &array));
1699: PetscCall(VecDestroy(&temp));
1700: }
1701: PetscCall(VecSetBlockSize(vec, bs));
1702: PetscCall(PetscViewerHDF5PopGroup(viewer));
1703: PetscCall(PetscViewerHDF5PopGroup(viewer));
1704: PetscCall(PetscViewerHDF5PopGroup(viewer));
1705: PetscCall(PetscViewerHDF5PopGroup(viewer));
1706: PetscCall(PetscViewerHDF5PopGroup(viewer));
1707: PetscCall(PetscViewerHDF5PopGroup(viewer));
1708: PetscFunctionReturn(PETSC_SUCCESS);
1709: }
1711: PetscErrorCode DMPlexLocalVectorView_HDF5_Internal(DM dm, PetscViewer viewer, DM sectiondm, Vec vec)
1712: {
1713: MPI_Comm comm;
1714: const char *topologydm_name;
1715: const char *sectiondm_name;
1716: const char *vec_name;
1717: PetscSection section;
1718: PetscBool includesConstraints;
1719: Vec gvec;
1720: PetscInt m, bs;
1722: PetscFunctionBegin;
1723: PetscCall(PetscObjectGetComm((PetscObject)dm, &comm));
1724: /* Check consistency */
1725: {
1726: PetscSF pointsf, pointsf1;
1728: PetscCall(DMGetPointSF(dm, &pointsf));
1729: PetscCall(DMGetPointSF(sectiondm, &pointsf1));
1730: PetscCheck(pointsf1 == pointsf, PETSC_COMM_SELF, PETSC_ERR_PLIB, "Mismatching point SFs for dm and sectiondm");
1731: }
1732: PetscCall(DMPlexGetHDF5Name_Private(dm, &topologydm_name));
1733: PetscCall(PetscObjectGetName((PetscObject)sectiondm, §iondm_name));
1734: PetscCall(PetscObjectGetName((PetscObject)vec, &vec_name));
1735: PetscCall(PetscViewerHDF5PushGroup(viewer, "topologies"));
1736: PetscCall(PetscViewerHDF5PushGroup(viewer, topologydm_name));
1737: PetscCall(PetscViewerHDF5PushGroup(viewer, "dms"));
1738: PetscCall(PetscViewerHDF5PushGroup(viewer, sectiondm_name));
1739: PetscCall(PetscViewerHDF5PushGroup(viewer, "vecs"));
1740: PetscCall(PetscViewerHDF5PushGroup(viewer, vec_name));
1741: PetscCall(VecGetBlockSize(vec, &bs));
1742: PetscCall(PetscViewerHDF5WriteAttribute(viewer, NULL, "blockSize", PETSC_INT, (void *)&bs));
1743: PetscCall(VecCreate(comm, &gvec));
1744: PetscCall(PetscObjectSetName((PetscObject)gvec, vec_name));
1745: PetscCall(DMGetGlobalSection(sectiondm, §ion));
1746: PetscCall(PetscSectionGetIncludesConstraints(section, &includesConstraints));
1747: if (includesConstraints) PetscCall(PetscSectionGetStorageSize(section, &m));
1748: else PetscCall(PetscSectionGetConstrainedStorageSize(section, &m));
1749: PetscCall(VecSetSizes(gvec, m, PETSC_DECIDE));
1750: PetscCall(VecSetUp(gvec));
1751: PetscCall(DMLocalToGlobalBegin(sectiondm, vec, INSERT_VALUES, gvec));
1752: PetscCall(DMLocalToGlobalEnd(sectiondm, vec, INSERT_VALUES, gvec));
1753: PetscCall(VecView(gvec, viewer));
1754: PetscCall(VecDestroy(&gvec));
1755: PetscCall(PetscViewerHDF5PopGroup(viewer));
1756: PetscCall(PetscViewerHDF5PopGroup(viewer));
1757: PetscCall(PetscViewerHDF5PopGroup(viewer));
1758: PetscCall(PetscViewerHDF5PopGroup(viewer));
1759: PetscCall(PetscViewerHDF5PopGroup(viewer));
1760: PetscCall(PetscViewerHDF5PopGroup(viewer));
1761: PetscFunctionReturn(PETSC_SUCCESS);
1762: }
1764: struct _n_LoadLabelsCtx {
1765: MPI_Comm comm;
1766: PetscMPIInt rank;
1767: DM dm;
1768: PetscViewer viewer;
1769: DMLabel label;
1770: PetscSF sfXC;
1771: PetscLayout layoutX;
1772: };
1773: typedef struct _n_LoadLabelsCtx *LoadLabelsCtx;
1775: static PetscErrorCode LoadLabelsCtxCreate(DM dm, PetscViewer viewer, PetscSF sfXC, LoadLabelsCtx *ctx)
1776: {
1777: PetscFunctionBegin;
1778: PetscCall(PetscNew(ctx));
1779: PetscCall(PetscObjectReference((PetscObject)((*ctx)->dm = dm)));
1780: PetscCall(PetscObjectReference((PetscObject)((*ctx)->viewer = viewer)));
1781: PetscCall(PetscObjectGetComm((PetscObject)dm, &(*ctx)->comm));
1782: PetscCallMPI(MPI_Comm_rank((*ctx)->comm, &(*ctx)->rank));
1783: (*ctx)->sfXC = sfXC;
1784: if (sfXC) {
1785: PetscInt nX;
1787: PetscCall(PetscObjectReference((PetscObject)sfXC));
1788: PetscCall(PetscSFGetGraph(sfXC, &nX, NULL, NULL, NULL));
1789: PetscCall(PetscLayoutCreateFromSizes((*ctx)->comm, nX, PETSC_DECIDE, 1, &(*ctx)->layoutX));
1790: }
1791: PetscFunctionReturn(PETSC_SUCCESS);
1792: }
1794: static PetscErrorCode LoadLabelsCtxDestroy(LoadLabelsCtx *ctx)
1795: {
1796: PetscFunctionBegin;
1797: if (!*ctx) PetscFunctionReturn(PETSC_SUCCESS);
1798: PetscCall(DMDestroy(&(*ctx)->dm));
1799: PetscCall(PetscViewerDestroy(&(*ctx)->viewer));
1800: PetscCall(PetscSFDestroy(&(*ctx)->sfXC));
1801: PetscCall(PetscLayoutDestroy(&(*ctx)->layoutX));
1802: PetscCall(PetscFree(*ctx));
1803: PetscFunctionReturn(PETSC_SUCCESS);
1804: }
1806: /*
1807: A: on-disk points
1808: X: global points [0, NX)
1809: C: distributed plex points
1810: */
1811: static herr_t ReadLabelStratumHDF5_Distribute_Private(IS stratumIS, LoadLabelsCtx ctx, IS *newStratumIS)
1812: {
1813: MPI_Comm comm = ctx->comm;
1814: PetscSF sfXC = ctx->sfXC;
1815: PetscLayout layoutX = ctx->layoutX;
1816: PetscSF sfXA;
1817: const PetscInt *A_points;
1818: PetscInt nX, nC;
1819: PetscInt n;
1821: PetscFunctionBegin;
1822: PetscCall(PetscSFGetGraph(sfXC, &nX, &nC, NULL, NULL));
1823: PetscCall(ISGetLocalSize(stratumIS, &n));
1824: PetscCall(ISGetIndices(stratumIS, &A_points));
1825: PetscCall(PetscSFCreate(comm, &sfXA));
1826: PetscCall(PetscSFSetGraphLayout(sfXA, layoutX, n, NULL, PETSC_USE_POINTER, A_points));
1827: PetscCall(ISCreate(comm, newStratumIS));
1828: PetscCall(ISSetType(*newStratumIS, ISGENERAL));
1829: {
1830: PetscInt i;
1831: PetscBool *A_mask, *X_mask, *C_mask;
1833: PetscCall(PetscCalloc3(n, &A_mask, nX, &X_mask, nC, &C_mask));
1834: for (i = 0; i < n; i++) A_mask[i] = PETSC_TRUE;
1835: PetscCall(PetscSFReduceBegin(sfXA, MPI_C_BOOL, A_mask, X_mask, MPI_REPLACE));
1836: PetscCall(PetscSFReduceEnd(sfXA, MPI_C_BOOL, A_mask, X_mask, MPI_REPLACE));
1837: PetscCall(PetscSFBcastBegin(sfXC, MPI_C_BOOL, X_mask, C_mask, MPI_LOR));
1838: PetscCall(PetscSFBcastEnd(sfXC, MPI_C_BOOL, X_mask, C_mask, MPI_LOR));
1839: PetscCall(ISGeneralSetIndicesFromMask(*newStratumIS, 0, nC, C_mask));
1840: PetscCall(PetscFree3(A_mask, X_mask, C_mask));
1841: }
1842: PetscCall(PetscSFDestroy(&sfXA));
1843: PetscCall(ISRestoreIndices(stratumIS, &A_points));
1844: PetscFunctionReturn(PETSC_SUCCESS);
1845: }
1847: static herr_t ReadLabelStratumHDF5_Static(hid_t g_id, const char *vname, const H5L_info_t *info, void *op_data)
1848: {
1849: LoadLabelsCtx ctx = (LoadLabelsCtx)op_data;
1850: PetscViewer viewer = ctx->viewer;
1851: DMLabel label = ctx->label;
1852: MPI_Comm comm = ctx->comm;
1853: IS stratumIS;
1854: const PetscInt *ind;
1855: PetscInt value, N, i;
1857: PetscCall(PetscOptionsStringToInt(vname, &value));
1858: PetscCall(ISCreate(comm, &stratumIS));
1859: PetscCall(PetscObjectSetName((PetscObject)stratumIS, "indices"));
1860: PetscCall(PetscViewerHDF5PushGroup(viewer, vname)); /* labels/<lname>/<vname> */
1862: if (!ctx->sfXC) {
1863: /* Force serial load */
1864: PetscCall(PetscViewerHDF5ReadSizes(viewer, "indices", NULL, &N));
1865: PetscCall(PetscLayoutSetLocalSize(stratumIS->map, !ctx->rank ? N : 0));
1866: PetscCall(PetscLayoutSetSize(stratumIS->map, N));
1867: }
1868: PetscCall(ISLoad(stratumIS, viewer));
1870: if (ctx->sfXC) {
1871: IS newStratumIS;
1873: PetscCallHDF5(ReadLabelStratumHDF5_Distribute_Private, (stratumIS, ctx, &newStratumIS));
1874: PetscCall(ISDestroy(&stratumIS));
1875: stratumIS = newStratumIS;
1876: }
1878: PetscCall(PetscViewerHDF5PopGroup(viewer));
1879: PetscCall(ISGetLocalSize(stratumIS, &N));
1880: PetscCall(ISGetIndices(stratumIS, &ind));
1881: for (i = 0; i < N; ++i) PetscCall(DMLabelSetValue(label, ind[i], value));
1882: PetscCall(ISRestoreIndices(stratumIS, &ind));
1883: PetscCall(ISDestroy(&stratumIS));
1884: return 0;
1885: }
1887: /* TODO: Fix this code, it is returning PETSc error codes when it should be translating them to herr_t codes */
1888: static herr_t ReadLabelHDF5_Static(hid_t g_id, const char *lname, const H5L_info_t *info, void *op_data)
