Actual source code: hdf5v.c
1: #include <petsc/private/viewerhdf5impl.h>
3: static PetscErrorCode PetscViewerHDF5Traverse_Internal(PetscViewer, const char[], PetscBool, PetscBool *, H5O_type_t *);
4: static PetscErrorCode PetscViewerHDF5HasAttribute_Internal(PetscViewer, const char[], const char[], PetscBool *);
5: static PetscErrorCode PetscViewerHDF5GetGroup_Internal(PetscViewer, const char *[]);
7: /*@C
8: PetscViewerHDF5GetGroup - Get the current HDF5 group name (full path), set with `PetscViewerHDF5PushGroup()`/`PetscViewerHDF5PopGroup()`.
10: Not Collective
12: Input Parameters:
13: + viewer - the `PetscViewer` of type `PETSCVIEWERHDF5`
14: - path - (Optional) The path relative to the pushed group
16: Output Parameter:
17: . abspath - The absolute HDF5 path (group)
19: Level: intermediate
21: Notes:
22: If path starts with '/', it is taken as an absolute path overriding currently pushed group, else path is relative to the current pushed group.
23: `NULL` or empty path means the current pushed group.
25: The output abspath is newly allocated so needs to be freed.
27: .seealso: [](sec_viewers), `PETSCVIEWERHDF5`, `PetscViewerHDF5Open()`, `PetscViewerHDF5PushGroup()`, `PetscViewerHDF5PopGroup()`, `PetscViewerHDF5OpenGroup()`, `PetscViewerHDF5WriteGroup()`
28: @*/
29: PetscErrorCode PetscViewerHDF5GetGroup(PetscViewer viewer, const char path[], const char *abspath[])
30: {
31: size_t len;
32: PetscBool relative = PETSC_FALSE;
33: const char *group;
34: char buf[PETSC_MAX_PATH_LEN] = "";
36: PetscFunctionBegin;
38: if (path) PetscAssertPointer(path, 2);
39: PetscAssertPointer(abspath, 3);
40: PetscCall(PetscViewerHDF5GetGroup_Internal(viewer, &group));
41: PetscCall(PetscStrlen(path, &len));
42: relative = (PetscBool)(!len || path[0] != '/');
43: if (relative) {
44: PetscCall(PetscStrncpy(buf, group, sizeof(buf)));
45: if (!group || len) PetscCall(PetscStrlcat(buf, "/", sizeof(buf)));
46: PetscCall(PetscStrlcat(buf, path, sizeof(buf)));
47: PetscCall(PetscStrallocpy(buf, (char **)abspath));
48: } else {
49: PetscCall(PetscStrallocpy(path, (char **)abspath));
50: }
51: PetscFunctionReturn(PETSC_SUCCESS);
52: }
54: static PetscErrorCode PetscViewerHDF5CheckNamedObject_Internal(PetscViewer viewer, PetscObject obj)
55: {
56: PetscBool has;
58: PetscFunctionBegin;
59: PetscCall(PetscViewerHDF5HasObject(viewer, obj, &has));
60: if (!has) {
61: const char *group;
62: PetscCall(PetscViewerHDF5GetGroup(viewer, NULL, &group));
63: SETERRQ(PetscObjectComm((PetscObject)viewer), PETSC_ERR_FILE_UNEXPECTED, "Object (dataset) \"%s\" not stored in group %s", obj->name, group);
64: }
65: PetscFunctionReturn(PETSC_SUCCESS);
66: }
68: static PetscErrorCode PetscViewerSetFromOptions_HDF5(PetscViewer v, PetscOptionItems PetscOptionsObject)
69: {
70: PetscBool flg = PETSC_FALSE, set;
71: PetscViewer_HDF5 *hdf5 = (PetscViewer_HDF5 *)v->data;
73: PetscFunctionBegin;
74: PetscOptionsHeadBegin(PetscOptionsObject, "HDF5 PetscViewer Options");
75: PetscCall(PetscOptionsBool("-viewer_hdf5_base_dimension2", "1d Vectors get 2 dimensions in HDF5", "PetscViewerHDF5SetBaseDimension2", hdf5->basedimension2, &hdf5->basedimension2, NULL));
76: PetscCall(PetscOptionsBool("-viewer_hdf5_sp_output", "Force data to be written in single precision", "PetscViewerHDF5SetSPOutput", hdf5->spoutput, &hdf5->spoutput, NULL));
77: PetscCall(PetscOptionsBool("-viewer_hdf5_collective", "Enable collective transfer mode", "PetscViewerHDF5SetCollective", flg, &flg, &set));
78: if (set) PetscCall(PetscViewerHDF5SetCollective(v, flg));
79: flg = PETSC_FALSE;
80: PetscCall(PetscOptionsBool("-viewer_hdf5_default_timestepping", "Set default timestepping state", "PetscViewerHDF5SetDefaultTimestepping", flg, &flg, &set));
81: if (set) PetscCall(PetscViewerHDF5SetDefaultTimestepping(v, flg));
82: PetscCall(PetscOptionsBool("-viewer_hdf5_compress", "Enable compression", "PetscViewerHDF5SetCompress", hdf5->compress, &hdf5->compress, NULL));
83: PetscOptionsHeadEnd();
84: PetscFunctionReturn(PETSC_SUCCESS);
85: }
87: static PetscErrorCode PetscViewerView_HDF5(PetscViewer v, PetscViewer viewer)
88: {
89: PetscViewer_HDF5 *hdf5 = (PetscViewer_HDF5 *)v->data;
90: PetscBool flg;
92: PetscFunctionBegin;
93: if (hdf5->filename) PetscCall(PetscViewerASCIIPrintf(viewer, "Filename: %s\n", hdf5->filename));
94: PetscCall(PetscViewerASCIIPrintf(viewer, "Vectors with blocksize 1 saved as 2D datasets: %s\n", PetscBools[hdf5->basedimension2]));
95: PetscCall(PetscViewerASCIIPrintf(viewer, "Enforce single precision storage: %s\n", PetscBools[hdf5->spoutput]));
96: PetscCall(PetscViewerHDF5GetCollective(v, &flg));
97: PetscCall(PetscViewerASCIIPrintf(viewer, "MPI-IO transfer mode: %s\n", flg ? "collective" : "independent"));
98: PetscCall(PetscViewerASCIIPrintf(viewer, "Default timestepping: %s\n", PetscBools[hdf5->defTimestepping]));
99: PetscCall(PetscViewerASCIIPrintf(viewer, "Compression: %s\n", PetscBools[hdf5->compress]));
100: PetscFunctionReturn(PETSC_SUCCESS);
101: }
103: static PetscErrorCode PetscViewerFileClose_HDF5(PetscViewer viewer)
104: {
105: PetscViewer_HDF5 *hdf5 = (PetscViewer_HDF5 *)viewer->data;
107: PetscFunctionBegin;
108: PetscCall(PetscFree(hdf5->filename));
109: if (hdf5->file_id) PetscCallHDF5(H5Fclose, (hdf5->file_id));
110: PetscFunctionReturn(PETSC_SUCCESS);
111: }
113: static PetscErrorCode PetscViewerFlush_HDF5(PetscViewer viewer)
114: {
115: PetscViewer_HDF5 *hdf5 = (PetscViewer_HDF5 *)viewer->data;
117: PetscFunctionBegin;
118: if (hdf5->file_id) PetscCallHDF5(H5Fflush, (hdf5->file_id, H5F_SCOPE_LOCAL));
119: PetscFunctionReturn(PETSC_SUCCESS);
120: }
122: static PetscErrorCode PetscViewerDestroy_HDF5(PetscViewer viewer)
123: {
124: PetscViewer_HDF5 *hdf5 = (PetscViewer_HDF5 *)viewer->data;
126: PetscFunctionBegin;
127: PetscCallHDF5(H5Pclose, (hdf5->dxpl_id));
128: PetscCall(PetscViewerFileClose_HDF5(viewer));
129: while (hdf5->groups) {
130: PetscViewerHDF5GroupList *tmp = hdf5->groups->next;
132: PetscCall(PetscFree(hdf5->groups->name));
133: PetscCall(PetscFree(hdf5->groups));
134: hdf5->groups = tmp;
135: }
136: PetscCall(PetscFree(hdf5));
137: PetscCall(PetscObjectComposeFunction((PetscObject)viewer, "PetscViewerFileSetName_C", NULL));
138: PetscCall(PetscObjectComposeFunction((PetscObject)viewer, "PetscViewerFileGetName_C", NULL));
139: PetscCall(PetscObjectComposeFunction((PetscObject)viewer, "PetscViewerFileSetMode_C", NULL));
140: PetscCall(PetscObjectComposeFunction((PetscObject)viewer, "PetscViewerFileGetMode_C", NULL));
141: PetscCall(PetscObjectComposeFunction((PetscObject)viewer, "PetscViewerHDF5SetBaseDimension2_C", NULL));
142: PetscCall(PetscObjectComposeFunction((PetscObject)viewer, "PetscViewerHDF5SetSPOutput_C", NULL));
143: PetscCall(PetscObjectComposeFunction((PetscObject)viewer, "PetscViewerHDF5SetCollective_C", NULL));
144: PetscCall(PetscObjectComposeFunction((PetscObject)viewer, "PetscViewerHDF5GetCollective_C", NULL));
145: PetscCall(PetscObjectComposeFunction((PetscObject)viewer, "PetscViewerHDF5GetDefaultTimestepping_C", NULL));
146: PetscCall(PetscObjectComposeFunction((PetscObject)viewer, "PetscViewerHDF5SetDefaultTimestepping_C", NULL));
147: PetscCall(PetscObjectComposeFunction((PetscObject)viewer, "PetscViewerHDF5SetCompress_C", NULL));
148: PetscCall(PetscObjectComposeFunction((PetscObject)viewer, "PetscViewerHDF5GetCompress_C", NULL));
149: PetscFunctionReturn(PETSC_SUCCESS);
150: }
152: static PetscErrorCode PetscViewerFileSetMode_HDF5(PetscViewer viewer, PetscFileMode type)
153: {
154: PetscViewer_HDF5 *hdf5 = (PetscViewer_HDF5 *)viewer->data;
156: PetscFunctionBegin;
157: hdf5->btype = type;
158: PetscFunctionReturn(PETSC_SUCCESS);
159: }
161: static PetscErrorCode PetscViewerFileGetMode_HDF5(PetscViewer viewer, PetscFileMode *type)
162: {
163: PetscViewer_HDF5 *hdf5 = (PetscViewer_HDF5 *)viewer->data;
165: PetscFunctionBegin;
166: *type = hdf5->btype;
167: PetscFunctionReturn(PETSC_SUCCESS);
168: }
170: static PetscErrorCode PetscViewerHDF5SetBaseDimension2_HDF5(PetscViewer viewer, PetscBool flg)
171: {
172: PetscViewer_HDF5 *hdf5 = (PetscViewer_HDF5 *)viewer->data;
174: PetscFunctionBegin;
175: hdf5->basedimension2 = flg;
176: PetscFunctionReturn(PETSC_SUCCESS);
177: }
179: /*@
180: PetscViewerHDF5SetBaseDimension2 - Vectors of 1 dimension (i.e. bs/dof is 1) will be saved in the HDF5 file with a
181: dimension of 2.
