Actual source code: ihdf5v.c
1: #include <petsc/private/viewerhdf5impl.h>
3: static PetscErrorCode PetscViewerHDF5Traverse_Inner_Internal(hid_t h5, const char name[], PetscBool createGroup, PetscBool *exists_)
4: {
5: htri_t exists;
6: hid_t group;
8: PetscFunctionBegin;
9: PetscCallHDF5Return(exists, H5Lexists, (h5, name, H5P_DEFAULT));
10: if (exists) PetscCallHDF5Return(exists, H5Oexists_by_name, (h5, name, H5P_DEFAULT));
11: if (!exists && createGroup) {
12: hid_t plist_id;
13: PetscCallHDF5Return(plist_id, H5Pcreate, (H5P_GROUP_CREATE));
14: PetscCallHDF5(H5Pset_link_creation_order, (plist_id, H5P_CRT_ORDER_TRACKED | H5P_CRT_ORDER_INDEXED));
15: PetscCallHDF5Return(group, H5Gcreate2, (h5, name, H5P_DEFAULT, plist_id, H5P_DEFAULT));
16: PetscCallHDF5(H5Pclose, (plist_id));
17: PetscCallHDF5(H5Gclose, (group));
18: exists = PETSC_TRUE;
19: }
20: *exists_ = (PetscBool)exists;
21: PetscFunctionReturn(PETSC_SUCCESS);
22: }
24: static PetscErrorCode PetscViewerHDF5Traverse_Internal(PetscViewer viewer, const char name[], PetscBool createGroup, PetscBool *has, H5O_type_t *otype)
25: {
26: const char rootGroupName[] = "/";
27: hid_t h5;
28: PetscBool exists = PETSC_FALSE;
29: int n;
30: char **hierarchy;
31: char buf[PETSC_MAX_PATH_LEN] = "";
33: PetscFunctionBegin;
35: if (name) PetscAssertPointer(name, 2);
36: else name = rootGroupName;
37: if (has) {
38: PetscAssertPointer(has, 4);
39: *has = PETSC_FALSE;
40: }
41: if (otype) {
42: PetscAssertPointer(otype, 5);
43: *otype = H5O_TYPE_UNKNOWN;
44: }
45: PetscCall(PetscViewerHDF5GetFileId(viewer, &h5));
47: /*
48: Unfortunately, H5Oexists_by_name() fails if any object in hierarchy is missing.
49: Hence, each of them needs to be tested separately:
50: 1) whether it's a valid link
51: 2) whether this link resolves to an object
52: See H5Oexists_by_name() documentation.
53: */
54: PetscCall(PetscStrToArray(name, '/', &n, &hierarchy));
55: if (!n) {
56: /* Assume group "/" always exists in accordance with HDF5 >= 1.10.0. See H5Lexists() documentation. */
57: if (has) *has = PETSC_TRUE;
58: if (otype) *otype = H5O_TYPE_GROUP;
59: PetscCall(PetscStrToArrayDestroy(n, hierarchy));
60: PetscFunctionReturn(PETSC_SUCCESS);
61: }
62: for (PetscInt i = 0; i < n; i++) {
63: PetscCall(PetscStrlcat(buf, "/", sizeof(buf)));
64: PetscCall(PetscStrlcat(buf, hierarchy[i], sizeof(buf)));
65: PetscCall(PetscViewerHDF5Traverse_Inner_Internal(h5, buf, createGroup, &exists));
66: if (!exists) break;
67: }
68: PetscCall(PetscStrToArrayDestroy(n, hierarchy));
70: /* If the object exists, get its type */
71: if (exists && otype) {
72: H5O_info_t info;
74: /* We could use H5Iget_type() here but that would require opening the object. This way we only need its name. */
75: PetscCallHDF5(H5Oget_info_by_name, (h5, name, &info, H5P_DEFAULT));
76: *otype = info.type;
77: }
78: if (has) *has = exists;
79: PetscFunctionReturn(PETSC_SUCCESS);
80: }
82: static PetscErrorCode PetscViewerHDF5GetGroup_Internal(PetscViewer viewer, const char *name[])
83: {
84: PetscViewer_HDF5 *hdf5 = (PetscViewer_HDF5 *)viewer->data;
86: PetscFunctionBegin;
88: PetscAssertPointer(name, 2);
89: if (hdf5->groups) *name = hdf5->groups->name;
90: else *name = NULL;
91: PetscFunctionReturn(PETSC_SUCCESS);
92: }
94: static PetscErrorCode PetscViewerHDF5HasAttribute_Internal(PetscViewer viewer, const char parent[], const char name[], PetscBool *has)
95: {
96: hid_t h5;
97: htri_t hhas;
99: PetscFunctionBegin;
100: PetscCall(PetscViewerHDF5GetFileId(viewer, &h5));
101: PetscCallHDF5Return(hhas, H5Aexists_by_name, (h5, parent, name, H5P_DEFAULT));
102: *has = hhas ? PETSC_TRUE : PETSC_FALSE;
103: PetscFunctionReturn(PETSC_SUCCESS);
104: }
106: static PetscErrorCode PetscViewerHDF5GetGroup_HDF5(PetscViewer viewer, const char path[], const char *abspath[])
107: {
108: size_t len;
109: PetscBool relative = PETSC_FALSE;
110: const char *group;
111: char buf[PETSC_MAX_PATH_LEN] = "";
113: PetscFunctionBegin;
114: PetscCall(PetscViewerHDF5GetGroup_Internal(viewer, &group));
115: PetscCall(PetscStrlen(path, &len));
116: relative = (PetscBool)(!len || path[0] != '/');
117: if (relative) {
118: PetscCall(PetscStrncpy(buf, group, sizeof(buf)));
119: if (!group || len) PetscCall(PetscStrlcat(buf, "/", sizeof(buf)));
120: PetscCall(PetscStrlcat(buf, path, sizeof(buf)));
121: PetscCall(PetscStrallocpy(buf, (char **)abspath));
122: } else {
123: PetscCall(PetscStrallocpy(path, (char **)abspath));
124: }
125: PetscFunctionReturn(PETSC_SUCCESS);
126: }
128: static PetscErrorCode PetscViewerSetFromOptions_HDF5(PetscViewer v, PetscOptionItems PetscOptionsObject)
129: {
130: PetscBool flg = PETSC_FALSE, set;
131: PetscViewer_HDF5 *hdf5 = (PetscViewer_HDF5 *)v->data;
133: PetscFunctionBegin;
134: PetscOptionsHeadBegin(PetscOptionsObject, "HDF5 PetscViewer Options");
135: PetscCall(PetscOptionsBool("-viewer_hdf5_base_dimension2", "1d Vectors get 2 dimensions in HDF5", "PetscViewerHDF5SetBaseDimension2", hdf5->basedimension2, &hdf5->basedimension2, NULL));
136: PetscCall(PetscOptionsBool("-viewer_hdf5_sp_output", "Force data to be written in single precision", "PetscViewerHDF5SetSPOutput", hdf5->spoutput, &hdf5->spoutput, NULL));