1889: {
1890: LoadLabelsCtx ctx = (LoadLabelsCtx)op_data;
1891: DM dm = ctx->dm;
1892: hsize_t idx = 0;
1893: PetscErrorCode ierr;
1894: PetscBool flg;
1895: herr_t err;
1897: PetscCall(DMHasLabel(dm, lname, &flg));
1898: if (flg) PetscCall(DMRemoveLabel(dm, lname, NULL));
1899: ierr = DMCreateLabel(dm, lname);
1900: if (ierr) return (herr_t)ierr;
1901: ierr = DMGetLabel(dm, lname, &ctx->label);
1902: if (ierr) return (herr_t)ierr;
1903: ierr = PetscViewerHDF5PushGroup(ctx->viewer, lname);
1904: if (ierr) return (herr_t)ierr;
1905: /* Iterate over the label's strata */
1906: PetscCallHDF5Return(err, H5Literate_by_name, (g_id, lname, H5_INDEX_NAME, H5_ITER_NATIVE, &idx, ReadLabelStratumHDF5_Static, op_data, 0));
1907: ierr = PetscViewerHDF5PopGroup(ctx->viewer);
1908: if (ierr) return (herr_t)ierr;
1909: return err;
1910: }
1912: PetscErrorCode DMPlexLabelsLoad_HDF5_Internal(DM dm, PetscViewer viewer, PetscSF sfXC)
1913: {
1914: const char *topologydm_name;
1915: LoadLabelsCtx ctx;
1916: hsize_t idx = 0;
1917: char group[PETSC_MAX_PATH_LEN];
1918: DMPlexStorageVersion version;
1919: PetscBool distributed, hasGroup;
1921: PetscFunctionBegin;
1922: PetscCall(DMPlexIsDistributed(dm, &distributed));
1923: if (distributed) PetscCheck(sfXC, PetscObjectComm((PetscObject)dm), PETSC_ERR_ARG_NULL, "PetscSF must be given for parallel load");
1924: PetscCall(LoadLabelsCtxCreate(dm, viewer, sfXC, &ctx));
1925: PetscCall(DMPlexGetHDF5Name_Private(dm, &topologydm_name));
1926: PetscCall(PetscViewerHDF5GetDMPlexStorageVersionReading(viewer, &version));
1927: if (DMPlexStorageVersionGE(version, 2, 0, 0)) {
1928: PetscCall(PetscSNPrintf(group, sizeof(group), "topologies/%s/labels", topologydm_name));
1929: } else {
1930: PetscCall(PetscStrncpy(group, "labels", sizeof(group)));
1931: }
1932: PetscCall(PetscViewerHDF5PushGroup(viewer, group));
1933: PetscCall(PetscViewerHDF5HasGroup(viewer, NULL, &hasGroup));
1934: if (hasGroup) {
1935: hid_t fileId, groupId;
1937: PetscCall(PetscViewerHDF5OpenGroup(viewer, NULL, &fileId, &groupId));
1938: /* Iterate over labels */
1939: PetscCallHDF5(H5Literate, (groupId, H5_INDEX_NAME, H5_ITER_NATIVE, &idx, ReadLabelHDF5_Static, ctx));
1940: PetscCallHDF5(H5Gclose, (groupId));
1941: }
1942: PetscCall(PetscViewerHDF5PopGroup(viewer));
1943: PetscCall(LoadLabelsCtxDestroy(&ctx));
1944: PetscFunctionReturn(PETSC_SUCCESS);
1945: }
1947: static PetscErrorCode DMPlexDistributionLoad_HDF5_Private(DM dm, PetscViewer viewer, PetscSF sf, PetscSF *distsf, DM *distdm)
1948: {
1949: MPI_Comm comm;
1950: PetscMPIInt size, rank;
1951: PetscInt dist_size;
1952: const char *distribution_name;
1953: PetscInt p, lsize;
1954: IS chartSizesIS, ownersIS, gpointsIS;
1955: const PetscInt *chartSize, *owners, *gpoints;
1956: PetscLayout layout;
1957: PetscBool has;
1959: PetscFunctionBegin;
1960: *distsf = NULL;
1961: *distdm = NULL;
1962: PetscCall(PetscObjectGetComm((PetscObject)dm, &comm));
1963: PetscCallMPI(MPI_Comm_size(comm, &size));
1964: PetscCallMPI(MPI_Comm_rank(comm, &rank));
1965: PetscCall(DMPlexDistributionGetName(dm, &distribution_name));
1966: if (!distribution_name) PetscFunctionReturn(PETSC_SUCCESS);
1967: PetscCall(PetscLogEventBegin(DMPLEX_DistributionLoad, viewer, 0, 0, 0));
1968: PetscCall(PetscViewerHDF5HasGroup(viewer, NULL, &has));
1969: if (!has) {
1970: const char *full_group;
1972: PetscCall(PetscViewerHDF5GetGroup(viewer, NULL, &full_group));
1973: 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);
1974: }
1975: PetscCall(PetscViewerHDF5ReadAttribute(viewer, NULL, "comm_size", PETSC_INT, NULL, (void *)&dist_size));
1976: 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);
1977: PetscCall(ISCreate(comm, &chartSizesIS));
1978: PetscCall(PetscObjectSetName((PetscObject)chartSizesIS, "chart_sizes"));
1979: PetscCall(ISCreate(comm, &ownersIS));
1980: PetscCall(PetscObjectSetName((PetscObject)ownersIS, "owners"));
1981: PetscCall(ISCreate(comm, &gpointsIS));
1982: PetscCall(PetscObjectSetName((PetscObject)gpointsIS, "global_point_numbers"));
1983: PetscCall(PetscLayoutSetLocalSize(chartSizesIS->map, 1));
1984: PetscCall(ISLoad(chartSizesIS, viewer));
1985: PetscCall(ISGetIndices(chartSizesIS, &chartSize));
1986: PetscCall(PetscLayoutSetLocalSize(ownersIS->map, *chartSize));
1987: PetscCall(PetscLayoutSetLocalSize(gpointsIS->map, *chartSize));
1988: PetscCall(ISLoad(ownersIS, viewer));
1989: PetscCall(ISLoad(gpointsIS, viewer));
1990: PetscCall(ISGetIndices(ownersIS, &owners));
1991: PetscCall(ISGetIndices(gpointsIS, &gpoints));
1992: PetscCall(PetscSFCreate(comm, distsf));
1993: PetscCall(PetscSFSetFromOptions(*distsf));
1994: PetscCall(PetscLayoutCreate(comm, &layout));
1995: PetscCall(PetscSFGetGraph(sf, &lsize, NULL, NULL, NULL));
1996: PetscCall(PetscLayoutSetLocalSize(layout, lsize));
1997: PetscCall(PetscLayoutSetBlockSize(layout, 1));
1998: PetscCall(PetscLayoutSetUp(layout));
1999: PetscCall(PetscSFSetGraphLayout(*distsf, layout, *chartSize, NULL, PETSC_OWN_POINTER, gpoints));
2000: PetscCall(PetscLayoutDestroy(&layout));
2001: /* Migrate DM */
2002: {
2003: PetscInt pStart, pEnd;
2004: PetscSFNode *buffer0, *buffer1, *buffer2;
2006: PetscCall(DMPlexGetChart(dm, &pStart, &pEnd));
2007: PetscCall(PetscMalloc2(pEnd - pStart, &buffer0, lsize, &buffer1));
2008: PetscCall(PetscMalloc1(*chartSize, &buffer2));
2009: {
2010: PetscSF workPointSF;
2011: PetscInt workNroots, workNleaves;
2012: const PetscInt *workIlocal;
2013: const PetscSFNode *workIremote;
2015: for (p = pStart; p < pEnd; ++p) {
2016: buffer0[p - pStart].rank = rank;
2017: buffer0[p - pStart].index = p - pStart;
2018: }
2019: PetscCall(DMGetPointSF(dm, &workPointSF));
2020: PetscCall(PetscSFGetGraph(workPointSF, &workNroots, &workNleaves, &workIlocal, &workIremote));
2021: for (p = 0; p < workNleaves; ++p) {
2022: PetscInt workIlocalp = (workIlocal ? workIlocal[p] : p);
2024: buffer0[workIlocalp].rank = -1;
2025: }
2026: }
2027: for (p = 0; p < lsize; ++p) buffer1[p].rank = -1;
2028: for (p = 0; p < *chartSize; ++p) buffer2[p].rank = -1;
2029: PetscCall(PetscSFReduceBegin(sf, MPIU_SF_NODE, buffer0, buffer1, MPI_MAXLOC));
2030: PetscCall(PetscSFReduceEnd(sf, MPIU_SF_NODE, buffer0, buffer1, MPI_MAXLOC));
2031: PetscCall(PetscSFBcastBegin(*distsf, MPIU_SF_NODE, buffer1, buffer2, MPI_REPLACE));
2032: PetscCall(PetscSFBcastEnd(*distsf, MPIU_SF_NODE, buffer1, buffer2, MPI_REPLACE));
2033: if (PetscDefined(USE_DEBUG)) {
2034: for (p = 0; p < *chartSize; ++p) 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);
2035: }
2036: PetscCall(PetscFree2(buffer0, buffer1));
2037: PetscCall(DMCreate(comm, distdm));
2038: PetscCall(DMSetType(*distdm, DMPLEX));
2039: PetscCall(PetscObjectSetName((PetscObject)*distdm, ((PetscObject)dm)->name));
2040: PetscCall(DMPlexDistributionSetName(*distdm, distribution_name));
2041: {
2042: PetscSF migrationSF;
2044: PetscCall(PetscSFCreate(comm, &migrationSF));
2045: PetscCall(PetscSFSetFromOptions(migrationSF));
2046: PetscCall(PetscSFSetGraph(migrationSF, pEnd - pStart, *chartSize, NULL, PETSC_OWN_POINTER, buffer2, PETSC_OWN_POINTER));
2047: PetscCall(PetscSFSetUp(migrationSF));
2048: PetscCall(DMPlexMigrate(dm, migrationSF, *distdm));
2049: PetscCall(PetscSFDestroy(&migrationSF));
2050: }
2051: }
2052: /* Set pointSF */
2053: {
2054: PetscSF pointSF;
2055: PetscInt *ilocal, nleaves, q;
2056: PetscSFNode *iremote, *buffer0, *buffer1;
2058: PetscCall(PetscMalloc2(*chartSize, &buffer0, lsize, &buffer1));
2059: for (p = 0, nleaves = 0; p < *chartSize; ++p) {
2060: if (owners[p] == rank) {
2061: buffer0[p].rank = rank;
2062: } else {
2063: buffer0[p].rank = -1;
2064: nleaves++;
2065: }
2066: buffer0[p].index = p;
2067: }
2068: for (p = 0; p < lsize; ++p) buffer1[p].rank = -1;