183: Logically Collective
185: Input Parameters:
186: + viewer - the `PetscViewer`; if it is a `PETSCVIEWERHDF5` then this command is ignored
187: - flg - if `PETSC_TRUE` the vector will always have at least a dimension of 2 even if that first dimension is of size 1
189: Options Database Key:
190: . -viewer_hdf5_base_dimension2 - turns on (true) or off (false) using a dimension of 2 in the HDF5 file even if the bs/dof of the vector is 1
192: Level: intermediate
194: Note:
195: Setting this option allegedly makes code that reads the HDF5 in easier since they do not have a "special case" of a bs/dof
196: of one when the dimension is lower. Others think the option is crazy.
198: .seealso: [](sec_viewers), `PETSCVIEWERHDF5`, `PetscViewerFileSetMode()`, `PetscViewerCreate()`, `PetscViewerSetType()`, `PetscViewerBinaryOpen()`
199: @*/
200: PetscErrorCode PetscViewerHDF5SetBaseDimension2(PetscViewer viewer, PetscBool flg)
201: {
202: PetscFunctionBegin;
204: PetscTryMethod(viewer, "PetscViewerHDF5SetBaseDimension2_C", (PetscViewer, PetscBool), (viewer, flg));
205: PetscFunctionReturn(PETSC_SUCCESS);
206: }
208: /*@
209: PetscViewerHDF5GetBaseDimension2 - Vectors of 1 dimension (i.e. bs/dof is 1) will be saved in the HDF5 file with a
210: dimension of 2.
212: Logically Collective
214: Input Parameter:
215: . viewer - the `PetscViewer`, must be `PETSCVIEWERHDF5`
217: Output Parameter:
218: . flg - if `PETSC_TRUE` the vector will always have at least a dimension of 2 even if that first dimension is of size 1
220: Level: intermediate
222: Note:
223: Setting this option allegedly makes code that reads the HDF5 in easier since they do not have a "special case" of a bs/dof
224: of one when the dimension is lower. Others think the option is crazy.
226: .seealso: [](sec_viewers), `PETSCVIEWERHDF5`, `PetscViewerFileSetMode()`, `PetscViewerCreate()`, `PetscViewerSetType()`, `PetscViewerBinaryOpen()`
227: @*/
228: PetscErrorCode PetscViewerHDF5GetBaseDimension2(PetscViewer viewer, PetscBool *flg)
229: {
230: PetscViewer_HDF5 *hdf5 = (PetscViewer_HDF5 *)viewer->data;
232: PetscFunctionBegin;
234: *flg = hdf5->basedimension2;
235: PetscFunctionReturn(PETSC_SUCCESS);
236: }
238: static PetscErrorCode PetscViewerHDF5SetSPOutput_HDF5(PetscViewer viewer, PetscBool flg)
239: {
240: PetscViewer_HDF5 *hdf5 = (PetscViewer_HDF5 *)viewer->data;
242: PetscFunctionBegin;
243: hdf5->spoutput = flg;
244: PetscFunctionReturn(PETSC_SUCCESS);
245: }
247: /*@
248: PetscViewerHDF5SetSPOutput - Data is written to disk in single precision even if PETSc is
249: compiled with double precision `PetscReal`.
251: Logically Collective
253: Input Parameters:
254: + viewer - the PetscViewer; if it is a `PETSCVIEWERHDF5` then this command is ignored
255: - flg - if `PETSC_TRUE` the data will be written to disk with single precision
257: Options Database Key:
258: . -viewer_hdf5_sp_output - turns on (true) or off (false) output in single precision
260: Level: intermediate
262: Note:
263: Setting this option does not make any difference if PETSc is compiled with single precision
264: in the first place. It does not affect reading datasets (HDF5 handle this internally).
266: .seealso: [](sec_viewers), `PETSCVIEWERHDF5`, `PetscViewerFileSetMode()`, `PetscViewerCreate()`, `PetscViewerSetType()`, `PetscViewerBinaryOpen()`,
267: `PetscReal`, `PetscViewerHDF5GetSPOutput()`
268: @*/
269: PetscErrorCode PetscViewerHDF5SetSPOutput(PetscViewer viewer, PetscBool flg)
270: {
271: PetscFunctionBegin;
273: PetscTryMethod(viewer, "PetscViewerHDF5SetSPOutput_C", (PetscViewer, PetscBool), (viewer, flg));
274: PetscFunctionReturn(PETSC_SUCCESS);
275: }
277: /*@
278: PetscViewerHDF5GetSPOutput - Data is written to disk in single precision even if PETSc is
279: compiled with double precision `PetscReal`.
281: Logically Collective
283: Input Parameter:
284: . viewer - the PetscViewer, must be of type `PETSCVIEWERHDF5`
286: Output Parameter:
287: . flg - if `PETSC_TRUE` the data will be written to disk with single precision
289: Level: intermediate
291: .seealso: [](sec_viewers), `PetscViewerFileSetMode()`, `PetscViewerCreate()`, `PetscViewerSetType()`, `PetscViewerBinaryOpen()`,
292: `PetscReal`, `PetscViewerHDF5SetSPOutput()`
293: @*/
294: PetscErrorCode PetscViewerHDF5GetSPOutput(PetscViewer viewer, PetscBool *flg)
295: {
296: PetscViewer_HDF5 *hdf5 = (PetscViewer_HDF5 *)viewer->data;
298: PetscFunctionBegin;
300: *flg = hdf5->spoutput;
301: PetscFunctionReturn(PETSC_SUCCESS);
302: }
304: static PetscErrorCode PetscViewerHDF5SetCollective_HDF5(PetscViewer viewer, PetscBool flg)
305: {
306: PetscFunctionBegin;
307: /* H5FD_MPIO_COLLECTIVE is wrong in hdf5 1.10.2, and is the same as H5FD_MPIO_INDEPENDENT in earlier versions
308: - see e.g. https://gitlab.cosma.dur.ac.uk/swift/swiftsim/issues/431 */
309: #if H5_VERSION_GE(1, 10, 3) && defined(H5_HAVE_PARALLEL)
310: {
311: PetscViewer_HDF5 *hdf5 = (PetscViewer_HDF5 *)viewer->data;
312: PetscCallHDF5(H5Pset_dxpl_mpio, (hdf5->dxpl_id, flg ? H5FD_MPIO_COLLECTIVE : H5FD_MPIO_INDEPENDENT));
313: }
314: #else
315: 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"));
316: #endif
317: PetscFunctionReturn(PETSC_SUCCESS);
318: }
320: /*@
321: PetscViewerHDF5SetCollective - Use collective MPI-IO transfer mode for HDF5 reads and writes.
323: Logically Collective; flg must contain common value
325: Input Parameters:
326: + viewer - the `PetscViewer`; if it is not `PETSCVIEWERHDF5` then this command is ignored
327: - flg - `PETSC_TRUE` for collective mode; `PETSC_FALSE` for independent mode (default)
329: Options Database Key:
330: . -viewer_hdf5_collective - turns on (true) or off (false) collective transfers
332: Level: intermediate
334: Note:
335: Collective mode gives the MPI-IO layer underneath HDF5 a chance to do some additional collective optimizations and hence can perform better.
336: However, this works correctly only since HDF5 1.10.3 and if HDF5 is installed for MPI; hence, we ignore this setting for older versions.
