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, (void **)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) {
369: PetscCall(PetscObjectGetName((PetscObject)dm, name));
370: } else {
371: *name = "plex";
372: }
373: PetscFunctionReturn(PETSC_SUCCESS);
374: }
376: PetscErrorCode DMSequenceGetLength_HDF5_Internal(DM dm, const char seqname[], PetscInt *seqlen, PetscViewer viewer)
377: {
378: hid_t file, group, dset, dspace;
379: hsize_t rdim, *dims;
380: const char *groupname;
381: PetscBool has;
383: PetscFunctionBegin;
384: PetscCall(PetscViewerHDF5GetGroup(viewer, NULL, &groupname));
385: PetscCall(PetscViewerHDF5HasDataset(viewer, seqname, &has));
386: PetscCheck(has, PetscObjectComm((PetscObject)viewer), PETSC_ERR_FILE_UNEXPECTED, "Object (dataset) \"%s\" not stored in group %s", seqname, groupname);
388: PetscCall(PetscViewerHDF5OpenGroup(viewer, NULL, &file, &group));
389: PetscCallHDF5Return(dset, H5Dopen2, (group, seqname, H5P_DEFAULT));
390: PetscCallHDF5Return(dspace, H5Dget_space, (dset));
391: PetscCallHDF5ReturnNoCheck(rdim, H5Sget_simple_extent_dims, (dspace, NULL, NULL));
392: PetscCall(PetscMalloc1(rdim, &dims));
393: PetscCallHDF5ReturnNoCheck(rdim, H5Sget_simple_extent_dims, (dspace, dims, NULL));
394: *seqlen = (PetscInt)dims[0];
395: PetscCall(PetscFree(dims));
396: PetscCallHDF5(H5Dclose, (dset));
397: PetscCallHDF5(H5Gclose, (group));
398: PetscFunctionReturn(PETSC_SUCCESS);
399: }
401: static PetscErrorCode DMSequenceView_HDF5(DM dm, const char seqname[], PetscInt seqnum, PetscScalar value, PetscViewer viewer)
402: {
403: Vec stamp;
404: PetscMPIInt rank;
406: PetscFunctionBegin;
407: if (seqnum < 0) PetscFunctionReturn(PETSC_SUCCESS);
408: PetscCallMPI(MPI_Comm_rank(PetscObjectComm((PetscObject)viewer), &rank));
409: PetscCall(VecCreateMPI(PetscObjectComm((PetscObject)viewer), rank ? 0 : 1, 1, &stamp));
410: PetscCall(VecSetBlockSize(stamp, 1));
411: PetscCall(PetscObjectSetName((PetscObject)stamp, seqname));
412: if (rank == 0) {
413: PetscReal timeScale;
414: PetscBool istime;
416: PetscCall(PetscStrncmp(seqname, "time", 5, &istime));
417: if (istime) {
418: PetscCall(DMPlexGetScale(dm, PETSC_UNIT_TIME, &timeScale));
419: value *= timeScale;
420: }
421: PetscCall(VecSetValue(stamp, 0, value, INSERT_VALUES));
422: }
423: PetscCall(VecAssemblyBegin(stamp));
424: PetscCall(VecAssemblyEnd(stamp));
425: PetscCall(PetscViewerHDF5PushGroup(viewer, "/"));
426: PetscCall(PetscViewerHDF5PushTimestepping(viewer));
427: PetscCall(PetscViewerHDF5SetTimestep(viewer, seqnum)); /* seqnum < 0 jumps out above */
428: PetscCall(VecView(stamp, viewer));
429: PetscCall(PetscViewerHDF5PopTimestepping(viewer));
430: PetscCall(PetscViewerHDF5PopGroup(viewer));
431: PetscCall(VecDestroy(&stamp));
432: PetscFunctionReturn(PETSC_SUCCESS);
433: }
435: PetscErrorCode DMSequenceLoad_HDF5_Internal(DM dm, const char seqname[], PetscInt seqnum, PetscScalar *value, PetscViewer viewer)
436: {
437: Vec stamp;
438: PetscMPIInt rank;
440: PetscFunctionBegin;
441: if (seqnum < 0) PetscFunctionReturn(PETSC_SUCCESS);
442: PetscCallMPI(MPI_Comm_rank(PetscObjectComm((PetscObject)viewer), &rank));
443: PetscCall(VecCreateMPI(PetscObjectComm((PetscObject)viewer), rank ? 0 : 1, 1, &stamp));
444: PetscCall(VecSetBlockSize(stamp, 1));
445: PetscCall(PetscObjectSetName((PetscObject)stamp, seqname));
446: PetscCall(PetscViewerHDF5PushGroup(viewer, "/"));
447: PetscCall(PetscViewerHDF5PushTimestepping(viewer));
448: PetscCall(PetscViewerHDF5SetTimestep(viewer, seqnum)); /* seqnum < 0 jumps out above */
449: PetscCall(VecLoad(stamp, viewer));
450: PetscCall(PetscViewerHDF5PopTimestepping(viewer));
451: PetscCall(PetscViewerHDF5PopGroup(viewer));
452: if (rank == 0) {
453: const PetscScalar *a;
454: PetscReal timeScale;
455: PetscBool istime;
457: PetscCall(VecGetArrayRead(stamp, &a));
458: *value = a[0];
459: PetscCall(VecRestoreArrayRead(stamp, &a));
460: PetscCall(PetscStrncmp(seqname, "time", 5, &istime));
461: if (istime) {
462: PetscCall(DMPlexGetScale(dm, PETSC_UNIT_TIME, &timeScale));
463: *value /= timeScale;
464: }
465: }
466: PetscCall(VecDestroy(&stamp));
467: PetscFunctionReturn(PETSC_SUCCESS);
468: }
470: static PetscErrorCode DMPlexCreateCutVertexLabel_Private(DM dm, DMLabel cutLabel, DMLabel *cutVertexLabel)
471: {
472: IS cutcells = NULL;
473: const PetscInt *cutc;
474: PetscInt cellHeight, vStart, vEnd, cStart, cEnd, c;
476: PetscFunctionBegin;
477: if (!cutLabel) PetscFunctionReturn(PETSC_SUCCESS);
478: PetscCall(DMPlexGetVTKCellHeight(dm, &cellHeight));
479: PetscCall(DMPlexGetHeightStratum(dm, cellHeight, &cStart, &cEnd));
480: PetscCall(DMPlexGetDepthStratum(dm, 0, &vStart, &vEnd));
481: /* Label vertices that should be duplicated */
482: PetscCall(DMLabelCreate(PETSC_COMM_SELF, "Cut Vertices", cutVertexLabel));
483: PetscCall(DMLabelGetStratumIS(cutLabel, 2, &cutcells));
484: if (cutcells) {
485: PetscInt n;
487: PetscCall(ISGetIndices(cutcells, &cutc));
488: PetscCall(ISGetLocalSize(cutcells, &n));
489: for (c = 0; c < n; ++c) {
490: if ((cutc[c] >= cStart) && (cutc[c] < cEnd)) {
491: PetscInt *closure = NULL;
492: PetscInt closureSize, cl, value;
494: PetscCall(DMPlexGetTransitiveClosure(dm, cutc[c], PETSC_TRUE, &closureSize, &closure));
495: for (cl = 0; cl < closureSize * 2; cl += 2) {
496: if ((closure[cl] >= vStart) && (closure[cl] < vEnd)) {
497: PetscCall(DMLabelGetValue(cutLabel, closure[cl], &value));
498: if (value == 1) PetscCall(DMLabelSetValue(*cutVertexLabel, closure[cl], 1));
499: }
500: }
501: PetscCall(DMPlexRestoreTransitiveClosure(dm, cutc[c], PETSC_TRUE, &closureSize, &closure));
502: }
503: }
504: PetscCall(ISRestoreIndices(cutcells, &cutc));
505: }
506: PetscCall(ISDestroy(&cutcells));
507: PetscFunctionReturn(PETSC_SUCCESS);
508: }
510: PetscErrorCode VecView_Plex_Local_HDF5_Internal(Vec v, PetscViewer viewer)
511: {
512: DMPlexStorageVersion version;
513: DM dm;
514: DM dmBC;
515: PetscSection section, sectionGlobal;
516: Vec gv;
517: const char *name;
518: PetscViewerFormat format;
519: PetscInt seqnum;
520: PetscReal seqval;
521: PetscBool isseq;
523: PetscFunctionBegin;
524: PetscCall(PetscViewerHDF5GetDMPlexStorageVersionWriting(viewer, &version));
525: PetscCall(PetscObjectTypeCompare((PetscObject)v, VECSEQ, &isseq));
526: PetscCall(VecGetDM(v, &dm));
527: PetscCall(DMGetLocalSection(dm, §ion));
528: PetscCall(DMGetOutputSequenceNumber(dm, &seqnum, &seqval));
529: PetscCall(DMSequenceView_HDF5(dm, "time", seqnum, (PetscScalar)seqval, viewer));
530: if (seqnum >= 0) {
531: PetscCall(PetscViewerHDF5PushTimestepping(viewer));
532: PetscCall(PetscViewerHDF5SetTimestep(viewer, seqnum));
533: }
534: PetscCall(PetscViewerGetFormat(viewer, &format));
535: PetscCall(DMGetOutputDM(dm, &dmBC));
536: PetscCall(DMGetGlobalSection(dmBC, §ionGlobal));
537: PetscCall(DMGetGlobalVector(dmBC, &gv));
538: PetscCall(PetscObjectGetName((PetscObject)v, &name));
539: PetscCall(PetscObjectSetName((PetscObject)gv, name));
540: PetscCall(DMLocalToGlobalBegin(dmBC, v, INSERT_VALUES, gv));
541: PetscCall(DMLocalToGlobalEnd(dmBC, v, INSERT_VALUES, gv));
542: PetscCall(PetscObjectTypeCompare((PetscObject)gv, VECSEQ, &isseq));
543: if (format == PETSC_VIEWER_HDF5_VIZ) {
544: /* Output visualization representation */
545: PetscInt numFields, f;
546: DMLabel cutLabel, cutVertexLabel = NULL;
548: PetscCall(PetscSectionGetNumFields(section, &numFields));
549: PetscCall(DMGetLabel(dm, "periodic_cut", &cutLabel));
550: for (f = 0; f < numFields; ++f) {
551: Vec subv;
552: IS is;
553: const char *fname, *fgroup, *componentName, *fname_def = "unnamed";
554: char subname[PETSC_MAX_PATH_LEN];
555: PetscInt Nc, Nt = 1;
556: PetscInt *pStart, *pEnd;
557: PetscViewerVTKFieldType *ft;
559: if (DMPlexStorageVersionEQ(version, 1, 1, 0)) PetscCall(DMPlexGetFieldTypes_Internal(dm, section, f, &Nt, &pStart, &pEnd, &ft));
560: else {
561: PetscCall(PetscMalloc3(Nt, &pStart, Nt, &pEnd, Nt, &ft));
562: PetscCall(DMPlexGetFieldType_Internal(dm, section, f, &pStart[0], &pEnd[0], &ft[0]));
563: }
564: for (PetscInt t = 0; t < Nt; ++t) {
565: size_t lname;
567: if (ft[t] == PETSC_VTK_INVALID) continue;
568: fgroup = (ft[t] == PETSC_VTK_POINT_VECTOR_FIELD) || (ft[t] == PETSC_VTK_POINT_FIELD) ? "/vertex_fields" : "/cell_fields";
569: PetscCall(PetscSectionGetFieldName(section, f, &fname));
570: if (!fname) fname = fname_def;
572: if (!t) {
573: PetscCall(PetscViewerHDF5PushGroup(viewer, fgroup));
574: } else {
575: char group[PETSC_MAX_PATH_LEN];
577: PetscCall(PetscSNPrintf(group, PETSC_MAX_PATH_LEN, "%s_%" PetscInt_FMT, fgroup, t));
578: PetscCall(PetscViewerHDF5PushGroup(viewer, group));
579: }
581: if (cutLabel) {
582: const PetscScalar *ga;
583: PetscScalar *suba;
584: PetscInt gstart, subSize = 0, extSize = 0, subOff = 0, newOff = 0;
586: PetscCall(DMPlexCreateCutVertexLabel_Private(dm, cutLabel, &cutVertexLabel));
587: PetscCall(PetscSectionGetFieldComponents(section, f, &Nc));
588: for (PetscInt p = pStart[t]; p < pEnd[t]; ++p) {
589: PetscInt gdof, fdof = 0, val;
591: PetscCall(PetscSectionGetDof(sectionGlobal, p, &gdof));
592: if (gdof > 0) PetscCall(PetscSectionGetFieldDof(section, p, f, &fdof));
593: subSize += fdof;
594: PetscCall(DMLabelGetValue(cutVertexLabel, p, &val));
595: if (val == 1) extSize += fdof;
596: }
597: PetscCall(VecCreate(PetscObjectComm((PetscObject)gv), &subv));
598: PetscCall(VecSetSizes(subv, subSize + extSize, PETSC_DETERMINE));
599: PetscCall(VecSetBlockSize(subv, Nc));
600: PetscCall(VecSetType(subv, VECSTANDARD));
601: PetscCall(VecGetOwnershipRange(gv, &gstart, NULL));
602: PetscCall(VecGetArrayRead(gv, &ga));
603: PetscCall(VecGetArray(subv, &suba));
604: for (PetscInt p = pStart[t]; p < pEnd[t]; ++p) {
605: PetscInt gdof, goff, val;
607: PetscCall(PetscSectionGetDof(sectionGlobal, p, &gdof));
608: if (gdof > 0) {
609: PetscInt fdof, fc, f2, poff = 0;
611: PetscCall(PetscSectionGetOffset(sectionGlobal, p, &goff));
612: /* Can get rid of this loop by storing field information in the global section */
613: for (f2 = 0; f2 < f; ++f2) {
614: PetscCall(PetscSectionGetFieldDof(section, p, f2, &fdof));
615: poff += fdof;
616: }
617: PetscCall(PetscSectionGetFieldDof(section, p, f, &fdof));
618: for (fc = 0; fc < fdof; ++fc, ++subOff) suba[subOff] = ga[goff + poff + fc - gstart];
619: PetscCall(DMLabelGetValue(cutVertexLabel, p, &val));
620: if (val == 1) {
621: for (fc = 0; fc < fdof; ++fc, ++newOff) suba[subSize + newOff] = ga[goff + poff + fc - gstart];
622: }
623: }
624: }
625: PetscCall(VecRestoreArrayRead(gv, &ga));
626: PetscCall(VecRestoreArray(subv, &suba));
627: PetscCall(DMLabelDestroy(&cutVertexLabel));
628: } else {
629: PetscCall(PetscSectionGetField_Internal(section, sectionGlobal, gv, f, pStart[t], pEnd[t], &is, &subv));
630: }
631: PetscCall(PetscStrlen(name, &lname));
632: if (lname) {
633: PetscCall(PetscStrncpy(subname, name, sizeof(subname)));
634: PetscCall(PetscStrlcat(subname, "_", sizeof(subname)));
635: }
636: PetscCall(PetscStrlcat(subname, fname, sizeof(subname)));
637: PetscCall(PetscObjectSetName((PetscObject)subv, subname));
638: if (isseq) PetscCall(VecView_Seq(subv, viewer));
639: else PetscCall(VecView_MPI(subv, viewer));
640: if (ft[t] == PETSC_VTK_POINT_VECTOR_FIELD || ft[t] == PETSC_VTK_CELL_VECTOR_FIELD) {
641: PetscCall(PetscViewerHDF5WriteObjectAttribute(viewer, (PetscObject)subv, "vector_field_type", PETSC_STRING, "vector"));
642: } else {
643: PetscCall(PetscViewerHDF5WriteObjectAttribute(viewer, (PetscObject)subv, "vector_field_type", PETSC_STRING, "scalar"));
644: }
646: /* Output the component names in the field if available */
647: PetscCall(PetscSectionGetFieldComponents(section, f, &Nc));
648: for (PetscInt c = 0; c < Nc; ++c) {
649: char componentNameLabel[PETSC_MAX_PATH_LEN];
650: PetscCall(PetscSectionGetComponentName(section, f, c, &componentName));
651: PetscCall(PetscSNPrintf(componentNameLabel, sizeof(componentNameLabel), "componentName%" PetscInt_FMT, c));
652: PetscCall(PetscViewerHDF5WriteObjectAttribute(viewer, (PetscObject)subv, componentNameLabel, PETSC_STRING, componentName));
653: }
655: if (cutLabel) PetscCall(VecDestroy(&subv));
656: else PetscCall(PetscSectionRestoreField_Internal(section, sectionGlobal, gv, f, pStart[t], pEnd[t], &is, &subv));
657: PetscCall(PetscViewerHDF5PopGroup(viewer));
658: }
659: if (!DMPlexStorageVersionEQ(version, 1, 1, 0)) PetscCall(PetscFree3(pStart, pEnd, ft));
660: }
661: } else {
662: /* Output full vector */
663: PetscCall(PetscViewerHDF5PushGroup(viewer, "/fields"));
664: if (isseq) PetscCall(VecView_Seq(gv, viewer));
665: else PetscCall(VecView_MPI(gv, viewer));
666: PetscCall(PetscViewerHDF5PopGroup(viewer));
667: }
668: if (seqnum >= 0) PetscCall(PetscViewerHDF5PopTimestepping(viewer));
669: PetscCall(DMRestoreGlobalVector(dmBC, &gv));
670: PetscFunctionReturn(PETSC_SUCCESS);
671: }
673: PetscErrorCode VecView_Plex_HDF5_Internal(Vec v, PetscViewer viewer)
674: {
675: DMPlexStorageVersion version;
676: DM dm;
677: Vec locv;
678: PetscObject isZero;
679: const char *name;
680: PetscReal time;
682: PetscFunctionBegin;
683: PetscCall(PetscViewerHDF5GetDMPlexStorageVersionWriting(viewer, &version));
684: PetscCall(PetscInfo(v, "Writing Vec %s storage version %d.%d.%d\n", v->hdr.name, version->major, version->minor, version->subminor));
686: PetscCall(VecGetDM(v, &dm));
687: PetscCall(DMGetLocalVector(dm, &locv));
688: PetscCall(PetscObjectGetName((PetscObject)v, &name));
689: PetscCall(PetscObjectSetName((PetscObject)locv, name));
690: PetscCall(PetscObjectQuery((PetscObject)v, "__Vec_bc_zero__", &isZero));
691: PetscCall(PetscObjectCompose((PetscObject)locv, "__Vec_bc_zero__", isZero));
692: PetscCall(DMGlobalToLocalBegin(dm, v, INSERT_VALUES, locv));
693: PetscCall(DMGlobalToLocalEnd(dm, v, INSERT_VALUES, locv));
694: PetscCall(DMGetOutputSequenceNumber(dm, NULL, &time));
695: PetscCall(DMPlexInsertBoundaryValues(dm, PETSC_TRUE, locv, time, NULL, NULL, NULL));
696: PetscCall(VecView_Plex_Local_HDF5_Internal(locv, viewer));
697: if (DMPlexStorageVersionEQ(version, 1, 1, 0)) {
698: PetscCall(PetscViewerHDF5PushGroup(viewer, "/fields"));
699: PetscCall(PetscViewerPushFormat(viewer, PETSC_VIEWER_HDF5_VIZ));
700: PetscCall(VecView_Plex_Local_HDF5_Internal(locv, viewer));
701: PetscCall(PetscViewerPopFormat(viewer));
702: PetscCall(PetscViewerHDF5PopGroup(viewer));
703: }
704: PetscCall(PetscObjectCompose((PetscObject)locv, "__Vec_bc_zero__", NULL));
705: PetscCall(DMRestoreLocalVector(dm, &locv));
706: PetscFunctionReturn(PETSC_SUCCESS);
707: }
709: PetscErrorCode VecView_Plex_HDF5_Native_Internal(Vec v, PetscViewer viewer)
710: {
711: PetscBool isseq;
713: PetscFunctionBegin;
714: PetscCall(PetscObjectTypeCompare((PetscObject)v, VECSEQ, &isseq));
715: PetscCall(PetscViewerHDF5PushGroup(viewer, "/fields"));
716: if (isseq) PetscCall(VecView_Seq(v, viewer));
717: else PetscCall(VecView_MPI(v, viewer));
718: PetscCall(PetscViewerHDF5PopGroup(viewer));
719: PetscFunctionReturn(PETSC_SUCCESS);
720: }
722: PetscErrorCode VecLoad_Plex_HDF5_Internal(Vec v, PetscViewer viewer)
723: {
724: DM dm;
725: Vec locv;
726: const char *name;
727: PetscInt seqnum;
729: PetscFunctionBegin;
730: PetscCall(VecGetDM(v, &dm));
731: PetscCall(DMGetLocalVector(dm, &locv));
732: PetscCall(PetscObjectGetName((PetscObject)v, &name));