2069: PetscCall(PetscSFReduceBegin(*distsf, MPIU_SF_NODE, buffer0, buffer1, MPI_MAXLOC));
2070: PetscCall(PetscSFReduceEnd(*distsf, MPIU_SF_NODE, buffer0, buffer1, MPI_MAXLOC));
2071: for (p = 0; p < *chartSize; ++p) buffer0[p].rank = -1;
2072: PetscCall(PetscSFBcastBegin(*distsf, MPIU_SF_NODE, buffer1, buffer0, MPI_REPLACE));
2073: PetscCall(PetscSFBcastEnd(*distsf, MPIU_SF_NODE, buffer1, buffer0, MPI_REPLACE));
2074: if (PetscDefined(USE_DEBUG)) {
2075: 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);
2076: }
2077: PetscCall(PetscMalloc1(nleaves, &ilocal));
2078: PetscCall(PetscMalloc1(nleaves, &iremote));
2079: for (p = 0, q = 0; p < *chartSize; ++p) {
2080: if (buffer0[p].rank != rank) {
2081: ilocal[q] = p;
2082: iremote[q].rank = buffer0[p].rank;
2083: iremote[q].index = buffer0[p].index;
2084: q++;
2085: }
2086: }
2087: PetscCheck(q == nleaves, PETSC_COMM_SELF, PETSC_ERR_PLIB, "Mismatching leaf sizes: %" PetscInt_FMT " != %" PetscInt_FMT, q, nleaves);
2088: PetscCall(PetscFree2(buffer0, buffer1));
2089: PetscCall(PetscSFCreate(comm, &pointSF));
2090: PetscCall(PetscSFSetFromOptions(pointSF));
2091: PetscCall(PetscSFSetGraph(pointSF, *chartSize, nleaves, ilocal, PETSC_OWN_POINTER, iremote, PETSC_OWN_POINTER));
2092: PetscCall(DMSetPointSF(*distdm, pointSF));
2093: {
2094: DM cdm;
2096: PetscCall(DMGetCoordinateDM(*distdm, &cdm));
2097: PetscCall(DMSetPointSF(cdm, pointSF));
2098: }
2099: PetscCall(PetscSFDestroy(&pointSF));
2100: }
2101: PetscCall(ISRestoreIndices(chartSizesIS, &chartSize));
2102: PetscCall(ISRestoreIndices(ownersIS, &owners));
2103: PetscCall(ISRestoreIndices(gpointsIS, &gpoints));
2104: PetscCall(ISDestroy(&chartSizesIS));
2105: PetscCall(ISDestroy(&ownersIS));
2106: PetscCall(ISDestroy(&gpointsIS));
2107: /* Record that overlap has been manually created. */
2108: /* This is to pass `DMPlexCheckPointSF()`, which checks that */
2109: /* pointSF does not contain cells in the leaves if overlap = 0. */
2110: PetscCall(DMPlexSetOverlap_Plex(*distdm, NULL, DMPLEX_OVERLAP_MANUAL));
2111: PetscCall(DMPlexDistributeSetDefault(*distdm, PETSC_FALSE));
2112: PetscCall(DMPlexReorderSetDefault(*distdm, DM_REORDER_DEFAULT_FALSE));
2113: PetscCall(PetscLogEventEnd(DMPLEX_DistributionLoad, viewer, 0, 0, 0));
2114: PetscFunctionReturn(PETSC_SUCCESS);
2115: }
2117: // Serial load of topology
2118: static PetscErrorCode DMPlexTopologyLoad_HDF5_Legacy_Private(DM dm, PetscViewer viewer, PetscSF *sf)
2119: {
2120: MPI_Comm comm;
2121: const char *pointsName, *coneSizesName, *conesName, *orientationsName;
2122: IS pointsIS, coneSizesIS, conesIS, orientationsIS;
2123: const PetscInt *points, *coneSizes, *cones, *orientations;
2124: PetscInt *cone, *ornt;
2125: PetscInt dim, N, Np, pEnd, p, q, maxConeSize = 0, c;
2126: PetscMPIInt size, rank;
2128: PetscFunctionBegin;
2129: pointsName = "order";
2130: coneSizesName = "cones";
2131: conesName = "cells";
2132: orientationsName = "orientation";
2133: PetscCall(PetscObjectGetComm((PetscObject)dm, &comm));
2134: PetscCallMPI(MPI_Comm_size(comm, &size));
2135: PetscCallMPI(MPI_Comm_rank(comm, &rank));
2136: PetscCall(ISCreate(comm, &pointsIS));
2137: PetscCall(PetscObjectSetName((PetscObject)pointsIS, pointsName));
2138: PetscCall(ISCreate(comm, &coneSizesIS));
2139: PetscCall(PetscObjectSetName((PetscObject)coneSizesIS, coneSizesName));
2140: PetscCall(ISCreate(comm, &conesIS));
2141: PetscCall(PetscObjectSetName((PetscObject)conesIS, conesName));
2142: PetscCall(ISCreate(comm, &orientationsIS));
2143: PetscCall(PetscObjectSetName((PetscObject)orientationsIS, orientationsName));
2144: PetscCall(PetscViewerHDF5ReadObjectAttribute(viewer, (PetscObject)conesIS, "cell_dim", PETSC_INT, NULL, &dim));
2145: PetscCall(DMSetDimension(dm, dim));
2146: {
2147: /* Force serial load */
2148: PetscCall(PetscInfo(dm, "Loading DM %s in serial\n", dm->hdr.name));
2149: PetscCall(PetscViewerHDF5ReadSizes(viewer, pointsName, NULL, &Np));
2150: PetscCall(PetscLayoutSetLocalSize(pointsIS->map, rank == 0 ? Np : 0));
2151: PetscCall(PetscLayoutSetSize(pointsIS->map, Np));
2152: pEnd = rank == 0 ? Np : 0;
2153: PetscCall(PetscViewerHDF5ReadSizes(viewer, coneSizesName, NULL, &Np));
2154: PetscCall(PetscLayoutSetLocalSize(coneSizesIS->map, rank == 0 ? Np : 0));
2155: PetscCall(PetscLayoutSetSize(coneSizesIS->map, Np));
2156: PetscCall(PetscViewerHDF5ReadSizes(viewer, conesName, NULL, &N));
2157: PetscCall(PetscLayoutSetLocalSize(conesIS->map, rank == 0 ? N : 0));
2158: PetscCall(PetscLayoutSetSize(conesIS->map, N));
2159: PetscCall(PetscViewerHDF5ReadSizes(viewer, orientationsName, NULL, &N));
2160: PetscCall(PetscLayoutSetLocalSize(orientationsIS->map, rank == 0 ? N : 0));
2161: PetscCall(PetscLayoutSetSize(orientationsIS->map, N));
2162: }
2163: PetscCall(ISLoad(pointsIS, viewer));
2164: PetscCall(ISLoad(coneSizesIS, viewer));
2165: PetscCall(ISLoad(conesIS, viewer));
2166: PetscCall(ISLoad(orientationsIS, viewer));
2167: /* Create Plex */
2168: PetscCall(DMPlexSetChart(dm, 0, pEnd));
2169: PetscCall(ISGetIndices(pointsIS, &points));
2170: PetscCall(ISGetIndices(coneSizesIS, &coneSizes));
2171: for (p = 0; p < pEnd; ++p) {
2172: PetscCall(DMPlexSetConeSize(dm, points[p], coneSizes[p]));
2173: maxConeSize = PetscMax(maxConeSize, coneSizes[p]);
2174: }
2175: PetscCall(DMSetUp(dm));
2176: PetscCall(ISGetIndices(conesIS, &cones));
2177: PetscCall(ISGetIndices(orientationsIS, &orientations));
2178: PetscCall(PetscMalloc2(maxConeSize, &cone, maxConeSize, &ornt));
2179: for (p = 0, q = 0; p < pEnd; ++p) {
2180: for (c = 0; c < coneSizes[p]; ++c, ++q) {
2181: cone[c] = cones[q];
2182: ornt[c] = orientations[q];
2183: }
2184: PetscCall(DMPlexSetCone(dm, points[p], cone));
2185: PetscCall(DMPlexSetConeOrientation(dm, points[p], ornt));
2186: }
2187: PetscCall(PetscFree2(cone, ornt));
2188: /* Create global section migration SF */
2189: if (sf) {
2190: PetscLayout layout;
2191: PetscInt *globalIndices;
2193: PetscCall(PetscMalloc1(pEnd, &globalIndices));
2194: /* plex point == globalPointNumber in this case */
2195: for (p = 0; p < pEnd; ++p) globalIndices[p] = p;
2196: PetscCall(PetscLayoutCreate(comm, &layout));
2197: PetscCall(PetscLayoutSetSize(layout, Np));
2198: PetscCall(PetscLayoutSetBlockSize(layout, 1));
2199: PetscCall(PetscLayoutSetUp(layout));
2200: PetscCall(PetscSFCreate(comm, sf));
2201: PetscCall(PetscSFSetFromOptions(*sf));
2202: PetscCall(PetscSFSetGraphLayout(*sf, layout, pEnd, NULL, PETSC_OWN_POINTER, globalIndices));
2203: PetscCall(PetscLayoutDestroy(&layout));
2204: PetscCall(PetscFree(globalIndices));
2205: }
2206: /* Clean-up */
2207: PetscCall(ISRestoreIndices(pointsIS, &points));
2208: PetscCall(ISRestoreIndices(coneSizesIS, &coneSizes));
2209: PetscCall(ISRestoreIndices(conesIS, &cones));
2210: PetscCall(ISRestoreIndices(orientationsIS, &orientations));
2211: PetscCall(ISDestroy(&pointsIS));
2212: PetscCall(ISDestroy(&coneSizesIS));
2213: PetscCall(ISDestroy(&conesIS));
2214: PetscCall(ISDestroy(&orientationsIS));
2215: /* Fill in the rest of the topology structure */
2216: PetscCall(DMPlexSymmetrize(dm));
2217: PetscCall(DMPlexStratify(dm));
2218: PetscFunctionReturn(PETSC_SUCCESS);
2219: }
2221: /* Representation of two DMPlex strata in 0-based global numbering */
2222: struct _n_PlexLayer {
2223: PetscInt d;
2224: IS conesIS, orientationsIS;
2225: PetscSection coneSizesSection;
2226: PetscLayout vertexLayout;
2227: PetscSF overlapSF, l2gSF; //TODO maybe confusing names (in DMPlex in general)
2228: PetscInt offset, conesOffset, leafOffset;
2229: };
2230: typedef struct _n_PlexLayer *PlexLayer;
2232: static PetscErrorCode PlexLayerDestroy(PlexLayer *layer)
2233: {
2234: PetscFunctionBegin;
2235: if (!*layer) PetscFunctionReturn(PETSC_SUCCESS);