338: Developer Notes:
339: In the HDF5 layer, `PETSC_TRUE` / `PETSC_FALSE` means `H5Pset_dxpl_mpio()` is called with `H5FD_MPIO_COLLECTIVE` / `H5FD_MPIO_INDEPENDENT`, respectively.
340: This in turn means use of MPI_File_{read,write}_all / MPI_File_{read,write} in the MPI-IO layer, respectively.
341: See HDF5 documentation and MPI-IO documentation for details.
343: .seealso: [](sec_viewers), `PETSCVIEWERHDF5`, `PetscViewerHDF5GetCollective()`, `PetscViewerCreate()`, `PetscViewerSetType()`, `PetscViewerHDF5Open()`
344: @*/
345: PetscErrorCode PetscViewerHDF5SetCollective(PetscViewer viewer, PetscBool flg)
346: {
347: PetscFunctionBegin;
350: PetscTryMethod(viewer, "PetscViewerHDF5SetCollective_C", (PetscViewer, PetscBool), (viewer, flg));
351: PetscFunctionReturn(PETSC_SUCCESS);
352: }
354: static PetscErrorCode PetscViewerHDF5GetCollective_HDF5(PetscViewer viewer, PetscBool *flg)
355: {
356: #if defined(H5_HAVE_PARALLEL)
357: PetscViewer_HDF5 *hdf5 = (PetscViewer_HDF5 *)viewer->data;
358: H5FD_mpio_xfer_t mode;
359: #endif
361: PetscFunctionBegin;
362: #if !defined(H5_HAVE_PARALLEL)
363: *flg = PETSC_FALSE;
364: #else
365: PetscCallHDF5(H5Pget_dxpl_mpio, (hdf5->dxpl_id, &mode));
366: *flg = (mode == H5FD_MPIO_COLLECTIVE) ? PETSC_TRUE : PETSC_FALSE;
367: #endif
368: PetscFunctionReturn(PETSC_SUCCESS);
369: }
371: /*@
372: PetscViewerHDF5GetCollective - Return flag whether collective MPI-IO transfer mode is used for HDF5 reads and writes.
374: Not Collective
376: Input Parameter:
377: . viewer - the `PETSCVIEWERHDF5` `PetscViewer`
379: Output Parameter:
380: . flg - the flag
382: Level: intermediate
384: Note:
385: This setting works correctly only since HDF5 1.10.3 and if HDF5 was installed for MPI. For older versions, `PETSC_FALSE` will be always returned.
386: For more details, see `PetscViewerHDF5SetCollective()`.
388: .seealso: [](sec_viewers), `PETSCVIEWERHDF5`, `PetscViewerHDF5SetCollective()`, `PetscViewerCreate()`, `PetscViewerSetType()`, `PetscViewerHDF5Open()`
389: @*/
390: PetscErrorCode PetscViewerHDF5GetCollective(PetscViewer viewer, PetscBool *flg)
391: {
392: PetscFunctionBegin;
394: PetscAssertPointer(flg, 2);
396: PetscUseMethod(viewer, "PetscViewerHDF5GetCollective_C", (PetscViewer, PetscBool *), (viewer, flg));
397: PetscFunctionReturn(PETSC_SUCCESS);
398: }
400: static PetscErrorCode PetscViewerFileSetName_HDF5(PetscViewer viewer, const char name[])
401: {
402: PetscViewer_HDF5 *hdf5 = (PetscViewer_HDF5 *)viewer->data;
403: hid_t plist_id;
405: PetscFunctionBegin;
406: if (hdf5->file_id) PetscCallHDF5(H5Fclose, (hdf5->file_id));
407: if (hdf5->filename) PetscCall(PetscFree(hdf5->filename));
408: PetscCall(PetscStrallocpy(name, &hdf5->filename));
409: /* Set up file access property list with parallel I/O access */
410: PetscCallHDF5Return(plist_id, H5Pcreate, (H5P_FILE_ACCESS));
411: #if defined(H5_HAVE_PARALLEL)
412: PetscCallHDF5(H5Pset_fapl_mpio, (plist_id, PetscObjectComm((PetscObject)viewer), MPI_INFO_NULL));
413: #endif
414: /* Create or open the file collectively */
415: switch (hdf5->btype) {
416: case FILE_MODE_READ:
417: if (PetscDefined(USE_DEBUG)) {
418: PetscMPIInt rank;
419: PetscBool flg;
421: PetscCallMPI(MPI_Comm_rank(PetscObjectComm((PetscObject)viewer), &rank));
422: if (rank == 0) {
423: PetscCall(PetscTestFile(hdf5->filename, 'r', &flg));
424: PetscCheck(flg, PETSC_COMM_SELF, PETSC_ERR_FILE_OPEN, "File %s requested for reading does not exist", hdf5->filename);
425: }
426: PetscCallMPI(MPI_Barrier(PetscObjectComm((PetscObject)viewer)));
427: }
428: PetscCallHDF5Return(hdf5->file_id, H5Fopen, (name, H5F_ACC_RDONLY, plist_id));
429: break;
430: case FILE_MODE_APPEND:
431: case FILE_MODE_UPDATE: {
432: PetscBool flg;
433: PetscCall(PetscTestFile(hdf5->filename, 'r', &flg));
434: if (flg) PetscCallHDF5Return(hdf5->file_id, H5Fopen, (name, H5F_ACC_RDWR, plist_id));
435: else PetscCallHDF5Return(hdf5->file_id, H5Fcreate, (name, H5F_ACC_EXCL, H5P_DEFAULT, plist_id));
436: break;
437: }
438: case FILE_MODE_WRITE:
439: PetscCallHDF5Return(hdf5->file_id, H5Fcreate, (name, H5F_ACC_TRUNC, H5P_DEFAULT, plist_id));
440: break;
441: case FILE_MODE_UNDEFINED:
442: SETERRQ(PetscObjectComm((PetscObject)viewer), PETSC_ERR_ORDER, "Must call PetscViewerFileSetMode() before PetscViewerFileSetName()");
443: default:
444: SETERRQ(PetscObjectComm((PetscObject)viewer), PETSC_ERR_SUP, "Unsupported file mode %s", PetscFileModes[hdf5->btype]);
445: }
446: PetscCheck(hdf5->file_id >= 0, PETSC_COMM_SELF, PETSC_ERR_LIB, "H5Fcreate failed for %s", name);
447: PetscCallHDF5(H5Pclose, (plist_id));
448: PetscCall(PetscViewerHDF5ResetAttachedDMPlexStorageVersion(viewer));
449: PetscFunctionReturn(PETSC_SUCCESS);
450: }
452: static PetscErrorCode PetscViewerFileGetName_HDF5(PetscViewer viewer, const char **name)
453: {
454: PetscViewer_HDF5 *vhdf5 = (PetscViewer_HDF5 *)viewer->data;
456: PetscFunctionBegin;
457: *name = vhdf5->filename;
458: PetscFunctionReturn(PETSC_SUCCESS);
459: }
461: static PetscErrorCode PetscViewerSetUp_HDF5(PetscViewer viewer)
462: {
463: /*
464: PetscViewer_HDF5 *hdf5 = (PetscViewer_HDF5*) viewer->data;
465: */
467: PetscFunctionBegin;
468: PetscFunctionReturn(PETSC_SUCCESS);
469: }
471: static PetscErrorCode PetscViewerHDF5SetDefaultTimestepping_HDF5(PetscViewer viewer, PetscBool flg)
472: {
473: PetscViewer_HDF5 *hdf5 = (PetscViewer_HDF5 *)viewer->data;
475: PetscFunctionBegin;
476: hdf5->defTimestepping = flg;
477: PetscFunctionReturn(PETSC_SUCCESS);
478: }
480: static PetscErrorCode PetscViewerHDF5GetDefaultTimestepping_HDF5(PetscViewer viewer, PetscBool *flg)
481: {
482: PetscViewer_HDF5 *hdf5 = (PetscViewer_HDF5 *)viewer->data;
484: PetscFunctionBegin;
485: *flg = hdf5->defTimestepping;
486: PetscFunctionReturn(PETSC_SUCCESS);
487: }
489: /*@
490: PetscViewerHDF5SetDefaultTimestepping - Set the flag for default timestepping
492: Logically Collective
494: Input Parameters:
495: + viewer - the `PetscViewer`; if it is not `PETSCVIEWERHDF5` then this command is ignored
496: - flg - if `PETSC_TRUE` we will assume that timestepping is on
498: Options Database Key:
499: . -viewer_hdf5_default_timestepping - turns on (true) or off (false) default timestepping
501: Level: intermediate
503: Note:
504: If the timestepping attribute is not found for an object, then the default timestepping is used
506: .seealso: [](sec_viewers), `PETSCVIEWERHDF5`, `PetscViewerHDF5GetDefaultTimestepping()`, `PetscViewerHDF5PushTimestepping()`, `PetscViewerHDF5GetTimestep()`
507: @*/
508: PetscErrorCode PetscViewerHDF5SetDefaultTimestepping(PetscViewer viewer, PetscBool flg)
509: {
510: PetscFunctionBegin;
512: PetscTryMethod(viewer, "PetscViewerHDF5SetDefaultTimestepping_C", (PetscViewer, PetscBool), (viewer, flg));
513: PetscFunctionReturn(PETSC_SUCCESS);
514: }
516: /*@
517: PetscViewerHDF5GetDefaultTimestepping - Get the flag for default timestepping
519: Not Collective
521: Input Parameter:
522: . viewer - the `PetscViewer` of type `PETSCVIEWERHDF5`
524: Output Parameter:
525: . flg - if `PETSC_TRUE` we will assume that timestepping is on
527: Level: intermediate
529: .seealso: [](sec_viewers), `PETSCVIEWERHDF5`, `PetscViewerHDF5SetDefaultTimestepping()`, `PetscViewerHDF5PushTimestepping()`, `PetscViewerHDF5GetTimestep()`
530: @*/
531: PetscErrorCode PetscViewerHDF5GetDefaultTimestepping(PetscViewer viewer, PetscBool *flg)
532: {
533: PetscFunctionBegin;
535: PetscUseMethod(viewer, "PetscViewerHDF5GetDefaultTimestepping_C", (PetscViewer, PetscBool *), (viewer, flg));
536: PetscFunctionReturn(PETSC_SUCCESS);
537: }
539: static PetscErrorCode PetscViewerHDF5SetCompress_HDF5(PetscViewer viewer, PetscBool flg)
540: {
541: PetscViewer_HDF5 *hdf5 = (PetscViewer_HDF5 *)viewer->data;
543: PetscFunctionBegin;
544: hdf5->compress = flg;
545: PetscFunctionReturn(PETSC_SUCCESS);
546: }
548: static PetscErrorCode PetscViewerHDF5GetCompress_HDF5(PetscViewer viewer, PetscBool *flg)
549: {
550: PetscViewer_HDF5 *hdf5 = (PetscViewer_HDF5 *)viewer->data;
552: PetscFunctionBegin;
553: *flg = hdf5->compress;
554: PetscFunctionReturn(PETSC_SUCCESS);
555: }
557: /*@
558: PetscViewerHDF5SetCompress - Set the flag for compression
560: Logically Collective
562: Input Parameters:
563: + viewer - the `PetscViewer`; if it is not `PETSCVIEWERHDF5` then this command is ignored
564: - flg - if `PETSC_TRUE` we will turn on compression
566: Options Database Key:
567: . -viewer_hdf5_compress - turns on (true) or off (false) compression
569: Level: intermediate
571: .seealso: [](sec_viewers), `PETSCVIEWERHDF5`, `PetscViewerHDF5GetCompress()`
572: @*/
573: PetscErrorCode PetscViewerHDF5SetCompress(PetscViewer viewer, PetscBool flg)
574: {
575: PetscFunctionBegin;
577: PetscTryMethod(viewer, "PetscViewerHDF5SetCompress_C", (PetscViewer, PetscBool), (viewer, flg));
578: PetscFunctionReturn(PETSC_SUCCESS);
579: }
581: /*@
582: PetscViewerHDF5GetCompress - Get the flag for compression
584: Not Collective
586: Input Parameter:
587: . viewer - the `PetscViewer` of type `PETSCVIEWERHDF5`
589: Output Parameter:
590: . flg - if `PETSC_TRUE` we will turn on compression
592: Level: intermediate
594: .seealso: [](sec_viewers), `PETSCVIEWERHDF5`, `PetscViewerHDF5SetCompress()`
595: @*/
596: PetscErrorCode PetscViewerHDF5GetCompress(PetscViewer viewer, PetscBool *flg)
597: {
598: PetscFunctionBegin;
600: PetscUseMethod(viewer, "PetscViewerHDF5GetCompress_C", (PetscViewer, PetscBool *), (viewer, flg));
601: PetscFunctionReturn(PETSC_SUCCESS);
602: }
604: /*MC
605: PETSCVIEWERHDF5 - A viewer that writes to an HDF5 file
607: Level: beginner
609: .seealso: [](sec_viewers), `PetscViewerHDF5Open()`, `PetscViewerStringSPrintf()`, `PetscViewerSocketOpen()`, `PetscViewerDrawOpen()`, `PETSCVIEWERSOCKET`,
610: `PetscViewerCreate()`, `PetscViewerASCIIOpen()`, `PetscViewerBinaryOpen()`, `PETSCVIEWERBINARY`, `PETSCVIEWERDRAW`, `PETSCVIEWERSTRING`,
611: `PetscViewerMatlabOpen()`, `VecView()`, `DMView()`, `PetscViewerMatlabPutArray()`, `PETSCVIEWERASCII`, `PETSCVIEWERMATLAB`,
612: `PetscViewerFileSetName()`, `PetscViewerFileSetMode()`, `PetscViewerFormat`, `PetscViewerType`, `PetscViewerSetType()`
613: M*/
615: PETSC_EXTERN PetscErrorCode PetscViewerCreate_HDF5(PetscViewer v)
616: {
617: PetscViewer_HDF5 *hdf5;
619: PetscFunctionBegin;
620: #if !defined(H5_HAVE_PARALLEL)
621: {
622: PetscMPIInt size;
623: PetscCallMPI(MPI_Comm_size(PetscObjectComm((PetscObject)v), &size));
624: 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)");
625: }
626: #endif
628: PetscCall(PetscNew(&hdf5));
630: v->data = (void *)hdf5;
631: v->ops->destroy = PetscViewerDestroy_HDF5;
632: v->ops->setfromoptions = PetscViewerSetFromOptions_HDF5;
633: v->ops->setup = PetscViewerSetUp_HDF5;
634: v->ops->view = PetscViewerView_HDF5;
635: v->ops->flush = PetscViewerFlush_HDF5;
636: hdf5->btype = FILE_MODE_UNDEFINED;
637: hdf5->filename = NULL;
638: hdf5->timestep = -1;
639: hdf5->groups = NULL;
641: PetscCallHDF5Return(hdf5->dxpl_id, H5Pcreate, (H5P_DATASET_XFER));
643: PetscCall(PetscObjectComposeFunction((PetscObject)v, "PetscViewerFileSetName_C", PetscViewerFileSetName_HDF5));
644: PetscCall(PetscObjectComposeFunction((PetscObject)v, "PetscViewerFileGetName_C", PetscViewerFileGetName_HDF5));
645: PetscCall(PetscObjectComposeFunction((PetscObject)v, "PetscViewerFileSetMode_C", PetscViewerFileSetMode_HDF5));
646: PetscCall(PetscObjectComposeFunction((PetscObject)v, "PetscViewerFileGetMode_C", PetscViewerFileGetMode_HDF5));
647: PetscCall(PetscObjectComposeFunction((PetscObject)v, "PetscViewerHDF5SetBaseDimension2_C", PetscViewerHDF5SetBaseDimension2_HDF5));
648: PetscCall(PetscObjectComposeFunction((PetscObject)v, "PetscViewerHDF5SetSPOutput_C", PetscViewerHDF5SetSPOutput_HDF5));
649: PetscCall(PetscObjectComposeFunction((PetscObject)v, "PetscViewerHDF5SetCollective_C", PetscViewerHDF5SetCollective_HDF5));
650: PetscCall(PetscObjectComposeFunction((PetscObject)v, "PetscViewerHDF5GetCollective_C", PetscViewerHDF5GetCollective_HDF5));
651: PetscCall(PetscObjectComposeFunction((PetscObject)v, "PetscViewerHDF5GetDefaultTimestepping_C", PetscViewerHDF5GetDefaultTimestepping_HDF5));
652: PetscCall(PetscObjectComposeFunction((PetscObject)v, "PetscViewerHDF5SetDefaultTimestepping_C", PetscViewerHDF5SetDefaultTimestepping_HDF5));
653: PetscCall(PetscObjectComposeFunction((PetscObject)v, "PetscViewerHDF5GetCompress_C", PetscViewerHDF5GetCompress_HDF5));
654: PetscCall(PetscObjectComposeFunction((PetscObject)v, "PetscViewerHDF5SetCompress_C", PetscViewerHDF5SetCompress_HDF5));
655: PetscFunctionReturn(PETSC_SUCCESS);
656: }
658: /*@C
659: PetscViewerHDF5Open - Opens a file for HDF5 input/output as a `PETSCVIEWERHDF5` `PetscViewer`
661: Collective
663: Input Parameters:
664: + comm - MPI communicator
665: . name - name of file
666: - type - type of file
668: Output Parameter:
669: . hdf5v - `PetscViewer` for HDF5 input/output to use with the specified file
671: Options Database Keys:
672: + -viewer_hdf5_base_dimension2 - turns on (true) or off (false) using a dimension of 2 in the HDF5 file even if the bs/dof of the vector is 1
673: - -viewer_hdf5_sp_output - forces (if true) the viewer to write data in single precision independent on the precision of PetscReal
675: Level: beginner
677: Notes:
678: Reading is always available, regardless of the mode. Available modes are
679: .vb
680: FILE_MODE_READ - open existing HDF5 file for read only access, fail if file does not exist [H5Fopen() with H5F_ACC_RDONLY]
681: FILE_MODE_WRITE - if file exists, fully overwrite it, else create new HDF5 file [H5FcreateH5Fcreate() with H5F_ACC_TRUNC]
682: FILE_MODE_APPEND - if file exists, keep existing contents [H5Fopen() with H5F_ACC_RDWR], else create new HDF5 file [H5FcreateH5Fcreate() with H5F_ACC_EXCL]
683: FILE_MODE_UPDATE - same as FILE_MODE_APPEND
684: .ve
686: In case of `FILE_MODE_APPEND` / `FILE_MODE_UPDATE`, any stored object (dataset, attribute) can be selectively overwritten if the same fully qualified name (/group/path/to/object) is specified.