137: PetscCall(PetscOptionsBool("-viewer_hdf5_collective", "Enable collective transfer mode", "PetscViewerHDF5SetCollective", flg, &flg, &set));
138: if (set) PetscCall(PetscViewerHDF5SetCollective(v, flg));
139: flg = PETSC_FALSE;
140: PetscCall(PetscOptionsBool("-viewer_hdf5_default_timestepping", "Set default timestepping state", "PetscViewerHDF5SetDefaultTimestepping", flg, &flg, &set));
141: if (set) PetscCall(PetscViewerHDF5SetDefaultTimestepping(v, flg));
142: PetscCall(PetscOptionsBool("-viewer_hdf5_compress", "Enable compression", "PetscViewerHDF5SetCompress", hdf5->compress, &hdf5->compress, NULL));
143: PetscOptionsHeadEnd();
144: PetscFunctionReturn(PETSC_SUCCESS);
145: }
147: static PetscErrorCode PetscViewerView_HDF5(PetscViewer v, PetscViewer viewer)
148: {
149: PetscViewer_HDF5 *hdf5 = (PetscViewer_HDF5 *)v->data;
150: PetscBool flg;
152: PetscFunctionBegin;
153: if (hdf5->filename) PetscCall(PetscViewerASCIIPrintf(viewer, "Filename: %s\n", hdf5->filename));
154: PetscCall(PetscViewerASCIIPrintf(viewer, "Vectors with blocksize 1 saved as 2D datasets: %s\n", PetscBools[hdf5->basedimension2]));
155: PetscCall(PetscViewerASCIIPrintf(viewer, "Enforce single precision storage: %s\n", PetscBools[hdf5->spoutput]));
156: PetscCall(PetscViewerHDF5GetCollective(v, &flg));
157: PetscCall(PetscViewerASCIIPrintf(viewer, "MPI-IO transfer mode: %s\n", flg ? "collective" : "independent"));
158: PetscCall(PetscViewerASCIIPrintf(viewer, "Default timestepping: %s\n", PetscBools[hdf5->defTimestepping]));
159: PetscCall(PetscViewerASCIIPrintf(viewer, "Compression: %s\n", PetscBools[hdf5->compress]));
160: PetscFunctionReturn(PETSC_SUCCESS);
161: }
163: static PetscErrorCode PetscViewerFileClose_HDF5(PetscViewer viewer)
164: {
165: PetscViewer_HDF5 *hdf5 = (PetscViewer_HDF5 *)viewer->data;
167: PetscFunctionBegin;
168: PetscCall(PetscFree(hdf5->filename));
169: if (hdf5->file_id) PetscCallHDF5(H5Fclose, (hdf5->file_id));
170: PetscFunctionReturn(PETSC_SUCCESS);
171: }
173: static PetscErrorCode PetscViewerFlush_HDF5(PetscViewer viewer)
174: {
175: PetscViewer_HDF5 *hdf5 = (PetscViewer_HDF5 *)viewer->data;
177: PetscFunctionBegin;
178: if (hdf5->file_id) PetscCallHDF5(H5Fflush, (hdf5->file_id, H5F_SCOPE_LOCAL));
179: PetscFunctionReturn(PETSC_SUCCESS);
180: }
182: static PetscErrorCode PetscViewerDestroy_HDF5(PetscViewer viewer)
183: {
184: PetscViewer_HDF5 *hdf5 = (PetscViewer_HDF5 *)viewer->data;
186: PetscFunctionBegin;
187: PetscCallHDF5(H5Pclose, (hdf5->dxpl_id));
188: PetscCall(PetscViewerFileClose_HDF5(viewer));
189: while (hdf5->groups) {
190: PetscViewerHDF5GroupList *tmp = hdf5->groups->next;
192: PetscCall(PetscFree(hdf5->groups->name));
193: PetscCall(PetscFree(hdf5->groups));
194: hdf5->groups = tmp;
195: }
196: PetscCall(PetscFree(hdf5));
197: PetscCall(PetscObjectComposeFunction((PetscObject)viewer, "PetscViewerFileSetName_C", NULL));
198: PetscCall(PetscObjectComposeFunction((PetscObject)viewer, "PetscViewerFileGetName_C", NULL));
199: PetscCall(PetscObjectComposeFunction((PetscObject)viewer, "PetscViewerFileSetMode_C", NULL));
200: PetscCall(PetscObjectComposeFunction((PetscObject)viewer, "PetscViewerFileGetMode_C", NULL));
201: PetscCall(PetscObjectComposeFunction((PetscObject)viewer, "PetscViewerHDF5SetBaseDimension2_C", NULL));
202: PetscCall(PetscObjectComposeFunction((PetscObject)viewer, "PetscViewerHDF5GetBaseDimension2_C", NULL));
203: PetscCall(PetscObjectComposeFunction((PetscObject)viewer, "PetscViewerHDF5SetSPOutput_C", NULL));
204: PetscCall(PetscObjectComposeFunction((PetscObject)viewer, "PetscViewerHDF5SetCollective_C", NULL));
205: PetscCall(PetscObjectComposeFunction((PetscObject)viewer, "PetscViewerHDF5GetCollective_C", NULL));
206: PetscCall(PetscObjectComposeFunction((PetscObject)viewer, "PetscViewerHDF5GetDefaultTimestepping_C", NULL));
207: PetscCall(PetscObjectComposeFunction((PetscObject)viewer, "PetscViewerHDF5SetDefaultTimestepping_C", NULL));
208: PetscCall(PetscObjectComposeFunction((PetscObject)viewer, "PetscViewerHDF5SetCompress_C", NULL));
209: PetscCall(PetscObjectComposeFunction((PetscObject)viewer, "PetscViewerHDF5GetCompress_C", NULL));
210: PetscCall(PetscObjectComposeFunction((PetscObject)viewer, "PetscViewerHDF5WriteGroup_C", NULL));
211: PetscCall(PetscObjectComposeFunction((PetscObject)viewer, "PetscViewerHDF5PushGroup_C", NULL));
212: PetscCall(PetscObjectComposeFunction((PetscObject)viewer, "PetscViewerHDF5PopGroup_C", NULL));
213: PetscCall(PetscObjectComposeFunction((PetscObject)viewer, "PetscViewerHDF5GetGroup_C", NULL));
214: PetscCall(PetscObjectComposeFunction((PetscObject)viewer, "PetscViewerHDF5PushTimestepping_C", NULL));
215: PetscCall(PetscObjectComposeFunction((PetscObject)viewer, "PetscViewerHDF5PopTimestepping_C", NULL));
216: PetscCall(PetscObjectComposeFunction((PetscObject)viewer, "PetscViewerHDF5IsTimestepping_C", NULL));
217: PetscCall(PetscObjectComposeFunction((PetscObject)viewer, "PetscViewerHDF5IncrementTimestep_C", NULL));
218: PetscCall(PetscObjectComposeFunction((PetscObject)viewer, "PetscViewerHDF5SetTimestep_C", NULL));
219: PetscCall(PetscObjectComposeFunction((PetscObject)viewer, "PetscViewerHDF5GetTimestep_C", NULL));