2236: PetscCall(PetscSectionDestroy(&(*layer)->coneSizesSection));
2237: PetscCall(ISDestroy(&(*layer)->conesIS));
2238: PetscCall(ISDestroy(&(*layer)->orientationsIS));
2239: PetscCall(PetscSFDestroy(&(*layer)->overlapSF));
2240: PetscCall(PetscSFDestroy(&(*layer)->l2gSF));
2241: PetscCall(PetscLayoutDestroy(&(*layer)->vertexLayout));
2242: PetscCall(PetscFree(*layer));
2243: PetscFunctionReturn(PETSC_SUCCESS);
2244: }
2246: static PetscErrorCode PlexLayerCreate_Private(PlexLayer *layer)
2247: {
2248: PetscFunctionBegin;
2249: PetscCall(PetscNew(layer));
2250: (*layer)->d = -1;
2251: (*layer)->offset = -1;
2252: (*layer)->conesOffset = -1;
2253: (*layer)->leafOffset = -1;
2254: PetscFunctionReturn(PETSC_SUCCESS);
2255: }
2257: // Parallel load of a depth stratum
2258: static PetscErrorCode PlexLayerLoad_Private(PlexLayer layer, PetscViewer viewer, PetscInt d, PetscLayout pointsLayout)
2259: {
2260: char path[128];
2261: MPI_Comm comm;
2262: const char *coneSizesName, *conesName, *orientationsName;
2263: IS coneSizesIS, conesIS, orientationsIS;
2264: PetscSection coneSizesSection;
2265: PetscLayout vertexLayout = NULL;
2266: PetscInt s;
2268: PetscFunctionBegin;
2269: coneSizesName = "cone_sizes";
2270: conesName = "cones";
2271: orientationsName = "orientations";
2272: PetscCall(PetscObjectGetComm((PetscObject)viewer, &comm));
2274: /* query size of next lower depth stratum (next lower dimension) */
2275: if (d > 0) {
2276: PetscInt NVertices;
2278: PetscCall(PetscSNPrintf(path, sizeof(path), "%" PetscInt_FMT "/%s", d - 1, coneSizesName));
2279: PetscCall(PetscViewerHDF5ReadSizes(viewer, path, NULL, &NVertices));
2280: PetscCall(PetscLayoutCreate(comm, &vertexLayout));
2281: PetscCall(PetscLayoutSetSize(vertexLayout, NVertices));
2282: PetscCall(PetscLayoutSetUp(vertexLayout));
2283: }
2285: PetscCall(PetscSNPrintf(path, sizeof(path), "%" PetscInt_FMT, d));
2286: PetscCall(PetscViewerHDF5PushGroup(viewer, path));
2288: /* create coneSizesSection from stored IS coneSizes */
2289: {
2290: const PetscInt *coneSizes;
2292: PetscCall(ISCreate(comm, &coneSizesIS));
2293: PetscCall(PetscObjectSetName((PetscObject)coneSizesIS, coneSizesName));
2294: if (pointsLayout) PetscCall(ISSetLayout(coneSizesIS, pointsLayout));
2295: PetscCall(ISLoad(coneSizesIS, viewer));
2296: if (!pointsLayout) PetscCall(ISGetLayout(coneSizesIS, &pointsLayout));
2297: PetscCall(ISGetIndices(coneSizesIS, &coneSizes));
2298: PetscCall(PetscSectionCreate(comm, &coneSizesSection));
2299: //TODO different start ?
2300: PetscCall(PetscSectionSetChart(coneSizesSection, 0, pointsLayout->n));
2301: for (s = 0; s < pointsLayout->n; ++s) PetscCall(PetscSectionSetDof(coneSizesSection, s, coneSizes[s]));
2302: PetscCall(PetscSectionSetUp(coneSizesSection));
2303: PetscCall(ISRestoreIndices(coneSizesIS, &coneSizes));
2304: {
2305: PetscLayout tmp = NULL;
2307: /* We need to keep the layout until the end of function */
2308: PetscCall(PetscLayoutReference((PetscLayout)pointsLayout, &tmp));
2309: }
2310: PetscCall(ISDestroy(&coneSizesIS));
2311: }
2313: /* use value layout of coneSizesSection as layout of cones and orientations */
2314: {
2315: PetscLayout conesLayout;
2317: PetscCall(PetscSectionGetValueLayout(comm, coneSizesSection, &conesLayout));
2318: PetscCall(ISCreate(comm, &conesIS));
2319: PetscCall(ISCreate(comm, &orientationsIS));
2320: PetscCall(PetscObjectSetName((PetscObject)conesIS, conesName));
2321: PetscCall(PetscObjectSetName((PetscObject)orientationsIS, orientationsName));
2322: PetscCall(PetscLayoutDuplicate(conesLayout, &conesIS->map));
2323: PetscCall(PetscLayoutDuplicate(conesLayout, &orientationsIS->map));
2324: PetscCall(ISLoad(conesIS, viewer));
2325: PetscCall(ISLoad(orientationsIS, viewer));
2326: PetscCall(PetscLayoutDestroy(&conesLayout));
2327: }
2329: /* check assertion that layout of points is the same as point layout of coneSizesSection */
2330: {
2331: PetscLayout pointsLayout0;
2332: PetscBool flg;
2334: PetscCall(PetscSectionGetPointLayout(comm, coneSizesSection, &pointsLayout0));
2335: PetscCall(PetscLayoutCompare(pointsLayout, pointsLayout0, &flg));
2336: PetscCheck(flg, comm, PETSC_ERR_PLIB, "points layout != coneSizesSection point layout");
2337: PetscCall(PetscLayoutDestroy(&pointsLayout0));
2338: }
2339: PetscCall(PetscViewerHDF5PopGroup(viewer));
2340: PetscCall(PetscLayoutDestroy(&pointsLayout));
2342: layer->d = d;
2343: layer->conesIS = conesIS;
2344: layer->coneSizesSection = coneSizesSection;
2345: layer->orientationsIS = orientationsIS;
2346: layer->vertexLayout = vertexLayout;
2347: PetscFunctionReturn(PETSC_SUCCESS);
2348: }
2350: static PetscErrorCode PlexLayerDistribute_Private(PlexLayer layer, PetscSF cellLocalToGlobalSF)
2351: {
2352: IS newConesIS, newOrientationsIS;
2353: PetscSection newConeSizesSection;
2354: MPI_Comm comm;
2356: PetscFunctionBegin;
2357: PetscCall(PetscObjectGetComm((PetscObject)cellLocalToGlobalSF, &comm));
2358: PetscCall(PetscSectionCreate(comm, &newConeSizesSection));
2359: //TODO rename to something like ISDistribute() with optional PetscSection argument
2360: PetscCall(DMPlexDistributeFieldIS(NULL, cellLocalToGlobalSF, layer->coneSizesSection, layer->conesIS, newConeSizesSection, &newConesIS));
2361: PetscCall(DMPlexDistributeFieldIS(NULL, cellLocalToGlobalSF, layer->coneSizesSection, layer->orientationsIS, newConeSizesSection, &newOrientationsIS));
2363: PetscCall(PetscObjectSetName((PetscObject)newConeSizesSection, ((PetscObject)layer->coneSizesSection)->name));
2364: PetscCall(PetscObjectSetName((PetscObject)newConesIS, ((PetscObject)layer->conesIS)->name));
2365: PetscCall(PetscObjectSetName((PetscObject)newOrientationsIS, ((PetscObject)layer->orientationsIS)->name));
2366: PetscCall(PetscSectionDestroy(&layer->coneSizesSection));
2367: PetscCall(ISDestroy(&layer->conesIS));
2368: PetscCall(ISDestroy(&layer->orientationsIS));
2369: layer->coneSizesSection = newConeSizesSection;
2370: layer->conesIS = newConesIS;
2371: layer->orientationsIS = newOrientationsIS;
2372: PetscFunctionReturn(PETSC_SUCCESS);
2373: }
2375: //TODO share code with DMPlexBuildFromCellListParallel()
2376: #include <petsc/private/hashseti.h>
2377: static PetscErrorCode PlexLayerCreateSFs_Private(PlexLayer layer, PetscSF *vertexOverlapSF, PetscSF *sfXC)
2378: {
2379: PetscLayout vertexLayout = layer->vertexLayout;
2380: PetscSection coneSection = layer->coneSizesSection;
2381: IS cellVertexData = layer->conesIS;
2382: IS coneOrientations = layer->orientationsIS;
2383: PetscSF vl2gSF, vOverlapSF;
2384: PetscInt *verticesAdj;
2385: PetscInt i, n, numVerticesAdj;
2386: const PetscInt *cvd, *co = NULL;
2387: MPI_Comm comm;
2389: PetscFunctionBegin;
2390: PetscCall(PetscObjectGetComm((PetscObject)coneSection, &comm));
2391: PetscCall(PetscSectionGetStorageSize(coneSection, &n));
2392: {
2393: PetscInt n0;
2395: PetscCall(ISGetLocalSize(cellVertexData, &n0));
2396: 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);
2397: PetscCall(ISGetIndices(cellVertexData, &cvd));
2398: }
2399: if (coneOrientations) {
2400: PetscInt n0;
2402: PetscCall(ISGetLocalSize(coneOrientations, &n0));
2403: 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);
2404: PetscCall(ISGetIndices(coneOrientations, &co));
2405: }
2406: /* Get/check global number of vertices */
2407: {
2408: PetscInt NVerticesInCells = PETSC_INT_MIN;
2410: /* NVerticesInCells = max(cellVertexData) + 1 */
2411: for (i = 0; i < n; i++)
2412: if (cvd[i] > NVerticesInCells) NVerticesInCells = cvd[i];
2413: ++NVerticesInCells;
2414: PetscCallMPI(MPIU_Allreduce(MPI_IN_PLACE, &NVerticesInCells, 1, MPIU_INT, MPI_MAX, comm));
2416: if (vertexLayout->n == PETSC_DECIDE && vertexLayout->N == PETSC_DECIDE) vertexLayout->N = NVerticesInCells;
2417: else