733: PetscCall(PetscObjectSetName((PetscObject)locv, name));
734: PetscCall(DMGetOutputSequenceNumber(dm, &seqnum, NULL));
735: PetscCall(PetscViewerHDF5PushGroup(viewer, "/fields"));
736: if (seqnum >= 0) {
737: PetscCall(PetscViewerHDF5PushTimestepping(viewer));
738: PetscCall(PetscViewerHDF5SetTimestep(viewer, seqnum));
739: }
740: PetscCall(VecLoad_Plex_Local(locv, viewer));
741: if (seqnum >= 0) PetscCall(PetscViewerHDF5PopTimestepping(viewer));
742: PetscCall(PetscViewerHDF5PopGroup(viewer));
743: PetscCall(DMLocalToGlobalBegin(dm, locv, INSERT_VALUES, v));
744: PetscCall(DMLocalToGlobalEnd(dm, locv, INSERT_VALUES, v));
745: PetscCall(DMRestoreLocalVector(dm, &locv));
746: PetscFunctionReturn(PETSC_SUCCESS);
747: }
749: PetscErrorCode VecLoad_Plex_HDF5_Native_Internal(Vec v, PetscViewer viewer)
750: {
751: DM dm;
752: PetscInt seqnum;
754: PetscFunctionBegin;
755: PetscCall(VecGetDM(v, &dm));
756: PetscCall(DMGetOutputSequenceNumber(dm, &seqnum, NULL));
757: PetscCall(PetscViewerHDF5PushGroup(viewer, "/fields"));
758: if (seqnum >= 0) {
759: PetscCall(PetscViewerHDF5PushTimestepping(viewer));
760: PetscCall(PetscViewerHDF5SetTimestep(viewer, seqnum));
761: }
762: PetscCall(VecLoad_Default(v, viewer));
763: if (seqnum >= 0) PetscCall(PetscViewerHDF5PopTimestepping(viewer));
764: PetscCall(PetscViewerHDF5PopGroup(viewer));
765: PetscFunctionReturn(PETSC_SUCCESS);
766: }
768: static PetscErrorCode DMPlexDistributionView_HDF5_Private(DM dm, IS globalPointNumbers, PetscViewer viewer)
769: {
770: DMPlexStorageVersion version;
771: MPI_Comm comm;
772: PetscMPIInt size, rank;
773: PetscInt size_petsc_int;
774: const char *topologydm_name, *distribution_name;
775: const PetscInt *gpoint;
776: PetscInt pStart, pEnd, p;
777: PetscSF pointSF;
778: PetscInt nroots, nleaves;
779: const PetscInt *ilocal;
780: const PetscSFNode *iremote;
781: IS chartSizesIS, ownersIS, gpointsIS;
782: PetscInt *chartSize, *owners, *gpoints;
783: PetscBool ocompress;
785: PetscFunctionBegin;
786: PetscCall(PetscViewerHDF5GetDMPlexStorageVersionWriting(viewer, &version));
787: PetscCall(PetscObjectGetComm((PetscObject)dm, &comm));
788: PetscCallMPI(MPI_Comm_size(comm, &size));
789: PetscCallMPI(MPI_Comm_rank(comm, &rank));
790: PetscCall(DMPlexGetHDF5Name_Private(dm, &topologydm_name));
791: PetscCall(DMPlexDistributionGetName(dm, &distribution_name));
792: if (!distribution_name) PetscFunctionReturn(PETSC_SUCCESS);
793: PetscCall(PetscLogEventBegin(DMPLEX_DistributionView, viewer, 0, 0, 0));
794: size_petsc_int = (PetscInt)size;
795: PetscCall(PetscViewerHDF5WriteAttribute(viewer, NULL, "comm_size", PETSC_INT, (void *)&size_petsc_int));
796: PetscCall(ISGetIndices(globalPointNumbers, &gpoint));
797: PetscCall(DMPlexGetChart(dm, &pStart, &pEnd));
798: PetscCall(PetscMalloc1(1, &chartSize));
799: *chartSize = pEnd - pStart;
800: PetscCall(PetscMalloc1(*chartSize, &owners));
801: PetscCall(PetscMalloc1(*chartSize, &gpoints));
802: PetscCall(DMGetPointSF(dm, &pointSF));
803: PetscCall(PetscSFGetGraph(pointSF, &nroots, &nleaves, &ilocal, &iremote));
804: for (p = pStart; p < pEnd; ++p) {
805: PetscInt gp = gpoint[p - pStart];
807: owners[p - pStart] = rank;
808: gpoints[p - pStart] = (gp < 0 ? -(gp + 1) : gp);
809: }
810: for (p = 0; p < nleaves; ++p) {
811: PetscInt ilocalp = (ilocal ? ilocal[p] : p);
813: owners[ilocalp] = iremote[p].rank;
814: }
815: PetscCall(ISCreateGeneral(comm, 1, chartSize, PETSC_OWN_POINTER, &chartSizesIS));
816: PetscCall(ISCreateGeneral(comm, *chartSize, owners, PETSC_OWN_POINTER, &ownersIS));
817: PetscCall(ISCreateGeneral(comm, *chartSize, gpoints, PETSC_OWN_POINTER, &gpointsIS));
818: if (DMPlexStorageVersionGE(version, 3, 1, 0)) {
819: PetscCall(PetscViewerHDF5GetCompress(viewer, &ocompress));
820: PetscCall(PetscViewerHDF5SetCompress(viewer, PETSC_TRUE));
821: }
822: PetscCall(PetscObjectSetName((PetscObject)chartSizesIS, "chart_sizes"));
823: PetscCall(PetscObjectSetName((PetscObject)ownersIS, "owners"));
824: PetscCall(PetscObjectSetName((PetscObject)gpointsIS, "global_point_numbers"));
825: PetscCall(ISView(chartSizesIS, viewer));
826: PetscCall(ISView(ownersIS, viewer));
827: PetscCall(ISView(gpointsIS, viewer));
828: PetscCall(ISDestroy(&chartSizesIS));
829: PetscCall(ISDestroy(&ownersIS));
830: PetscCall(ISDestroy(&gpointsIS));
831: PetscCall(ISRestoreIndices(globalPointNumbers, &gpoint));
832: if (DMPlexStorageVersionGE(version, 3, 1, 0)) PetscCall(PetscViewerHDF5SetCompress(viewer, ocompress));
833: PetscCall(PetscLogEventEnd(DMPLEX_DistributionView, viewer, 0, 0, 0));
834: PetscFunctionReturn(PETSC_SUCCESS);
835: }
837: 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[])
838: {
839: DMPlexStorageVersion version;
840: IS coneSizesIS, conesIS, orientationsIS;
841: PetscInt *coneSizes, *cones, *orientations;
842: const PetscInt *gpoint;
843: PetscInt nPoints = 0, conesSize = 0;
844: PetscInt p, c, s;
845: PetscBool ocompress;
846: MPI_Comm comm;
848: PetscFunctionBegin;
849: PetscCall(PetscViewerHDF5GetDMPlexStorageVersionWriting(viewer, &version));
850: PetscCall(PetscObjectGetComm((PetscObject)dm, &comm));
851: PetscCall(ISGetIndices(globalPointNumbers, &gpoint));
852: for (p = pStart; p < pEnd; ++p) {
853: if (gpoint[p] >= 0) {
854: PetscInt coneSize;
856: PetscCall(DMPlexGetConeSize(dm, p, &coneSize));
857: nPoints += 1;
858: conesSize += coneSize;
859: }
860: }
861: PetscCall(PetscMalloc1(nPoints, &coneSizes));
862: PetscCall(PetscMalloc1(conesSize, &cones));
863: PetscCall(PetscMalloc1(conesSize, &orientations));
864: for (p = pStart, c = 0, s = 0; p < pEnd; ++p) {
865: if (gpoint[p] >= 0) {
866: const PetscInt *cone, *ornt;
867: PetscInt coneSize, cp;
869: PetscCall(DMPlexGetConeSize(dm, p, &coneSize));
870: PetscCall(DMPlexGetCone(dm, p, &cone));
871: PetscCall(DMPlexGetConeOrientation(dm, p, &ornt));
872: coneSizes[s] = coneSize;
873: for (cp = 0; cp < coneSize; ++cp, ++c) {
874: cones[c] = gpoint[cone[cp]] < 0 ? -(gpoint[cone[cp]] + 1) : gpoint[cone[cp]];
875: orientations[c] = ornt[cp];
876: }
877: ++s;
878: }
879: }
880: PetscCheck(s == nPoints, PETSC_COMM_SELF, PETSC_ERR_LIB, "Total number of points %" PetscInt_FMT " != %" PetscInt_FMT, s, nPoints);
881: PetscCheck(c == conesSize, PETSC_COMM_SELF, PETSC_ERR_LIB, "Total number of cone points %" PetscInt_FMT " != %" PetscInt_FMT, c, conesSize);
882: PetscCall(ISCreateGeneral(comm, nPoints, coneSizes, PETSC_OWN_POINTER, &coneSizesIS));
883: PetscCall(ISCreateGeneral(comm, conesSize, cones, PETSC_OWN_POINTER, &conesIS));
884: PetscCall(ISCreateGeneral(comm, conesSize, orientations, PETSC_OWN_POINTER, &orientationsIS));
885: PetscCall(PetscObjectSetName((PetscObject)coneSizesIS, coneSizesName));
886: PetscCall(PetscObjectSetName((PetscObject)conesIS, conesName));
887: PetscCall(PetscObjectSetName((PetscObject)orientationsIS, orientationsName));
888: if (DMPlexStorageVersionGE(version, 3, 1, 0)) {
889: PetscCall(PetscViewerHDF5GetCompress(viewer, &ocompress));
890: PetscCall(PetscViewerHDF5SetCompress(viewer, PETSC_TRUE));
891: }
892: PetscCall(ISView(coneSizesIS, viewer));
893: PetscCall(ISView(conesIS, viewer));
894: PetscCall(ISView(orientationsIS, viewer));
895: PetscCall(ISDestroy(&coneSizesIS));
896: PetscCall(ISDestroy(&conesIS));
897: PetscCall(ISDestroy(&orientationsIS));
898: if (pointsName) {
899: IS pointsIS;
900: PetscInt *points;
902: PetscCall(PetscMalloc1(nPoints, &points));
903: for (p = pStart, c = 0, s = 0; p < pEnd; ++p) {
904: if (gpoint[p] >= 0) {
905: points[s] = gpoint[p];
906: ++s;
907: }
908: }
909: PetscCall(ISCreateGeneral(comm, nPoints, points, PETSC_OWN_POINTER, &pointsIS));
910: PetscCall(PetscObjectSetName((PetscObject)pointsIS, pointsName));
911: PetscCall(ISView(pointsIS, viewer));
912: PetscCall(ISDestroy(&pointsIS));
913: }
914: PetscCall(ISRestoreIndices(globalPointNumbers, &gpoint));
915: if (DMPlexStorageVersionGE(version, 3, 1, 0)) PetscCall(PetscViewerHDF5SetCompress(viewer, ocompress));
916: PetscFunctionReturn(PETSC_SUCCESS);
917: }
919: static PetscErrorCode DMPlexTopologyView_HDF5_Legacy_Private(DM dm, IS globalPointNumbers, PetscViewer viewer)
920: {
921: const char *pointsName, *coneSizesName, *conesName, *orientationsName;
922: PetscInt pStart, pEnd, dim;
924: PetscFunctionBegin;
925: pointsName = "order";
926: coneSizesName = "cones";
927: conesName = "cells";
928: orientationsName = "orientation";
929: PetscCall(DMPlexGetChart(dm, &pStart, &pEnd));
930: PetscCall(DMPlexTopologyView_HDF5_Inner_Private(dm, globalPointNumbers, viewer, pStart, pEnd, pointsName, coneSizesName, conesName, orientationsName));
931: PetscCall(DMGetDimension(dm, &dim));
932: PetscCall(PetscViewerHDF5WriteAttribute(viewer, conesName, "cell_dim", PETSC_INT, (void *)&dim));
933: PetscFunctionReturn(PETSC_SUCCESS);
934: }
936: //TODO get this numbering right away without needing this function
937: /* Renumber global point numbers so that they are 0-based per stratum */
938: static PetscErrorCode RenumberGlobalPointNumbersPerStratum_Private(DM dm, IS globalPointNumbers, IS *newGlobalPointNumbers, IS *strataPermutation)
939: {
940: PetscInt d, depth, p, n;
941: PetscInt *offsets;
942: const PetscInt *gpn;
943: PetscInt *ngpn;
944: MPI_Comm comm;
946: PetscFunctionBegin;
947: PetscCall(PetscObjectGetComm((PetscObject)dm, &comm));
948: PetscCall(ISGetLocalSize(globalPointNumbers, &n));
949: PetscCall(ISGetIndices(globalPointNumbers, &gpn));
950: PetscCall(PetscMalloc1(n, &ngpn));
951: PetscCall(DMPlexGetDepth(dm, &depth));
952: PetscCall(PetscMalloc1(depth + 1, &offsets));
953: for (d = 0; d <= depth; d++) {
954: PetscInt pStart, pEnd;
956: PetscCall(DMPlexGetDepthStratum(dm, d, &pStart, &pEnd));
957: offsets[d] = PETSC_INT_MAX;
958: for (p = pStart; p < pEnd; p++) {
959: if (gpn[p] >= 0 && gpn[p] < offsets[d]) offsets[d] = gpn[p];
960: }
961: }
962: PetscCallMPI(MPIU_Allreduce(MPI_IN_PLACE, offsets, depth + 1, MPIU_INT, MPI_MIN, comm));
963: for (d = 0; d <= depth; d++) {
964: PetscInt pStart, pEnd;
966: PetscCall(DMPlexGetDepthStratum(dm, d, &pStart, &pEnd));
967: for (p = pStart; p < pEnd; p++) ngpn[p] = gpn[p] - PetscSign(gpn[p]) * offsets[d];
968: }
969: PetscCall(ISRestoreIndices(globalPointNumbers, &gpn));
970: PetscCall(ISCreateGeneral(PetscObjectComm((PetscObject)globalPointNumbers), n, ngpn, PETSC_OWN_POINTER, newGlobalPointNumbers));
971: {
972: PetscInt *perm;
974: PetscCall(PetscMalloc1(depth + 1, &perm));
975: for (d = 0; d <= depth; d++) perm[d] = d;
976: PetscCall(PetscSortIntWithPermutation(depth + 1, offsets, perm));
977: PetscCall(ISCreateGeneral(PETSC_COMM_SELF, depth + 1, perm, PETSC_OWN_POINTER, strataPermutation));
978: }
979: PetscCall(PetscFree(offsets));
980: PetscFunctionReturn(PETSC_SUCCESS);
981: }
983: static PetscErrorCode DMPlexTopologyView_HDF5_Private(DM dm, IS globalPointNumbers, PetscViewer viewer)
984: {
985: IS globalPointNumbers0, strataPermutation;
986: const char *coneSizesName, *conesName, *orientationsName;
987: PetscInt depth, d;
988: MPI_Comm comm;
990: PetscFunctionBegin;
991: coneSizesName = "cone_sizes";
992: conesName = "cones";
993: orientationsName = "orientations";
994: PetscCall(PetscObjectGetComm((PetscObject)dm, &comm));
995: PetscCall(DMPlexGetDepth(dm, &depth));
996: {
997: PetscInt dim;
999: PetscCall(DMGetDimension(dm, &dim));
1000: PetscCall(PetscViewerHDF5WriteAttribute(viewer, NULL, "cell_dim", PETSC_INT, &dim));
1001: PetscCall(PetscViewerHDF5WriteAttribute(viewer, NULL, "depth", PETSC_INT, &depth));
1002: }
1004: PetscCall(RenumberGlobalPointNumbersPerStratum_Private(dm, globalPointNumbers, &globalPointNumbers0, &strataPermutation));
1005: /* TODO dirty trick to save serial IS using the same parallel viewer */
1006: {
1007: IS spOnComm;
1008: PetscInt n = 0, N;
1009: const PetscInt *idx = NULL;
1010: const PetscInt *old;
1011: PetscMPIInt rank;
1013: PetscCallMPI(MPI_Comm_rank(comm, &rank));
1014: PetscCall(ISGetLocalSize(strataPermutation, &N));
1015: PetscCall(ISGetIndices(strataPermutation, &old));
1016: if (!rank) {
1017: n = N;
1018: idx = old;
1019: }
1020: PetscCall(ISCreateGeneral(comm, n, idx, PETSC_COPY_VALUES, &spOnComm));
1021: PetscCall(ISRestoreIndices(strataPermutation, &old));
1022: PetscCall(ISDestroy(&strataPermutation));
1023: strataPermutation = spOnComm;
1024: }
1025: PetscCall(PetscObjectSetName((PetscObject)strataPermutation, "permutation"));
1026: PetscCall(ISView(strataPermutation, viewer));
1027: PetscCall(PetscViewerHDF5PushGroup(viewer, "strata"));
1028: for (d = 0; d <= depth; d++) {
1029: PetscInt pStart, pEnd;
1030: char group[128];
1032: PetscCall(PetscSNPrintf(group, sizeof(group), "%" PetscInt_FMT, d));
1033: PetscCall(PetscViewerHDF5PushGroup(viewer, group));
1034: PetscCall(DMPlexGetDepthStratum(dm, d, &pStart, &pEnd));
1035: PetscCall(DMPlexTopologyView_HDF5_Inner_Private(dm, globalPointNumbers0, viewer, pStart, pEnd, NULL, coneSizesName, conesName, orientationsName));
1036: PetscCall(PetscViewerHDF5PopGroup(viewer));
1037: }
1038: PetscCall(PetscViewerHDF5PopGroup(viewer)); /* strata */
1039: PetscCall(ISDestroy(&globalPointNumbers0));
1040: PetscCall(ISDestroy(&strataPermutation));
1041: PetscFunctionReturn(PETSC_SUCCESS);
1042: }
1044: PetscErrorCode DMPlexTopologyView_HDF5_Internal(DM dm, IS globalPointNumbers, PetscViewer viewer)
1045: {
1046: DMPlexStorageVersion version;
1047: const char *topologydm_name;
1048: char group[PETSC_MAX_PATH_LEN];
1050: PetscFunctionBegin;
1051: PetscCall(PetscViewerHDF5GetDMPlexStorageVersionWriting(viewer, &version));
1052: PetscCall(PetscInfo(dm, "Writing DM %s storage version %d.%d.%d\n", dm->hdr.name, version->major, version->minor, version->subminor));
1053: PetscCall(DMPlexGetHDF5Name_Private(dm, &topologydm_name));
1054: if (DMPlexStorageVersionGE(version, 2, 0, 0)) {
1055: PetscCall(PetscSNPrintf(group, sizeof(group), "topologies/%s", topologydm_name));
1056: } else {
1057: PetscCall(PetscStrncpy(group, "/", sizeof(group)));
1058: }
1059: PetscCall(PetscViewerHDF5PushGroup(viewer, group));
1061: PetscCall(PetscViewerHDF5PushGroup(viewer, "topology"));
1062: if (version->major < 3) {
1063: PetscCall(DMPlexTopologyView_HDF5_Legacy_Private(dm, globalPointNumbers, viewer));
1064: } else {
1065: /* since DMPlexStorageVersion 3.0.0 */
1066: PetscCall(DMPlexTopologyView_HDF5_Private(dm, globalPointNumbers, viewer));
1067: }
1068: PetscCall(PetscViewerHDF5PopGroup(viewer)); /* "topology" */
1070: if (DMPlexStorageVersionGE(version, 2, 1, 0)) {
1071: const char *distribution_name;
1073: PetscCall(DMPlexDistributionGetName(dm, &distribution_name));
1074: PetscCall(PetscViewerHDF5PushGroup(viewer, "distributions"));
1075: PetscCall(PetscViewerHDF5WriteGroup(viewer, NULL));
1076: PetscCall(PetscViewerHDF5PushGroup(viewer, distribution_name));
1077: PetscCall(DMPlexDistributionView_HDF5_Private(dm, globalPointNumbers, viewer));
1078: PetscCall(PetscViewerHDF5PopGroup(viewer)); /* distribution_name */
1079: PetscCall(PetscViewerHDF5PopGroup(viewer)); /* "distributions" */
1080: }
1082: PetscCall(PetscViewerHDF5PopGroup(viewer));
1083: PetscFunctionReturn(PETSC_SUCCESS);
1084: }
1086: static PetscErrorCode CreateConesIS_Private(DM dm, PetscInt cStart, PetscInt cEnd, IS globalCellNumbers, PetscInt *numCorners, IS *cellIS)
1087: {
1088: PetscSF sfPoint;
1089: DMLabel cutLabel, cutVertexLabel = NULL;