220: PetscCall(PetscObjectComposeFunction((PetscObject)viewer, "PetscViewerHDF5WriteAttribute_C", NULL));
221: PetscCall(PetscObjectComposeFunction((PetscObject)viewer, "PetscViewerHDF5ReadAttribute_C", NULL));
222: PetscCall(PetscObjectComposeFunction((PetscObject)viewer, "PetscViewerHDF5HasGroup_C", NULL));
223: PetscCall(PetscObjectComposeFunction((PetscObject)viewer, "PetscViewerHDF5HasDataset_C", NULL));
224: PetscCall(PetscObjectComposeFunction((PetscObject)viewer, "PetscViewerHDF5HasAttribute_C", NULL));
225: PetscCall(PetscObjectComposeFunction((PetscObject)viewer, "PetscViewerHDF5GetSPOutput_C", NULL));
226: PetscFunctionReturn(PETSC_SUCCESS);
227: }
229: static PetscErrorCode PetscViewerFileSetMode_HDF5(PetscViewer viewer, PetscFileMode type)
230: {
231: PetscViewer_HDF5 *hdf5 = (PetscViewer_HDF5 *)viewer->data;
233: PetscFunctionBegin;
234: hdf5->btype = type;
235: PetscFunctionReturn(PETSC_SUCCESS);
236: }
238: static PetscErrorCode PetscViewerFileGetMode_HDF5(PetscViewer viewer, PetscFileMode *type)
239: {
240: PetscViewer_HDF5 *hdf5 = (PetscViewer_HDF5 *)viewer->data;
242: PetscFunctionBegin;
243: *type = hdf5->btype;
244: PetscFunctionReturn(PETSC_SUCCESS);
245: }
247: static PetscErrorCode PetscViewerHDF5SetBaseDimension2_HDF5(PetscViewer viewer, PetscBool flg)
248: {
249: PetscViewer_HDF5 *hdf5 = (PetscViewer_HDF5 *)viewer->data;
251: PetscFunctionBegin;
252: hdf5->basedimension2 = flg;
253: PetscFunctionReturn(PETSC_SUCCESS);
254: }
256: static PetscErrorCode PetscViewerHDF5GetBaseDimension2_HDF5(PetscViewer viewer, PetscBool *flg)
257: {
258: PetscViewer_HDF5 *hdf5 = (PetscViewer_HDF5 *)viewer->data;
260: PetscFunctionBegin;
261: *flg = hdf5->basedimension2;
262: PetscFunctionReturn(PETSC_SUCCESS);
263: }
265: static PetscErrorCode PetscViewerHDF5SetSPOutput_HDF5(PetscViewer viewer, PetscBool flg)
266: {
267: PetscViewer_HDF5 *hdf5 = (PetscViewer_HDF5 *)viewer->data;
269: PetscFunctionBegin;
270: hdf5->spoutput = flg;
271: PetscFunctionReturn(PETSC_SUCCESS);
272: }
274: static PetscErrorCode PetscViewerHDF5GetSPOutput_HDF5(PetscViewer viewer, PetscBool *flg)
275: {
276: PetscViewer_HDF5 *hdf5 = (PetscViewer_HDF5 *)viewer->data;
278: PetscFunctionBegin;
279: *flg = hdf5->spoutput;
280: PetscFunctionReturn(PETSC_SUCCESS);
281: }
283: static PetscErrorCode PetscViewerHDF5SetCollective_HDF5(PetscViewer viewer, PetscBool flg)
284: {
285: PetscFunctionBegin;
286: /* H5FD_MPIO_COLLECTIVE is wrong in hdf5 1.10.2, and is the same as H5FD_MPIO_INDEPENDENT in earlier versions
287: - see e.g. https://gitlab.cosma.dur.ac.uk/swift/swiftsim/issues/431 */
288: #if H5_VERSION_GE(1, 10, 3) && defined(H5_HAVE_PARALLEL)
289: {
290: PetscViewer_HDF5 *hdf5 = (PetscViewer_HDF5 *)viewer->data;
291: PetscCallHDF5(H5Pset_dxpl_mpio, (hdf5->dxpl_id, flg ? H5FD_MPIO_COLLECTIVE : H5FD_MPIO_INDEPENDENT));
292: }
293: #else
294: if (flg) PetscCall(PetscPrintf(PetscObjectComm((PetscObject)viewer), "Warning: PetscViewerHDF5SetCollective(viewer,PETSC_TRUE) is ignored for HDF5 versions prior to 1.10.3 or if built without MPI support\n"));
295: #endif
296: PetscFunctionReturn(PETSC_SUCCESS);
297: }
299: static PetscErrorCode PetscViewerHDF5GetCollective_HDF5(PetscViewer viewer, PetscBool *flg)
300: {
301: #if defined(H5_HAVE_PARALLEL)
302: PetscViewer_HDF5 *hdf5 = (PetscViewer_HDF5 *)viewer->data;
303: H5FD_mpio_xfer_t mode;
304: #endif
306: PetscFunctionBegin;
307: #if !defined(H5_HAVE_PARALLEL)
308: *flg = PETSC_FALSE;
309: #else
310: PetscCallHDF5(H5Pget_dxpl_mpio, (hdf5->dxpl_id, &mode));
311: *flg = (mode == H5FD_MPIO_COLLECTIVE) ? PETSC_TRUE : PETSC_FALSE;
312: #endif
313: PetscFunctionReturn(PETSC_SUCCESS);
314: }
316: static PetscErrorCode PetscViewerFileSetName_HDF5(PetscViewer viewer, const char name[])
317: {
318: PetscViewer_HDF5 *hdf5 = (PetscViewer_HDF5 *)viewer->data;
319: hid_t plist_access_id;
320: hid_t plist_create_id;
322: PetscFunctionBegin;
323: if (hdf5->file_id) PetscCallHDF5(H5Fclose, (hdf5->file_id));
324: PetscCall(PetscFree(hdf5->filename));
325: PetscCall(PetscStrallocpy(name, &hdf5->filename));
326: PetscCallHDF5Return(plist_create_id, H5Pcreate, (H5P_FILE_CREATE));
327: PetscCallHDF5(H5Pset_link_creation_order, (plist_create_id, H5P_CRT_ORDER_TRACKED | H5P_CRT_ORDER_INDEXED));
328: PetscCallHDF5Return(plist_access_id, H5Pcreate, (H5P_FILE_ACCESS));
329: #if defined(H5_HAVE_PARALLEL)
330: PetscCallHDF5(H5Pset_fapl_mpio, (plist_access_id, PetscObjectComm((PetscObject)viewer), MPI_INFO_NULL));
331: #endif
332: /* Create or open the file collectively */
333: switch (hdf5->btype) {
334: case FILE_MODE_READ:
335: if (PetscDefined(USE_DEBUG)) {
336: PetscMPIInt rank;
337: PetscBool flg;
339: PetscCallMPI(MPI_Comm_rank(PetscObjectComm((PetscObject)viewer), &rank));
340: if (rank == 0) {
341: PetscCall(PetscTestFile(hdf5->filename, 'r', &flg));
342: PetscCheck(flg, PETSC_COMM_SELF, PETSC_ERR_FILE_OPEN, "File %s requested for reading does not exist", hdf5->filename);
343: }
344: PetscCallMPI(MPI_Barrier(PetscObjectComm((PetscObject)viewer)));
345: }
346: PetscCallHDF5Return(hdf5->file_id, H5Fopen, (name, H5F_ACC_RDONLY, plist_access_id));
347: break;