2418: 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,
2419: vertexLayout->N, NVerticesInCells);
2420: PetscCall(PetscLayoutSetUp(vertexLayout));
2421: }
2422: /* Find locally unique vertices in cellVertexData */
2423: {
2424: PetscHSetI vhash;
2425: PetscInt off = 0;
2427: PetscCall(PetscHSetICreate(&vhash));
2428: for (i = 0; i < n; ++i) PetscCall(PetscHSetIAdd(vhash, cvd[i]));
2429: PetscCall(PetscHSetIGetSize(vhash, &numVerticesAdj));
2430: PetscCall(PetscMalloc1(numVerticesAdj, &verticesAdj));
2431: PetscCall(PetscHSetIGetElems(vhash, &off, verticesAdj));
2432: PetscAssert(off == numVerticesAdj, PETSC_COMM_SELF, PETSC_ERR_PLIB, "Assertion failed: off == numVerticesAdj (%" PetscInt_FMT " != %" PetscInt_FMT ")", off, numVerticesAdj);
2433: PetscCall(PetscHSetIDestroy(&vhash));
2434: }
2435: /* We must sort vertices to preserve numbering */
2436: PetscCall(PetscSortInt(numVerticesAdj, verticesAdj));
2437: /* Connect locally unique vertices with star forest */
2438: PetscCall(PetscSFCreateByMatchingIndices(vertexLayout, numVerticesAdj, verticesAdj, NULL, 0, numVerticesAdj, verticesAdj, NULL, 0, &vl2gSF, &vOverlapSF));
2439: PetscCall(PetscObjectSetName((PetscObject)vOverlapSF, "overlapSF"));
2440: PetscCall(PetscObjectSetName((PetscObject)vl2gSF, "localToGlobalSF"));
2442: PetscCall(PetscFree(verticesAdj));
2443: *vertexOverlapSF = vOverlapSF;
2444: *sfXC = vl2gSF;
2445: PetscFunctionReturn(PETSC_SUCCESS);
2446: }
2448: static PetscErrorCode PlexLayerCreateCellSFs_Private(PlexLayer layer, PetscSF *cellOverlapSF, PetscSF *cellLocalToGlobalSF)
2449: {
2450: PetscSection coneSection = layer->coneSizesSection;
2451: PetscInt nCells;
2452: MPI_Comm comm;
2454: PetscFunctionBegin;
2455: PetscCall(PetscObjectGetComm((PetscObject)coneSection, &comm));
2456: {
2457: PetscInt cStart;
2459: PetscCall(PetscSectionGetChart(coneSection, &cStart, &nCells));
2460: PetscCheck(cStart == 0, comm, PETSC_ERR_ARG_OUTOFRANGE, "coneSection must start at 0");
2461: }
2462: /* Create overlapSF as empty SF with the right number of roots */
2463: PetscCall(PetscSFCreate(comm, cellOverlapSF));
2464: PetscCall(PetscSFSetGraph(*cellOverlapSF, nCells, 0, NULL, PETSC_USE_POINTER, NULL, PETSC_USE_POINTER));
2465: PetscCall(PetscSFSetUp(*cellOverlapSF));
2466: /* Create localToGlobalSF as identity mapping */
2467: {
2468: PetscLayout map;
2470: PetscCall(PetscLayoutCreateFromSizes(comm, nCells, PETSC_DECIDE, 1, &map));
2471: PetscCall(PetscSFCreateFromLayouts(map, map, cellLocalToGlobalSF));
2472: PetscCall(PetscSFSetUp(*cellLocalToGlobalSF));
2473: PetscCall(PetscLayoutDestroy(&map));
2474: }
2475: PetscFunctionReturn(PETSC_SUCCESS);
2476: }
2478: static PetscErrorCode DMPlexTopologyBuildFromLayers_Private(DM dm, PetscInt depth, PlexLayer *layers, IS strataPermutation)
2479: {
2480: const PetscInt *permArr;
2481: PetscInt d, nPoints;
2482: MPI_Comm comm;
2484: PetscFunctionBegin;
2485: PetscCall(PetscObjectGetComm((PetscObject)dm, &comm));
2486: PetscCall(ISGetIndices(strataPermutation, &permArr));
2488: /* Count points, strata offsets and cones offsets (taking strataPermutation into account) */
2489: {
2490: PetscInt stratumOffset = 0;
2491: PetscInt conesOffset = 0;
2493: for (d = 0; d <= depth; d++) {
2494: const PetscInt e = permArr[d];
2495: const PlexLayer l = layers[e];
2496: PetscInt lo, n, size;
2498: PetscCall(PetscSectionGetChart(l->coneSizesSection, &lo, &n));
2499: PetscCall(PetscSectionGetStorageSize(l->coneSizesSection, &size));
2500: PetscCheck(lo == 0, comm, PETSC_ERR_PLIB, "starting point should be 0 in coneSizesSection %" PetscInt_FMT, d);
2501: l->offset = stratumOffset;
2502: l->conesOffset = conesOffset;
2503: stratumOffset += n;
2504: conesOffset += size;
2505: }
2506: nPoints = stratumOffset;
2507: }
2509: /* Set interval for all plex points */
2510: //TODO we should store starting point of plex
2511: PetscCall(DMPlexSetChart(dm, 0, nPoints));
2513: /* Set up plex coneSection from layer coneSections */
2514: {
2515: PetscSection coneSection;
2517: PetscCall(DMPlexGetConeSection(dm, &coneSection));
2518: for (d = 0; d <= depth; d++) {
2519: const PlexLayer l = layers[d];
2520: PetscInt n, q;
2522: PetscCall(PetscSectionGetChart(l->coneSizesSection, NULL, &n));
2523: for (q = 0; q < n; q++) {
2524: const PetscInt p = l->offset + q;
2525: PetscInt coneSize;
2527: PetscCall(PetscSectionGetDof(l->coneSizesSection, q, &coneSize));
2528: PetscCall(PetscSectionSetDof(coneSection, p, coneSize));
2529: }
2530: }
2531: }
2532: //TODO this is terrible, DMSetUp_Plex() should be DMPlexSetUpSections() or so
2533: PetscCall(DMSetUp(dm));
2535: /* Renumber cones points from layer-global numbering to plex-local numbering */
2536: {
2537: PetscInt *cones, *ornts;
2539: PetscCall(DMPlexGetCones(dm, &cones));
2540: PetscCall(DMPlexGetConeOrientations(dm, &ornts));
2541: for (d = 1; d <= depth; d++) {
2542: const PlexLayer l = layers[d];
2543: PetscInt i, lConesSize;
2544: PetscInt *lCones;
2545: const PetscInt *lOrnts;
2546: PetscInt *pCones = &cones[l->conesOffset];
2547: PetscInt *pOrnts = &ornts[l->conesOffset];
2549: PetscCall(PetscSectionGetStorageSize(l->coneSizesSection, &lConesSize));
2550: /* Get cones in local plex numbering */
2551: {
2552: ISLocalToGlobalMapping l2g;
2553: PetscLayout vertexLayout = l->vertexLayout;
2554: PetscSF vertexSF = layers[d - 1]->l2gSF; /* vertices of this layer are cells of previous layer */
2555: const PetscInt *gCones;
2556: PetscInt lConesSize0;
2558: PetscCall(ISGetLocalSize(l->conesIS, &lConesSize0));
2559: PetscCheck(lConesSize0 == lConesSize, comm, PETSC_ERR_PLIB, "layer %" PetscInt_FMT " size(conesIS) = %" PetscInt_FMT " != %" PetscInt_FMT " = storageSize(coneSizesSection)", d, lConesSize0, lConesSize);
2560: PetscCall(ISGetLocalSize(l->orientationsIS, &lConesSize0));
2561: PetscCheck(lConesSize0 == lConesSize, comm, PETSC_ERR_PLIB, "layer %" PetscInt_FMT " size(orientationsIS) = %" PetscInt_FMT " != %" PetscInt_FMT " = storageSize(coneSizesSection)", d, lConesSize0, lConesSize);
2563: PetscCall(PetscMalloc1(lConesSize, &lCones));
2564: PetscCall(ISGetIndices(l->conesIS, &gCones));
2565: PetscCall(ISLocalToGlobalMappingCreateSF(vertexSF, vertexLayout->rstart, &l2g));
2566: PetscCall(ISGlobalToLocalMappingApply(l2g, IS_GTOLM_MASK, lConesSize, gCones, &lConesSize0, lCones));
2567: PetscCheck(lConesSize0 == lConesSize, comm, PETSC_ERR_PLIB, "global to local does not cover all indices (%" PetscInt_FMT " of %" PetscInt_FMT ")", lConesSize0, lConesSize);
2568: PetscCall(ISLocalToGlobalMappingDestroy(&l2g));
2569: PetscCall(ISRestoreIndices(l->conesIS, &gCones));
2570: }
2571: PetscCall(ISGetIndices(l->orientationsIS, &lOrnts));
2572: /* Set cones, need to add stratum offset */
2573: for (i = 0; i < lConesSize; i++) {
2574: pCones[i] = lCones[i] + layers[d - 1]->offset; /* cone points of current layer are points of previous layer */
2575: pOrnts[i] = lOrnts[i];
2576: }
2577: PetscCall(PetscFree(lCones));
2578: PetscCall(ISRestoreIndices(l->orientationsIS, &lOrnts));
2579: }
2580: }
2581: PetscCall(DMPlexSymmetrize(dm));
2582: PetscCall(DMPlexStratify(dm));
2583: PetscCall(ISRestoreIndices(strataPermutation, &permArr));
2584: PetscFunctionReturn(PETSC_SUCCESS);
2585: }
2587: static PetscErrorCode PlexLayerConcatenateSFs_Private(MPI_Comm comm, PetscInt depth, PlexLayer layers[], IS strataPermutation, PetscSF *overlapSF, PetscSF *l2gSF)
2588: {
2589: PetscInt d;
2590: PetscSF *osfs, *lsfs;
2591: PetscInt *leafOffsets;
2592: const PetscInt *permArr;
2594: PetscFunctionBegin;
2595: PetscCall(ISGetIndices(strataPermutation, &permArr));
2596: PetscCall(PetscCalloc3(depth + 1, &osfs, depth + 1, &lsfs, depth + 1, &leafOffsets));
2597: for (d = 0; d <= depth; d++) {
2598: const PetscInt e = permArr[d];