1090: IS globalVertexNumbers, cutvertices = NULL;
1091: const PetscInt *gcell, *gvertex, *cutverts = NULL;
1092: PetscInt *vertices;
1093: PetscInt conesSize = 0;
1094: PetscInt dim, numCornersLocal = 0, cell, vStart, vEnd, vExtra = 0, v;
1096: PetscFunctionBegin;
1097: *numCorners = 0;
1098: PetscCall(DMGetDimension(dm, &dim));
1099: PetscCall(DMPlexGetDepthStratum(dm, 0, &vStart, &vEnd));
1100: PetscCall(ISGetIndices(globalCellNumbers, &gcell));
1102: for (cell = cStart; cell < cEnd; ++cell) {
1103: PetscInt *closure = NULL;
1104: PetscInt closureSize, v, Nc = 0;
1106: if (gcell[cell] < 0) continue;
1107: PetscCall(DMPlexGetTransitiveClosure(dm, cell, PETSC_TRUE, &closureSize, &closure));
1108: for (v = 0; v < closureSize * 2; v += 2) {
1109: if ((closure[v] >= vStart) && (closure[v] < vEnd)) ++Nc;
1110: }
1111: PetscCall(DMPlexRestoreTransitiveClosure(dm, cell, PETSC_TRUE, &closureSize, &closure));
1112: conesSize += Nc;
1113: if (!numCornersLocal) numCornersLocal = Nc;
1114: else if (numCornersLocal != Nc) numCornersLocal = 1;
1115: }
1116: PetscCallMPI(MPIU_Allreduce(&numCornersLocal, numCorners, 1, MPIU_INT, MPI_MAX, PetscObjectComm((PetscObject)dm)));
1117: PetscCheck(!numCornersLocal || !(numCornersLocal != *numCorners || *numCorners == 0), PETSC_COMM_SELF, PETSC_ERR_SUP, "Visualization topology currently only supports identical cell shapes");
1118: /* Handle periodic cuts by identifying vertices which should be duplicated */
1119: PetscCall(DMGetLabel(dm, "periodic_cut", &cutLabel));
1120: PetscCall(DMPlexCreateCutVertexLabel_Private(dm, cutLabel, &cutVertexLabel));
1121: if (cutVertexLabel) PetscCall(DMLabelGetStratumIS(cutVertexLabel, 1, &cutvertices));
1122: if (cutvertices) {
1123: PetscCall(ISGetIndices(cutvertices, &cutverts));
1124: PetscCall(ISGetLocalSize(cutvertices, &vExtra));
1125: }
1126: PetscCall(DMGetPointSF(dm, &sfPoint));
1127: if (cutLabel) {
1128: const PetscInt *ilocal;
1129: const PetscSFNode *iremote;
1130: PetscInt nroots, nleaves;
1132: PetscCall(PetscSFGetGraph(sfPoint, &nroots, &nleaves, &ilocal, &iremote));
1133: if (nleaves < 0) {
1134: PetscCall(PetscObjectReference((PetscObject)sfPoint));
1135: } else {
1136: PetscCall(PetscSFCreate(PetscObjectComm((PetscObject)sfPoint), &sfPoint));
1137: PetscCall(PetscSFSetGraph(sfPoint, nroots + vExtra, nleaves, (PetscInt *)ilocal, PETSC_COPY_VALUES, (PetscSFNode *)iremote, PETSC_COPY_VALUES));
1138: }
1139: } else {
1140: PetscCall(PetscObjectReference((PetscObject)sfPoint));
1141: }
1142: /* Number all vertices */
1143: PetscCall(DMPlexCreateNumbering_Plex(dm, vStart, vEnd + vExtra, 0, NULL, sfPoint, &globalVertexNumbers));
1144: PetscCall(PetscSFDestroy(&sfPoint));
1145: /* Create cones */
1146: PetscCall(ISGetIndices(globalVertexNumbers, &gvertex));
1147: PetscCall(PetscMalloc1(conesSize, &vertices));
1148: for (cell = cStart, v = 0; cell < cEnd; ++cell) {
1149: PetscInt *closure = NULL;
1150: PetscInt closureSize, Nc = 0, p, value = -1;
1151: PetscBool replace;
1153: if (gcell[cell] < 0) continue;
1154: if (cutLabel) PetscCall(DMLabelGetValue(cutLabel, cell, &value));
1155: replace = (value == 2) ? PETSC_TRUE : PETSC_FALSE;
1156: PetscCall(DMPlexGetTransitiveClosure(dm, cell, PETSC_TRUE, &closureSize, &closure));
1157: for (p = 0; p < closureSize * 2; p += 2) {
1158: if ((closure[p] >= vStart) && (closure[p] < vEnd)) closure[Nc++] = closure[p];
1159: }
1160: PetscCall(DMPlexReorderCell(dm, cell, closure));
1161: for (p = 0; p < Nc; ++p) {
1162: PetscInt nv, gv = gvertex[closure[p] - vStart];
1164: if (replace) {
1165: PetscCall(PetscFindInt(closure[p], vExtra, cutverts, &nv));
1166: if (nv >= 0) gv = gvertex[vEnd - vStart + nv];
1167: }
1168: vertices[v++] = gv < 0 ? -(gv + 1) : gv;
1169: }
1170: PetscCall(DMPlexRestoreTransitiveClosure(dm, cell, PETSC_TRUE, &closureSize, &closure));
1171: }
1172: PetscCall(ISRestoreIndices(globalVertexNumbers, &gvertex));
1173: PetscCall(ISDestroy(&globalVertexNumbers));
1174: PetscCall(ISRestoreIndices(globalCellNumbers, &gcell));
1175: if (cutvertices) PetscCall(ISRestoreIndices(cutvertices, &cutverts));
1176: PetscCall(ISDestroy(&cutvertices));
1177: PetscCall(DMLabelDestroy(&cutVertexLabel));
1178: PetscCheck(v == conesSize, PETSC_COMM_SELF, PETSC_ERR_LIB, "Total number of cell vertices %" PetscInt_FMT " != %" PetscInt_FMT, v, conesSize);
1179: PetscCall(ISCreateGeneral(PetscObjectComm((PetscObject)dm), conesSize, vertices, PETSC_OWN_POINTER, cellIS));
1180: PetscCall(PetscLayoutSetBlockSize((*cellIS)->map, *numCorners));
1181: PetscCall(PetscObjectSetName((PetscObject)*cellIS, "cells"));
1182: PetscFunctionReturn(PETSC_SUCCESS);
1183: }
1185: static PetscErrorCode DMPlexTopologyView_HDF5_XDMF_Private(DM dm, IS globalCellNumbers, PetscViewer viewer)
1186: {
1187: DM cdm;
1188: DMLabel depthLabel, ctLabel;
1189: IS cellIS;
1190: PetscInt dim, depth, cellHeight, c, n = 0;
1192: PetscFunctionBegin;
1193: PetscCall(PetscViewerHDF5PushGroup(viewer, "/viz"));
1194: PetscCall(PetscViewerHDF5WriteGroup(viewer, NULL));
1196: PetscCall(PetscViewerHDF5PopGroup(viewer));
1197: PetscCall(DMGetDimension(dm, &dim));
1198: PetscCall(DMPlexGetDepth(dm, &depth));
1199: PetscCall(DMGetCoordinateDM(dm, &cdm));
1200: PetscCall(DMPlexGetVTKCellHeight(dm, &cellHeight));
1201: PetscCall(DMPlexGetDepthLabel(dm, &depthLabel));
1202: PetscCall(DMPlexGetCellTypeLabel(dm, &ctLabel));
1203: for (c = 0; c < DM_NUM_POLYTOPES; ++c) {
1204: const DMPolytopeType ict = (DMPolytopeType)c;
1205: PetscInt pStart, pEnd, dep, numCorners;
1206: PetscBool output = PETSC_FALSE, doOutput;
1208: if (ict == DM_POLYTOPE_FV_GHOST) continue;
1209: PetscCall(DMLabelGetStratumBounds(ctLabel, ict, &pStart, &pEnd));
1210: if (pStart >= 0) {
1211: PetscCall(DMLabelGetValue(depthLabel, pStart, &dep));
1212: if (dep == depth - cellHeight) output = PETSC_TRUE;
1213: }
1214: PetscCallMPI(MPIU_Allreduce(&output, &doOutput, 1, MPI_C_BOOL, MPI_LOR, PetscObjectComm((PetscObject)dm)));
1215: if (!doOutput) continue;
1216: PetscCall(CreateConesIS_Private(dm, pStart, pEnd, globalCellNumbers, &numCorners, &cellIS));
1217: if (!n) {
1218: PetscCall(PetscViewerHDF5PushGroup(viewer, "/viz/topology"));
1219: } else {
1220: char group[PETSC_MAX_PATH_LEN];
1222: PetscCall(PetscSNPrintf(group, PETSC_MAX_PATH_LEN, "/viz/topology_%" PetscInt_FMT, n));
1223: PetscCall(PetscViewerHDF5PushGroup(viewer, group));
1224: }
1225: PetscCall(ISView(cellIS, viewer));
1226: PetscCall(PetscViewerHDF5WriteObjectAttribute(viewer, (PetscObject)cellIS, "cell_corners", PETSC_INT, (void *)&numCorners));
1227: PetscCall(PetscViewerHDF5WriteObjectAttribute(viewer, (PetscObject)cellIS, "cell_dim", PETSC_INT, (void *)&dim));
1228: PetscCall(ISDestroy(&cellIS));
1229: PetscCall(PetscViewerHDF5PopGroup(viewer));
1230: ++n;
1231: }
1232: PetscFunctionReturn(PETSC_SUCCESS);
1233: }
1235: static PetscErrorCode DMPlexCoordinatesView_HDF5_Legacy_Private(DM dm, PetscViewer viewer)
1236: {
1237: DM cdm;
1238: Vec coordinates, newcoords;
1239: PetscReal lengthScale;
1240: PetscInt m, M, bs;
1242: PetscFunctionBegin;
1243: PetscCall(DMPlexGetScale(dm, PETSC_UNIT_LENGTH, &lengthScale));
1244: PetscCall(DMGetCoordinateDM(dm, &cdm));
1245: PetscCall(DMGetCoordinates(dm, &coordinates));
1246: PetscCall(VecCreate(PetscObjectComm((PetscObject)coordinates), &newcoords));
1247: PetscCall(PetscObjectSetName((PetscObject)newcoords, "vertices"));
1248: PetscCall(VecGetSize(coordinates, &M));
1249: PetscCall(VecGetLocalSize(coordinates, &m));
1250: PetscCall(VecSetSizes(newcoords, m, M));
1251: PetscCall(VecGetBlockSize(coordinates, &bs));
1252: PetscCall(VecSetBlockSize(newcoords, bs));
1253: PetscCall(VecSetType(newcoords, VECSTANDARD));
1254: PetscCall(VecCopy(coordinates, newcoords));
1255: PetscCall(VecScale(newcoords, lengthScale));
1256: /* Did not use DMGetGlobalVector() in order to bypass default group assignment */
1257: PetscCall(PetscViewerHDF5PushGroup(viewer, "/geometry"));
1258: PetscCall(PetscViewerPushFormat(viewer, PETSC_VIEWER_NATIVE));
1259: PetscCall(VecView(newcoords, viewer));
1260: PetscCall(PetscViewerPopFormat(viewer));
1261: PetscCall(PetscViewerHDF5PopGroup(viewer));
1262: PetscCall(VecDestroy(&newcoords));
1263: PetscFunctionReturn(PETSC_SUCCESS);
1264: }
1266: PetscErrorCode DMPlexCoordinatesView_HDF5_Internal(DM dm, PetscViewer viewer)
1267: {
1268: DM cdm;
1269: Vec coords, newcoords;
1270: PetscInt m, M, bs;
1271: PetscReal lengthScale;
1272: PetscBool viewSection = PETSC_TRUE, ocompress;
1273: const char *topologydm_name, *coordinatedm_name, *coordinates_name;
1274: PetscViewerFormat format;
1275: DMPlexStorageVersion version;
1277: PetscFunctionBegin;
1278: PetscCall(PetscViewerGetFormat(viewer, &format));
1279: PetscCall(PetscViewerHDF5GetDMPlexStorageVersionWriting(viewer, &version));
1280: if (!DMPlexStorageVersionGE(version, 2, 0, 0) || format == PETSC_VIEWER_HDF5_XDMF || format == PETSC_VIEWER_HDF5_VIZ) {
1281: PetscCall(DMPlexCoordinatesView_HDF5_Legacy_Private(dm, viewer));
1282: PetscFunctionReturn(PETSC_SUCCESS);
1283: }
1284: /* since 2.0.0 */
1285: if (DMPlexStorageVersionGE(version, 3, 1, 0)) {
1286: PetscCall(PetscViewerHDF5GetCompress(viewer, &ocompress));
1287: PetscCall(PetscViewerHDF5SetCompress(viewer, PETSC_TRUE));
1288: }
1289: PetscCall(PetscOptionsGetBool(NULL, dm->hdr.prefix, "-dm_plex_view_coordinate_section", &viewSection, NULL));
1290: PetscCall(DMGetCoordinateDM(dm, &cdm));
1291: PetscCall(DMGetCoordinates(dm, &coords));
1292: PetscCall(PetscObjectGetName((PetscObject)cdm, &coordinatedm_name));
1293: PetscCall(PetscObjectGetName((PetscObject)coords, &coordinates_name));
1294: PetscCall(DMPlexGetHDF5Name_Private(dm, &topologydm_name));
1295: PetscCall(PetscViewerHDF5PushGroup(viewer, "topologies"));
1296: PetscCall(PetscViewerHDF5PushGroup(viewer, topologydm_name));
1297: PetscCall(PetscViewerHDF5WriteAttribute(viewer, NULL, "coordinateDMName", PETSC_STRING, coordinatedm_name));
1298: PetscCall(PetscViewerHDF5WriteAttribute(viewer, NULL, "coordinatesName", PETSC_STRING, coordinates_name));
1299: PetscCall(PetscViewerHDF5PopGroup(viewer));
1300: PetscCall(PetscViewerHDF5PopGroup(viewer));
1301: if (viewSection) PetscCall(DMPlexSectionView(dm, viewer, cdm));
1302: PetscCall(VecCreate(PetscObjectComm((PetscObject)coords), &newcoords));
1303: PetscCall(PetscObjectSetName((PetscObject)newcoords, coordinates_name));
1304: PetscCall(VecGetSize(coords, &M));
1305: PetscCall(VecGetLocalSize(coords, &m));
1306: PetscCall(VecSetSizes(newcoords, m, M));
1307: PetscCall(VecGetBlockSize(coords, &bs));
1308: PetscCall(VecSetBlockSize(newcoords, bs));
1309: PetscCall(VecSetType(newcoords, VECSTANDARD));
1310: PetscCall(VecCopy(coords, newcoords));
1311: PetscCall(DMPlexGetScale(dm, PETSC_UNIT_LENGTH, &lengthScale));
1312: PetscCall(VecScale(newcoords, lengthScale));
1313: PetscCall(PetscViewerPushFormat(viewer, PETSC_VIEWER_NATIVE));
1314: PetscCall(DMPlexGlobalVectorView(dm, viewer, cdm, newcoords));
1315: PetscCall(PetscViewerPopFormat(viewer));
1316: PetscCall(VecDestroy(&newcoords));
1317: if (DMPlexStorageVersionGE(version, 3, 1, 0)) PetscCall(PetscViewerHDF5SetCompress(viewer, ocompress));
1318: PetscFunctionReturn(PETSC_SUCCESS);
1319: }
1321: static PetscErrorCode DMPlexCoordinatesView_HDF5_XDMF_Private(DM dm, PetscViewer viewer)
1322: {
1323: DM cdm;
1324: Vec coordinatesLocal, newcoords;
1325: PetscSection cSection, cGlobalSection;
1326: PetscScalar *coords, *ncoords;
1327: DMLabel cutLabel, cutVertexLabel = NULL;
1328: const PetscReal *L;
1329: PetscReal lengthScale;
1330: PetscInt vStart, vEnd, v, bs, N, coordSize, dof, off, d;
1331: PetscBool localized, embedded;
1333: PetscFunctionBegin;
1334: PetscCall(DMPlexGetDepthStratum(dm, 0, &vStart, &vEnd));
1335: PetscCall(DMPlexGetScale(dm, PETSC_UNIT_LENGTH, &lengthScale));
1336: PetscCall(DMGetCoordinatesLocal(dm, &coordinatesLocal));
1337: PetscCall(VecGetBlockSize(coordinatesLocal, &bs));
1338: PetscCall(DMGetCoordinatesLocalized(dm, &localized));
1339: if (localized == PETSC_FALSE) PetscFunctionReturn(PETSC_SUCCESS);
1340: PetscCall(DMGetPeriodicity(dm, NULL, NULL, &L));
1341: PetscCall(DMGetCoordinateDM(dm, &cdm));
1342: PetscCall(DMGetLocalSection(cdm, &cSection));
1343: PetscCall(DMGetGlobalSection(cdm, &cGlobalSection));
1344: PetscCall(DMGetLabel(dm, "periodic_cut", &cutLabel));
1345: N = 0;
1347: PetscCall(DMPlexCreateCutVertexLabel_Private(dm, cutLabel, &cutVertexLabel));
1348: PetscCall(VecCreate(PetscObjectComm((PetscObject)dm), &newcoords));
1349: PetscCall(PetscSectionGetDof(cSection, vStart, &dof));
1350: PetscCall(PetscPrintf(PETSC_COMM_SELF, "DOF: %" PetscInt_FMT "\n", dof));
1351: embedded = (PetscBool)(L && dof == 2 && !cutLabel);
1352: if (cutVertexLabel) {
1353: PetscCall(DMLabelGetStratumSize(cutVertexLabel, 1, &v));
1354: N += dof * v;
1355: }
1356: for (v = vStart; v < vEnd; ++v) {
1357: PetscCall(PetscSectionGetDof(cGlobalSection, v, &dof));
1358: if (dof < 0) continue;
1359: if (embedded) N += dof + 1;
1360: else N += dof;
1361: }
1362: if (embedded) PetscCall(VecSetBlockSize(newcoords, bs + 1));
1363: else PetscCall(VecSetBlockSize(newcoords, bs));
1364: PetscCall(VecSetSizes(newcoords, N, PETSC_DETERMINE));
1365: PetscCall(VecSetType(newcoords, VECSTANDARD));
1366: PetscCall(VecGetArray(coordinatesLocal, &coords));
1367: PetscCall(VecGetArray(newcoords, &ncoords));
1368: coordSize = 0;
1369: for (v = vStart; v < vEnd; ++v) {
1370: PetscCall(PetscSectionGetDof(cGlobalSection, v, &dof));
1371: PetscCall(PetscSectionGetOffset(cSection, v, &off));
1372: if (dof < 0) continue;
1373: if (embedded) {
1374: if (L && (L[0] > 0.0) && (L[1] > 0.0)) {
1375: PetscReal theta, phi, r, R;
1376: /* XY-periodic */
1377: /* Suppose its an y-z circle, then
1378: \hat r = (0, cos(th), sin(th)) \hat x = (1, 0, 0)
1379: and the circle in that plane is
1380: \hat r cos(phi) + \hat x sin(phi) */
1381: theta = 2.0 * PETSC_PI * PetscRealPart(coords[off + 1]) / L[1];
1382: phi = 2.0 * PETSC_PI * PetscRealPart(coords[off + 0]) / L[0];
1383: r = L[0] / (2.0 * PETSC_PI * 2.0 * L[1]);
1384: R = L[1] / (2.0 * PETSC_PI);
1385: ncoords[coordSize++] = PetscSinReal(phi) * r;
1386: ncoords[coordSize++] = -PetscCosReal(theta) * (R + r * PetscCosReal(phi));
1387: ncoords[coordSize++] = PetscSinReal(theta) * (R + r * PetscCosReal(phi));
1388: } else if (L && (L[0] > 0.0)) {
1389: /* X-periodic */
1390: ncoords[coordSize++] = -PetscCosReal(2.0 * PETSC_PI * PetscRealPart(coords[off + 0]) / L[0]) * (L[0] / (2.0 * PETSC_PI));
1391: ncoords[coordSize++] = coords[off + 1];
1392: ncoords[coordSize++] = PetscSinReal(2.0 * PETSC_PI * PetscRealPart(coords[off + 0]) / L[0]) * (L[0] / (2.0 * PETSC_PI));
1393: } else if (L && (L[1] > 0.0)) {
1394: /* Y-periodic */
1395: ncoords[coordSize++] = coords[off + 0];
1396: ncoords[coordSize++] = PetscSinReal(2.0 * PETSC_PI * PetscRealPart(coords[off + 1]) / L[1]) * (L[1] / (2.0 * PETSC_PI));
1397: ncoords[coordSize++] = -PetscCosReal(2.0 * PETSC_PI * PetscRealPart(coords[off + 1]) / L[1]) * (L[1] / (2.0 * PETSC_PI));
1398: #if 0
1399: } else if ((bd[0] == DM_BOUNDARY_TWIST)) {
1400: PetscReal phi, r, R;
1401: /* Mobius strip */
1402: /* Suppose its an x-z circle, then
1403: \hat r = (-cos(phi), 0, sin(phi)) \hat y = (0, 1, 0)
1404: and in that plane we rotate by pi as we go around the circle