688: This PetscViewer should be destroyed with PetscViewerDestroy().
690: .seealso: [](sec_viewers), `PETSCVIEWERHDF5`, `PetscViewerASCIIOpen()`, `PetscViewerPushFormat()`, `PetscViewerDestroy()`, `PetscViewerHDF5SetBaseDimension2()`,
691: `PetscViewerHDF5SetSPOutput()`, `PetscViewerHDF5GetBaseDimension2()`, `VecView()`, `MatView()`, `VecLoad()`,
692: `MatLoad()`, `PetscFileMode`, `PetscViewer`, `PetscViewerSetType()`, `PetscViewerFileSetMode()`, `PetscViewerFileSetName()`
693: @*/
694: PetscErrorCode PetscViewerHDF5Open(MPI_Comm comm, const char name[], PetscFileMode type, PetscViewer *hdf5v)
695: {
696: PetscFunctionBegin;
697: PetscCall(PetscViewerCreate(comm, hdf5v));
698: PetscCall(PetscViewerSetType(*hdf5v, PETSCVIEWERHDF5));
699: PetscCall(PetscViewerFileSetMode(*hdf5v, type));
700: PetscCall(PetscViewerFileSetName(*hdf5v, name));
701: PetscCall(PetscViewerSetFromOptions(*hdf5v));
702: PetscFunctionReturn(PETSC_SUCCESS);
703: }
705: /*@C
706: PetscViewerHDF5GetFileId - Retrieve the file id, this file ID then can be used in direct HDF5 calls
708: Not Collective
710: Input Parameter:
711: . viewer - the `PetscViewer`
713: Output Parameter:
714: . file_id - The file id
716: Level: intermediate
718: .seealso: [](sec_viewers), `PETSCVIEWERHDF5`, `PetscViewerHDF5Open()`
719: @*/
720: PetscErrorCode PetscViewerHDF5GetFileId(PetscViewer viewer, hid_t *file_id)
721: {
722: PetscViewer_HDF5 *hdf5 = (PetscViewer_HDF5 *)viewer->data;
724: PetscFunctionBegin;
726: if (file_id) *file_id = hdf5->file_id;
727: PetscFunctionReturn(PETSC_SUCCESS);
728: }
730: /*@C
731: PetscViewerHDF5PushGroup - Set the current HDF5 group for output
733: Not Collective
735: Input Parameters:
736: + viewer - the `PetscViewer` of type `PETSCVIEWERHDF5`
737: - name - The group name
739: Level: intermediate
741: Notes:
742: This is designed to mnemonically resemble the Unix cd command.
743: .vb
744: If name begins with '/', it is interpreted as an absolute path fully replacing current group, otherwise it is taken as relative to the current group.
745: `NULL`, empty string, or any sequence of all slashes (e.g. "///") is interpreted as the root group "/".
746: "." means the current group is pushed again.
747: .ve
749: Example:
750: Suppose the current group is "/a".
751: .vb
752: If name is `NULL`, empty string, or a sequence of all slashes (e.g. "///"), then the new group will be "/".
753: If name is ".", then the new group will be "/a".
754: If name is "b", then the new group will be "/a/b".
755: If name is "/b", then the new group will be "/b".
756: .ve
758: Developer Notes:
759: The root group "/" is internally stored as `NULL`.
761: .seealso: [](sec_viewers), `PETSCVIEWERHDF5`, `PetscViewerHDF5Open()`, `PetscViewerHDF5PopGroup()`, `PetscViewerHDF5GetGroup()`, `PetscViewerHDF5OpenGroup()`, `PetscViewerHDF5WriteGroup()`
762: @*/
763: PetscErrorCode PetscViewerHDF5PushGroup(PetscViewer viewer, const char name[])
764: {
765: PetscViewer_HDF5 *hdf5 = (PetscViewer_HDF5 *)viewer->data;
766: PetscViewerHDF5GroupList *groupNode;
767: size_t i, len;
768: char buf[PETSC_MAX_PATH_LEN];
769: const char *gname;
771: PetscFunctionBegin;
773: if (name) PetscAssertPointer(name, 2);
774: PetscCall(PetscStrlen(name, &len));
775: gname = NULL;
776: if (len) {
777: if (len == 1 && name[0] == '.') {
778: /* use current name */
779: gname = (hdf5->groups && hdf5->groups->name) ? hdf5->groups->name : NULL;
780: } else if (name[0] == '/') {
781: /* absolute */
782: for (i = 1; i < len; i++) {
783: if (name[i] != '/') {
784: gname = name;
785: break;
786: }
787: }
788: } else {
789: /* relative */
790: const char *parent = (hdf5->groups && hdf5->groups->name) ? hdf5->groups->name : "";
791: PetscCall(PetscSNPrintf(buf, sizeof(buf), "%s/%s", parent, name));
792: gname = buf;
793: }
794: }
795: PetscCall(PetscNew(&groupNode));
796: PetscCall(PetscStrallocpy(gname, (char **)&groupNode->name));
797: groupNode->next = hdf5->groups;
798: hdf5->groups = groupNode;
799: PetscFunctionReturn(PETSC_SUCCESS);
800: }
802: /*@
803: PetscViewerHDF5PopGroup - Return the current HDF5 group for output to the previous value
805: Not Collective
807: Input Parameter:
808: . viewer - the `PetscViewer` of type `PETSCVIEWERHDF5`
810: Level: intermediate
812: .seealso: [](sec_viewers), `PETSCVIEWERHDF5`, `PetscViewerHDF5Open()`, `PetscViewerHDF5PushGroup()`, `PetscViewerHDF5GetGroup()`, `PetscViewerHDF5OpenGroup()`, `PetscViewerHDF5WriteGroup()`
813: @*/
814: PetscErrorCode PetscViewerHDF5PopGroup(PetscViewer viewer)
815: {
816: PetscViewer_HDF5 *hdf5 = (PetscViewer_HDF5 *)viewer->data;
817: PetscViewerHDF5GroupList *groupNode;
819: PetscFunctionBegin;
821: PetscCheck(hdf5->groups, PetscObjectComm((PetscObject)viewer), PETSC_ERR_ARG_WRONGSTATE, "HDF5 group stack is empty, cannot pop");
822: groupNode = hdf5->groups;
823: hdf5->groups = hdf5->groups->next;
824: PetscCall(PetscFree(groupNode->name));
825: PetscCall(PetscFree(groupNode));
826: PetscFunctionReturn(PETSC_SUCCESS);
827: }
829: static PetscErrorCode PetscViewerHDF5GetGroup_Internal(PetscViewer viewer, const char *name[])
830: {
831: PetscViewer_HDF5 *hdf5 = (PetscViewer_HDF5 *)viewer->data;
833: PetscFunctionBegin;
835: PetscAssertPointer(name, 2);
836: if (hdf5->groups) *name = hdf5->groups->name;
837: else *name = NULL;
838: PetscFunctionReturn(PETSC_SUCCESS);
839: }
841: /*@C
842: PetscViewerHDF5OpenGroup - Open the HDF5 group with the name (full path) returned by `PetscViewerHDF5GetGroup()`,
843: and return this group's ID and file ID.
844: If `PetscViewerHDF5GetGroup()` yields NULL, then group ID is file ID.
846: Not Collective
848: Input Parameters:
849: + viewer - the `PetscViewer` of type `PETSCVIEWERHDF5`
850: - path - (Optional) The path relative to the pushed group
852: Output Parameters:
853: + fileId - The HDF5 file ID
854: - groupId - The HDF5 group ID
856: Level: intermediate
858: Note:
859: If path starts with '/', it is taken as an absolute path overriding currently pushed group, else path is relative to the current pushed group.
860: `NULL` or empty path means the current pushed group.
862: If the viewer is writable, the group is created if it doesn't exist yet.
864: .seealso: [](sec_viewers), `PETSCVIEWERHDF5`, `PetscViewerHDF5Open()`, `PetscViewerHDF5PushGroup()`, `PetscViewerHDF5PopGroup()`, `PetscViewerHDF5GetGroup()`, `PetscViewerHDF5WriteGroup()`
865: @*/
866: PetscErrorCode PetscViewerHDF5OpenGroup(PetscViewer viewer, const char path[], hid_t *fileId, hid_t *groupId)
867: {
868: hid_t file_id;
869: H5O_type_t type;
870: const char *fileName = NULL;
871: const char *groupName = NULL;
872: PetscBool writable, has;
874: PetscFunctionBegin;
875: PetscCall(PetscViewerWritable(viewer, &writable));
876: PetscCall(PetscViewerHDF5GetFileId(viewer, &file_id));
877: PetscCall(PetscViewerFileGetName(viewer, &fileName));
878: PetscCall(PetscViewerHDF5GetGroup(viewer, path, &groupName));
879: PetscCall(PetscViewerHDF5Traverse_Internal(viewer, groupName, writable, &has, &type));
880: if (!has) {
881: PetscCheck(writable, PetscObjectComm((PetscObject)viewer), PETSC_ERR_FILE_UNEXPECTED, "Group %s does not exist and file %s is not open for writing", groupName, fileName);
882: SETERRQ(PetscObjectComm((PetscObject)viewer), PETSC_ERR_LIB, "HDF5 failed to create group %s although file %s is open for writing", groupName, fileName);
883: }
884: 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);
885: PetscCallHDF5Return(*groupId, H5Gopen2, (file_id, groupName, H5P_DEFAULT));
886: PetscCall(PetscFree(groupName));
887: *fileId = file_id;
888: PetscFunctionReturn(PETSC_SUCCESS);
889: }
891: /*@C
892: PetscViewerHDF5WriteGroup - Ensure the HDF5 group exists in the HDF5 file
894: Not Collective
896: Input Parameters:
897: + viewer - the `PetscViewer` of type `PETSCVIEWERHDF5`
898: - path - (Optional) The path relative to the pushed group
900: Level: intermediate
902: Note:
903: If path starts with '/', it is taken as an absolute path overriding currently pushed group, else path is relative to the current pushed group.