2600: PetscAssert(e == layers[e]->d, PETSC_COMM_SELF, PETSC_ERR_PLIB, "assertion: e == layers[e]->d");
2601: osfs[d] = layers[e]->overlapSF;
2602: lsfs[d] = layers[e]->l2gSF;
2603: leafOffsets[d] = layers[e]->offset;
2604: }
2605: PetscCall(PetscSFConcatenate(comm, depth + 1, osfs, PETSCSF_CONCATENATE_ROOTMODE_LOCAL, leafOffsets, overlapSF));
2606: PetscCall(PetscSFConcatenate(comm, depth + 1, lsfs, PETSCSF_CONCATENATE_ROOTMODE_GLOBAL, leafOffsets, l2gSF));
2607: PetscCall(PetscFree3(osfs, lsfs, leafOffsets));
2608: PetscCall(ISRestoreIndices(strataPermutation, &permArr));
2609: PetscFunctionReturn(PETSC_SUCCESS);
2610: }
2612: // Parallel load of topology
2613: static PetscErrorCode DMPlexTopologyLoad_HDF5_Private(DM dm, PetscViewer viewer, PetscSF *sfXC)
2614: {
2615: PlexLayer *layers;
2616: IS strataPermutation;
2617: PetscLayout pointsLayout;
2618: PetscInt depth;
2619: PetscInt d;
2620: MPI_Comm comm;
2622: PetscFunctionBegin;
2623: {
2624: PetscInt dim;
2626: PetscCall(PetscViewerHDF5ReadAttribute(viewer, NULL, "depth", PETSC_INT, NULL, &depth));
2627: PetscCall(PetscViewerHDF5ReadAttribute(viewer, NULL, "cell_dim", PETSC_INT, NULL, &dim));
2628: PetscCall(DMSetDimension(dm, dim));
2629: }
2630: PetscCall(PetscObjectGetComm((PetscObject)dm, &comm));
2632: PetscCall(PetscInfo(dm, "Loading DM %s in parallel\n", dm->hdr.name));
2633: {
2634: IS spOnComm;
2636: PetscCall(ISCreate(comm, &spOnComm));
2637: PetscCall(PetscObjectSetName((PetscObject)spOnComm, "permutation"));
2638: PetscCall(ISLoad(spOnComm, viewer));
2639: /* have the same serial IS on every rank */
2640: PetscCall(ISAllGather(spOnComm, &strataPermutation));
2641: PetscCall(PetscObjectSetName((PetscObject)strataPermutation, ((PetscObject)spOnComm)->name));
2642: PetscCall(ISDestroy(&spOnComm));
2643: }
2645: /* Create layers, load raw data for each layer */
2646: PetscCall(PetscViewerHDF5PushGroup(viewer, "strata"));
2647: PetscCall(PetscMalloc1(depth + 1, &layers));
2648: for (d = depth, pointsLayout = NULL; d >= 0; pointsLayout = layers[d]->vertexLayout, d--) {
2649: PetscCall(PlexLayerCreate_Private(&layers[d]));
2650: PetscCall(PlexLayerLoad_Private(layers[d], viewer, d, pointsLayout));
2651: }
2652: PetscCall(PetscViewerHDF5PopGroup(viewer)); /* strata */
2654: for (d = depth; d >= 0; d--) {
2655: /* Redistribute cells and vertices for each applicable layer */
2656: if (d < depth) PetscCall(PlexLayerDistribute_Private(layers[d], layers[d]->l2gSF));
2657: /* Create vertex overlap SF and vertex localToGlobal SF for each applicable layer */
2658: if (d > 0) PetscCall(PlexLayerCreateSFs_Private(layers[d], &layers[d - 1]->overlapSF, &layers[d - 1]->l2gSF));
2659: }
2660: /* Build trivial SFs for the cell layer as well */
2661: PetscCall(PlexLayerCreateCellSFs_Private(layers[depth], &layers[depth]->overlapSF, &layers[depth]->l2gSF));
2663: /* Build DMPlex topology from the layers */
2664: PetscCall(DMPlexTopologyBuildFromLayers_Private(dm, depth, layers, strataPermutation));
2666: /* Build overall point SF alias overlap SF */
2667: {
2668: PetscSF overlapSF;
2670: PetscCall(PlexLayerConcatenateSFs_Private(comm, depth, layers, strataPermutation, &overlapSF, sfXC));
2671: PetscCall(DMSetPointSF(dm, overlapSF));
2672: PetscCall(PetscSFDestroy(&overlapSF));
2673: }
2675: for (d = depth; d >= 0; d--) PetscCall(PlexLayerDestroy(&layers[d]));
2676: PetscCall(PetscFree(layers));
2677: PetscCall(ISDestroy(&strataPermutation));
2678: PetscFunctionReturn(PETSC_SUCCESS);
2679: }
2681: PetscErrorCode DMPlexTopologyLoad_HDF5_Internal(DM dm, PetscViewer viewer, PetscSF *sfXC)
2682: {
2683: DMPlexStorageVersion version;
2684: const char *topologydm_name;
2685: char group[PETSC_MAX_PATH_LEN];
2686: PetscSF sfwork = NULL;
2688: PetscFunctionBegin;
2689: PetscCall(DMPlexGetHDF5Name_Private(dm, &topologydm_name));
2690: PetscCall(PetscViewerHDF5GetDMPlexStorageVersionReading(viewer, &version));
2691: if (DMPlexStorageVersionGE(version, 2, 0, 0)) {
2692: PetscCall(PetscSNPrintf(group, sizeof(group), "topologies/%s", topologydm_name));
2693: } else {
2694: PetscCall(PetscStrncpy(group, "/", sizeof(group)));
2695: }
2696: PetscCall(PetscViewerHDF5PushGroup(viewer, group));
2698: PetscCall(PetscViewerHDF5PushGroup(viewer, "topology"));
2699: if (version->major < 3) {
2700: PetscCall(DMPlexTopologyLoad_HDF5_Legacy_Private(dm, viewer, &sfwork));
2701: } else {
2702: /* since DMPlexStorageVersion 3.0.0 */
2703: PetscCall(DMPlexTopologyLoad_HDF5_Private(dm, viewer, &sfwork));
2704: }
2705: PetscCall(PetscViewerHDF5PopGroup(viewer)); /* "topology" */
2707: if (DMPlexStorageVersionGE(version, 2, 0, 0)) {
2708: DM distdm;
2709: PetscSF distsf;
2710: const char *distribution_name;
2711: PetscBool exists;
2713: PetscCall(DMPlexDistributionGetName(dm, &distribution_name));
2714: /* this group is guaranteed to be present since DMPlexStorageVersion 2.1.0 */
2715: PetscCall(PetscViewerHDF5PushGroup(viewer, "distributions"));
2716: PetscCall(PetscViewerHDF5HasGroup(viewer, NULL, &exists));
2717: if (exists) {
2718: PetscCall(PetscViewerHDF5PushGroup(viewer, distribution_name));
2719: PetscCall(DMPlexDistributionLoad_HDF5_Private(dm, viewer, sfwork, &distsf, &distdm));
2720: if (distdm) {
2721: PetscCall(DMPlexReplace_Internal(dm, &distdm));
2722: PetscCall(PetscSFDestroy(&sfwork));
2723: sfwork = distsf;
2724: }
2725: PetscCall(PetscViewerHDF5PopGroup(viewer)); /* distribution_name */
2726: }
2727: PetscCall(PetscViewerHDF5PopGroup(viewer)); /* "distributions" */
2728: }
2729: if (sfXC) {
2730: *sfXC = sfwork;
2731: } else {
2732: PetscCall(PetscSFDestroy(&sfwork));
2733: }
2735: PetscCall(PetscViewerHDF5PopGroup(viewer));
2736: PetscFunctionReturn(PETSC_SUCCESS);
2737: }
2739: /* If the file is old, it not only has different path to the coordinates, but */
2740: /* does not contain coordinateDMs, so must fall back to the old implementation. */
2741: static PetscErrorCode DMPlexCoordinatesLoad_HDF5_Legacy_Private(DM dm, PetscViewer viewer)
2742: {
2743: PetscSection coordSection;
2744: Vec coordinates;
2745: PetscReal lengthScale;
2746: PetscInt spatialDim, N, numVertices, vStart, vEnd, v;
2747: PetscMPIInt rank;
2749: PetscFunctionBegin;
2750: PetscCallMPI(MPI_Comm_rank(PetscObjectComm((PetscObject)dm), &rank));
2751: /* Read geometry */
2752: PetscCall(PetscViewerHDF5PushGroup(viewer, "/geometry"));
2753: PetscCall(VecCreate(PetscObjectComm((PetscObject)dm), &coordinates));
2754: PetscCall(PetscObjectSetName((PetscObject)coordinates, "vertices"));
2755: {
2756: /* Force serial load */
2757: PetscCall(PetscViewerHDF5ReadSizes(viewer, "vertices", &spatialDim, &N));
2758: PetscCall(VecSetSizes(coordinates, rank == 0 ? N : 0, N));
2759: PetscCall(VecSetBlockSize(coordinates, spatialDim));
2760: }
2761: PetscCall(VecLoad(coordinates, viewer));
2762: PetscCall(PetscViewerHDF5PopGroup(viewer));
2763: PetscCall(DMPlexGetScale(dm, PETSC_UNIT_LENGTH, &lengthScale));
2764: PetscCall(VecScale(coordinates, 1.0 / lengthScale));
2765: PetscCall(VecGetLocalSize(coordinates, &numVertices));
2766: PetscCall(VecGetBlockSize(coordinates, &spatialDim));
2767: numVertices /= spatialDim;
2768: /* Create coordinates */
2769: PetscCall(DMPlexGetDepthStratum(dm, 0, &vStart, &vEnd));
2770: 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);
2771: PetscCall(DMGetCoordinateSection(dm, &coordSection));
2772: PetscCall(PetscSectionSetNumFields(coordSection, 1));
2773: PetscCall(PetscSectionSetFieldComponents(coordSection, 0, spatialDim));
2774: PetscCall(PetscSectionSetChart(coordSection, vStart, vEnd));
2775: for (v = vStart; v < vEnd; ++v) {
2776: PetscCall(PetscSectionSetDof(coordSection, v, spatialDim));
2777: PetscCall(PetscSectionSetFieldDof(coordSection, v, 0, spatialDim));
2778: }
2779: PetscCall(PetscSectionSetUp(coordSection));