1405: \hat r cos(phi/2) + \hat y sin(phi/2) */
1406: phi = 2.0*PETSC_PI*PetscRealPart(coords[off+0])/L[0];
1407: R = L[0];
1408: r = PetscRealPart(coords[off+1]) - L[1]/2.0;
1409: ncoords[coordSize++] = -PetscCosReal(phi) * (R + r * PetscCosReal(phi/2.0));
1410: ncoords[coordSize++] = PetscSinReal(phi/2.0) * r;
1411: ncoords[coordSize++] = PetscSinReal(phi) * (R + r * PetscCosReal(phi/2.0));
1412: #endif
1413: } else SETERRQ(PetscObjectComm((PetscObject)dm), PETSC_ERR_SUP, "Cannot handle periodicity in this domain");
1414: } else {
1415: for (d = 0; d < dof; ++d, ++coordSize) ncoords[coordSize] = coords[off + d];
1416: }
1417: }
1418: if (cutVertexLabel) {
1419: IS vertices;
1420: const PetscInt *verts;
1421: PetscInt n;
1423: PetscCall(DMLabelGetStratumIS(cutVertexLabel, 1, &vertices));
1424: if (vertices) {
1425: PetscCall(ISGetIndices(vertices, &verts));
1426: PetscCall(ISGetLocalSize(vertices, &n));
1427: for (v = 0; v < n; ++v) {
1428: PetscCall(PetscSectionGetDof(cSection, verts[v], &dof));
1429: PetscCall(PetscSectionGetOffset(cSection, verts[v], &off));
1430: for (d = 0; d < dof; ++d) ncoords[coordSize++] = coords[off + d] + ((L[d] > 0.) ? L[d] : 0.0);
1431: }
1432: PetscCall(ISRestoreIndices(vertices, &verts));
1433: PetscCall(ISDestroy(&vertices));
1434: }
1435: }
1436: PetscCheck(coordSize == N, PETSC_COMM_SELF, PETSC_ERR_PLIB, "Mismatched sizes: %" PetscInt_FMT " != %" PetscInt_FMT, coordSize, N);
1437: PetscCall(DMLabelDestroy(&cutVertexLabel));
1438: PetscCall(VecRestoreArray(coordinatesLocal, &coords));
1439: PetscCall(VecRestoreArray(newcoords, &ncoords));
1440: PetscCall(PetscObjectSetName((PetscObject)newcoords, "vertices"));
1441: PetscCall(VecScale(newcoords, lengthScale));
1442: PetscCall(PetscViewerHDF5PushGroup(viewer, "/viz"));
1443: PetscCall(PetscViewerHDF5WriteGroup(viewer, NULL));
1444: PetscCall(PetscViewerHDF5PopGroup(viewer));
1445: PetscCall(PetscViewerHDF5PushGroup(viewer, "/viz/geometry"));
1446: PetscCall(VecView(newcoords, viewer));
1447: PetscCall(PetscViewerHDF5PopGroup(viewer));
1448: PetscCall(VecDestroy(&newcoords));
1449: PetscFunctionReturn(PETSC_SUCCESS);
1450: }
1452: PetscErrorCode DMPlexLabelsView_HDF5_Internal(DM dm, IS globalPointNumbers, PetscViewer viewer)
1453: {
1454: const char *topologydm_name;
1455: const PetscInt *gpoint;
1456: PetscInt numLabels;
1457: PetscBool omitCelltypes = PETSC_FALSE, ocompress;
1458: DMPlexStorageVersion version;
1459: char group[PETSC_MAX_PATH_LEN];
1461: PetscFunctionBegin;
1462: PetscCall(PetscOptionsGetBool(NULL, dm->hdr.prefix, "-dm_plex_omit_celltypes", &omitCelltypes, NULL));
1463: PetscCall(PetscViewerHDF5GetDMPlexStorageVersionWriting(viewer, &version));
1464: if (DMPlexStorageVersionGE(version, 3, 1, 0)) {
1465: PetscCall(PetscViewerHDF5GetCompress(viewer, &ocompress));
1466: PetscCall(PetscViewerHDF5SetCompress(viewer, PETSC_TRUE));
1467: }
1468: PetscCall(ISGetIndices(globalPointNumbers, &gpoint));
1469: PetscCall(DMPlexGetHDF5Name_Private(dm, &topologydm_name));
1470: if (DMPlexStorageVersionGE(version, 2, 0, 0)) {
1471: PetscCall(PetscSNPrintf(group, sizeof(group), "topologies/%s/labels", topologydm_name));
1472: } else {
1473: PetscCall(PetscStrncpy(group, "/labels", sizeof(group)));
1474: }
1475: PetscCall(PetscViewerHDF5PushGroup(viewer, group));
1476: PetscCall(DMGetNumLabels(dm, &numLabels));
1477: for (PetscInt l = 0; l < numLabels; ++l) {
1478: DMLabel label;
1479: const char *name;
1480: IS valueIS, pvalueIS, globalValueIS;
1481: const PetscInt *values;
1482: PetscInt numValues, v;
1483: PetscBool isDepth, isCelltype, output;
1485: PetscCall(DMGetLabelByNum(dm, l, &label));
1486: PetscCall(PetscObjectGetName((PetscObject)label, &name));
1487: PetscCall(DMGetLabelOutput(dm, name, &output));
1488: PetscCall(PetscStrncmp(name, "depth", 10, &isDepth));
1489: PetscCall(PetscStrncmp(name, "celltype", 10, &isCelltype));
1490: // TODO Should only filter out celltype if it can be calculated
1491: if (isDepth || (isCelltype && omitCelltypes) || !output) continue;
1492: PetscCall(PetscViewerHDF5PushGroup(viewer, name));
1493: PetscCall(DMLabelGetValueIS(label, &valueIS));
1494: /* Must copy to a new IS on the global comm */
1495: PetscCall(ISGetLocalSize(valueIS, &numValues));
1496: PetscCall(ISGetIndices(valueIS, &values));
1497: PetscCall(ISCreateGeneral(PetscObjectComm((PetscObject)dm), numValues, values, PETSC_COPY_VALUES, &pvalueIS));
1498: PetscCall(ISRestoreIndices(valueIS, &values));
1499: PetscCall(ISAllGather(pvalueIS, &globalValueIS));
1500: PetscCall(ISDestroy(&pvalueIS));
1501: PetscCall(ISSortRemoveDups(globalValueIS));
1502: PetscCall(ISGetLocalSize(globalValueIS, &numValues));
1503: PetscCall(ISGetIndices(globalValueIS, &values));
1504: for (v = 0; v < numValues; ++v) {
1505: IS stratumIS, globalStratumIS;
1506: const PetscInt *spoints = NULL;
1507: PetscInt *gspoints, n = 0, gn, p;
1508: const char *iname = "indices";
1509: char group[PETSC_MAX_PATH_LEN];
1511: PetscCall(PetscSNPrintf(group, sizeof(group), "%" PetscInt_FMT, values[v]));
1512: PetscCall(PetscViewerHDF5PushGroup(viewer, group));
1513: PetscCall(DMLabelGetStratumIS(label, values[v], &stratumIS));
1515: if (stratumIS) PetscCall(ISGetLocalSize(stratumIS, &n));
1516: if (stratumIS) PetscCall(ISGetIndices(stratumIS, &spoints));
1517: for (gn = 0, p = 0; p < n; ++p)
1518: if (gpoint[spoints[p]] >= 0) ++gn;
1519: PetscCall(PetscMalloc1(gn, &gspoints));
1520: for (gn = 0, p = 0; p < n; ++p)
1521: if (gpoint[spoints[p]] >= 0) gspoints[gn++] = gpoint[spoints[p]];
1522: if (stratumIS) PetscCall(ISRestoreIndices(stratumIS, &spoints));
1523: PetscCall(ISCreateGeneral(PetscObjectComm((PetscObject)dm), gn, gspoints, PETSC_OWN_POINTER, &globalStratumIS));
1524: PetscCall(PetscObjectSetName((PetscObject)globalStratumIS, iname));
1525: PetscCall(ISView(globalStratumIS, viewer));
1526: PetscCall(ISDestroy(&globalStratumIS));
1527: PetscCall(ISDestroy(&stratumIS));
1528: PetscCall(PetscViewerHDF5PopGroup(viewer));
1529: }
1530: PetscCall(ISRestoreIndices(globalValueIS, &values));
1531: PetscCall(ISDestroy(&globalValueIS));
1532: PetscCall(ISDestroy(&valueIS));
1533: PetscCall(PetscViewerHDF5PopGroup(viewer));
1534: }
1535: PetscCall(ISRestoreIndices(globalPointNumbers, &gpoint));
1536: PetscCall(PetscViewerHDF5PopGroup(viewer));
1537: if (DMPlexStorageVersionGE(version, 3, 1, 0)) PetscCall(PetscViewerHDF5SetCompress(viewer, ocompress));
1538: PetscFunctionReturn(PETSC_SUCCESS);
1539: }
1541: /* We only write cells and vertices. Does this screw up parallel reading? */
1542: PetscErrorCode DMPlexView_HDF5_Internal(DM dm, PetscViewer viewer)
1543: {
1544: IS globalPointNumbers;
1545: PetscViewerFormat format;
1546: PetscBool viz_geom = PETSC_FALSE, xdmf_topo = PETSC_FALSE, petsc_topo = PETSC_FALSE, view_rank = PETSC_FALSE;
1548: PetscFunctionBegin;
1549: PetscCall(DMPlexCreatePointNumbering(dm, &globalPointNumbers));
1550: PetscCall(DMPlexCoordinatesView_HDF5_Internal(dm, viewer));
1552: PetscCall(PetscViewerGetFormat(viewer, &format));
1553: switch (format) {
1554: case PETSC_VIEWER_HDF5_VIZ:
1555: viz_geom = PETSC_TRUE;
1556: xdmf_topo = PETSC_TRUE;
1557: view_rank = PETSC_TRUE;
1558: break;
1559: case PETSC_VIEWER_HDF5_XDMF:
1560: xdmf_topo = PETSC_TRUE;
1561: break;
1562: case PETSC_VIEWER_HDF5_PETSC:
1563: petsc_topo = PETSC_TRUE;
1564: break;
1565: case PETSC_VIEWER_DEFAULT:
1566: case PETSC_VIEWER_NATIVE:
1567: viz_geom = PETSC_TRUE;
1568: xdmf_topo = PETSC_TRUE;
1569: petsc_topo = PETSC_TRUE;
1570: break;
1571: default:
1572: SETERRQ(PetscObjectComm((PetscObject)dm), PETSC_ERR_SUP, "PetscViewerFormat %s not supported for HDF5 output.", PetscViewerFormats[format]);
1573: }
1575: if (viz_geom) PetscCall(DMPlexCoordinatesView_HDF5_XDMF_Private(dm, viewer));
1576: if (xdmf_topo) PetscCall(DMPlexTopologyView_HDF5_XDMF_Private(dm, globalPointNumbers, viewer));
1577: if (petsc_topo) {
1578: PetscBool viewLabels = PETSC_TRUE;
1580: PetscCall(DMPlexTopologyView_HDF5_Internal(dm, globalPointNumbers, viewer));
1581: PetscCall(PetscOptionsGetBool(NULL, dm->hdr.prefix, "-dm_plex_view_labels", &viewLabels, NULL));
1582: if (viewLabels) PetscCall(DMPlexLabelsView_HDF5_Internal(dm, globalPointNumbers, viewer));
1583: }
1584: if (view_rank) {
1585: Vec v;
1587: PetscCall(DMPlexCreateRankField(dm, &v));
1588: PetscCall(VecView(v, viewer));
1589: PetscCall(VecDestroy(&v));
1590: }
1591: PetscCall(ISDestroy(&globalPointNumbers));
1592: PetscFunctionReturn(PETSC_SUCCESS);
1593: }
1595: PetscErrorCode DMPlexSectionView_HDF5_Internal(DM dm, PetscViewer viewer, DM sectiondm)
1596: {
1597: DMPlexStorageVersion version;
1598: MPI_Comm comm;
1599: const char *topologydm_name;
1600: const char *sectiondm_name;
1601: PetscSection gsection;
1602: PetscBool ocompress;
1604: PetscFunctionBegin;
1605: PetscCall(PetscViewerHDF5GetDMPlexStorageVersionWriting(viewer, &version));
1606: if (DMPlexStorageVersionGE(version, 3, 1, 0)) {
1607: PetscCall(PetscViewerHDF5GetCompress(viewer, &ocompress));
1608: PetscCall(PetscViewerHDF5SetCompress(viewer, PETSC_TRUE));
1609: }
1610: PetscCall(PetscObjectGetComm((PetscObject)sectiondm, &comm));
1611: PetscCall(DMPlexGetHDF5Name_Private(dm, &topologydm_name));
1612: PetscCall(PetscObjectGetName((PetscObject)sectiondm, §iondm_name));
1613: PetscCall(PetscViewerHDF5PushGroup(viewer, "topologies"));
1614: PetscCall(PetscViewerHDF5PushGroup(viewer, topologydm_name));
1615: PetscCall(PetscViewerHDF5PushGroup(viewer, "dms"));
1616: PetscCall(PetscViewerHDF5PushGroup(viewer, sectiondm_name));
1617: PetscCall(DMGetGlobalSection(sectiondm, &gsection));
1618: /* Save raw section */
1619: PetscCall(PetscSectionView(gsection, viewer));
1620: /* Save plex wrapper */
1621: {
1622: PetscInt pStart, pEnd, p, n;
1623: IS globalPointNumbers;
1624: const PetscInt *gpoints;
1625: IS orderIS;
1626: PetscInt *order;
1628: PetscCall(PetscSectionGetChart(gsection, &pStart, &pEnd));
1629: PetscCall(DMPlexCreatePointNumbering(dm, &globalPointNumbers));
1630: PetscCall(ISGetIndices(globalPointNumbers, &gpoints));
1631: for (p = pStart, n = 0; p < pEnd; ++p)
1632: if (gpoints[p] >= 0) n++;
1633: /* "order" is an array of global point numbers.
1634: When loading, it is used with topology/order array
1635: to match section points with plex topology points. */
1636: PetscCall(PetscMalloc1(n, &order));
1637: for (p = pStart, n = 0; p < pEnd; ++p)
1638: if (gpoints[p] >= 0) order[n++] = gpoints[p];
1639: PetscCall(ISRestoreIndices(globalPointNumbers, &gpoints));
1640: PetscCall(ISDestroy(&globalPointNumbers));
1641: PetscCall(ISCreateGeneral(comm, n, order, PETSC_OWN_POINTER, &orderIS));
1642: PetscCall(PetscObjectSetName((PetscObject)orderIS, "order"));
1643: PetscCall(ISView(orderIS, viewer));
1644: PetscCall(ISDestroy(&orderIS));
1645: }
1646: PetscCall(PetscViewerHDF5PopGroup(viewer));
1647: PetscCall(PetscViewerHDF5PopGroup(viewer));
1648: PetscCall(PetscViewerHDF5PopGroup(viewer));
1649: PetscCall(PetscViewerHDF5PopGroup(viewer));
1650: if (DMPlexStorageVersionGE(version, 3, 1, 0)) PetscCall(PetscViewerHDF5SetCompress(viewer, ocompress));
1651: PetscFunctionReturn(PETSC_SUCCESS);
1652: }
1654: PetscErrorCode DMPlexGlobalVectorView_HDF5_Internal(DM dm, PetscViewer viewer, DM sectiondm, Vec vec)
1655: {
1656: const char *topologydm_name;
1657: const char *sectiondm_name;
1658: const char *vec_name;
1659: PetscInt bs;
1661: PetscFunctionBegin;
1662: /* Check consistency */
1663: {
1664: PetscSF pointsf, pointsf1;
1666: PetscCall(DMGetPointSF(dm, &pointsf));
1667: PetscCall(DMGetPointSF(sectiondm, &pointsf1));
1668: PetscCheck(pointsf1 == pointsf, PETSC_COMM_SELF, PETSC_ERR_PLIB, "Mismatching point SFs for dm and sectiondm");
1669: }
1670: PetscCall(DMPlexGetHDF5Name_Private(dm, &topologydm_name));
1671: PetscCall(PetscObjectGetName((PetscObject)sectiondm, §iondm_name));
1672: PetscCall(PetscObjectGetName((PetscObject)vec, &vec_name));
1673: PetscCall(PetscViewerHDF5PushGroup(viewer, "topologies"));
1674: PetscCall(PetscViewerHDF5PushGroup(viewer, topologydm_name));
1675: PetscCall(PetscViewerHDF5PushGroup(viewer, "dms"));
1676: PetscCall(PetscViewerHDF5PushGroup(viewer, sectiondm_name));
1677: PetscCall(PetscViewerHDF5PushGroup(viewer, "vecs"));
1678: PetscCall(PetscViewerHDF5PushGroup(viewer, vec_name));
1679: PetscCall(VecGetBlockSize(vec, &bs));
1680: PetscCall(PetscViewerHDF5WriteAttribute(viewer, NULL, "blockSize", PETSC_INT, (void *)&bs));
1681: PetscCall(VecSetBlockSize(vec, 1));
1682: /* VecView(vec, viewer) would call (*vec->opt->view)(vec, viewer), but, */
1683: /* if vec was created with DMGet{Global, Local}Vector(), vec->opt->view */
1684: /* is set to VecView_Plex, which would save vec in a predefined location. */
1685: /* To save vec in where we want, we create a new Vec (temp) with */
1686: /* VecCreate(), wrap the vec data in temp, and call VecView(temp, viewer). */
1687: {
1688: Vec temp;
1689: const PetscScalar *array;
1690: PetscLayout map;
1692: PetscCall(VecCreate(PetscObjectComm((PetscObject)vec), &temp));
1693: PetscCall(PetscObjectSetName((PetscObject)temp, vec_name));
1694: PetscCall(VecGetLayout(vec, &map));
1695: PetscCall(VecSetLayout(temp, map));
1696: PetscCall(VecSetUp(temp));
1697: PetscCall(VecGetArrayRead(vec, &array));
1698: PetscCall(VecPlaceArray(temp, array));
1699: PetscCall(VecView(temp, viewer));
1700: PetscCall(VecResetArray(temp));
1701: PetscCall(VecRestoreArrayRead(vec, &array));
1702: PetscCall(VecDestroy(&temp));
1703: }
1704: PetscCall(VecSetBlockSize(vec, bs));
1705: PetscCall(PetscViewerHDF5PopGroup(viewer));
1706: PetscCall(PetscViewerHDF5PopGroup(viewer));
1707: PetscCall(PetscViewerHDF5PopGroup(viewer));
1708: PetscCall(PetscViewerHDF5PopGroup(viewer));
1709: PetscCall(PetscViewerHDF5PopGroup(viewer));
1710: PetscCall(PetscViewerHDF5PopGroup(viewer));
1711: PetscFunctionReturn(PETSC_SUCCESS);
1712: }
1714: PetscErrorCode DMPlexLocalVectorView_HDF5_Internal(DM dm, PetscViewer viewer, DM sectiondm, Vec vec)
1715: {
1716: MPI_Comm comm;
1717: const char *topologydm_name;
1718: const char *sectiondm_name;
1719: const char *vec_name;
1720: PetscSection section;
1721: PetscBool includesConstraints;
1722: Vec gvec;
1723: PetscInt m, bs;
1725: PetscFunctionBegin;
1726: PetscCall(PetscObjectGetComm((PetscObject)dm, &comm));
1727: /* Check consistency */
1728: {
1729: PetscSF pointsf, pointsf1;
1731: PetscCall(DMGetPointSF(dm, &pointsf));
1732: PetscCall(DMGetPointSF(sectiondm, &pointsf1));
1733: PetscCheck(pointsf1 == pointsf, PETSC_COMM_SELF, PETSC_ERR_PLIB, "Mismatching point SFs for dm and sectiondm");
1734: }
1735: PetscCall(DMPlexGetHDF5Name_Private(dm, &topologydm_name));
1736: PetscCall(PetscObjectGetName((PetscObject)sectiondm, §iondm_name));
1737: PetscCall(PetscObjectGetName((PetscObject)vec, &vec_name));
1738: PetscCall(PetscViewerHDF5PushGroup(viewer, "topologies"));
1739: PetscCall(PetscViewerHDF5PushGroup(viewer, topologydm_name));
1740: PetscCall(PetscViewerHDF5PushGroup(viewer, "dms"));
1741: PetscCall(PetscViewerHDF5PushGroup(viewer, sectiondm_name));
1742: PetscCall(PetscViewerHDF5PushGroup(viewer, "vecs"));
1743: PetscCall(PetscViewerHDF5PushGroup(viewer, vec_name));
1744: PetscCall(VecGetBlockSize(vec, &bs));
1745: PetscCall(PetscViewerHDF5WriteAttribute(viewer, NULL, "blockSize", PETSC_INT, (void *)&bs));
1746: PetscCall(VecCreate(comm, &gvec));