904: `NULL` or empty path means the current pushed group.
906: This will fail if the viewer is not writable.
908: .seealso: [](sec_viewers), `PETSCVIEWERHDF5`, `PetscViewerHDF5Open()`, `PetscViewerHDF5PushGroup()`, `PetscViewerHDF5PopGroup()`, `PetscViewerHDF5GetGroup()`, `PetscViewerHDF5OpenGroup()`
909: @*/
910: PetscErrorCode PetscViewerHDF5WriteGroup(PetscViewer viewer, const char path[])
911: {
912: hid_t fileId, groupId;
914: PetscFunctionBegin;
915: PetscCall(PetscViewerHDF5OpenGroup(viewer, path, &fileId, &groupId)); // make sure group is actually created
916: PetscCallHDF5(H5Gclose, (groupId));
917: PetscFunctionReturn(PETSC_SUCCESS);
918: }
920: /*@
921: PetscViewerHDF5PushTimestepping - Activate timestepping mode for subsequent HDF5 reading and writing.
923: Not Collective
925: Input Parameter:
926: . viewer - the `PetscViewer` of type `PETSCVIEWERHDF5`
928: Level: intermediate
930: Notes:
931: On first `PetscViewerHDF5PushTimestepping()`, the initial time step is set to 0.
932: Next timesteps can then be set using `PetscViewerHDF5IncrementTimestep()` or `PetscViewerHDF5SetTimestep()`.
933: Current timestep value determines which timestep is read from or written to any dataset on the next HDF5 I/O operation [e.g. `VecView()`].
934: Use `PetscViewerHDF5PopTimestepping()` to deactivate timestepping mode; calling it by the end of the program is NOT mandatory.
935: Current timestep is remembered between `PetscViewerHDF5PopTimestepping()` and the next `PetscViewerHDF5PushTimestepping()`.
937: If a dataset was stored with timestepping, it can be loaded only in the timestepping mode again.
938: Loading a timestepped dataset with timestepping disabled, or vice-versa results in an error.
940: Developer Notes:
941: Timestepped HDF5 dataset has an extra dimension and attribute "timestepping" set to true.
943: .seealso: [](sec_viewers), `PETSCVIEWERHDF5`, `PetscViewerHDF5Open()`, `PetscViewerHDF5PopTimestepping()`, `PetscViewerHDF5IsTimestepping()`, `PetscViewerHDF5SetTimestep()`, `PetscViewerHDF5IncrementTimestep()`, `PetscViewerHDF5GetTimestep()`
944: @*/
945: PetscErrorCode PetscViewerHDF5PushTimestepping(PetscViewer viewer)
946: {
947: PetscViewer_HDF5 *hdf5 = (PetscViewer_HDF5 *)viewer->data;
949: PetscFunctionBegin;
951: PetscCheck(!hdf5->timestepping, PetscObjectComm((PetscObject)viewer), PETSC_ERR_ARG_WRONGSTATE, "Timestepping is already pushed");
952: hdf5->timestepping = PETSC_TRUE;
953: if (hdf5->timestep < 0) hdf5->timestep = 0;
954: PetscFunctionReturn(PETSC_SUCCESS);
955: }
957: /*@
958: PetscViewerHDF5PopTimestepping - Deactivate timestepping mode for subsequent HDF5 reading and writing.
960: Not Collective
962: Input Parameter:
963: . viewer - the `PetscViewer` of type `PETSCVIEWERHDF5`
965: Level: intermediate
967: Note:
968: See `PetscViewerHDF5PushTimestepping()` for details.
970: .seealso: [](sec_viewers), `PETSCVIEWERHDF5`, `PetscViewerHDF5Open()`, `PetscViewerHDF5PushTimestepping()`, `PetscViewerHDF5IsTimestepping()`, `PetscViewerHDF5SetTimestep()`, `PetscViewerHDF5IncrementTimestep()`, `PetscViewerHDF5GetTimestep()`
971: @*/
972: PetscErrorCode PetscViewerHDF5PopTimestepping(PetscViewer viewer)
973: {
974: PetscViewer_HDF5 *hdf5 = (PetscViewer_HDF5 *)viewer->data;
976: PetscFunctionBegin;
978: PetscCheck(hdf5->timestepping, PetscObjectComm((PetscObject)viewer), PETSC_ERR_ARG_WRONGSTATE, "Timestepping has not been pushed yet. Call PetscViewerHDF5PushTimestepping() first");
979: hdf5->timestepping = PETSC_FALSE;
980: PetscFunctionReturn(PETSC_SUCCESS);
981: }
983: /*@
984: PetscViewerHDF5IsTimestepping - Ask the viewer whether it is in timestepping mode currently.
986: Not Collective
988: Input Parameter:
989: . viewer - the `PetscViewer` of type `PETSCVIEWERHDF5`
991: Output Parameter:
992: . flg - is timestepping active?
994: Level: intermediate
996: Note:
997: See `PetscViewerHDF5PushTimestepping()` for details.
999: .seealso: [](sec_viewers), `PETSCVIEWERHDF5`, `PetscViewerHDF5Open()`, `PetscViewerHDF5PushTimestepping()`, `PetscViewerHDF5PopTimestepping()`, `PetscViewerHDF5SetTimestep()`, `PetscViewerHDF5IncrementTimestep()`, `PetscViewerHDF5GetTimestep()`
1000: @*/
1001: PetscErrorCode PetscViewerHDF5IsTimestepping(PetscViewer viewer, PetscBool *flg)
1002: {
1003: PetscViewer_HDF5 *hdf5 = (PetscViewer_HDF5 *)viewer->data;
1005: PetscFunctionBegin;
1007: *flg = hdf5->timestepping;
1008: PetscFunctionReturn(PETSC_SUCCESS);
1009: }
1011: /*@
1012: PetscViewerHDF5IncrementTimestep - Increments current timestep for the HDF5 output. Fields are stacked in time.
1014: Not Collective
1016: Input Parameter:
1017: . viewer - the `PetscViewer` of type `PETSCVIEWERHDF5`
1019: Level: intermediate
1021: Note:
1022: This can be called only if the viewer is in timestepping mode. See `PetscViewerHDF5PushTimestepping()` for details.
1024: .seealso: [](sec_viewers), `PETSCVIEWERHDF5`, `PetscViewerHDF5Open()`, `PetscViewerHDF5PushTimestepping()`, `PetscViewerHDF5SetTimestep()`, `PetscViewerHDF5GetTimestep()`
1025: @*/
1026: PetscErrorCode PetscViewerHDF5IncrementTimestep(PetscViewer viewer)
1027: {
1028: PetscViewer_HDF5 *hdf5 = (PetscViewer_HDF5 *)viewer->data;
1030: PetscFunctionBegin;
1032: PetscCheck(hdf5->timestepping, PetscObjectComm((PetscObject)viewer), PETSC_ERR_ARG_WRONGSTATE, "Timestepping has not been pushed yet. Call PetscViewerHDF5PushTimestepping() first");
1033: ++hdf5->timestep;
1034: PetscFunctionReturn(PETSC_SUCCESS);
1035: }
1037: /*@
1038: PetscViewerHDF5SetTimestep - Set the current timestep for the HDF5 output. Fields are stacked in time.
1040: Logically Collective
1042: Input Parameters:
1043: + viewer - the `PetscViewer` of type `PETSCVIEWERHDF5`
1044: - timestep - The timestep
1046: Level: intermediate
1048: Note:
1049: This can be called only if the viewer is in timestepping mode. See `PetscViewerHDF5PushTimestepping()` for details.
1051: .seealso: [](sec_viewers), `PETSCVIEWERHDF5`, `PetscViewerHDF5Open()`, `PetscViewerHDF5PushTimestepping()`, `PetscViewerHDF5IncrementTimestep()`, `PetscViewerHDF5GetTimestep()`
1052: @*/
1053: PetscErrorCode PetscViewerHDF5SetTimestep(PetscViewer viewer, PetscInt timestep)
1054: {
1055: PetscViewer_HDF5 *hdf5 = (PetscViewer_HDF5 *)viewer->data;
1057: PetscFunctionBegin;
1060: PetscCheck(timestep >= 0, PetscObjectComm((PetscObject)viewer), PETSC_ERR_ARG_WRONGSTATE, "Timestep %" PetscInt_FMT " is negative", timestep);
1061: PetscCheck(hdf5->timestepping, PetscObjectComm((PetscObject)viewer), PETSC_ERR_ARG_WRONGSTATE, "Timestepping has not been pushed yet. Call PetscViewerHDF5PushTimestepping() first");
1062: hdf5->timestep = timestep;
1063: PetscFunctionReturn(PETSC_SUCCESS);
1064: }
1066: /*@
1067: PetscViewerHDF5GetTimestep - Get the current timestep for the HDF5 output. Fields are stacked in time.