348: case FILE_MODE_APPEND:
349: case FILE_MODE_UPDATE: {
350: PetscBool flg;
351: PetscCall(PetscTestFile(hdf5->filename, 'r', &flg));
352: if (flg) PetscCallHDF5Return(hdf5->file_id, H5Fopen, (name, H5F_ACC_RDWR, plist_access_id));
353: else PetscCallHDF5Return(hdf5->file_id, H5Fcreate, (name, H5F_ACC_EXCL, plist_create_id, plist_access_id));
354: break;
355: }
356: case FILE_MODE_WRITE:
357: PetscCallHDF5Return(hdf5->file_id, H5Fcreate, (name, H5F_ACC_TRUNC, plist_create_id, plist_access_id));
358: break;
359: case FILE_MODE_UNDEFINED:
360: SETERRQ(PetscObjectComm((PetscObject)viewer), PETSC_ERR_ORDER, "Must call PetscViewerFileSetMode() before PetscViewerFileSetName()");
361: default:
362: SETERRQ(PetscObjectComm((PetscObject)viewer), PETSC_ERR_SUP, "Unsupported file mode %s", PetscFileModes[hdf5->btype]);
363: }
364: PetscCheck(hdf5->file_id >= 0, PETSC_COMM_SELF, PETSC_ERR_LIB, "H5Fcreate failed for %s", name);
365: PetscCallHDF5(H5Pclose, (plist_access_id));
366: PetscCallHDF5(H5Pclose, (plist_create_id));
367: PetscCall(PetscViewerHDF5ResetAttachedDMPlexStorageVersion(viewer));
368: PetscFunctionReturn(PETSC_SUCCESS);
369: }
371: static PetscErrorCode PetscViewerFileGetName_HDF5(PetscViewer viewer, const char **name)
372: {
373: PetscViewer_HDF5 *vhdf5 = (PetscViewer_HDF5 *)viewer->data;
375: PetscFunctionBegin;
376: *name = vhdf5->filename;
377: PetscFunctionReturn(PETSC_SUCCESS);
378: }
380: static PetscErrorCode PetscViewerSetUp_HDF5(PETSC_UNUSED PetscViewer viewer)
381: {
382: PetscFunctionBegin;
383: PetscFunctionReturn(PETSC_SUCCESS);
384: }
386: static PetscErrorCode PetscViewerHDF5SetDefaultTimestepping_HDF5(PetscViewer viewer, PetscBool flg)
387: {
388: PetscViewer_HDF5 *hdf5 = (PetscViewer_HDF5 *)viewer->data;
390: PetscFunctionBegin;
391: hdf5->defTimestepping = flg;
392: PetscFunctionReturn(PETSC_SUCCESS);
393: }
395: static PetscErrorCode PetscViewerHDF5GetDefaultTimestepping_HDF5(PetscViewer viewer, PetscBool *flg)
396: {
397: PetscViewer_HDF5 *hdf5 = (PetscViewer_HDF5 *)viewer->data;
399: PetscFunctionBegin;
400: *flg = hdf5->defTimestepping;
401: PetscFunctionReturn(PETSC_SUCCESS);
402: }
404: static PetscErrorCode PetscViewerHDF5SetCompress_HDF5(PetscViewer viewer, PetscBool flg)
405: {
406: PetscViewer_HDF5 *hdf5 = (PetscViewer_HDF5 *)viewer->data;
408: PetscFunctionBegin;
409: hdf5->compress = flg;
410: PetscFunctionReturn(PETSC_SUCCESS);
411: }
413: static PetscErrorCode PetscViewerHDF5GetCompress_HDF5(PetscViewer viewer, PetscBool *flg)
414: {
415: PetscViewer_HDF5 *hdf5 = (PetscViewer_HDF5 *)viewer->data;
417: PetscFunctionBegin;
418: *flg = hdf5->compress;
419: PetscFunctionReturn(PETSC_SUCCESS);
420: }
422: /*@C
423: PetscViewerHDF5GetFileId - Retrieve the file id, this file ID then can be used in direct HDF5 calls
425: Not Collective
427: Input Parameter:
428: . viewer - the `PetscViewer`
430: Output Parameter:
431: . file_id - The file id
433: Level: intermediate
435: .seealso: [](sec_viewers), `PETSCVIEWERHDF5`, `PetscViewerHDF5Open()`
436: @*/
437: PetscErrorCode PetscViewerHDF5GetFileId(PetscViewer viewer, hid_t *file_id)
438: {
439: PetscViewer_HDF5 *hdf5 = (PetscViewer_HDF5 *)viewer->data;
441: PetscFunctionBegin;
443: if (file_id) *file_id = hdf5->file_id;
444: PetscFunctionReturn(PETSC_SUCCESS);
445: }
447: static PetscErrorCode PetscViewerHDF5PushGroup_HDF5(PetscViewer viewer, const char name[])
448: {
449: PetscViewer_HDF5 *hdf5 = (PetscViewer_HDF5 *)viewer->data;
450: PetscViewerHDF5GroupList *groupNode;
451: size_t i, len;
452: char buf[PETSC_MAX_PATH_LEN];
453: const char *gname;
455: PetscFunctionBegin;
456: PetscCall(PetscStrlen(name, &len));
457: gname = NULL;
458: if (len) {
459: if (len == 1 && name[0] == '.') {
460: /* use current name */
461: gname = (hdf5->groups && hdf5->groups->name) ? hdf5->groups->name : NULL;
462: } else if (name[0] == '/') {
463: /* absolute */
464: for (i = 1; i < len; i++) {
465: if (name[i] != '/') {
466: gname = name;
467: break;
468: }
469: }
470: } else {
471: /* relative */
472: const char *parent = (hdf5->groups && hdf5->groups->name) ? hdf5->groups->name : "";
473: PetscCall(PetscSNPrintf(buf, sizeof(buf), "%s/%s", parent, name));
474: gname = buf;
475: }
476: }
477: PetscCall(PetscNew(&groupNode));
478: PetscCall(PetscStrallocpy(gname, (char **)&groupNode->name));
479: groupNode->next = hdf5->groups;
480: hdf5->groups = groupNode;
481: PetscFunctionReturn(PETSC_SUCCESS);
482: }
484: static PetscErrorCode PetscViewerHDF5PopGroup_HDF5(PetscViewer viewer)
485: {
486: PetscViewer_HDF5 *hdf5 = (PetscViewer_HDF5 *)viewer->data;
487: PetscViewerHDF5GroupList *groupNode;
489: PetscFunctionBegin;
490: PetscCheck(hdf5->groups, PetscObjectComm((PetscObject)viewer), PETSC_ERR_ARG_WRONGSTATE, "HDF5 group stack is empty, cannot pop");
491: groupNode = hdf5->groups;
492: hdf5->groups = hdf5->groups->next;
493: PetscCall(PetscFree(groupNode->name));
494: PetscCall(PetscFree(groupNode));
495: PetscFunctionReturn(PETSC_SUCCESS);
496: }
498: /*@C
499: PetscViewerHDF5OpenGroup - Open the HDF5 group with the name (full path) returned by `PetscViewerHDF5GetGroup()`,
500: and return this group's ID and file ID.