1747: PetscCall(PetscObjectSetName((PetscObject)gvec, vec_name));
1748: PetscCall(DMGetGlobalSection(sectiondm, §ion));
1749: PetscCall(PetscSectionGetIncludesConstraints(section, &includesConstraints));
1750: if (includesConstraints) PetscCall(PetscSectionGetStorageSize(section, &m));
1751: else PetscCall(PetscSectionGetConstrainedStorageSize(section, &m));
1752: PetscCall(VecSetSizes(gvec, m, PETSC_DECIDE));
1753: PetscCall(VecSetUp(gvec));
1754: PetscCall(DMLocalToGlobalBegin(sectiondm, vec, INSERT_VALUES, gvec));
1755: PetscCall(DMLocalToGlobalEnd(sectiondm, vec, INSERT_VALUES, gvec));
1756: PetscCall(VecView(gvec, viewer));
1757: PetscCall(VecDestroy(&gvec));
1758: PetscCall(PetscViewerHDF5PopGroup(viewer));
1759: PetscCall(PetscViewerHDF5PopGroup(viewer));
1760: PetscCall(PetscViewerHDF5PopGroup(viewer));
1761: PetscCall(PetscViewerHDF5PopGroup(viewer));
1762: PetscCall(PetscViewerHDF5PopGroup(viewer));
1763: PetscCall(PetscViewerHDF5PopGroup(viewer));
1764: PetscFunctionReturn(PETSC_SUCCESS);
1765: }
1767: struct _n_LoadLabelsCtx {
1768: MPI_Comm comm;
1769: PetscMPIInt rank;
1770: DM dm;
1771: PetscViewer viewer;
1772: DMLabel label;
1773: PetscSF sfXC;
1774: PetscLayout layoutX;
1775: };
1776: typedef struct _n_LoadLabelsCtx *LoadLabelsCtx;
1778: static PetscErrorCode LoadLabelsCtxCreate(DM dm, PetscViewer viewer, PetscSF sfXC, LoadLabelsCtx *ctx)
1779: {
1780: PetscFunctionBegin;
1781: PetscCall(PetscNew(ctx));
1782: PetscCall(PetscObjectReference((PetscObject)((*ctx)->dm = dm)));
1783: PetscCall(PetscObjectReference((PetscObject)((*ctx)->viewer = viewer)));
1784: PetscCall(PetscObjectGetComm((PetscObject)dm, &(*ctx)->comm));
1785: PetscCallMPI(MPI_Comm_rank((*ctx)->comm, &(*ctx)->rank));
1786: (*ctx)->sfXC = sfXC;
1787: if (sfXC) {
1788: PetscInt nX;
1790: PetscCall(PetscObjectReference((PetscObject)sfXC));
1791: PetscCall(PetscSFGetGraph(sfXC, &nX, NULL, NULL, NULL));
1792: PetscCall(PetscLayoutCreateFromSizes((*ctx)->comm, nX, PETSC_DECIDE, 1, &(*ctx)->layoutX));
1793: }
1794: PetscFunctionReturn(PETSC_SUCCESS);
1795: }
1797: static PetscErrorCode LoadLabelsCtxDestroy(LoadLabelsCtx *ctx)
1798: {
1799: PetscFunctionBegin;
1800: if (!*ctx) PetscFunctionReturn(PETSC_SUCCESS);
1801: PetscCall(DMDestroy(&(*ctx)->dm));
1802: PetscCall(PetscViewerDestroy(&(*ctx)->viewer));
1803: PetscCall(PetscSFDestroy(&(*ctx)->sfXC));
1804: PetscCall(PetscLayoutDestroy(&(*ctx)->layoutX));
1805: PetscCall(PetscFree(*ctx));
1806: PetscFunctionReturn(PETSC_SUCCESS);
1807: }
1809: /*
1810: A: on-disk points
1811: X: global points [0, NX)
1812: C: distributed plex points
1813: */
1814: static herr_t ReadLabelStratumHDF5_Distribute_Private(IS stratumIS, LoadLabelsCtx ctx, IS *newStratumIS)
1815: {
1816: MPI_Comm comm = ctx->comm;
1817: PetscSF sfXC = ctx->sfXC;
1818: PetscLayout layoutX = ctx->layoutX;
1819: PetscSF sfXA;
1820: const PetscInt *A_points;
1821: PetscInt nX, nC;
1822: PetscInt n;
1824: PetscFunctionBegin;
1825: PetscCall(PetscSFGetGraph(sfXC, &nX, &nC, NULL, NULL));
1826: PetscCall(ISGetLocalSize(stratumIS, &n));
1827: PetscCall(ISGetIndices(stratumIS, &A_points));
1828: PetscCall(PetscSFCreate(comm, &sfXA));
1829: PetscCall(PetscSFSetGraphLayout(sfXA, layoutX, n, NULL, PETSC_USE_POINTER, A_points));
1830: PetscCall(ISCreate(comm, newStratumIS));
1831: PetscCall(ISSetType(*newStratumIS, ISGENERAL));
1832: {
1833: PetscInt i;
1834: PetscBool *A_mask, *X_mask, *C_mask;
1836: PetscCall(PetscCalloc3(n, &A_mask, nX, &X_mask, nC, &C_mask));
1837: for (i = 0; i < n; i++) A_mask[i] = PETSC_TRUE;
1838: PetscCall(PetscSFReduceBegin(sfXA, MPI_C_BOOL, A_mask, X_mask, MPI_REPLACE));
1839: PetscCall(PetscSFReduceEnd(sfXA, MPI_C_BOOL, A_mask, X_mask, MPI_REPLACE));
1840: PetscCall(PetscSFBcastBegin(sfXC, MPI_C_BOOL, X_mask, C_mask, MPI_LOR));
1841: PetscCall(PetscSFBcastEnd(sfXC, MPI_C_BOOL, X_mask, C_mask, MPI_LOR));
1842: PetscCall(ISGeneralSetIndicesFromMask(*newStratumIS, 0, nC, C_mask));
1843: PetscCall(PetscFree3(A_mask, X_mask, C_mask));
1844: }
1845: PetscCall(PetscSFDestroy(&sfXA));
1846: PetscCall(ISRestoreIndices(stratumIS, &A_points));
1847: PetscFunctionReturn(PETSC_SUCCESS);
1848: }
1850: static herr_t ReadLabelStratumHDF5_Static(hid_t g_id, const char *vname, const H5L_info_t *info, void *op_data)
1851: {
1852: LoadLabelsCtx ctx = (LoadLabelsCtx)op_data;
1853: PetscViewer viewer = ctx->viewer;
1854: DMLabel label = ctx->label;
1855: MPI_Comm comm = ctx->comm;
1856: IS stratumIS;
1857: const PetscInt *ind;
1858: PetscInt value, N, i;
1860: PetscCall(PetscOptionsStringToInt(vname, &value));
1861: PetscCall(ISCreate(comm, &stratumIS));
1862: PetscCall(PetscObjectSetName((PetscObject)stratumIS, "indices"));
1863: PetscCall(PetscViewerHDF5PushGroup(viewer, vname)); /* labels/<lname>/<vname> */
1865: if (!ctx->sfXC) {
1866: /* Force serial load */
1867: PetscCall(PetscViewerHDF5ReadSizes(viewer, "indices", NULL, &N));
1868: PetscCall(PetscLayoutSetLocalSize(stratumIS->map, !ctx->rank ? N : 0));
1869: PetscCall(PetscLayoutSetSize(stratumIS->map, N));
1870: }
1871: PetscCall(ISLoad(stratumIS, viewer));
1873: if (ctx->sfXC) {
1874: IS newStratumIS;
1876: PetscCallHDF5(ReadLabelStratumHDF5_Distribute_Private, (stratumIS, ctx, &newStratumIS));
1877: PetscCall(ISDestroy(&stratumIS));
1878: stratumIS = newStratumIS;
1879: }
1881: PetscCall(PetscViewerHDF5PopGroup(viewer));
1882: PetscCall(ISGetLocalSize(stratumIS, &N));
1883: PetscCall(ISGetIndices(stratumIS, &ind));
1884: for (i = 0; i < N; ++i) PetscCall(DMLabelSetValue(label, ind[i], value));
1885: PetscCall(ISRestoreIndices(stratumIS, &ind));
1886: PetscCall(ISDestroy(&stratumIS));
1887: return 0;
1888: }
1890: /* TODO: Fix this code, it is returning PETSc error codes when it should be translating them to herr_t codes */
1891: static herr_t ReadLabelHDF5_Static(hid_t g_id, const char *lname, const H5L_info_t *info, void *op_data)
1892: {
1893: LoadLabelsCtx ctx = (LoadLabelsCtx)op_data;
1894: DM dm = ctx->dm;
1895: hsize_t idx = 0;
1896: PetscErrorCode ierr;
1897: PetscBool flg;
1898: herr_t err;
1900: PetscCall(DMHasLabel(dm, lname, &flg));
1901: if (flg) PetscCall(DMRemoveLabel(dm, lname, NULL));
1902: ierr = DMCreateLabel(dm, lname);
1903: if (ierr) return (herr_t)ierr;
1904: ierr = DMGetLabel(dm, lname, &ctx->label);
1905: if (ierr) return (herr_t)ierr;
1906: ierr = PetscViewerHDF5PushGroup(ctx->viewer, lname);
1907: if (ierr) return (herr_t)ierr;
1908: /* Iterate over the label's strata */
1909: PetscCallHDF5Return(err, H5Literate_by_name, (g_id, lname, H5_INDEX_NAME, H5_ITER_NATIVE, &idx, ReadLabelStratumHDF5_Static, op_data, 0));
1910: ierr = PetscViewerHDF5PopGroup(ctx->viewer);
1911: if (ierr) return (herr_t)ierr;
1912: return err;
1913: }
1915: PetscErrorCode DMPlexLabelsLoad_HDF5_Internal(DM dm, PetscViewer viewer, PetscSF sfXC)
1916: {
1917: const char *topologydm_name;
1918: LoadLabelsCtx ctx;
1919: hsize_t idx = 0;
1920: char group[PETSC_MAX_PATH_LEN];
1921: DMPlexStorageVersion version;
1922: PetscBool distributed, hasGroup;
1924: PetscFunctionBegin;
1925: PetscCall(DMPlexIsDistributed(dm, &distributed));
1926: if (distributed) PetscCheck(sfXC, PetscObjectComm((PetscObject)dm), PETSC_ERR_ARG_NULL, "PetscSF must be given for parallel load");
1927: PetscCall(LoadLabelsCtxCreate(dm, viewer, sfXC, &ctx));
1928: PetscCall(DMPlexGetHDF5Name_Private(dm, &topologydm_name));
1929: PetscCall(PetscViewerHDF5GetDMPlexStorageVersionReading(viewer, &version));
1930: if (DMPlexStorageVersionGE(version, 2, 0, 0)) {
1931: PetscCall(PetscSNPrintf(group, sizeof(group), "topologies/%s/labels", topologydm_name));
1932: } else {
1933: PetscCall(PetscStrncpy(group, "labels", sizeof(group)));
1934: }
1935: PetscCall(PetscViewerHDF5PushGroup(viewer, group));
1936: PetscCall(PetscViewerHDF5HasGroup(viewer, NULL, &hasGroup));
1937: if (hasGroup) {
1938: hid_t fileId, groupId;
1940: PetscCall(PetscViewerHDF5OpenGroup(viewer, NULL, &fileId, &groupId));
1941: /* Iterate over labels */
1942: PetscCallHDF5(H5Literate, (groupId, H5_INDEX_NAME, H5_ITER_NATIVE, &idx, ReadLabelHDF5_Static, ctx));
1943: PetscCallHDF5(H5Gclose, (groupId));
1944: }
1945: PetscCall(PetscViewerHDF5PopGroup(viewer));
1946: PetscCall(LoadLabelsCtxDestroy(&ctx));
1947: PetscFunctionReturn(PETSC_SUCCESS);
1948: }
1950: static PetscErrorCode DMPlexDistributionLoad_HDF5_Private(DM dm, PetscViewer viewer, PetscSF sf, PetscSF *distsf, DM *distdm)
1951: {
1952: MPI_Comm comm;
1953: PetscMPIInt size, rank;
1954: PetscInt dist_size;
1955: const char *distribution_name;
1956: PetscInt p, lsize;
1957: IS chartSizesIS, ownersIS, gpointsIS;
1958: const PetscInt *chartSize, *owners, *gpoints;
1959: PetscLayout layout;
1960: PetscBool has;
1962: PetscFunctionBegin;
1963: *distsf = NULL;
1964: *distdm = NULL;
1965: PetscCall(PetscObjectGetComm((PetscObject)dm, &comm));
1966: PetscCallMPI(MPI_Comm_size(comm, &size));
1967: PetscCallMPI(MPI_Comm_rank(comm, &rank));
1968: PetscCall(DMPlexDistributionGetName(dm, &distribution_name));
1969: if (!distribution_name) PetscFunctionReturn(PETSC_SUCCESS);
1970: PetscCall(PetscLogEventBegin(DMPLEX_DistributionLoad, viewer, 0, 0, 0));
1971: PetscCall(PetscViewerHDF5HasGroup(viewer, NULL, &has));
1972: if (!has) {
1973: const char *full_group;
1975: PetscCall(PetscViewerHDF5GetGroup(viewer, NULL, &full_group));
1976: 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);
1977: }
1978: PetscCall(PetscViewerHDF5ReadAttribute(viewer, NULL, "comm_size", PETSC_INT, NULL, (void *)&dist_size));
1979: 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);
1980: PetscCall(ISCreate(comm, &chartSizesIS));
1981: PetscCall(PetscObjectSetName((PetscObject)chartSizesIS, "chart_sizes"));
1982: PetscCall(ISCreate(comm, &ownersIS));
1983: PetscCall(PetscObjectSetName((PetscObject)ownersIS, "owners"));
1984: PetscCall(ISCreate(comm, &gpointsIS));
1985: PetscCall(PetscObjectSetName((PetscObject)gpointsIS, "global_point_numbers"));
1986: PetscCall(PetscLayoutSetLocalSize(chartSizesIS->map, 1));
1987: PetscCall(ISLoad(chartSizesIS, viewer));
1988: PetscCall(ISGetIndices(chartSizesIS, &chartSize));
1989: PetscCall(PetscLayoutSetLocalSize(ownersIS->map, *chartSize));
1990: PetscCall(PetscLayoutSetLocalSize(gpointsIS->map, *chartSize));
1991: PetscCall(ISLoad(ownersIS, viewer));
1992: PetscCall(ISLoad(gpointsIS, viewer));
1993: PetscCall(ISGetIndices(ownersIS, &owners));
1994: PetscCall(ISGetIndices(gpointsIS, &gpoints));
1995: PetscCall(PetscSFCreate(comm, distsf));
1996: PetscCall(PetscSFSetFromOptions(*distsf));
1997: PetscCall(PetscLayoutCreate(comm, &layout));
1998: PetscCall(PetscSFGetGraph(sf, &lsize, NULL, NULL, NULL));
1999: PetscCall(PetscLayoutSetLocalSize(layout, lsize));
2000: PetscCall(PetscLayoutSetBlockSize(layout, 1));
2001: PetscCall(PetscLayoutSetUp(layout));
2002: PetscCall(PetscSFSetGraphLayout(*distsf, layout, *chartSize, NULL, PETSC_OWN_POINTER, gpoints));
2003: PetscCall(PetscLayoutDestroy(&layout));
2004: /* Migrate DM */
2005: {
2006: PetscInt pStart, pEnd;
2007: PetscSFNode *buffer0, *buffer1, *buffer2;
2009: PetscCall(DMPlexGetChart(dm, &pStart, &pEnd));
2010: PetscCall(PetscMalloc2(pEnd - pStart, &buffer0, lsize, &buffer1));
2011: PetscCall(PetscMalloc1(*chartSize, &buffer2));
2012: {
2013: PetscSF workPointSF;
2014: PetscInt workNroots, workNleaves;
2015: const PetscInt *workIlocal;
2016: const PetscSFNode *workIremote;
2018: for (p = pStart; p < pEnd; ++p) {
2019: buffer0[p - pStart].rank = rank;
2020: buffer0[p - pStart].index = p - pStart;
2021: }
2022: PetscCall(DMGetPointSF(dm, &workPointSF));
2023: PetscCall(PetscSFGetGraph(workPointSF, &workNroots, &workNleaves, &workIlocal, &workIremote));
2024: for (p = 0; p < workNleaves; ++p) {
2025: PetscInt workIlocalp = (workIlocal ? workIlocal[p] : p);
2027: buffer0[workIlocalp].rank = -1;
2028: }
2029: }
2030: for (p = 0; p < lsize; ++p) buffer1[p].rank = -1;
2031: for (p = 0; p < *chartSize; ++p) buffer2[p].rank = -1;
2032: PetscCall(PetscSFReduceBegin(sf, MPIU_SF_NODE, buffer0, buffer1, MPI_MAXLOC));
2033: PetscCall(PetscSFReduceEnd(sf, MPIU_SF_NODE, buffer0, buffer1, MPI_MAXLOC));
2034: PetscCall(PetscSFBcastBegin(*distsf, MPIU_SF_NODE, buffer1, buffer2, MPI_REPLACE));
2035: PetscCall(PetscSFBcastEnd(*distsf, MPIU_SF_NODE, buffer1, buffer2, MPI_REPLACE));
2036: if (PetscDefined(USE_DEBUG)) {
2037: 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);
2038: }
2039: PetscCall(PetscFree2(buffer0, buffer1));
2040: PetscCall(DMCreate(comm, distdm));
2041: PetscCall(DMSetType(*distdm, DMPLEX));
2042: PetscCall(PetscObjectSetName((PetscObject)*distdm, ((PetscObject)dm)->name));
2043: PetscCall(DMPlexDistributionSetName(*distdm, distribution_name));
2044: {
2045: PetscSF migrationSF;
2047: PetscCall(PetscSFCreate(comm, &migrationSF));
2048: PetscCall(PetscSFSetFromOptions(migrationSF));
2049: PetscCall(PetscSFSetGraph(migrationSF, pEnd - pStart, *chartSize, NULL, PETSC_OWN_POINTER, buffer2, PETSC_OWN_POINTER));
2050: PetscCall(PetscSFSetUp(migrationSF));
2051: PetscCall(DMPlexMigrate(dm, migrationSF, *distdm));
2052: PetscCall(PetscSFDestroy(&migrationSF));
2053: }
2054: }
2055: /* Set pointSF */
2056: {
2057: PetscSF pointSF;
2058: PetscInt *ilocal, nleaves, q;
2059: PetscSFNode *iremote, *buffer0, *buffer1;
2061: PetscCall(PetscMalloc2(*chartSize, &buffer0, lsize, &buffer1));
2062: for (p = 0, nleaves = 0; p < *chartSize; ++p) {
2063: if (owners[p] == rank) {
2064: buffer0[p].rank = rank;
2065: } else {
2066: buffer0[p].rank = -1;
2067: nleaves++;
2068: }
2069: buffer0[p].index = p;
2070: }
2071: for (p = 0; p < lsize; ++p) buffer1[p].rank = -1;
2072: PetscCall(PetscSFReduceBegin(*distsf, MPIU_SF_NODE, buffer0, buffer1, MPI_MAXLOC));
2073: PetscCall(PetscSFReduceEnd(*distsf, MPIU_SF_NODE, buffer0, buffer1, MPI_MAXLOC));
2074: for (p = 0; p < *chartSize; ++p) buffer0[p].rank = -1;
2075: PetscCall(PetscSFBcastBegin(*distsf, MPIU_SF_NODE, buffer1, buffer0, MPI_REPLACE));
2076: PetscCall(PetscSFBcastEnd(*distsf, MPIU_SF_NODE, buffer1, buffer0, MPI_REPLACE));
2077: if (PetscDefined(USE_DEBUG)) {
2078: 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);
2079: }
2080: PetscCall(PetscMalloc1(nleaves, &ilocal));
2081: PetscCall(PetscMalloc1(nleaves, &iremote));
2082: for (p = 0, q = 0; p < *chartSize; ++p) {
2083: if (buffer0[p].rank != rank) {
2084: ilocal[q] = p;
2085: iremote[q].rank = buffer0[p].rank;
2086: iremote[q].index = buffer0[p].index;
2087: q++;
2088: }
2089: }
2090: PetscCheck(q == nleaves, PETSC_COMM_SELF, PETSC_ERR_PLIB, "Mismatching leaf sizes: %" PetscInt_FMT " != %" PetscInt_FMT, q, nleaves);
2091: PetscCall(PetscFree2(buffer0, buffer1));
2092: PetscCall(PetscSFCreate(comm, &pointSF));
2093: PetscCall(PetscSFSetFromOptions(pointSF));
2094: PetscCall(PetscSFSetGraph(pointSF, *chartSize, nleaves, ilocal, PETSC_OWN_POINTER, iremote, PETSC_OWN_POINTER));
2095: PetscCall(DMSetPointSF(*distdm, pointSF));
2096: {
2097: DM cdm;
2099: PetscCall(DMGetCoordinateDM(*distdm, &cdm));
2100: PetscCall(DMSetPointSF(cdm, pointSF));
2101: }
2102: PetscCall(PetscSFDestroy(&pointSF));
2103: }
2104: PetscCall(ISRestoreIndices(chartSizesIS, &chartSize));
2105: PetscCall(ISRestoreIndices(ownersIS, &owners));
2106: PetscCall(ISRestoreIndices(gpointsIS, &gpoints));
2107: PetscCall(ISDestroy(&chartSizesIS));
2108: PetscCall(ISDestroy(&ownersIS));