2780: PetscCall(DMSetCoordinates(dm, coordinates));
2781: PetscCall(VecDestroy(&coordinates));
2782: PetscFunctionReturn(PETSC_SUCCESS);
2783: }
2785: PetscErrorCode DMPlexCoordinatesLoad_HDF5_Internal(DM dm, PetscViewer viewer, PetscSF sfXC)
2786: {
2787: DMPlexStorageVersion version;
2788: DM cdm;
2789: Vec coords;
2790: PetscInt blockSize;
2791: PetscReal lengthScale;
2792: PetscSF lsf;
2793: const char *topologydm_name;
2794: char *coordinatedm_name, *coordinates_name;
2796: PetscFunctionBegin;
2797: PetscCall(PetscViewerHDF5GetDMPlexStorageVersionReading(viewer, &version));
2798: if (!DMPlexStorageVersionGE(version, 2, 0, 0)) {
2799: PetscCall(DMPlexCoordinatesLoad_HDF5_Legacy_Private(dm, viewer));
2800: PetscFunctionReturn(PETSC_SUCCESS);
2801: }
2802: /* else: since DMPlexStorageVersion 2.0.0 */
2803: PetscCheck(sfXC, PetscObjectComm((PetscObject)dm), PETSC_ERR_ARG_NULL, "PetscSF must be given for parallel load");
2804: PetscCall(DMPlexGetHDF5Name_Private(dm, &topologydm_name));
2805: PetscCall(PetscViewerHDF5PushGroup(viewer, "topologies"));
2806: PetscCall(PetscViewerHDF5PushGroup(viewer, topologydm_name));
2807: PetscCall(PetscViewerHDF5ReadAttribute(viewer, NULL, "coordinateDMName", PETSC_STRING, NULL, &coordinatedm_name));
2808: PetscCall(PetscViewerHDF5ReadAttribute(viewer, NULL, "coordinatesName", PETSC_STRING, NULL, &coordinates_name));
2809: PetscCall(PetscViewerHDF5PopGroup(viewer));
2810: PetscCall(PetscViewerHDF5PopGroup(viewer));
2811: PetscCall(DMGetCoordinateDM(dm, &cdm));
2812: PetscCall(PetscObjectSetName((PetscObject)cdm, coordinatedm_name));
2813: PetscCall(PetscFree(coordinatedm_name));
2814: /* lsf: on-disk data -> in-memory local vector associated with cdm's local section */
2815: PetscCall(DMPlexSectionLoad(dm, viewer, cdm, sfXC, NULL, &lsf));
2816: PetscCall(DMCreateLocalVector(cdm, &coords));
2817: PetscCall(PetscObjectSetName((PetscObject)coords, coordinates_name));
2818: PetscCall(PetscFree(coordinates_name));
2819: PetscCall(PetscViewerPushFormat(viewer, PETSC_VIEWER_NATIVE));
2820: PetscCall(DMPlexLocalVectorLoad(dm, viewer, cdm, lsf, coords));
2821: PetscCall(PetscViewerPopFormat(viewer));
2822: PetscCall(DMPlexGetScale(dm, PETSC_UNIT_LENGTH, &lengthScale));
2823: PetscCall(VecScale(coords, 1.0 / lengthScale));
2824: PetscCall(DMSetCoordinatesLocal(dm, coords));
2825: PetscCall(VecGetBlockSize(coords, &blockSize));
2826: PetscCall(DMSetCoordinateDim(dm, blockSize));
2827: PetscCall(VecDestroy(&coords));
2828: PetscCall(PetscSFDestroy(&lsf));
2829: PetscFunctionReturn(PETSC_SUCCESS);
2830: }
2832: PetscErrorCode DMPlexLoad_HDF5_Internal(DM dm, PetscViewer viewer)
2833: {
2834: DMPlexStorageVersion version;
2836: PetscFunctionBegin;
2837: PetscCall(PetscViewerHDF5GetDMPlexStorageVersionReading(viewer, &version));
2838: PetscCall(PetscInfo(dm, "Loading DM %s storage version %d.%d.%d\n", dm->hdr.name, version->major, version->minor, version->subminor));
2839: if (!DMPlexStorageVersionGE(version, 2, 0, 0)) {
2840: PetscCall(DMPlexTopologyLoad_HDF5_Internal(dm, viewer, NULL));
2841: PetscCall(DMPlexLabelsLoad_HDF5_Internal(dm, viewer, NULL));
2842: PetscCall(DMPlexCoordinatesLoad_HDF5_Legacy_Private(dm, viewer));
2843: } else {
2844: PetscSF sfXC;
2846: /* since DMPlexStorageVersion 2.0.0 */
2847: PetscCall(DMPlexTopologyLoad_HDF5_Internal(dm, viewer, &sfXC));
2848: PetscCall(DMPlexLabelsLoad_HDF5_Internal(dm, viewer, sfXC));
2849: PetscCall(DMPlexCoordinatesLoad_HDF5_Internal(dm, viewer, sfXC));
2850: PetscCall(PetscSFDestroy(&sfXC));
2851: }
2852: PetscFunctionReturn(PETSC_SUCCESS);
2853: }
2855: static PetscErrorCode DMPlexSectionLoad_HDF5_Internal_CreateDataSF(PetscSection rootSection, PetscLayout layout, PetscInt globalOffsets[], PetscSection leafSection, PetscSF *sectionSF)
2856: {
2857: MPI_Comm comm;
2858: PetscInt pStart, pEnd, p, m;
2859: PetscInt *goffs, *ilocal;
2860: PetscBool rootIncludeConstraints, leafIncludeConstraints;
2862: PetscFunctionBegin;
2863: PetscCall(PetscObjectGetComm((PetscObject)leafSection, &comm));
2864: PetscCall(PetscSectionGetChart(leafSection, &pStart, &pEnd));
2865: PetscCall(PetscSectionGetIncludesConstraints(rootSection, &rootIncludeConstraints));
2866: PetscCall(PetscSectionGetIncludesConstraints(leafSection, &leafIncludeConstraints));
2867: if (rootIncludeConstraints && leafIncludeConstraints) PetscCall(PetscSectionGetStorageSize(leafSection, &m));
2868: else PetscCall(PetscSectionGetConstrainedStorageSize(leafSection, &m));
2869: PetscCall(PetscMalloc1(m, &ilocal));
2870: PetscCall(PetscMalloc1(m, &goffs));
2871: /* Currently, PetscSFDistributeSection() returns globalOffsets[] only */
2872: /* for the top-level section (not for each field), so one must have */
2873: /* rootSection->pointMajor == PETSC_TRUE. */
2874: PetscCheck(rootSection->pointMajor, PETSC_COMM_SELF, PETSC_ERR_SUP, "No support for field major ordering");
2875: /* Currently, we also assume that leafSection->pointMajor == PETSC_TRUE. */
2876: PetscCheck(leafSection->pointMajor, PETSC_COMM_SELF, PETSC_ERR_SUP, "No support for field major ordering");
2877: for (p = pStart, m = 0; p < pEnd; ++p) {
2878: PetscInt dof, cdof, i, j, off, goff;
2879: const PetscInt *cinds;
2881: PetscCall(PetscSectionGetDof(leafSection, p, &dof));
2882: if (dof < 0) continue;
2883: goff = globalOffsets[p - pStart];
2884: PetscCall(PetscSectionGetOffset(leafSection, p, &off));
2885: PetscCall(PetscSectionGetConstraintDof(leafSection, p, &cdof));
2886: PetscCall(PetscSectionGetConstraintIndices(leafSection, p, &cinds));
2887: for (i = 0, j = 0; i < dof; ++i) {
2888: PetscBool constrained = (PetscBool)(j < cdof && i == cinds[j]);
2890: if (!constrained || (leafIncludeConstraints && rootIncludeConstraints)) {
2891: ilocal[m] = off++;
2892: goffs[m++] = goff++;
2893: } else if (leafIncludeConstraints && !rootIncludeConstraints) ++off;
2894: else if (!leafIncludeConstraints && rootIncludeConstraints) ++goff;
2895: if (constrained) ++j;
2896: }
2897: }
2898: PetscCall(PetscSFCreate(comm, sectionSF));
2899: PetscCall(PetscSFSetFromOptions(*sectionSF));
2900: PetscCall(PetscSFSetGraphLayout(*sectionSF, layout, m, ilocal, PETSC_OWN_POINTER, goffs));
2901: PetscCall(PetscFree(goffs));
2902: PetscFunctionReturn(PETSC_SUCCESS);
2903: }
2905: PetscErrorCode DMPlexSectionLoad_HDF5_Internal(DM dm, PetscViewer viewer, DM sectiondm, PetscSF sfXB, PetscSF *gsf, PetscSF *lsf)
2906: {
2907: MPI_Comm comm;
2908: PetscMPIInt size, rank;
2909: const char *topologydm_name;
2910: const char *sectiondm_name;
2911: PetscSection sectionA, sectionB;
2912: PetscBool has;
2913: PetscInt nX, n, i;
2914: PetscSF sfAB;
2916: PetscFunctionBegin;
2917: PetscCall(PetscObjectGetComm((PetscObject)dm, &comm));
2918: PetscCallMPI(MPI_Comm_size(comm, &size));
2919: PetscCallMPI(MPI_Comm_rank(comm, &rank));
2920: PetscCall(DMPlexGetHDF5Name_Private(dm, &topologydm_name));
2921: PetscCall(PetscObjectGetName((PetscObject)sectiondm, §iondm_name));
2922: PetscCall(PetscViewerHDF5PushGroup(viewer, "topologies"));
2923: PetscCall(PetscViewerHDF5PushGroup(viewer, topologydm_name));
2924: PetscCall(PetscViewerHDF5PushGroup(viewer, "dms"));
2925: PetscCall(PetscViewerHDF5PushGroup(viewer, sectiondm_name));
2926: /* A: on-disk points */
2927: /* X: list of global point numbers, [0, NX) */
2928: /* B: plex points */
2929: /* Load raw section (sectionA) */
2930: PetscCall(PetscSectionCreate(comm, §ionA));
2931: PetscCall(PetscViewerHDF5HasGroup(viewer, "section", &has));
2932: if (has) PetscCall(PetscSectionLoad(sectionA, viewer));
2933: else {
2934: // TODO If section is missing, create the default affine section with dim dofs on each vertex. Use PetscSplitOwnership() to split vertices.
2935: // How do I know the total number of vertices?