501: If `PetscViewerHDF5GetGroup()` yields NULL, then group ID is file ID.
503: Not Collective
505: Input Parameters:
506: + viewer - the `PetscViewer` of type `PETSCVIEWERHDF5`
507: - path - (Optional) The path relative to the pushed group
509: Output Parameters:
510: + fileId - The HDF5 file ID
511: - groupId - The HDF5 group ID
513: Level: intermediate
515: Note:
516: If path starts with '/', it is taken as an absolute path overriding currently pushed group, else path is relative to the current pushed group.
517: `NULL` or empty path means the current pushed group.
519: If the viewer is writable, the group is created if it doesn't exist yet.
521: .seealso: [](sec_viewers), `PETSCVIEWERHDF5`, `PetscViewerHDF5Open()`, `PetscViewerHDF5PushGroup()`, `PetscViewerHDF5PopGroup()`, `PetscViewerHDF5GetGroup()`, `PetscViewerHDF5WriteGroup()`
522: @*/
523: PetscErrorCode PetscViewerHDF5OpenGroup(PetscViewer viewer, const char path[], hid_t *fileId, hid_t *groupId)
524: {
525: hid_t file_id;
526: H5O_type_t type;
527: const char *fileName = NULL;
528: const char *groupName = NULL;
529: PetscBool writable, has;
531: PetscFunctionBegin;
533: if (path) PetscAssertPointer(path, 2);
534: PetscAssertPointer(fileId, 3);
535: PetscAssertPointer(groupId, 4);
536: PetscCall(PetscViewerWritable(viewer, &writable));
537: PetscCall(PetscViewerHDF5GetFileId(viewer, &file_id));
538: PetscCall(PetscViewerFileGetName(viewer, &fileName));
539: PetscCall(PetscViewerHDF5GetGroup(viewer, path, &groupName));
540: PetscCall(PetscViewerHDF5Traverse_Internal(viewer, groupName, writable, &has, &type));
541: if (!has) {
542: PetscCheck(writable, PetscObjectComm((PetscObject)viewer), PETSC_ERR_FILE_UNEXPECTED, "Group %s does not exist and file %s is not open for writing", groupName, fileName);
543: SETERRQ(PetscObjectComm((PetscObject)viewer), PETSC_ERR_LIB, "HDF5 failed to create group %s although file %s is open for writing", groupName, fileName);
544: }
545: PetscCheck(type == H5O_TYPE_GROUP, PetscObjectComm((PetscObject)viewer), PETSC_ERR_FILE_UNEXPECTED, "Path %s in file %s resolves to something which is not a group", groupName, fileName);
546: PetscCallHDF5Return(*groupId, H5Gopen2, (file_id, groupName, H5P_DEFAULT));
547: PetscCall(PetscFree(groupName));
548: *fileId = file_id;
549: PetscFunctionReturn(PETSC_SUCCESS);
550: }
552: static PetscErrorCode PetscViewerHDF5WriteGroup_HDF5(PetscViewer viewer, const char path[])
553: {
554: hid_t fileId, groupId;
556: PetscFunctionBegin;
557: PetscCall(PetscViewerHDF5OpenGroup(viewer, path, &fileId, &groupId)); // make sure group is actually created
558: PetscCallHDF5(H5Gclose, (groupId));
559: PetscFunctionReturn(PETSC_SUCCESS);
560: }
562: static PetscErrorCode PetscViewerHDF5PushTimestepping_HDF5(PetscViewer viewer)
563: {
564: PetscViewer_HDF5 *hdf5 = (PetscViewer_HDF5 *)viewer->data;
566: PetscFunctionBegin;
567: PetscCheck(!hdf5->timestepping, PetscObjectComm((PetscObject)viewer), PETSC_ERR_ARG_WRONGSTATE, "Timestepping is already pushed");
568: hdf5->timestepping = PETSC_TRUE;
569: if (hdf5->timestep < 0) hdf5->timestep = 0;
570: PetscFunctionReturn(PETSC_SUCCESS);
571: }
573: static PetscErrorCode PetscViewerHDF5PopTimestepping_HDF5(PetscViewer viewer)
574: {
575: PetscViewer_HDF5 *hdf5 = (PetscViewer_HDF5 *)viewer->data;
577: PetscFunctionBegin;
578: PetscCheck(hdf5->timestepping, PetscObjectComm((PetscObject)viewer), PETSC_ERR_ARG_WRONGSTATE, "Timestepping has not been pushed yet. Call PetscViewerHDF5PushTimestepping() first");
579: hdf5->timestepping = PETSC_FALSE;
580: PetscFunctionReturn(PETSC_SUCCESS);
581: }
583: static PetscErrorCode PetscViewerHDF5IsTimestepping_HDF5(PetscViewer viewer, PetscBool *flg)
584: {
585: PetscViewer_HDF5 *hdf5 = (PetscViewer_HDF5 *)viewer->data;
587: PetscFunctionBegin;
588: *flg = hdf5->timestepping;
589: PetscFunctionReturn(PETSC_SUCCESS);
590: }
592: static PetscErrorCode PetscViewerHDF5IncrementTimestep_HDF5(PetscViewer viewer)
593: {
594: PetscViewer_HDF5 *hdf5 = (PetscViewer_HDF5 *)viewer->data;
596: PetscFunctionBegin;
597: PetscCheck(hdf5->timestepping, PetscObjectComm((PetscObject)viewer), PETSC_ERR_ARG_WRONGSTATE, "Timestepping has not been pushed yet. Call PetscViewerHDF5PushTimestepping() first");
598: ++hdf5->timestep;
599: PetscFunctionReturn(PETSC_SUCCESS);
600: }
602: static PetscErrorCode PetscViewerHDF5SetTimestep_HDF5(PetscViewer viewer, PetscInt timestep)
603: {
604: PetscViewer_HDF5 *hdf5 = (PetscViewer_HDF5 *)viewer->data;
606: PetscFunctionBegin;
607: PetscCheck(timestep >= 0, PetscObjectComm((PetscObject)viewer), PETSC_ERR_ARG_WRONGSTATE, "Timestep %" PetscInt_FMT " is negative", timestep);
608: PetscCheck(hdf5->timestepping, PetscObjectComm((PetscObject)viewer), PETSC_ERR_ARG_WRONGSTATE, "Timestepping has not been pushed yet. Call PetscViewerHDF5PushTimestepping() first");
609: hdf5->timestep = timestep;
610: PetscFunctionReturn(PETSC_SUCCESS);
611: }
613: static PetscErrorCode PetscViewerHDF5GetTimestep_HDF5(PetscViewer viewer, PetscInt *timestep)
614: {
615: PetscViewer_HDF5 *hdf5 = (PetscViewer_HDF5 *)viewer->data;
617: PetscFunctionBegin;
618: PetscCheck(hdf5->timestepping, PetscObjectComm((PetscObject)viewer), PETSC_ERR_ARG_WRONGSTATE, "Timestepping has not been pushed yet. Call PetscViewerHDF5PushTimestepping() first");
619: *timestep = hdf5->timestep;
620: PetscFunctionReturn(PETSC_SUCCESS);
621: }
623: /*@C
624: PetscDataTypeToHDF5DataType - Converts the PETSc name of a datatype to its HDF5 name.