2109: PetscCall(ISDestroy(&gpointsIS));
2110: /* Record that overlap has been manually created. */
2111: /* This is to pass `DMPlexCheckPointSF()`, which checks that */
2112: /* pointSF does not contain cells in the leaves if overlap = 0. */
2113: PetscCall(DMPlexSetOverlap_Plex(*distdm, NULL, DMPLEX_OVERLAP_MANUAL));
2114: PetscCall(DMPlexDistributeSetDefault(*distdm, PETSC_FALSE));
2115: PetscCall(DMPlexReorderSetDefault(*distdm, DM_REORDER_DEFAULT_FALSE));
2116: PetscCall(PetscLogEventEnd(DMPLEX_DistributionLoad, viewer, 0, 0, 0));
2117: PetscFunctionReturn(PETSC_SUCCESS);
2118: }
2120: // Serial load of topology
2121: static PetscErrorCode DMPlexTopologyLoad_HDF5_Legacy_Private(DM dm, PetscViewer viewer, PetscSF *sf)
2122: {
2123: MPI_Comm comm;
2124: const char *pointsName, *coneSizesName, *conesName, *orientationsName;
2125: IS pointsIS, coneSizesIS, conesIS, orientationsIS;
2126: const PetscInt *points, *coneSizes, *cones, *orientations;
2127: PetscInt *cone, *ornt;
2128: PetscInt dim, N, Np, pEnd, p, q, maxConeSize = 0, c;
2129: PetscMPIInt size, rank;
2131: PetscFunctionBegin;
2132: pointsName = "order";
2133: coneSizesName = "cones";
2134: conesName = "cells";
2135: orientationsName = "orientation";
2136: PetscCall(PetscObjectGetComm((PetscObject)dm, &comm));
2137: PetscCallMPI(MPI_Comm_size(comm, &size));
2138: PetscCallMPI(MPI_Comm_rank(comm, &rank));
2139: PetscCall(ISCreate(comm, &pointsIS));
2140: PetscCall(PetscObjectSetName((PetscObject)pointsIS, pointsName));
2141: PetscCall(ISCreate(comm, &coneSizesIS));
2142: PetscCall(PetscObjectSetName((PetscObject)coneSizesIS, coneSizesName));
2143: PetscCall(ISCreate(comm, &conesIS));
2144: PetscCall(PetscObjectSetName((PetscObject)conesIS, conesName));
2145: PetscCall(ISCreate(comm, &orientationsIS));
2146: PetscCall(PetscObjectSetName((PetscObject)orientationsIS, orientationsName));
2147: PetscCall(PetscViewerHDF5ReadObjectAttribute(viewer, (PetscObject)conesIS, "cell_dim", PETSC_INT, NULL, &dim));
2148: PetscCall(DMSetDimension(dm, dim));
2149: {
2150: /* Force serial load */
2151: PetscCall(PetscInfo(dm, "Loading DM %s in serial\n", dm->hdr.name));
2152: PetscCall(PetscViewerHDF5ReadSizes(viewer, pointsName, NULL, &Np));
2153: PetscCall(PetscLayoutSetLocalSize(pointsIS->map, rank == 0 ? Np : 0));
2154: PetscCall(PetscLayoutSetSize(pointsIS->map, Np));
2155: pEnd = rank == 0 ? Np : 0;
2156: PetscCall(PetscViewerHDF5ReadSizes(viewer, coneSizesName, NULL, &Np));
2157: PetscCall(PetscLayoutSetLocalSize(coneSizesIS->map, rank == 0 ? Np : 0));
2158: PetscCall(PetscLayoutSetSize(coneSizesIS->map, Np));
2159: PetscCall(PetscViewerHDF5ReadSizes(viewer, conesName, NULL, &N));
2160: PetscCall(PetscLayoutSetLocalSize(conesIS->map, rank == 0 ? N : 0));
2161: PetscCall(PetscLayoutSetSize(conesIS->map, N));
2162: PetscCall(PetscViewerHDF5ReadSizes(viewer, orientationsName, NULL, &N));
2163: PetscCall(PetscLayoutSetLocalSize(orientationsIS->map, rank == 0 ? N : 0));
2164: PetscCall(PetscLayoutSetSize(orientationsIS->map, N));
2165: }
2166: PetscCall(ISLoad(pointsIS, viewer));
2167: PetscCall(ISLoad(coneSizesIS, viewer));
2168: PetscCall(ISLoad(conesIS, viewer));
2169: PetscCall(ISLoad(orientationsIS, viewer));
2170: /* Create Plex */
2171: PetscCall(DMPlexSetChart(dm, 0, pEnd));
2172: PetscCall(ISGetIndices(pointsIS, &points));
2173: PetscCall(ISGetIndices(coneSizesIS, &coneSizes));
2174: for (p = 0; p < pEnd; ++p) {
2175: PetscCall(DMPlexSetConeSize(dm, points[p], coneSizes[p]));
2176: maxConeSize = PetscMax(maxConeSize, coneSizes[p]);
2177: }
2178: PetscCall(DMSetUp(dm));
2179: PetscCall(ISGetIndices(conesIS, &cones));
2180: PetscCall(ISGetIndices(orientationsIS, &orientations));
2181: PetscCall(PetscMalloc2(maxConeSize, &cone, maxConeSize, &ornt));
2182: for (p = 0, q = 0; p < pEnd; ++p) {
2183: for (c = 0; c < coneSizes[p]; ++c, ++q) {
2184: cone[c] = cones[q];
2185: ornt[c] = orientations[q];
2186: }
2187: PetscCall(DMPlexSetCone(dm, points[p], cone));
2188: PetscCall(DMPlexSetConeOrientation(dm, points[p], ornt));
2189: }
2190: PetscCall(PetscFree2(cone, ornt));
2191: /* Create global section migration SF */
2192: if (sf) {
2193: PetscLayout layout;
2194: PetscInt *globalIndices;
2196: PetscCall(PetscMalloc1(pEnd, &globalIndices));
2197: /* plex point == globalPointNumber in this case */
2198: for (p = 0; p < pEnd; ++p) globalIndices[p] = p;
2199: PetscCall(PetscLayoutCreate(comm, &layout));
2200: PetscCall(PetscLayoutSetSize(layout, Np));
2201: PetscCall(PetscLayoutSetBlockSize(layout, 1));
2202: PetscCall(PetscLayoutSetUp(layout));
2203: PetscCall(PetscSFCreate(comm, sf));
2204: PetscCall(PetscSFSetFromOptions(*sf));
2205: PetscCall(PetscSFSetGraphLayout(*sf, layout, pEnd, NULL, PETSC_OWN_POINTER, globalIndices));
2206: PetscCall(PetscLayoutDestroy(&layout));
2207: PetscCall(PetscFree(globalIndices));
2208: }
2209: /* Clean-up */
2210: PetscCall(ISRestoreIndices(pointsIS, &points));
2211: PetscCall(ISRestoreIndices(coneSizesIS, &coneSizes));
2212: PetscCall(ISRestoreIndices(conesIS, &cones));
2213: PetscCall(ISRestoreIndices(orientationsIS, &orientations));
2214: PetscCall(ISDestroy(&pointsIS));
2215: PetscCall(ISDestroy(&coneSizesIS));
2216: PetscCall(ISDestroy(&conesIS));
2217: PetscCall(ISDestroy(&orientationsIS));
2218: /* Fill in the rest of the topology structure */
2219: PetscCall(DMPlexSymmetrize(dm));
2220: PetscCall(DMPlexStratify(dm));
2221: PetscFunctionReturn(PETSC_SUCCESS);
2222: }
2224: /* Representation of two DMPlex strata in 0-based global numbering */
2225: struct _n_PlexLayer {
2226: PetscInt d;
2227: IS conesIS, orientationsIS;
2228: PetscSection coneSizesSection;
2229: PetscLayout vertexLayout;
2230: PetscSF overlapSF, l2gSF; //TODO maybe confusing names (in DMPlex in general)
2231: PetscInt offset, conesOffset, leafOffset;
2232: };
2233: typedef struct _n_PlexLayer *PlexLayer;
2235: static PetscErrorCode PlexLayerDestroy(PlexLayer *layer)
2236: {
2237: PetscFunctionBegin;
2238: if (!*layer) PetscFunctionReturn(PETSC_SUCCESS);
2239: PetscCall(PetscSectionDestroy(&(*layer)->coneSizesSection));
2240: PetscCall(ISDestroy(&(*layer)->conesIS));
2241: PetscCall(ISDestroy(&(*layer)->orientationsIS));
2242: PetscCall(PetscSFDestroy(&(*layer)->overlapSF));
2243: PetscCall(PetscSFDestroy(&(*layer)->l2gSF));
2244: PetscCall(PetscLayoutDestroy(&(*layer)->vertexLayout));
2245: PetscCall(PetscFree(*layer));
2246: PetscFunctionReturn(PETSC_SUCCESS);
2247: }
2249: static PetscErrorCode PlexLayerCreate_Private(PlexLayer *layer)
2250: {
2251: PetscFunctionBegin;
2252: PetscCall(PetscNew(layer));
2253: (*layer)->d = -1;
2254: (*layer)->offset = -1;
2255: (*layer)->conesOffset = -1;
2256: (*layer)->leafOffset = -1;
2257: PetscFunctionReturn(PETSC_SUCCESS);
2258: }
2260: // Parallel load of a depth stratum
2261: static PetscErrorCode PlexLayerLoad_Private(PlexLayer layer, PetscViewer viewer, PetscInt d, PetscLayout pointsLayout)
2262: {
2263: char path[128];
2264: MPI_Comm comm;
2265: const char *coneSizesName, *conesName, *orientationsName;
2266: IS coneSizesIS, conesIS, orientationsIS;
2267: PetscSection coneSizesSection;
2268: PetscLayout vertexLayout = NULL;
2269: PetscInt s;
2271: PetscFunctionBegin;
2272: coneSizesName = "cone_sizes";
2273: conesName = "cones";
2274: orientationsName = "orientations";
2275: PetscCall(PetscObjectGetComm((PetscObject)viewer, &comm));
2277: /* query size of next lower depth stratum (next lower dimension) */
2278: if (d > 0) {
2279: PetscInt NVertices;
2281: PetscCall(PetscSNPrintf(path, sizeof(path), "%" PetscInt_FMT "/%s", d - 1, coneSizesName));
2282: PetscCall(PetscViewerHDF5ReadSizes(viewer, path, NULL, &NVertices));
2283: PetscCall(PetscLayoutCreate(comm, &vertexLayout));
2284: PetscCall(PetscLayoutSetSize(vertexLayout, NVertices));
2285: PetscCall(PetscLayoutSetUp(vertexLayout));
2286: }
2288: PetscCall(PetscSNPrintf(path, sizeof(path), "%" PetscInt_FMT, d));
2289: PetscCall(PetscViewerHDF5PushGroup(viewer, path));
2291: /* create coneSizesSection from stored IS coneSizes */
2292: {
2293: const PetscInt *coneSizes;
2295: PetscCall(ISCreate(comm, &coneSizesIS));
2296: PetscCall(PetscObjectSetName((PetscObject)coneSizesIS, coneSizesName));
2297: if (pointsLayout) PetscCall(ISSetLayout(coneSizesIS, pointsLayout));
2298: PetscCall(ISLoad(coneSizesIS, viewer));
2299: if (!pointsLayout) PetscCall(ISGetLayout(coneSizesIS, &pointsLayout));
2300: PetscCall(ISGetIndices(coneSizesIS, &coneSizes));
2301: PetscCall(PetscSectionCreate(comm, &coneSizesSection));
2302: //TODO different start ?
2303: PetscCall(PetscSectionSetChart(coneSizesSection, 0, pointsLayout->n));
2304: for (s = 0; s < pointsLayout->n; ++s) PetscCall(PetscSectionSetDof(coneSizesSection, s, coneSizes[s]));
2305: PetscCall(PetscSectionSetUp(coneSizesSection));
2306: PetscCall(ISRestoreIndices(coneSizesIS, &coneSizes));
2307: {
2308: PetscLayout tmp = NULL;
2310: /* We need to keep the layout until the end of function */
2311: PetscCall(PetscLayoutReference((PetscLayout)pointsLayout, &tmp));
2312: }
2313: PetscCall(ISDestroy(&coneSizesIS));
2314: }
2316: /* use value layout of coneSizesSection as layout of cones and orientations */
2317: {
2318: PetscLayout conesLayout;
2320: PetscCall(PetscSectionGetValueLayout(comm, coneSizesSection, &conesLayout));
2321: PetscCall(ISCreate(comm, &conesIS));
2322: PetscCall(ISCreate(comm, &orientationsIS));
2323: PetscCall(PetscObjectSetName((PetscObject)conesIS, conesName));
2324: PetscCall(PetscObjectSetName((PetscObject)orientationsIS, orientationsName));
2325: PetscCall(PetscLayoutDuplicate(conesLayout, &conesIS->map));
2326: PetscCall(PetscLayoutDuplicate(conesLayout, &orientationsIS->map));
2327: PetscCall(ISLoad(conesIS, viewer));
2328: PetscCall(ISLoad(orientationsIS, viewer));
2329: PetscCall(PetscLayoutDestroy(&conesLayout));
2330: }
2332: /* check assertion that layout of points is the same as point layout of coneSizesSection */
2333: {
2334: PetscLayout pointsLayout0;
2335: PetscBool flg;
2337: PetscCall(PetscSectionGetPointLayout(comm, coneSizesSection, &pointsLayout0));
2338: PetscCall(PetscLayoutCompare(pointsLayout, pointsLayout0, &flg));
2339: PetscCheck(flg, comm, PETSC_ERR_PLIB, "points layout != coneSizesSection point layout");
2340: PetscCall(PetscLayoutDestroy(&pointsLayout0));
2341: }
2342: PetscCall(PetscViewerHDF5PopGroup(viewer));
2343: PetscCall(PetscLayoutDestroy(&pointsLayout));
2345: layer->d = d;
2346: layer->conesIS = conesIS;
2347: layer->coneSizesSection = coneSizesSection;
2348: layer->orientationsIS = orientationsIS;
2349: layer->vertexLayout = vertexLayout;
2350: PetscFunctionReturn(PETSC_SUCCESS);
2351: }
2353: static PetscErrorCode PlexLayerDistribute_Private(PlexLayer layer, PetscSF cellLocalToGlobalSF)
2354: {
2355: IS newConesIS, newOrientationsIS;
2356: PetscSection newConeSizesSection;
2357: MPI_Comm comm;
2359: PetscFunctionBegin;
2360: PetscCall(PetscObjectGetComm((PetscObject)cellLocalToGlobalSF, &comm));
2361: PetscCall(PetscSectionCreate(comm, &newConeSizesSection));
2362: //TODO rename to something like ISDistribute() with optional PetscSection argument
2363: PetscCall(DMPlexDistributeFieldIS(NULL, cellLocalToGlobalSF, layer->coneSizesSection, layer->conesIS, newConeSizesSection, &newConesIS));
2364: PetscCall(DMPlexDistributeFieldIS(NULL, cellLocalToGlobalSF, layer->coneSizesSection, layer->orientationsIS, newConeSizesSection, &newOrientationsIS));
2366: PetscCall(PetscObjectSetName((PetscObject)newConeSizesSection, ((PetscObject)layer->coneSizesSection)->name));
2367: PetscCall(PetscObjectSetName((PetscObject)newConesIS, ((PetscObject)layer->conesIS)->name));
2368: PetscCall(PetscObjectSetName((PetscObject)newOrientationsIS, ((PetscObject)layer->orientationsIS)->name));
2369: PetscCall(PetscSectionDestroy(&layer->coneSizesSection));
2370: PetscCall(ISDestroy(&layer->conesIS));
2371: PetscCall(ISDestroy(&layer->orientationsIS));
2372: layer->coneSizesSection = newConeSizesSection;
2373: layer->conesIS = newConesIS;
2374: layer->orientationsIS = newOrientationsIS;
2375: PetscFunctionReturn(PETSC_SUCCESS);
2376: }
2378: //TODO share code with DMPlexBuildFromCellListParallel()
2379: #include <petsc/private/hashseti.h>
2380: static PetscErrorCode PlexLayerCreateSFs_Private(PlexLayer layer, PetscSF *vertexOverlapSF, PetscSF *sfXC)
2381: {
2382: PetscLayout vertexLayout = layer->vertexLayout;
2383: PetscSection coneSection = layer->coneSizesSection;
2384: IS cellVertexData = layer->conesIS;
2385: IS coneOrientations = layer->orientationsIS;
2386: PetscSF vl2gSF, vOverlapSF;
2387: PetscInt *verticesAdj;
2388: PetscInt i, n, numVerticesAdj;
2389: const PetscInt *cvd, *co = NULL;
2390: MPI_Comm comm;
2392: PetscFunctionBegin;
2393: PetscCall(PetscObjectGetComm((PetscObject)coneSection, &comm));
2394: PetscCall(PetscSectionGetStorageSize(coneSection, &n));
2395: {
2396: PetscInt n0;
2398: PetscCall(ISGetLocalSize(cellVertexData, &n0));
2399: 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);
2400: PetscCall(ISGetIndices(cellVertexData, &cvd));
2401: }
2402: if (coneOrientations) {
2403: PetscInt n0;
2405: PetscCall(ISGetLocalSize(coneOrientations, &n0));
2406: 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);
2407: PetscCall(ISGetIndices(coneOrientations, &co));
2408: }
2409: /* Get/check global number of vertices */
2410: {
2411: PetscInt NVerticesInCells = PETSC_INT_MIN;
2413: /* NVerticesInCells = max(cellVertexData) + 1 */
2414: for (i = 0; i < n; i++)
2415: if (cvd[i] > NVerticesInCells) NVerticesInCells = cvd[i];
2416: ++NVerticesInCells;
2417: PetscCallMPI(MPIU_Allreduce(MPI_IN_PLACE, &NVerticesInCells, 1, MPIU_INT, MPI_MAX, comm));
2419: if (vertexLayout->n == PETSC_DECIDE && vertexLayout->N == PETSC_DECIDE) vertexLayout->N = NVerticesInCells;
2420: else
2421: 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,
2422: vertexLayout->N, NVerticesInCells);
2423: PetscCall(PetscLayoutSetUp(vertexLayout));
2424: }
2425: /* Find locally unique vertices in cellVertexData */
2426: {
2427: PetscHSetI vhash;
2428: PetscInt off = 0;
2430: PetscCall(PetscHSetICreate(&vhash));
2431: for (i = 0; i < n; ++i) PetscCall(PetscHSetIAdd(vhash, cvd[i]));
2432: PetscCall(PetscHSetIGetSize(vhash, &numVerticesAdj));
2433: PetscCall(PetscMalloc1(numVerticesAdj, &verticesAdj));
2434: PetscCall(PetscHSetIGetElems(vhash, &off, verticesAdj));
2435: PetscAssert(off == numVerticesAdj, PETSC_COMM_SELF, PETSC_ERR_PLIB, "Assertion failed: off == numVerticesAdj (%" PetscInt_FMT " != %" PetscInt_FMT ")", off, numVerticesAdj);
2436: PetscCall(PetscHSetIDestroy(&vhash));
2437: }
2438: /* We must sort vertices to preserve numbering */
2439: PetscCall(PetscSortInt(numVerticesAdj, verticesAdj));
2440: /* Connect locally unique vertices with star forest */
2441: PetscCall(PetscSFCreateByMatchingIndices(vertexLayout, numVerticesAdj, verticesAdj, NULL, 0, numVerticesAdj, verticesAdj, NULL, 0, &vl2gSF, &vOverlapSF));
2442: PetscCall(PetscObjectSetName((PetscObject)vOverlapSF, "overlapSF"));
2443: PetscCall(PetscObjectSetName((PetscObject)vl2gSF, "localToGlobalSF"));
2445: PetscCall(PetscFree(verticesAdj));
2446: *vertexOverlapSF = vOverlapSF;
2447: *sfXC = vl2gSF;
2448: PetscFunctionReturn(PETSC_SUCCESS);
2449: }
2451: static PetscErrorCode PlexLayerCreateCellSFs_Private(PlexLayer layer, PetscSF *cellOverlapSF, PetscSF *cellLocalToGlobalSF)