2936: PetscInt dim, Nf = 1, Nv, nv = PETSC_DECIDE;
2938: PetscCall(DMGetDimension(dm, &dim));
2939: PetscCall(DMPlexGetDepthStratumGlobalSize(dm, 0, &Nv));
2940: PetscCall(PetscSectionSetNumFields(sectionA, Nf));
2941: PetscCall(PetscSectionSetFieldName(sectionA, 0, "Cartesian"));
2942: PetscCall(PetscSectionSetFieldComponents(sectionA, 0, dim));
2943: for (PetscInt c = 0; c < dim; ++c) {
2944: char axis = 'X' + (char)c;
2946: PetscCall(PetscSectionSetComponentName(sectionA, 0, c, &axis));
2947: }
2948: PetscCall(PetscSplitOwnership(comm, &nv, &Nv));
2949: PetscCall(PetscSectionSetChart(sectionA, 0, nv));
2950: for (PetscInt p = 0; p < nv; ++p) {
2951: PetscCall(PetscSectionSetDof(sectionA, p, dim));
2952: PetscCall(PetscSectionSetFieldDof(sectionA, p, 0, dim));
2953: }
2954: PetscCall(PetscSectionSetUp(sectionA));
2955: }
2956: PetscCall(PetscSectionGetChart(sectionA, NULL, &n));
2957: /* Create sfAB: A -> B */
2958: #if defined(PETSC_USE_DEBUG)
2959: {
2960: PetscInt N, N1;
2962: PetscCall(PetscViewerHDF5ReadSizes(viewer, "order", NULL, &N1));
2963: PetscCallMPI(MPIU_Allreduce(&n, &N, 1, MPIU_INT, MPI_SUM, comm));
2964: 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);
2965: }
2966: #endif
2967: {
2968: IS orderIS;
2969: const PetscInt *gpoints;
2970: PetscSF sfXA, sfAX;
2971: PetscLayout layout;
2972: PetscSFNode *owners, *buffer;
2973: PetscInt nleaves;
2974: PetscInt *ilocal;
2975: PetscSFNode *iremote;
2977: /* Create sfAX: A -> X */
2978: PetscCall(ISCreate(comm, &orderIS));
2979: PetscCall(PetscObjectSetName((PetscObject)orderIS, "order"));
2980: PetscCall(PetscLayoutSetLocalSize(orderIS->map, n));
2981: PetscCall(ISLoad(orderIS, viewer));
2982: PetscCall(PetscLayoutCreate(comm, &layout));
2983: PetscCall(PetscSFGetGraph(sfXB, &nX, NULL, NULL, NULL));
2984: PetscCall(PetscLayoutSetLocalSize(layout, nX));
2985: PetscCall(PetscLayoutSetBlockSize(layout, 1));
2986: PetscCall(PetscLayoutSetUp(layout));
2987: PetscCall(PetscSFCreate(comm, &sfXA));
2988: PetscCall(ISGetIndices(orderIS, &gpoints));
2989: PetscCall(PetscSFSetGraphLayout(sfXA, layout, n, NULL, PETSC_OWN_POINTER, gpoints));
2990: PetscCall(ISRestoreIndices(orderIS, &gpoints));
2991: PetscCall(ISDestroy(&orderIS));
2992: PetscCall(PetscLayoutDestroy(&layout));
2993: PetscCall(PetscMalloc1(n, &owners));
2994: PetscCall(PetscMalloc1(nX, &buffer));
2995: for (i = 0; i < n; ++i) {
2996: owners[i].rank = rank;
2997: owners[i].index = i;
2998: }
2999: for (i = 0; i < nX; ++i) {
3000: buffer[i].rank = -1;
3001: buffer[i].index = -1;
3002: }
3003: PetscCall(PetscSFReduceBegin(sfXA, MPIU_SF_NODE, owners, buffer, MPI_MAXLOC));
3004: PetscCall(PetscSFReduceEnd(sfXA, MPIU_SF_NODE, owners, buffer, MPI_MAXLOC));
3005: PetscCall(PetscSFDestroy(&sfXA));
3006: PetscCall(PetscFree(owners));
3007: for (i = 0, nleaves = 0; i < nX; ++i)
3008: if (buffer[i].rank >= 0) nleaves++;
3009: PetscCall(PetscMalloc1(nleaves, &ilocal));
3010: PetscCall(PetscMalloc1(nleaves, &iremote));
3011: for (i = 0, nleaves = 0; i < nX; ++i) {
3012: if (buffer[i].rank >= 0) {
3013: ilocal[nleaves] = i;
3014: iremote[nleaves].rank = buffer[i].rank;
3015: iremote[nleaves].index = buffer[i].index;
3016: nleaves++;
3017: }
3018: }
3019: PetscCall(PetscFree(buffer));
3020: PetscCall(PetscSFCreate(comm, &sfAX));
3021: PetscCall(PetscSFSetFromOptions(sfAX));
3022: PetscCall(PetscSFSetGraph(sfAX, n, nleaves, ilocal, PETSC_OWN_POINTER, iremote, PETSC_OWN_POINTER));
3023: PetscCall(PetscSFCompose(sfAX, sfXB, &sfAB));
3024: PetscCall(PetscSFDestroy(&sfAX));
3025: }
3026: PetscCall(PetscViewerHDF5PopGroup(viewer));
3027: PetscCall(PetscViewerHDF5PopGroup(viewer));
3028: PetscCall(PetscViewerHDF5PopGroup(viewer));
3029: PetscCall(PetscViewerHDF5PopGroup(viewer));
3030: /* Create plex section (sectionB) */
3031: PetscCall(DMGetLocalSection(sectiondm, §ionB));
3032: if (lsf || gsf) {
3033: PetscLayout layout;
3034: PetscInt M, m;
3035: PetscInt *offsetsA;
3036: PetscBool includesConstraintsA;
3038: PetscCall(PetscSFDistributeSection(sfAB, sectionA, &offsetsA, sectionB));
3039: PetscCall(PetscSectionGetIncludesConstraints(sectionA, &includesConstraintsA));
3040: if (includesConstraintsA) PetscCall(PetscSectionGetStorageSize(sectionA, &m));
3041: else PetscCall(PetscSectionGetConstrainedStorageSize(sectionA, &m));
3042: PetscCallMPI(MPIU_Allreduce(&m, &M, 1, MPIU_INT, MPI_SUM, comm));
3043: PetscCall(PetscLayoutCreate(comm, &layout));
3044: PetscCall(PetscLayoutSetSize(layout, M));
3045: PetscCall(PetscLayoutSetUp(layout));
3046: if (lsf) {
3047: PetscSF lsfABdata;
3049: PetscCall(DMPlexSectionLoad_HDF5_Internal_CreateDataSF(sectionA, layout, offsetsA, sectionB, &lsfABdata));
3050: *lsf = lsfABdata;
3051: }
3052: if (gsf) {
3053: PetscSection gsectionB, gsectionB1;
3054: PetscBool includesConstraintsB;
3055: PetscSF gsfABdata, pointsf;
3057: PetscCall(DMGetGlobalSection(sectiondm, &gsectionB1));
3058: PetscCall(PetscSectionGetIncludesConstraints(gsectionB1, &includesConstraintsB));
3059: PetscCall(DMGetPointSF(sectiondm, &pointsf));
3060: PetscCall(PetscSectionCreateGlobalSection(sectionB, pointsf, PETSC_TRUE, includesConstraintsB, PETSC_TRUE, &gsectionB));
3061: PetscCall(DMPlexSectionLoad_HDF5_Internal_CreateDataSF(sectionA, layout, offsetsA, gsectionB, &gsfABdata));
3062: PetscCall(PetscSectionDestroy(&gsectionB));
3063: *gsf = gsfABdata;
3064: }
3065: PetscCall(PetscLayoutDestroy(&layout));
3066: PetscCall(PetscFree(offsetsA));
3067: } else {
3068: PetscCall(PetscSFDistributeSection(sfAB, sectionA, NULL, sectionB));
3069: }
3070: PetscCall(PetscSFDestroy(&sfAB));
3071: PetscCall(PetscSectionDestroy(§ionA));
3072: PetscFunctionReturn(PETSC_SUCCESS);
3073: }
3075: PetscErrorCode DMPlexVecLoad_HDF5_Internal(DM dm, PetscViewer viewer, DM sectiondm, PetscSF sf, Vec vec)
3076: {
3077: MPI_Comm comm;
3078: const char *topologydm_name;
3079: const char *sectiondm_name;
3080: const char *vec_name;
3081: Vec vecA;
3082: PetscInt mA, m, bs;
3083: const PetscInt *ilocal;
3084: const PetscScalar *src;
3085: PetscScalar *dest;
3087: PetscFunctionBegin;
3088: PetscCall(PetscObjectGetComm((PetscObject)dm, &comm));
3089: PetscCall(DMPlexGetHDF5Name_Private(dm, &topologydm_name));
3090: PetscCall(PetscObjectGetName((PetscObject)sectiondm, §iondm_name));
3091: PetscCall(PetscObjectGetName((PetscObject)vec, &vec_name));
3092: PetscCall(PetscViewerHDF5PushGroup(viewer, "topologies"));
3093: PetscCall(PetscViewerHDF5PushGroup(viewer, topologydm_name));
3094: PetscCall(PetscViewerHDF5PushGroup(viewer, "dms"));
3095: PetscCall(PetscViewerHDF5PushGroup(viewer, sectiondm_name));
3096: PetscCall(PetscViewerHDF5PushGroup(viewer, "vecs"));
3097: PetscCall(PetscViewerHDF5PushGroup(viewer, vec_name));
3098: PetscCall(VecCreate(comm, &vecA));
3099: PetscCall(PetscObjectSetName((PetscObject)vecA, vec_name));
3100: PetscCall(PetscSFGetGraph(sf, &mA, &m, &ilocal, NULL));
3101: /* Check consistency */
3102: {
3103: PetscSF pointsf, pointsf1;
3104: PetscInt m1, i, j;
3106: PetscCall(DMGetPointSF(dm, &pointsf));
3107: PetscCall(DMGetPointSF(sectiondm, &pointsf1));
3108: PetscCheck(pointsf1 == pointsf, PETSC_COMM_SELF, PETSC_ERR_PLIB, "Mismatching point SFs for dm and sectiondm");
3109: #if defined(PETSC_USE_DEBUG)
3110: {
3111: PetscInt MA, MA1;
3113: PetscCallMPI(MPIU_Allreduce(&mA, &MA, 1, MPIU_INT, MPI_SUM, comm));
3114: PetscCall(PetscViewerHDF5ReadSizes(viewer, vec_name, NULL, &MA1));
3115: PetscCheck(MA1 == MA, PETSC_COMM_SELF, PETSC_ERR_PLIB, "Total SF root size (%" PetscInt_FMT ") != On-disk vector data size (%" PetscInt_FMT ")", MA, MA1);
3116: }
3117: #endif
3118: PetscCall(VecGetLocalSize(vec, &m1));
3119: PetscCheck(m1 >= m, PETSC_COMM_SELF, PETSC_ERR_PLIB, "Target vector size (%" PetscInt_FMT ") < SF leaf size (%" PetscInt_FMT ")", m1, m);
3120: for (i = 0; i < m; ++i) {
3121: j = ilocal ? ilocal[i] : i;
3122: 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);
3123: }
3124: }
3125: PetscCall(VecSetSizes(vecA, mA, PETSC_DECIDE));
3126: PetscCall(VecLoad(vecA, viewer));
3127: PetscCall(VecGetArrayRead(vecA, &src));
3128: PetscCall(VecGetArray(vec, &dest));
3129: PetscCall(PetscSFBcastBegin(sf, MPIU_SCALAR, src, dest, MPI_REPLACE));
3130: PetscCall(PetscSFBcastEnd(sf, MPIU_SCALAR, src, dest, MPI_REPLACE));
3131: PetscCall(VecRestoreArray(vec, &dest));
3132: PetscCall(VecRestoreArrayRead(vecA, &src));
3133: PetscCall(VecDestroy(&vecA));
3134: PetscCall(PetscViewerHDF5ReadAttribute(viewer, NULL, "blockSize", PETSC_INT, NULL, (void *)&bs));
3135: PetscCall(VecSetBlockSize(vec, bs));
3136: PetscCall(PetscViewerHDF5PopGroup(viewer));
3137: PetscCall(PetscViewerHDF5PopGroup(viewer));
3138: PetscCall(PetscViewerHDF5PopGroup(viewer));
3139: PetscCall(PetscViewerHDF5PopGroup(viewer));
3140: PetscCall(PetscViewerHDF5PopGroup(viewer));
3141: PetscCall(PetscViewerHDF5PopGroup(viewer));
3142: PetscFunctionReturn(PETSC_SUCCESS);
3143: }