1069: Not Collective
1071: Input Parameter:
1072: . viewer - the `PetscViewer` of type `PETSCVIEWERHDF5`
1074: Output Parameter:
1075: . timestep - The timestep
1077: Level: intermediate
1079: Note:
1080: This can be called only if the viewer is in the timestepping mode. See `PetscViewerHDF5PushTimestepping()` for details.
1082: .seealso: [](sec_viewers), `PETSCVIEWERHDF5`, `PetscViewerHDF5Open()`, `PetscViewerHDF5PushTimestepping()`, `PetscViewerHDF5IncrementTimestep()`, `PetscViewerHDF5SetTimestep()`
1083: @*/
1084: PetscErrorCode PetscViewerHDF5GetTimestep(PetscViewer viewer, PetscInt *timestep)
1085: {
1086: PetscViewer_HDF5 *hdf5 = (PetscViewer_HDF5 *)viewer->data;
1088: PetscFunctionBegin;
1090: PetscAssertPointer(timestep, 2);
1091: PetscCheck(hdf5->timestepping, PetscObjectComm((PetscObject)viewer), PETSC_ERR_ARG_WRONGSTATE, "Timestepping has not been pushed yet. Call PetscViewerHDF5PushTimestepping() first");
1092: *timestep = hdf5->timestep;
1093: PetscFunctionReturn(PETSC_SUCCESS);
1094: }
1096: /*@C
1097: PetscDataTypeToHDF5DataType - Converts the PETSc name of a datatype to its HDF5 name.
1099: Not Collective
1101: Input Parameter:
1102: . ptype - the PETSc datatype name (for example `PETSC_DOUBLE`)
1104: Output Parameter:
1105: . htype - the HDF5 datatype
1107: Level: advanced
1109: .seealso: [](sec_viewers), `PetscDataType`, `PetscHDF5DataTypeToPetscDataType()`
1110: @*/
1111: PetscErrorCode PetscDataTypeToHDF5DataType(PetscDataType ptype, hid_t *htype)
1112: {
1113: PetscFunctionBegin;
1114: if (ptype == PETSC_INT)
1115: #if defined(PETSC_USE_64BIT_INDICES)
1116: *htype = H5T_NATIVE_LLONG;
1117: #else
1118: *htype = H5T_NATIVE_INT;
1119: #endif
1120: else if (ptype == PETSC_DOUBLE) *htype = H5T_NATIVE_DOUBLE;
1121: else if (ptype == PETSC_LONG) *htype = H5T_NATIVE_LONG;
1122: else if (ptype == PETSC_SHORT) *htype = H5T_NATIVE_SHORT;
1123: else if (ptype == PETSC_ENUM) *htype = H5T_NATIVE_INT;
1124: else if (ptype == PETSC_BOOL) *htype = H5T_NATIVE_HBOOL;
1125: else if (ptype == PETSC_FLOAT) *htype = H5T_NATIVE_FLOAT;
1126: else if (ptype == PETSC_CHAR) *htype = H5T_NATIVE_CHAR;
1127: else if (ptype == PETSC_BIT_LOGICAL) *htype = H5T_NATIVE_UCHAR;
1128: else if (ptype == PETSC_STRING) *htype = H5Tcopy(H5T_C_S1);
1129: else SETERRQ(PETSC_COMM_SELF, PETSC_ERR_ARG_OUTOFRANGE, "Unsupported PETSc datatype");
1130: PetscFunctionReturn(PETSC_SUCCESS);
1131: }
1133: /*@C
1134: PetscHDF5DataTypeToPetscDataType - Finds the PETSc name of a datatype from its HDF5 name
1136: Not Collective
1138: Input Parameter:
1139: . htype - the HDF5 datatype (for example `H5T_NATIVE_DOUBLE`, ...)
1141: Output Parameter:
1142: . ptype - the PETSc datatype name (for example `PETSC_DOUBLE`)
1144: Level: advanced
1146: .seealso: [](sec_viewers), `PetscDataType`
1147: @*/
1148: PetscErrorCode PetscHDF5DataTypeToPetscDataType(hid_t htype, PetscDataType *ptype)
1149: {
1150: PetscFunctionBegin;
1151: #if defined(PETSC_USE_64BIT_INDICES)
1152: if (htype == H5T_NATIVE_INT) *ptype = PETSC_LONG;
1153: else if (htype == H5T_NATIVE_LLONG) *ptype = PETSC_INT;
1154: #else
1155: if (htype == H5T_NATIVE_INT) *ptype = PETSC_INT;
1156: #endif
1157: else if (htype == H5T_NATIVE_DOUBLE) *ptype = PETSC_DOUBLE;
1158: else if (htype == H5T_NATIVE_LONG) *ptype = PETSC_LONG;
1159: else if (htype == H5T_NATIVE_SHORT) *ptype = PETSC_SHORT;
1160: else if (htype == H5T_NATIVE_HBOOL) *ptype = PETSC_BOOL;
1161: else if (htype == H5T_NATIVE_FLOAT) *ptype = PETSC_FLOAT;
1162: else if (htype == H5T_NATIVE_CHAR) *ptype = PETSC_CHAR;
1163: else if (htype == H5T_NATIVE_UCHAR) *ptype = PETSC_CHAR;
1164: else if (htype == H5T_C_S1) *ptype = PETSC_STRING;
1165: else SETERRQ(PETSC_COMM_SELF, PETSC_ERR_ARG_OUTOFRANGE, "Unsupported HDF5 datatype");
1166: PetscFunctionReturn(PETSC_SUCCESS);
1167: }
1169: /*@C
1170: PetscViewerHDF5WriteAttribute - Write an attribute
1172: Collective
1174: Input Parameters:
1175: + viewer - The `PETSCVIEWERHDF5` viewer
1176: . parent - The parent dataset/group name
1177: . name - The attribute name
1178: . datatype - The attribute type
1179: - value - The attribute value
1181: Level: advanced
1183: Note:
1184: If parent starts with '/', it is taken as an absolute path overriding currently pushed group, else parent is relative to the current pushed group. NULL means the current pushed group.
1186: .seealso: [](sec_viewers), `PETSCVIEWERHDF5`, `PetscViewerHDF5Open()`, `PetscViewerHDF5WriteObjectAttribute()`, `PetscViewerHDF5ReadAttribute()`, `PetscViewerHDF5HasAttribute()`,
1187: `PetscViewerHDF5PushGroup()`, `PetscViewerHDF5PopGroup()`, `PetscViewerHDF5GetGroup()`
1188: @*/
1189: PetscErrorCode PetscViewerHDF5WriteAttribute(PetscViewer viewer, const char parent[], const char name[], PetscDataType datatype, const void *value)
1190: {
1191: const char *parentAbsPath;
1192: hid_t h5, dataspace, obj, attribute, dtype;
1193: PetscBool has;
1195: PetscFunctionBegin;
1197: if (parent) PetscAssertPointer(parent, 2);
1198: PetscAssertPointer(name, 3);
1200: PetscAssertPointer(value, 5);
1201: PetscCall(PetscViewerHDF5GetGroup(viewer, parent, &parentAbsPath));
1202: PetscCall(PetscViewerHDF5Traverse_Internal(viewer, parentAbsPath, PETSC_TRUE, NULL, NULL));
1203: PetscCall(PetscViewerHDF5HasAttribute_Internal(viewer, parentAbsPath, name, &has));
1204: PetscCall(PetscDataTypeToHDF5DataType(datatype, &dtype));
1205: if (datatype == PETSC_STRING) {
1206: size_t len;
1207: PetscCall(PetscStrlen((const char *)value, &len));
1208: PetscCallHDF5(H5Tset_size, (dtype, len + 1));
1209: }
1210: PetscCall(PetscViewerHDF5GetFileId(viewer, &h5));
1211: PetscCallHDF5Return(dataspace, H5Screate, (H5S_SCALAR));
1212: PetscCallHDF5Return(obj, H5Oopen, (h5, parentAbsPath, H5P_DEFAULT));
1213: if (has) {
1214: PetscCallHDF5Return(attribute, H5Aopen_name, (obj, name));
1215: } else {
1216: PetscCallHDF5Return(attribute, H5Acreate2, (obj, name, dtype, dataspace, H5P_DEFAULT, H5P_DEFAULT));
1217: }
1218: PetscCallHDF5(H5Awrite, (attribute, dtype, value));
1219: if (datatype == PETSC_STRING) PetscCallHDF5(H5Tclose, (dtype));
1220: PetscCallHDF5(H5Aclose, (attribute));
1221: PetscCallHDF5(H5Oclose, (obj));
1222: PetscCallHDF5(H5Sclose, (dataspace));
1223: PetscCall(PetscFree(parentAbsPath));
1224: PetscFunctionReturn(PETSC_SUCCESS);
1225: }
1227: /*@C
1228: PetscViewerHDF5WriteObjectAttribute - Write an attribute to the dataset matching the given `PetscObject` by name
1230: Collective
1232: Input Parameters:
1233: + viewer - The `PETSCVIEWERHDF5` viewer
1234: . obj - The object whose name is used to lookup the parent dataset, relative to the current group.