2452: {
2453: PetscSection coneSection = layer->coneSizesSection;
2454: PetscInt nCells;
2455: MPI_Comm comm;
2457: PetscFunctionBegin;
2458: PetscCall(PetscObjectGetComm((PetscObject)coneSection, &comm));
2459: {
2460: PetscInt cStart;
2462: PetscCall(PetscSectionGetChart(coneSection, &cStart, &nCells));
2463: PetscCheck(cStart == 0, comm, PETSC_ERR_ARG_OUTOFRANGE, "coneSection must start at 0");
2464: }
2465: /* Create overlapSF as empty SF with the right number of roots */
2466: PetscCall(PetscSFCreate(comm, cellOverlapSF));
2467: PetscCall(PetscSFSetGraph(*cellOverlapSF, nCells, 0, NULL, PETSC_USE_POINTER, NULL, PETSC_USE_POINTER));
2468: PetscCall(PetscSFSetUp(*cellOverlapSF));
2469: /* Create localToGlobalSF as identity mapping */
2470: {
2471: PetscLayout map;
2473: PetscCall(PetscLayoutCreateFromSizes(comm, nCells, PETSC_DECIDE, 1, &map));
2474: PetscCall(PetscSFCreateFromLayouts(map, map, cellLocalToGlobalSF));
2475: PetscCall(PetscSFSetUp(*cellLocalToGlobalSF));
2476: PetscCall(PetscLayoutDestroy(&map));
2477: }
2478: PetscFunctionReturn(PETSC_SUCCESS);
2479: }
2481: static PetscErrorCode DMPlexTopologyBuildFromLayers_Private(DM dm, PetscInt depth, PlexLayer *layers, IS strataPermutation)
2482: {
2483: const PetscInt *permArr;
2484: PetscInt d, nPoints;
2485: MPI_Comm comm;
2487: PetscFunctionBegin;
2488: PetscCall(PetscObjectGetComm((PetscObject)dm, &comm));
2489: PetscCall(ISGetIndices(strataPermutation, &permArr));
2491: /* Count points, strata offsets and cones offsets (taking strataPermutation into account) */
2492: {
2493: PetscInt stratumOffset = 0;
2494: PetscInt conesOffset = 0;
2496: for (d = 0; d <= depth; d++) {
2497: const PetscInt e = permArr[d];
2498: const PlexLayer l = layers[e];
2499: PetscInt lo, n, size;
2501: PetscCall(PetscSectionGetChart(l->coneSizesSection, &lo, &n));
2502: PetscCall(PetscSectionGetStorageSize(l->coneSizesSection, &size));
2503: PetscCheck(lo == 0, comm, PETSC_ERR_PLIB, "starting point should be 0 in coneSizesSection %" PetscInt_FMT, d);
2504: l->offset = stratumOffset;
2505: l->conesOffset = conesOffset;
2506: stratumOffset += n;
2507: conesOffset += size;
2508: }
2509: nPoints = stratumOffset;
2510: }
2512: /* Set interval for all plex points */
2513: //TODO we should store starting point of plex
2514: PetscCall(DMPlexSetChart(dm, 0, nPoints));
2516: /* Set up plex coneSection from layer coneSections */
2517: {
2518: PetscSection coneSection;
2520: PetscCall(DMPlexGetConeSection(dm, &coneSection));
2521: for (d = 0; d <= depth; d++) {
2522: const PlexLayer l = layers[d];
2523: PetscInt n, q;
2525: PetscCall(PetscSectionGetChart(l->coneSizesSection, NULL, &n));
2526: for (q = 0; q < n; q++) {
2527: const PetscInt p = l->offset + q;
2528: PetscInt coneSize;
2530: PetscCall(PetscSectionGetDof(l->coneSizesSection, q, &coneSize));
2531: PetscCall(PetscSectionSetDof(coneSection, p, coneSize));
2532: }
2533: }
2534: }
2535: //TODO this is terrible, DMSetUp_Plex() should be DMPlexSetUpSections() or so
2536: PetscCall(DMSetUp(dm));
2538: /* Renumber cones points from layer-global numbering to plex-local numbering */
2539: {
2540: PetscInt *cones, *ornts;
2542: PetscCall(DMPlexGetCones(dm, &cones));
2543: PetscCall(DMPlexGetConeOrientations(dm, &ornts));
2544: for (d = 1; d <= depth; d++) {
2545: const PlexLayer l = layers[d];
2546: PetscInt i, lConesSize;
2547: PetscInt *lCones;
2548: const PetscInt *lOrnts;
2549: PetscInt *pCones = &cones[l->conesOffset];
2550: PetscInt *pOrnts = &ornts[l->conesOffset];
2552: PetscCall(PetscSectionGetStorageSize(l->coneSizesSection, &lConesSize));
2553: /* Get cones in local plex numbering */
2554: {
2555: ISLocalToGlobalMapping l2g;
2556: PetscLayout vertexLayout = l->vertexLayout;
2557: PetscSF vertexSF = layers[d - 1]->l2gSF; /* vertices of this layer are cells of previous layer */
2558: const PetscInt *gCones;
2559: PetscInt lConesSize0;
2561: PetscCall(ISGetLocalSize(l->conesIS, &lConesSize0));
2562: PetscCheck(lConesSize0 == lConesSize, comm, PETSC_ERR_PLIB, "layer %" PetscInt_FMT " size(conesIS) = %" PetscInt_FMT " != %" PetscInt_FMT " = storageSize(coneSizesSection)", d, lConesSize0, lConesSize);
2563: PetscCall(ISGetLocalSize(l->orientationsIS, &lConesSize0));
2564: PetscCheck(lConesSize0 == lConesSize, comm, PETSC_ERR_PLIB, "layer %" PetscInt_FMT " size(orientationsIS) = %" PetscInt_FMT " != %" PetscInt_FMT " = storageSize(coneSizesSection)", d, lConesSize0, lConesSize);
2566: PetscCall(PetscMalloc1(lConesSize, &lCones));
2567: PetscCall(ISGetIndices(l->conesIS, &gCones));
2568: PetscCall(ISLocalToGlobalMappingCreateSF(vertexSF, vertexLayout->rstart, &l2g));
2569: PetscCall(ISGlobalToLocalMappingApply(l2g, IS_GTOLM_MASK, lConesSize, gCones, &lConesSize0, lCones));
2570: PetscCheck(lConesSize0 == lConesSize, comm, PETSC_ERR_PLIB, "global to local does not cover all indices (%" PetscInt_FMT " of %" PetscInt_FMT ")", lConesSize0, lConesSize);
2571: PetscCall(ISLocalToGlobalMappingDestroy(&l2g));
2572: PetscCall(ISRestoreIndices(l->conesIS, &gCones));
2573: }
2574: PetscCall(ISGetIndices(l->orientationsIS, &lOrnts));
2575: /* Set cones, need to add stratum offset */
2576: for (i = 0; i < lConesSize; i++) {
2577: pCones[i] = lCones[i] + layers[d - 1]->offset; /* cone points of current layer are points of previous layer */
2578: pOrnts[i] = lOrnts[i];
2579: }
2580: PetscCall(PetscFree(lCones));
2581: PetscCall(ISRestoreIndices(l->orientationsIS, &lOrnts));
2582: }
2583: }
2584: PetscCall(DMPlexSymmetrize(dm));
2585: PetscCall(DMPlexStratify(dm));
2586: PetscCall(ISRestoreIndices(strataPermutation, &permArr));
2587: PetscFunctionReturn(PETSC_SUCCESS);
2588: }
2590: static PetscErrorCode PlexLayerConcatenateSFs_Private(MPI_Comm comm, PetscInt depth, PlexLayer layers[], IS strataPermutation, PetscSF *overlapSF, PetscSF *l2gSF)
2591: {
2592: PetscInt d;
2593: PetscSF *osfs, *lsfs;
2594: PetscInt *leafOffsets;
2595: const PetscInt *permArr;
2597: PetscFunctionBegin;
2598: PetscCall(ISGetIndices(strataPermutation, &permArr));
2599: PetscCall(PetscCalloc3(depth + 1, &osfs, depth + 1, &lsfs, depth + 1, &leafOffsets));
2600: for (d = 0; d <= depth; d++) {
2601: const PetscInt e = permArr[d];
2603: PetscAssert(e == layers[e]->d, PETSC_COMM_SELF, PETSC_ERR_PLIB, "assertion: e == layers[e]->d");
2604: osfs[d] = layers[e]->overlapSF;
2605: lsfs[d] = layers[e]->l2gSF;
2606: leafOffsets[d] = layers[e]->offset;
2607: }
2608: PetscCall(PetscSFConcatenate(comm, depth + 1, osfs, PETSCSF_CONCATENATE_ROOTMODE_LOCAL, leafOffsets, overlapSF));
2609: PetscCall(PetscSFConcatenate(comm, depth + 1, lsfs, PETSCSF_CONCATENATE_ROOTMODE_GLOBAL, leafOffsets, l2gSF));
2610: PetscCall(PetscFree3(osfs, lsfs, leafOffsets));
2611: PetscCall(ISRestoreIndices(strataPermutation, &permArr));
2612: PetscFunctionReturn(PETSC_SUCCESS);
2613: }
2615: // Parallel load of topology
2616: static PetscErrorCode DMPlexTopologyLoad_HDF5_Private(DM dm, PetscViewer viewer, PetscSF *sfXC)
2617: {
2618: PlexLayer *layers;
2619: IS strataPermutation;
2620: PetscLayout pointsLayout;
2621: PetscInt depth;
2622: PetscInt d;
2623: MPI_Comm comm;
2625: PetscFunctionBegin;
2626: {
2627: PetscInt dim;
2629: PetscCall(PetscViewerHDF5ReadAttribute(viewer, NULL, "depth", PETSC_INT, NULL, &depth));
2630: PetscCall(PetscViewerHDF5ReadAttribute(viewer, NULL, "cell_dim", PETSC_INT, NULL, &dim));
2631: PetscCall(DMSetDimension(dm, dim));
2632: }
2633: PetscCall(PetscObjectGetComm((PetscObject)dm, &comm));
2635: PetscCall(PetscInfo(dm, "Loading DM %s in parallel\n", dm->hdr.name));
2636: {
2637: IS spOnComm;
2639: PetscCall(ISCreate(comm, &spOnComm));
2640: PetscCall(PetscObjectSetName((PetscObject)spOnComm, "permutation"));
2641: PetscCall(ISLoad(spOnComm, viewer));
2642: /* have the same serial IS on every rank */
2643: PetscCall(ISAllGather(spOnComm, &strataPermutation));
2644: PetscCall(PetscObjectSetName((PetscObject)strataPermutation, ((PetscObject)spOnComm)->name));
2645: PetscCall(ISDestroy(&spOnComm));
2646: }
2648: /* Create layers, load raw data for each layer */
2649: PetscCall(PetscViewerHDF5PushGroup(viewer, "strata"));
2650: PetscCall(PetscMalloc1(depth + 1, &layers));
2651: for (d = depth, pointsLayout = NULL; d >= 0; pointsLayout = layers[d]->vertexLayout, d--) {
2652: PetscCall(PlexLayerCreate_Private(&layers[d]));
2653: PetscCall(PlexLayerLoad_Private(layers[d], viewer, d, pointsLayout));
2654: }
2655: PetscCall(PetscViewerHDF5PopGroup(viewer)); /* strata */
2657: for (d = depth; d >= 0; d--) {
2658: /* Redistribute cells and vertices for each applicable layer */
2659: if (d < depth) PetscCall(PlexLayerDistribute_Private(layers[d], layers[d]->l2gSF));
2660: /* Create vertex overlap SF and vertex localToGlobal SF for each applicable layer */
2661: if (d > 0) PetscCall(PlexLayerCreateSFs_Private(layers[d], &layers[d - 1]->overlapSF, &layers[d - 1]->l2gSF));
2662: }
2663: /* Build trivial SFs for the cell layer as well */
2664: PetscCall(PlexLayerCreateCellSFs_Private(layers[depth], &layers[depth]->overlapSF, &layers[depth]->l2gSF));
2666: /* Build DMPlex topology from the layers */
2667: PetscCall(DMPlexTopologyBuildFromLayers_Private(dm, depth, layers, strataPermutation));
2669: /* Build overall point SF alias overlap SF */
2670: {
2671: PetscSF overlapSF;
2673: PetscCall(PlexLayerConcatenateSFs_Private(comm, depth, layers, strataPermutation, &overlapSF, sfXC));
2674: PetscCall(DMSetPointSF(dm, overlapSF));
2675: PetscCall(PetscSFDestroy(&overlapSF));
2676: }
2678: for (d = depth; d >= 0; d--) PetscCall(PlexLayerDestroy(&layers[d]));
2679: PetscCall(PetscFree(layers));
2680: PetscCall(ISDestroy(&strataPermutation));
2681: PetscFunctionReturn(PETSC_SUCCESS);
2682: }
2684: PetscErrorCode DMPlexTopologyLoad_HDF5_Internal(DM dm, PetscViewer viewer, PetscSF *sfXC)
2685: {
2686: DMPlexStorageVersion version;
2687: const char *topologydm_name;
2688: char group[PETSC_MAX_PATH_LEN];
2689: PetscSF sfwork = NULL;
2691: PetscFunctionBegin;
2692: PetscCall(DMPlexGetHDF5Name_Private(dm, &topologydm_name));
2693: PetscCall(PetscViewerHDF5GetDMPlexStorageVersionReading(viewer, &version));
2694: if (DMPlexStorageVersionGE(version, 2, 0, 0)) {
2695: PetscCall(PetscSNPrintf(group, sizeof(group), "topologies/%s", topologydm_name));
2696: } else {
2697: PetscCall(PetscStrncpy(group, "/", sizeof(group)));
2698: }
2699: PetscCall(PetscViewerHDF5PushGroup(viewer, group));
2701: PetscCall(PetscViewerHDF5PushGroup(viewer, "topology"));
2702: if (version->major < 3) {
2703: PetscCall(DMPlexTopologyLoad_HDF5_Legacy_Private(dm, viewer, &sfwork));
2704: } else {
2705: /* since DMPlexStorageVersion 3.0.0 */
2706: PetscCall(DMPlexTopologyLoad_HDF5_Private(dm, viewer, &sfwork));
2707: }
2708: PetscCall(PetscViewerHDF5PopGroup(viewer)); /* "topology" */
2710: if (DMPlexStorageVersionGE(version, 2, 0, 0)) {
2711: DM distdm;
2712: PetscSF distsf;
2713: const char *distribution_name;
2714: PetscBool exists;
2716: PetscCall(DMPlexDistributionGetName(dm, &distribution_name));
2717: /* this group is guaranteed to be present since DMPlexStorageVersion 2.1.0 */
2718: PetscCall(PetscViewerHDF5PushGroup(viewer, "distributions"));
2719: PetscCall(PetscViewerHDF5HasGroup(viewer, NULL, &exists));
2720: if (exists) {
2721: PetscCall(PetscViewerHDF5PushGroup(viewer, distribution_name));
2722: PetscCall(DMPlexDistributionLoad_HDF5_Private(dm, viewer, sfwork, &distsf, &distdm));
2723: if (distdm) {
2724: PetscCall(DMPlexReplace_Internal(dm, &distdm));
2725: PetscCall(PetscSFDestroy(&sfwork));
2726: sfwork = distsf;
2727: }
2728: PetscCall(PetscViewerHDF5PopGroup(viewer)); /* distribution_name */
2729: }
2730: PetscCall(PetscViewerHDF5PopGroup(viewer)); /* "distributions" */
2731: }
2732: if (sfXC) {
2733: *sfXC = sfwork;
2734: } else {
2735: PetscCall(PetscSFDestroy(&sfwork));
2736: }
2738: PetscCall(PetscViewerHDF5PopGroup(viewer));
2739: PetscFunctionReturn(PETSC_SUCCESS);
2740: }
2742: /* If the file is old, it not only has different path to the coordinates, but */
2743: /* does not contain coordinateDMs, so must fall back to the old implementation. */
2744: static PetscErrorCode DMPlexCoordinatesLoad_HDF5_Legacy_Private(DM dm, PetscViewer viewer)
2745: {
2746: PetscSection coordSection;
2747: Vec coordinates;
2748: PetscReal lengthScale;
2749: PetscInt spatialDim, N, numVertices, vStart, vEnd, v;
2750: PetscMPIInt rank;
2752: PetscFunctionBegin;
2753: PetscCallMPI(MPI_Comm_rank(PetscObjectComm((PetscObject)dm), &rank));
2754: /* Read geometry */
2755: PetscCall(PetscViewerHDF5PushGroup(viewer, "/geometry"));
2756: PetscCall(VecCreate(PetscObjectComm((PetscObject)dm), &coordinates));
2757: PetscCall(PetscObjectSetName((PetscObject)coordinates, "vertices"));
2758: {
2759: /* Force serial load */
2760: PetscCall(PetscViewerHDF5ReadSizes(viewer, "vertices", &spatialDim, &N));
2761: PetscCall(VecSetSizes(coordinates, rank == 0 ? N : 0, N));
2762: PetscCall(VecSetBlockSize(coordinates, spatialDim));
2763: }
2764: PetscCall(VecLoad(coordinates, viewer));
2765: PetscCall(PetscViewerHDF5PopGroup(viewer));
2766: PetscCall(DMPlexGetScale(dm, PETSC_UNIT_LENGTH, &lengthScale));
2767: PetscCall(VecScale(coordinates, 1.0 / lengthScale));
2768: PetscCall(VecGetLocalSize(coordinates, &numVertices));
2769: PetscCall(VecGetBlockSize(coordinates, &spatialDim));
2770: numVertices /= spatialDim;
2771: /* Create coordinates */
2772: PetscCall(DMPlexGetDepthStratum(dm, 0, &vStart, &vEnd));
2773: 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);
2774: PetscCall(DMGetCoordinateSection(dm, &coordSection));
2775: PetscCall(PetscSectionSetNumFields(coordSection, 1));
2776: PetscCall(PetscSectionSetFieldComponents(coordSection, 0, spatialDim));
2777: PetscCall(PetscSectionSetChart(coordSection, vStart, vEnd));
2778: for (v = vStart; v < vEnd; ++v) {
2779: PetscCall(PetscSectionSetDof(coordSection, v, spatialDim));
2780: PetscCall(PetscSectionSetFieldDof(coordSection, v, 0, spatialDim));
2781: }
2782: PetscCall(PetscSectionSetUp(coordSection));
2783: PetscCall(DMSetCoordinates(dm, coordinates));
2784: PetscCall(VecDestroy(&coordinates));
2785: PetscFunctionReturn(PETSC_SUCCESS);
2786: }
2788: PetscErrorCode DMPlexCoordinatesLoad_HDF5_Internal(DM dm, PetscViewer viewer, PetscSF sfXC)
2789: {
2790: DMPlexStorageVersion version;
2791: DM cdm;
2792: Vec coords;
2793: PetscInt blockSize;
2794: PetscReal lengthScale;
2795: PetscSF lsf;
2796: const char *topologydm_name;
2797: char *coordinatedm_name, *coordinates_name;
2799: PetscFunctionBegin;
2800: PetscCall(PetscViewerHDF5GetDMPlexStorageVersionReading(viewer, &version));
2801: if (!DMPlexStorageVersionGE(version, 2, 0, 0)) {
2802: PetscCall(DMPlexCoordinatesLoad_HDF5_Legacy_Private(dm, viewer));
2803: PetscFunctionReturn(PETSC_SUCCESS);
2804: }
2805: /* else: since DMPlexStorageVersion 2.0.0 */
2806: PetscCheck(sfXC, PetscObjectComm((PetscObject)dm), PETSC_ERR_ARG_NULL, "PetscSF must be given for parallel load");
2807: PetscCall(DMPlexGetHDF5Name_Private(dm, &topologydm_name));
2808: PetscCall(PetscViewerHDF5PushGroup(viewer, "topologies"));
2809: PetscCall(PetscViewerHDF5PushGroup(viewer, topologydm_name));
2810: PetscCall(PetscViewerHDF5ReadAttribute(viewer, NULL, "coordinateDMName", PETSC_STRING, NULL, &coordinatedm_name));
2811: PetscCall(PetscViewerHDF5ReadAttribute(viewer, NULL, "coordinatesName", PETSC_STRING, NULL, &coordinates_name));