626: Not Collective
628: Input Parameter:
629: . ptype - the PETSc datatype name (for example `PETSC_DOUBLE`)
631: Output Parameter:
632: . htype - the HDF5 datatype
634: Level: advanced
636: .seealso: [](sec_viewers), `PetscDataType`, `PetscHDF5DataTypeToPetscDataType()`
637: @*/
638: PetscErrorCode PetscDataTypeToHDF5DataType(PetscDataType ptype, hid_t *htype)
639: {
640: PetscFunctionBegin;
641: if (ptype == PETSC_INT) *htype = PetscDefined(USE_64BIT_INDICES) ? H5T_NATIVE_LLONG : H5T_NATIVE_INT;
642: else if (ptype == PETSC_DOUBLE) *htype = H5T_NATIVE_DOUBLE;
643: else if (ptype == PETSC_LONG) *htype = H5T_NATIVE_LONG;
644: else if (ptype == PETSC_SHORT) *htype = H5T_NATIVE_SHORT;
645: else if (ptype == PETSC_ENUM) *htype = H5T_NATIVE_INT;
646: else if (ptype == PETSC_BOOL) *htype = H5T_NATIVE_HBOOL;
647: else if (ptype == PETSC_FLOAT) *htype = H5T_NATIVE_FLOAT;
648: else if (ptype == PETSC_CHAR) *htype = H5T_NATIVE_CHAR;
649: else if (ptype == PETSC_BIT_LOGICAL) *htype = H5T_NATIVE_UCHAR;
650: else if (ptype == PETSC_STRING) *htype = H5Tcopy(H5T_C_S1);
651: else SETERRQ(PETSC_COMM_SELF, PETSC_ERR_ARG_OUTOFRANGE, "Unsupported PETSc datatype");
652: PetscFunctionReturn(PETSC_SUCCESS);
653: }
655: /*@C
656: PetscHDF5DataTypeToPetscDataType - Finds the PETSc name of a datatype from its HDF5 name
658: Not Collective
660: Input Parameter:
661: . htype - the HDF5 datatype (for example `H5T_NATIVE_DOUBLE`, ...)
663: Output Parameter:
664: . ptype - the PETSc datatype name (for example `PETSC_DOUBLE`)
666: Level: advanced
668: .seealso: [](sec_viewers), `PetscDataType`
669: @*/
670: PetscErrorCode PetscHDF5DataTypeToPetscDataType(hid_t htype, PetscDataType *ptype)
671: {
672: PetscFunctionBegin;
673: if (htype == H5T_NATIVE_INT) *ptype = PetscDefined(USE_64BIT_INDICES) ? PETSC_LONG : PETSC_INT;
674: #if defined(PETSC_USE_64BIT_INDICES)
675: else if (htype == H5T_NATIVE_LLONG) *ptype = PETSC_INT;
676: #endif
677: else if (htype == H5T_NATIVE_DOUBLE) *ptype = PETSC_DOUBLE;
678: else if (htype == H5T_NATIVE_LONG) *ptype = PETSC_LONG;
679: else if (htype == H5T_NATIVE_SHORT) *ptype = PETSC_SHORT;
680: else if (htype == H5T_NATIVE_HBOOL) *ptype = PETSC_BOOL;
681: else if (htype == H5T_NATIVE_FLOAT) *ptype = PETSC_FLOAT;
682: else if (htype == H5T_NATIVE_CHAR) *ptype = PETSC_CHAR;
683: else if (htype == H5T_NATIVE_UCHAR) *ptype = PETSC_CHAR;
684: else if (htype == H5T_C_S1) *ptype = PETSC_STRING;
685: else SETERRQ(PETSC_COMM_SELF, PETSC_ERR_ARG_OUTOFRANGE, "Unsupported HDF5 datatype");
686: PetscFunctionReturn(PETSC_SUCCESS);
687: }
689: static PetscErrorCode PetscViewerHDF5WriteAttribute_HDF5(PetscViewer viewer, const char parent[], const char name[], PetscDataType datatype, const void *value)
690: {
691: const char *parentAbsPath;
692: hid_t h5, dataspace, obj, attribute, dtype;
693: PetscBool has;
695: PetscFunctionBegin;
696: PetscCall(PetscViewerHDF5GetGroup(viewer, parent, &parentAbsPath));
697: PetscCall(PetscViewerHDF5Traverse_Internal(viewer, parentAbsPath, PETSC_TRUE, NULL, NULL));
698: PetscCall(PetscViewerHDF5HasAttribute_Internal(viewer, parentAbsPath, name, &has));
699: PetscCall(PetscDataTypeToHDF5DataType(datatype, &dtype));
700: if (datatype == PETSC_STRING) {
701: size_t len;
702: PetscCall(PetscStrlen((const char *)value, &len));
703: PetscCallHDF5(H5Tset_size, (dtype, len + 1));
704: }
705: PetscCall(PetscViewerHDF5GetFileId(viewer, &h5));
706: PetscCallHDF5Return(dataspace, H5Screate, (H5S_SCALAR));
707: PetscCallHDF5Return(obj, H5Oopen, (h5, parentAbsPath, H5P_DEFAULT));
708: if (has) {
709: PetscCallHDF5Return(attribute, H5Aopen_name, (obj, name));
710: } else {
711: PetscCallHDF5Return(attribute, H5Acreate2, (obj, name, dtype, dataspace, H5P_DEFAULT, H5P_DEFAULT));
712: }
713: PetscCallHDF5(H5Awrite, (attribute, dtype, value));
714: if (datatype == PETSC_STRING) PetscCallHDF5(H5Tclose, (dtype));
715: PetscCallHDF5(H5Aclose, (attribute));
716: PetscCallHDF5(H5Oclose, (obj));
717: PetscCallHDF5(H5Sclose, (dataspace));
718: PetscCall(PetscFree(parentAbsPath));
719: PetscFunctionReturn(PETSC_SUCCESS);
720: }
722: static PetscErrorCode PetscViewerHDF5ReadAttribute_HDF5(PetscViewer viewer, const char parent[], const char name[], PetscDataType datatype, const void *defaultValue, void *value)
723: {
724: const char *parentAbsPath;
725: hid_t h5, obj, attribute, dtype;
726: PetscBool has;