2812: PetscCall(PetscViewerHDF5PopGroup(viewer));
2813: PetscCall(PetscViewerHDF5PopGroup(viewer));
2814: PetscCall(DMGetCoordinateDM(dm, &cdm));
2815: PetscCall(PetscObjectSetName((PetscObject)cdm, coordinatedm_name));
2816: PetscCall(PetscFree(coordinatedm_name));
2817: /* lsf: on-disk data -> in-memory local vector associated with cdm's local section */
2818: PetscCall(DMPlexSectionLoad(dm, viewer, cdm, sfXC, NULL, &lsf));
2819: PetscCall(DMCreateLocalVector(cdm, &coords));
2820: PetscCall(PetscObjectSetName((PetscObject)coords, coordinates_name));
2821: PetscCall(PetscFree(coordinates_name));
2822: PetscCall(PetscViewerPushFormat(viewer, PETSC_VIEWER_NATIVE));
2823: PetscCall(DMPlexLocalVectorLoad(dm, viewer, cdm, lsf, coords));
2824: PetscCall(PetscViewerPopFormat(viewer));
2825: PetscCall(DMPlexGetScale(dm, PETSC_UNIT_LENGTH, &lengthScale));
2826: PetscCall(VecScale(coords, 1.0 / lengthScale));
2827: PetscCall(DMSetCoordinatesLocal(dm, coords));
2828: PetscCall(VecGetBlockSize(coords, &blockSize));
2829: PetscCall(DMSetCoordinateDim(dm, blockSize));
2830: PetscCall(VecDestroy(&coords));
2831: PetscCall(PetscSFDestroy(&lsf));
2832: PetscFunctionReturn(PETSC_SUCCESS);
2833: }
2835: PetscErrorCode DMPlexLoad_HDF5_Internal(DM dm, PetscViewer viewer)
2836: {
2837: DMPlexStorageVersion version;
2839: PetscFunctionBegin;
2840: PetscCall(PetscViewerHDF5GetDMPlexStorageVersionReading(viewer, &version));
2841: PetscCall(PetscInfo(dm, "Loading DM %s storage version %d.%d.%d\n", dm->hdr.name, version->major, version->minor, version->subminor));
2842: if (!DMPlexStorageVersionGE(version, 2, 0, 0)) {
2843: PetscCall(DMPlexTopologyLoad_HDF5_Internal(dm, viewer, NULL));
2844: PetscCall(DMPlexLabelsLoad_HDF5_Internal(dm, viewer, NULL));
2845: PetscCall(DMPlexCoordinatesLoad_HDF5_Legacy_Private(dm, viewer));
2846: } else {
2847: PetscSF sfXC;
2849: /* since DMPlexStorageVersion 2.0.0 */
2850: PetscCall(DMPlexTopologyLoad_HDF5_Internal(dm, viewer, &sfXC));
2851: PetscCall(DMPlexLabelsLoad_HDF5_Internal(dm, viewer, sfXC));
2852: PetscCall(DMPlexCoordinatesLoad_HDF5_Internal(dm, viewer, sfXC));
2853: PetscCall(PetscSFDestroy(&sfXC));
2854: }
2855: PetscFunctionReturn(PETSC_SUCCESS);
2856: }
2858: static PetscErrorCode DMPlexSectionLoad_HDF5_Internal_CreateDataSF(PetscSection rootSection, PetscLayout layout, PetscInt globalOffsets[], PetscSection leafSection, PetscSF *sectionSF)
2859: {
2860: MPI_Comm comm;
2861: PetscInt pStart, pEnd, p, m;
2862: PetscInt *goffs, *ilocal;
2863: PetscBool rootIncludeConstraints, leafIncludeConstraints;
2865: PetscFunctionBegin;
2866: PetscCall(PetscObjectGetComm((PetscObject)leafSection, &comm));
2867: PetscCall(PetscSectionGetChart(leafSection, &pStart, &pEnd));
2868: PetscCall(PetscSectionGetIncludesConstraints(rootSection, &rootIncludeConstraints));
2869: PetscCall(PetscSectionGetIncludesConstraints(leafSection, &leafIncludeConstraints));
2870: if (rootIncludeConstraints && leafIncludeConstraints) PetscCall(PetscSectionGetStorageSize(leafSection, &m));
2871: else PetscCall(PetscSectionGetConstrainedStorageSize(leafSection, &m));
2872: PetscCall(PetscMalloc1(m, &ilocal));
2873: PetscCall(PetscMalloc1(m, &goffs));
2874: /* Currently, PetscSFDistributeSection() returns globalOffsets[] only */
2875: /* for the top-level section (not for each field), so one must have */
2876: /* rootSection->pointMajor == PETSC_TRUE. */
2877: PetscCheck(rootSection->pointMajor, PETSC_COMM_SELF, PETSC_ERR_SUP, "No support for field major ordering");
2878: /* Currently, we also assume that leafSection->pointMajor == PETSC_TRUE. */
2879: PetscCheck(leafSection->pointMajor, PETSC_COMM_SELF, PETSC_ERR_SUP, "No support for field major ordering");
2880: for (p = pStart, m = 0; p < pEnd; ++p) {
2881: PetscInt dof, cdof, i, j, off, goff;
2882: const PetscInt *cinds;
2884: PetscCall(PetscSectionGetDof(leafSection, p, &dof));
2885: if (dof < 0) continue;
2886: goff = globalOffsets[p - pStart];
2887: PetscCall(PetscSectionGetOffset(leafSection, p, &off));
2888: PetscCall(PetscSectionGetConstraintDof(leafSection, p, &cdof));
2889: PetscCall(PetscSectionGetConstraintIndices(leafSection, p, &cinds));
2890: for (i = 0, j = 0; i < dof; ++i) {
2891: PetscBool constrained = (PetscBool)(j < cdof && i == cinds[j]);
2893: if (!constrained || (leafIncludeConstraints && rootIncludeConstraints)) {
2894: ilocal[m] = off++;
2895: goffs[m++] = goff++;
2896: } else if (leafIncludeConstraints && !rootIncludeConstraints) ++off;
2897: else if (!leafIncludeConstraints && rootIncludeConstraints) ++goff;
2898: if (constrained) ++j;
2899: }
2900: }
2901: PetscCall(PetscSFCreate(comm, sectionSF));
2902: PetscCall(PetscSFSetFromOptions(*sectionSF));
2903: PetscCall(PetscSFSetGraphLayout(*sectionSF, layout, m, ilocal, PETSC_OWN_POINTER, goffs));
2904: PetscCall(PetscFree(goffs));
2905: PetscFunctionReturn(PETSC_SUCCESS);
2906: }
2908: PetscErrorCode DMPlexSectionLoad_HDF5_Internal(DM dm, PetscViewer viewer, DM sectiondm, PetscSF sfXB, PetscSF *gsf, PetscSF *lsf)
2909: {
2910: MPI_Comm comm;
2911: PetscMPIInt size, rank;
2912: const char *topologydm_name;
2913: const char *sectiondm_name;
2914: PetscSection sectionA, sectionB;
2915: PetscBool has;
2916: PetscInt nX, n, i;
2917: PetscSF sfAB;
2919: PetscFunctionBegin;
2920: PetscCall(PetscObjectGetComm((PetscObject)dm, &comm));
2921: PetscCallMPI(MPI_Comm_size(comm, &size));
2922: PetscCallMPI(MPI_Comm_rank(comm, &rank));
2923: PetscCall(DMPlexGetHDF5Name_Private(dm, &topologydm_name));
2924: PetscCall(PetscObjectGetName((PetscObject)sectiondm, §iondm_name));
2925: PetscCall(PetscViewerHDF5PushGroup(viewer, "topologies"));
2926: PetscCall(PetscViewerHDF5PushGroup(viewer, topologydm_name));
2927: PetscCall(PetscViewerHDF5PushGroup(viewer, "dms"));
2928: PetscCall(PetscViewerHDF5PushGroup(viewer, sectiondm_name));
2929: /* A: on-disk points */
2930: /* X: list of global point numbers, [0, NX) */
2931: /* B: plex points */
2932: /* Load raw section (sectionA) */
2933: PetscCall(PetscSectionCreate(comm, §ionA));
2934: PetscCall(PetscViewerHDF5HasGroup(viewer, "section", &has));
2935: if (has) PetscCall(PetscSectionLoad(sectionA, viewer));
2936: else {
2937: // TODO If section is missing, create the default affine section with dim dofs on each vertex. Use PetscSplitOwnership() to split vertices.
2938: // How do I know the total number of vertices?
2939: PetscInt dim, Nf = 1, Nv, nv = PETSC_DECIDE;
2941: PetscCall(DMGetDimension(dm, &dim));
2942: PetscCall(DMPlexGetDepthStratumGlobalSize(dm, 0, &Nv));
2943: PetscCall(PetscSectionSetNumFields(sectionA, Nf));
2944: PetscCall(PetscSectionSetFieldName(sectionA, 0, "Cartesian"));
2945: PetscCall(PetscSectionSetFieldComponents(sectionA, 0, dim));
2946: for (PetscInt c = 0; c < dim; ++c) {
2947: char axis = 'X' + (char)c;
2949: PetscCall(PetscSectionSetComponentName(sectionA, 0, c, &axis));
2950: }
2951: PetscCall(PetscSplitOwnership(comm, &nv, &Nv));
2952: PetscCall(PetscSectionSetChart(sectionA, 0, nv));
2953: for (PetscInt p = 0; p < nv; ++p) {
2954: PetscCall(PetscSectionSetDof(sectionA, p, dim));
2955: PetscCall(PetscSectionSetFieldDof(sectionA, p, 0, dim));
2956: }
2957: PetscCall(PetscSectionSetUp(sectionA));
2958: }
2959: PetscCall(PetscSectionGetChart(sectionA, NULL, &n));
2960: /* Create sfAB: A -> B */
2961: #if defined(PETSC_USE_DEBUG)
2962: {
2963: PetscInt N, N1;
2965: PetscCall(PetscViewerHDF5ReadSizes(viewer, "order", NULL, &N1));
2966: PetscCallMPI(MPIU_Allreduce(&n, &N, 1, MPIU_INT, MPI_SUM, comm));
2967: 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);
2968: }
2969: #endif
2970: {
2971: IS orderIS;
2972: const PetscInt *gpoints;
2973: PetscSF sfXA, sfAX;
2974: PetscLayout layout;
2975: PetscSFNode *owners, *buffer;
2976: PetscInt nleaves;
2977: PetscInt *ilocal;
2978: PetscSFNode *iremote;
2980: /* Create sfAX: A -> X */
2981: PetscCall(ISCreate(comm, &orderIS));
2982: PetscCall(PetscObjectSetName((PetscObject)orderIS, "order"));
2983: PetscCall(PetscLayoutSetLocalSize(orderIS->map, n));
2984: PetscCall(ISLoad(orderIS, viewer));
2985: PetscCall(PetscLayoutCreate(comm, &layout));
2986: PetscCall(PetscSFGetGraph(sfXB, &nX, NULL, NULL, NULL));
2987: PetscCall(PetscLayoutSetLocalSize(layout, nX));
2988: PetscCall(PetscLayoutSetBlockSize(layout, 1));
2989: PetscCall(PetscLayoutSetUp(layout));
2990: PetscCall(PetscSFCreate(comm, &sfXA));
2991: PetscCall(ISGetIndices(orderIS, &gpoints));
2992: PetscCall(PetscSFSetGraphLayout(sfXA, layout, n, NULL, PETSC_OWN_POINTER, gpoints));
2993: PetscCall(ISRestoreIndices(orderIS, &gpoints));
2994: PetscCall(ISDestroy(&orderIS));
2995: PetscCall(PetscLayoutDestroy(&layout));
2996: PetscCall(PetscMalloc1(n, &owners));
2997: PetscCall(PetscMalloc1(nX, &buffer));
2998: for (i = 0; i < n; ++i) {
2999: owners[i].rank = rank;
3000: owners[i].index = i;
3001: }
3002: for (i = 0; i < nX; ++i) {
3003: buffer[i].rank = -1;
3004: buffer[i].index = -1;
3005: }
3006: PetscCall(PetscSFReduceBegin(sfXA, MPIU_SF_NODE, owners, buffer, MPI_MAXLOC));
3007: PetscCall(PetscSFReduceEnd(sfXA, MPIU_SF_NODE, owners, buffer, MPI_MAXLOC));
3008: PetscCall(PetscSFDestroy(&sfXA));
3009: PetscCall(PetscFree(owners));
3010: for (i = 0, nleaves = 0; i < nX; ++i)
3011: if (buffer[i].rank >= 0) nleaves++;
3012: PetscCall(PetscMalloc1(nleaves, &ilocal));
3013: PetscCall(PetscMalloc1(nleaves, &iremote));
3014: for (i = 0, nleaves = 0; i < nX; ++i) {
3015: if (buffer[i].rank >= 0) {
3016: ilocal[nleaves] = i;
3017: iremote[nleaves].rank = buffer[i].rank;
3018: iremote[nleaves].index = buffer[i].index;
3019: nleaves++;
3020: }
3021: }
3022: PetscCall(PetscFree(buffer));
3023: PetscCall(PetscSFCreate(comm, &sfAX));
3024: PetscCall(PetscSFSetFromOptions(sfAX));
3025: PetscCall(PetscSFSetGraph(sfAX, n, nleaves, ilocal, PETSC_OWN_POINTER, iremote, PETSC_OWN_POINTER));
3026: PetscCall(PetscSFCompose(sfAX, sfXB, &sfAB));
3027: PetscCall(PetscSFDestroy(&sfAX));
3028: }
3029: PetscCall(PetscViewerHDF5PopGroup(viewer));
3030: PetscCall(PetscViewerHDF5PopGroup(viewer));
3031: PetscCall(PetscViewerHDF5PopGroup(viewer));
3032: PetscCall(PetscViewerHDF5PopGroup(viewer));
3033: /* Create plex section (sectionB) */
3034: PetscCall(DMGetLocalSection(sectiondm, §ionB));
3035: if (lsf || gsf) {
3036: PetscLayout layout;
3037: PetscInt M, m;
3038: PetscInt *offsetsA;
3039: PetscBool includesConstraintsA;
3041: PetscCall(PetscSFDistributeSection(sfAB, sectionA, &offsetsA, sectionB));
3042: PetscCall(PetscSectionGetIncludesConstraints(sectionA, &includesConstraintsA));
3043: if (includesConstraintsA) PetscCall(PetscSectionGetStorageSize(sectionA, &m));
3044: else PetscCall(PetscSectionGetConstrainedStorageSize(sectionA, &m));
3045: PetscCallMPI(MPIU_Allreduce(&m, &M, 1, MPIU_INT, MPI_SUM, comm));
3046: PetscCall(PetscLayoutCreate(comm, &layout));
3047: PetscCall(PetscLayoutSetSize(layout, M));
3048: PetscCall(PetscLayoutSetUp(layout));
3049: if (lsf) {
3050: PetscSF lsfABdata;
3052: PetscCall(DMPlexSectionLoad_HDF5_Internal_CreateDataSF(sectionA, layout, offsetsA, sectionB, &lsfABdata));
3053: *lsf = lsfABdata;
3054: }
3055: if (gsf) {
3056: PetscSection gsectionB, gsectionB1;
3057: PetscBool includesConstraintsB;
3058: PetscSF gsfABdata, pointsf;
3060: PetscCall(DMGetGlobalSection(sectiondm, &gsectionB1));
3061: PetscCall(PetscSectionGetIncludesConstraints(gsectionB1, &includesConstraintsB));
3062: PetscCall(DMGetPointSF(sectiondm, &pointsf));
3063: PetscCall(PetscSectionCreateGlobalSection(sectionB, pointsf, PETSC_TRUE, includesConstraintsB, PETSC_TRUE, &gsectionB));
3064: PetscCall(DMPlexSectionLoad_HDF5_Internal_CreateDataSF(sectionA, layout, offsetsA, gsectionB, &gsfABdata));
3065: PetscCall(PetscSectionDestroy(&gsectionB));
3066: *gsf = gsfABdata;
3067: }
3068: PetscCall(PetscLayoutDestroy(&layout));
3069: PetscCall(PetscFree(offsetsA));
3070: } else {
3071: PetscCall(PetscSFDistributeSection(sfAB, sectionA, NULL, sectionB));
3072: }
3073: PetscCall(PetscSFDestroy(&sfAB));
3074: PetscCall(PetscSectionDestroy(§ionA));
3075: PetscFunctionReturn(PETSC_SUCCESS);
3076: }
3078: PetscErrorCode DMPlexVecLoad_HDF5_Internal(DM dm, PetscViewer viewer, DM sectiondm, PetscSF sf, Vec vec)
3079: {
3080: MPI_Comm comm;
3081: const char *topologydm_name;
3082: const char *sectiondm_name;
3083: const char *vec_name;
3084: Vec vecA;
3085: PetscInt mA, m, bs;
3086: const PetscInt *ilocal;
3087: const PetscScalar *src;
3088: PetscScalar *dest;
3090: PetscFunctionBegin;
3091: PetscCall(PetscObjectGetComm((PetscObject)dm, &comm));
3092: PetscCall(DMPlexGetHDF5Name_Private(dm, &topologydm_name));
3093: PetscCall(PetscObjectGetName((PetscObject)sectiondm, §iondm_name));
3094: PetscCall(PetscObjectGetName((PetscObject)vec, &vec_name));
3095: PetscCall(PetscViewerHDF5PushGroup(viewer, "topologies"));
3096: PetscCall(PetscViewerHDF5PushGroup(viewer, topologydm_name));
3097: PetscCall(PetscViewerHDF5PushGroup(viewer, "dms"));
3098: PetscCall(PetscViewerHDF5PushGroup(viewer, sectiondm_name));
3099: PetscCall(PetscViewerHDF5PushGroup(viewer, "vecs"));
3100: PetscCall(PetscViewerHDF5PushGroup(viewer, vec_name));
3101: PetscCall(VecCreate(comm, &vecA));
3102: PetscCall(PetscObjectSetName((PetscObject)vecA, vec_name));
3103: PetscCall(PetscSFGetGraph(sf, &mA, &m, &ilocal, NULL));
3104: /* Check consistency */
3105: {
3106: PetscSF pointsf, pointsf1;
3107: PetscInt m1, i, j;
3109: PetscCall(DMGetPointSF(dm, &pointsf));
3110: PetscCall(DMGetPointSF(sectiondm, &pointsf1));
3111: PetscCheck(pointsf1 == pointsf, PETSC_COMM_SELF, PETSC_ERR_PLIB, "Mismatching point SFs for dm and sectiondm");
3112: #if defined(PETSC_USE_DEBUG)
3113: {
3114: PetscInt MA, MA1;
3116: PetscCallMPI(MPIU_Allreduce(&mA, &MA, 1, MPIU_INT, MPI_SUM, comm));
3117: PetscCall(PetscViewerHDF5ReadSizes(viewer, vec_name, NULL, &MA1));
3118: PetscCheck(MA1 == MA, PETSC_COMM_SELF, PETSC_ERR_PLIB, "Total SF root size (%" PetscInt_FMT ") != On-disk vector data size (%" PetscInt_FMT ")", MA, MA1);
3119: }
3120: #endif
3121: PetscCall(VecGetLocalSize(vec, &m1));
3122: PetscCheck(m1 >= m, PETSC_COMM_SELF, PETSC_ERR_PLIB, "Target vector size (%" PetscInt_FMT ") < SF leaf size (%" PetscInt_FMT ")", m1, m);
3123: for (i = 0; i < m; ++i) {
3124: j = ilocal ? ilocal[i] : i;
3125: 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);
3126: }
3127: }
3128: PetscCall(VecSetSizes(vecA, mA, PETSC_DECIDE));
3129: PetscCall(VecLoad(vecA, viewer));
3130: PetscCall(VecGetArrayRead(vecA, &src));
3131: PetscCall(VecGetArray(vec, &dest));
3132: PetscCall(PetscSFBcastBegin(sf, MPIU_SCALAR, src, dest, MPI_REPLACE));
3133: PetscCall(PetscSFBcastEnd(sf, MPIU_SCALAR, src, dest, MPI_REPLACE));
3134: PetscCall(VecRestoreArray(vec, &dest));
3135: PetscCall(VecRestoreArrayRead(vecA, &src));
3136: PetscCall(VecDestroy(&vecA));
3137: PetscCall(PetscViewerHDF5ReadAttribute(viewer, NULL, "blockSize", PETSC_INT, NULL, (void *)&bs));
3138: PetscCall(VecSetBlockSize(vec, bs));
3139: PetscCall(PetscViewerHDF5PopGroup(viewer));
3140: PetscCall(PetscViewerHDF5PopGroup(viewer));
3141: PetscCall(PetscViewerHDF5PopGroup(viewer));
3142: PetscCall(PetscViewerHDF5PopGroup(viewer));
3143: PetscCall(PetscViewerHDF5PopGroup(viewer));
3144: PetscCall(PetscViewerHDF5PopGroup(viewer));
3145: PetscFunctionReturn(PETSC_SUCCESS);
3146: }