728: PetscFunctionBegin;
729: PetscCall(PetscDataTypeToHDF5DataType(datatype, &dtype));
730: PetscCall(PetscViewerHDF5GetGroup(viewer, parent, &parentAbsPath));
731: PetscCall(PetscViewerHDF5Traverse_Internal(viewer, parentAbsPath, PETSC_FALSE, &has, NULL));
732: if (has) PetscCall(PetscViewerHDF5HasAttribute_Internal(viewer, parentAbsPath, name, &has));
733: if (!has) {
734: if (defaultValue) {
735: if (defaultValue != value) {
736: if (datatype == PETSC_STRING) {
737: PetscCall(PetscStrallocpy(*(char **)defaultValue, (char **)value));
738: } else {
739: size_t len;
740: PetscCallHDF5ReturnNoCheck(len, H5Tget_size, (dtype));
741: PetscCall(PetscMemcpy(value, defaultValue, len));
742: }
743: }
744: PetscCall(PetscFree(parentAbsPath));
745: PetscFunctionReturn(PETSC_SUCCESS);
746: } else SETERRQ(PetscObjectComm((PetscObject)viewer), PETSC_ERR_FILE_UNEXPECTED, "Attribute %s/%s does not exist and default value not provided", parentAbsPath, name);
747: }
748: PetscCall(PetscViewerHDF5GetFileId(viewer, &h5));
749: PetscCallHDF5Return(obj, H5Oopen, (h5, parentAbsPath, H5P_DEFAULT));
750: PetscCallHDF5Return(attribute, H5Aopen_name, (obj, name));
751: if (datatype == PETSC_STRING) {
752: size_t len;
753: hid_t atype;
754: PetscCallHDF5Return(atype, H5Aget_type, (attribute));
755: PetscCallHDF5ReturnNoCheck(len, H5Tget_size, (atype));
756: PetscCall(PetscMalloc((len + 1) * sizeof(char), value));
757: PetscCallHDF5(H5Tset_size, (dtype, len + 1));
758: PetscCallHDF5(H5Aread, (attribute, dtype, *(char **)value));
759: } else {
760: PetscCallHDF5(H5Aread, (attribute, dtype, value));
761: }
762: PetscCallHDF5(H5Aclose, (attribute));
763: /* H5Oclose can be used to close groups, datasets, or committed datatypes */
764: PetscCallHDF5(H5Oclose, (obj));
765: PetscCall(PetscFree(parentAbsPath));
766: PetscFunctionReturn(PETSC_SUCCESS);
767: }
769: static PetscErrorCode PetscViewerHDF5HasGroup_HDF5(PetscViewer viewer, const char path[], PetscBool *has)
770: {
771: H5O_type_t type;
772: const char *abspath;
774: PetscFunctionBegin;
775: PetscCall(PetscViewerHDF5GetGroup(viewer, path, &abspath));
776: PetscCall(PetscViewerHDF5Traverse_Internal(viewer, abspath, PETSC_FALSE, NULL, &type));
777: *has = (PetscBool)(type == H5O_TYPE_GROUP);
778: PetscCall(PetscFree(abspath));
779: PetscFunctionReturn(PETSC_SUCCESS);
780: }
782: static PetscErrorCode PetscViewerHDF5HasDataset_HDF5(PetscViewer viewer, const char path[], PetscBool *has)
783: {
784: H5O_type_t type;
785: const char *abspath;
787: PetscFunctionBegin;
788: PetscCall(PetscViewerHDF5GetGroup(viewer, path, &abspath));
789: PetscCall(PetscViewerHDF5Traverse_Internal(viewer, abspath, PETSC_FALSE, NULL, &type));
790: *has = (PetscBool)(type == H5O_TYPE_DATASET);
791: PetscCall(PetscFree(abspath));
792: PetscFunctionReturn(PETSC_SUCCESS);
793: }
795: static PetscErrorCode PetscViewerHDF5HasAttribute_HDF5(PetscViewer viewer, const char parent[], const char name[], PetscBool *has)
796: {
797: const char *parentAbsPath;
799: PetscFunctionBegin;
800: PetscCall(PetscViewerHDF5GetGroup(viewer, parent, &parentAbsPath));
801: PetscCall(PetscViewerHDF5Traverse_Internal(viewer, parentAbsPath, PETSC_FALSE, has, NULL));
802: if (*has) PetscCall(PetscViewerHDF5HasAttribute_Internal(viewer, parentAbsPath, name, has));
803: PetscCall(PetscFree(parentAbsPath));
804: PetscFunctionReturn(PETSC_SUCCESS);
805: }
807: /*MC
808: PETSCVIEWERHDF5 - A viewer that writes to an HDF5 file
810: Level: beginner
812: .seealso: [](sec_viewers), `PetscViewerHDF5Open()`, `PetscViewerStringSPrintf()`, `PetscViewerSocketOpen()`, `PetscViewerDrawOpen()`, `PETSCVIEWERSOCKET`,
813: `PetscViewerCreate()`, `PetscViewerASCIIOpen()`, `PetscViewerBinaryOpen()`, `PETSCVIEWERBINARY`, `PETSCVIEWERDRAW`, `PETSCVIEWERSTRING`,
814: `PetscViewerMatlabOpen()`, `VecView()`, `DMView()`, `PetscViewerMatlabPutArray()`, `PETSCVIEWERASCII`, `PETSCVIEWERMATLAB`,
815: `PetscViewerFileSetName()`, `PetscViewerFileSetMode()`, `PetscViewerFormat`, `PetscViewerType`, `PetscViewerSetType()`
816: M*/
818: PETSC_EXTERN PetscErrorCode PetscViewerCreate_HDF5(PetscViewer v)
819: {
820: PetscViewer_HDF5 *hdf5;
822: PetscFunctionBegin;
823: #if !defined(H5_HAVE_PARALLEL)
824: {
825: PetscMPIInt size;
826: PetscCallMPI(MPI_Comm_size(PetscObjectComm((PetscObject)v), &size));
827: PetscCheck(size <= 1, PetscObjectComm((PetscObject)v), PETSC_ERR_SUP, "Cannot use parallel HDF5 viewer since the given HDF5 does not support parallel I/O (H5_HAVE_PARALLEL is unset)");
828: }
829: #endif
831: PetscCall(PetscNew(&hdf5));
833: v->data = (void *)hdf5;
834: v->ops->destroy = PetscViewerDestroy_HDF5;
835: v->ops->setfromoptions = PetscViewerSetFromOptions_HDF5;
836: v->ops->setup = PetscViewerSetUp_HDF5;
837: v->ops->view = PetscViewerView_HDF5;
838: v->ops->flush = PetscViewerFlush_HDF5;
839: hdf5->btype = FILE_MODE_UNDEFINED;
840: hdf5->filename = NULL;
841: hdf5->timestep = -1;
842: hdf5->groups = NULL;
844: PetscCallHDF5Return(hdf5->dxpl_id, H5Pcreate, (H5P_DATASET_XFER));
846: PetscCall(PetscObjectComposeFunction((PetscObject)v, "PetscViewerFileSetName_C", PetscViewerFileSetName_HDF5));
847: PetscCall(PetscObjectComposeFunction((PetscObject)v, "PetscViewerFileGetName_C", PetscViewerFileGetName_HDF5));
848: PetscCall(PetscObjectComposeFunction((PetscObject)v, "PetscViewerFileSetMode_C", PetscViewerFileSetMode_HDF5));
849: PetscCall(PetscObjectComposeFunction((PetscObject)v, "PetscViewerFileGetMode_C", PetscViewerFileGetMode_HDF5));
850: PetscCall(PetscObjectComposeFunction((PetscObject)v, "PetscViewerHDF5SetBaseDimension2_C", PetscViewerHDF5SetBaseDimension2_HDF5));
851: PetscCall(PetscObjectComposeFunction((PetscObject)v, "PetscViewerHDF5GetBaseDimension2_C", PetscViewerHDF5GetBaseDimension2_HDF5));
852: PetscCall(PetscObjectComposeFunction((PetscObject)v, "PetscViewerHDF5SetSPOutput_C", PetscViewerHDF5SetSPOutput_HDF5));
853: PetscCall(PetscObjectComposeFunction((PetscObject)v, "PetscViewerHDF5SetCollective_C", PetscViewerHDF5SetCollective_HDF5));
854: PetscCall(PetscObjectComposeFunction((PetscObject)v, "PetscViewerHDF5GetCollective_C", PetscViewerHDF5GetCollective_HDF5));
855: PetscCall(PetscObjectComposeFunction((PetscObject)v, "PetscViewerHDF5GetDefaultTimestepping_C", PetscViewerHDF5GetDefaultTimestepping_HDF5));
856: PetscCall(PetscObjectComposeFunction((PetscObject)v, "PetscViewerHDF5SetDefaultTimestepping_C", PetscViewerHDF5SetDefaultTimestepping_HDF5));
857: PetscCall(PetscObjectComposeFunction((PetscObject)v, "PetscViewerHDF5GetCompress_C", PetscViewerHDF5GetCompress_HDF5));
858: PetscCall(PetscObjectComposeFunction((PetscObject)v, "PetscViewerHDF5SetCompress_C", PetscViewerHDF5SetCompress_HDF5));
859: PetscCall(PetscObjectComposeFunction((PetscObject)v, "PetscViewerHDF5WriteGroup_C", PetscViewerHDF5WriteGroup_HDF5));
860: PetscCall(PetscObjectComposeFunction((PetscObject)v, "PetscViewerHDF5PushGroup_C", PetscViewerHDF5PushGroup_HDF5));
861: PetscCall(PetscObjectComposeFunction((PetscObject)v, "PetscViewerHDF5PopGroup_C", PetscViewerHDF5PopGroup_HDF5));
862: PetscCall(PetscObjectComposeFunction((PetscObject)v, "PetscViewerHDF5GetGroup_C", PetscViewerHDF5GetGroup_HDF5));
863: PetscCall(PetscObjectComposeFunction((PetscObject)v, "PetscViewerHDF5PushTimestepping_C", PetscViewerHDF5PushTimestepping_HDF5));
864: PetscCall(PetscObjectComposeFunction((PetscObject)v, "PetscViewerHDF5PopTimestepping_C", PetscViewerHDF5PopTimestepping_HDF5));
865: PetscCall(PetscObjectComposeFunction((PetscObject)v, "PetscViewerHDF5IsTimestepping_C", PetscViewerHDF5IsTimestepping_HDF5));
866: PetscCall(PetscObjectComposeFunction((PetscObject)v, "PetscViewerHDF5IncrementTimestep_C", PetscViewerHDF5IncrementTimestep_HDF5));
867: PetscCall(PetscObjectComposeFunction((PetscObject)v, "PetscViewerHDF5SetTimestep_C", PetscViewerHDF5SetTimestep_HDF5));
868: PetscCall(PetscObjectComposeFunction((PetscObject)v, "PetscViewerHDF5GetTimestep_C", PetscViewerHDF5GetTimestep_HDF5));
869: PetscCall(PetscObjectComposeFunction((PetscObject)v, "PetscViewerHDF5WriteAttribute_C", PetscViewerHDF5WriteAttribute_HDF5));
870: PetscCall(PetscObjectComposeFunction((PetscObject)v, "PetscViewerHDF5ReadAttribute_C", PetscViewerHDF5ReadAttribute_HDF5));
871: PetscCall(PetscObjectComposeFunction((PetscObject)v, "PetscViewerHDF5HasGroup_C", PetscViewerHDF5HasGroup_HDF5));
872: PetscCall(PetscObjectComposeFunction((PetscObject)v, "PetscViewerHDF5HasDataset_C", PetscViewerHDF5HasDataset_HDF5));
873: PetscCall(PetscObjectComposeFunction((PetscObject)v, "PetscViewerHDF5HasAttribute_C", PetscViewerHDF5HasAttribute_HDF5));
874: PetscCall(PetscObjectComposeFunction((PetscObject)v, "PetscViewerHDF5GetSPOutput_C", PetscViewerHDF5GetSPOutput_HDF5));
875: PetscFunctionReturn(PETSC_SUCCESS);
876: }