1235: . name - The attribute name
1236: . datatype - The attribute type
1237: - value - The attribute value
1239: Level: advanced
1241: Note:
1242: This fails if the path current_group/object_name doesn't resolve to a dataset (the path doesn't exist or is not a dataset).
1243: You might want to check first if it does using `PetscViewerHDF5HasObject()`.
1245: .seealso: [](sec_viewers), `PETSCVIEWERHDF5`, `PetscViewerHDF5Open()`, `PetscViewerHDF5WriteAttribute()`, `PetscViewerHDF5ReadObjectAttribute()`, `PetscViewerHDF5HasObjectAttribute()`,
1246: `PetscViewerHDF5HasObject()`, `PetscViewerHDF5PushGroup()`, `PetscViewerHDF5PopGroup()`, `PetscViewerHDF5GetGroup()`
1247: @*/
1248: PetscErrorCode PetscViewerHDF5WriteObjectAttribute(PetscViewer viewer, PetscObject obj, const char name[], PetscDataType datatype, const void *value)
1249: {
1250: PetscFunctionBegin;
1253: PetscAssertPointer(name, 3);
1254: PetscAssertPointer(value, 5);
1255: PetscCall(PetscViewerHDF5CheckNamedObject_Internal(viewer, obj));
1256: PetscCall(PetscViewerHDF5WriteAttribute(viewer, obj->name, name, datatype, value));
1257: PetscFunctionReturn(PETSC_SUCCESS);
1258: }
1260: /*@C
1261: PetscViewerHDF5ReadAttribute - Read an attribute
1263: Collective
1265: Input Parameters:
1266: + viewer - The `PETSCVIEWERHDF5` viewer
1267: . parent - The parent dataset/group name
1268: . name - The attribute name
1269: . datatype - The attribute type
1270: - defaultValue - The pointer to the default value
1272: Output Parameter:
1273: . value - The pointer to the read HDF5 attribute value
1275: Level: advanced
1277: Notes:
1278: If defaultValue is `NULL` and the attribute is not found, an error occurs.
1280: If defaultValue is not `NULL` and the attribute is not found, `defaultValue` is copied to value.
1282: The pointers `defaultValue` and value can be the same; for instance
1283: .vb
1284: flg = PETSC_FALSE;
1285: PetscCall(`PetscViewerHDF5ReadAttribute`(viewer,name,"attr",PETSC_BOOL,&flg,&flg));
1286: .ve
1287: is valid, but make sure the default value is initialized.
1289: If the datatype is `PETSC_STRING`, the output string is newly allocated so one must `PetscFree()` it when no longer needed.
1291: If parent starts with '/', it is taken as an absolute path overriding currently pushed group, else parent is relative to the current pushed group. `NULL` means the current pushed group.
1293: .seealso: [](sec_viewers), `PETSCVIEWERHDF5`, `PetscViewerHDF5Open()`, `PetscViewerHDF5ReadObjectAttribute()`, `PetscViewerHDF5WriteAttribute()`, `PetscViewerHDF5HasAttribute()`, `PetscViewerHDF5HasObject()`, `PetscViewerHDF5PushGroup()`, `PetscViewerHDF5PopGroup()`, `PetscViewerHDF5GetGroup()`
1294: @*/
1295: PetscErrorCode PetscViewerHDF5ReadAttribute(PetscViewer viewer, const char parent[], const char name[], PetscDataType datatype, const void *defaultValue, void *value)
1296: {
1297: const char *parentAbsPath;
1298: hid_t h5, obj, attribute, dtype;
1299: PetscBool has;
1301: PetscFunctionBegin;
1303: if (parent) PetscAssertPointer(parent, 2);
1304: PetscAssertPointer(name, 3);
1305: if (defaultValue) PetscAssertPointer(defaultValue, 5);
1306: PetscAssertPointer(value, 6);
1307: PetscCall(PetscDataTypeToHDF5DataType(datatype, &dtype));
1308: PetscCall(PetscViewerHDF5GetGroup(viewer, parent, &parentAbsPath));
1309: PetscCall(PetscViewerHDF5Traverse_Internal(viewer, parentAbsPath, PETSC_FALSE, &has, NULL));
1310: if (has) PetscCall(PetscViewerHDF5HasAttribute_Internal(viewer, parentAbsPath, name, &has));
1311: if (!has) {
1312: if (defaultValue) {
1313: if (defaultValue != value) {
1314: if (datatype == PETSC_STRING) {
1315: PetscCall(PetscStrallocpy(*(char **)defaultValue, (char **)value));
1316: } else {
1317: size_t len;
1318: PetscCallHDF5ReturnNoCheck(len, H5Tget_size, (dtype));
1319: PetscCall(PetscMemcpy(value, defaultValue, len));
1320: }
1321: }
1322: PetscCall(PetscFree(parentAbsPath));
1323: PetscFunctionReturn(PETSC_SUCCESS);
1324: } else SETERRQ(PetscObjectComm((PetscObject)viewer), PETSC_ERR_FILE_UNEXPECTED, "Attribute %s/%s does not exist and default value not provided", parentAbsPath, name);
1325: }
1326: PetscCall(PetscViewerHDF5GetFileId(viewer, &h5));
1327: PetscCallHDF5Return(obj, H5Oopen, (h5, parentAbsPath, H5P_DEFAULT));
1328: PetscCallHDF5Return(attribute, H5Aopen_name, (obj, name));
1329: if (datatype == PETSC_STRING) {
1330: size_t len;
1331: hid_t atype;
1332: PetscCallHDF5Return(atype, H5Aget_type, (attribute));
1333: PetscCallHDF5ReturnNoCheck(len, H5Tget_size, (atype));
1334: PetscCall(PetscMalloc((len + 1) * sizeof(char), value));
1335: PetscCallHDF5(H5Tset_size, (dtype, len + 1));
1336: PetscCallHDF5(H5Aread, (attribute, dtype, *(char **)value));
1337: } else {
1338: PetscCallHDF5(H5Aread, (attribute, dtype, value));
1339: }
1340: PetscCallHDF5(H5Aclose, (attribute));
1341: /* H5Oclose can be used to close groups, datasets, or committed datatypes */
1342: PetscCallHDF5(H5Oclose, (obj));
1343: PetscCall(PetscFree(parentAbsPath));
1344: PetscFunctionReturn(PETSC_SUCCESS);
1345: }
1347: /*@C
1348: PetscViewerHDF5ReadObjectAttribute - Read an attribute from the dataset matching the given `PetscObject` by name
1350: Collective
1352: Input Parameters:
1353: + viewer - The `PETSCVIEWERHDF5` viewer
1354: . obj - The object whose name is used to lookup the parent dataset, relative to the current group.
1355: . name - The attribute name
1356: . datatype - The attribute type
1357: - defaultValue - The default attribute value
1359: Output Parameter:
1360: . value - The attribute value
1362: Level: advanced
1364: Note:
1365: This fails if current_group/object_name doesn't resolve to a dataset (the path doesn't exist or is not a dataset).
1366: You might want to check first if it does using `PetscViewerHDF5HasObject()`.
1368: .seealso: [](sec_viewers), `PETSCVIEWERHDF5`, `PetscViewerHDF5Open()`, `PetscViewerHDF5ReadAttribute()` `PetscViewerHDF5WriteObjectAttribute()`, `PetscViewerHDF5HasObjectAttribute()`, `PetscViewerHDF5PushGroup()`, `PetscViewerHDF5PopGroup()`, `PetscViewerHDF5GetGroup()`
1369: @*/
1370: PetscErrorCode PetscViewerHDF5ReadObjectAttribute(PetscViewer viewer, PetscObject obj, const char name[], PetscDataType datatype, void *defaultValue, void *value)
1371: {
1372: PetscFunctionBegin;
1375: PetscAssertPointer(name, 3);
1376: PetscAssertPointer(value, 6);
1377: PetscCall(PetscViewerHDF5CheckNamedObject_Internal(viewer, obj));
1378: PetscCall(PetscViewerHDF5ReadAttribute(viewer, obj->name, name, datatype, defaultValue, value));
1379: PetscFunctionReturn(PETSC_SUCCESS);
1380: }
1382: static PetscErrorCode PetscViewerHDF5Traverse_Inner_Internal(hid_t h5, const char name[], PetscBool createGroup, PetscBool *exists_)
1383: {
1384: htri_t exists;
1385: hid_t group;
1387: PetscFunctionBegin;
1388: PetscCallHDF5Return(exists, H5Lexists, (h5, name, H5P_DEFAULT));
1389: if (exists) PetscCallHDF5Return(exists, H5Oexists_by_name, (h5, name, H5P_DEFAULT));
1390: if (!exists && createGroup) {
1391: PetscCallHDF5Return(group, H5Gcreate2, (h5, name, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT));
1392: PetscCallHDF5(H5Gclose, (group));
1393: exists = PETSC_TRUE;
1394: }
1395: *exists_ = (PetscBool)exists;
1396: PetscFunctionReturn(PETSC_SUCCESS);
1397: }
1399: static PetscErrorCode PetscViewerHDF5Traverse_Internal(PetscViewer viewer, const char name[], PetscBool createGroup, PetscBool *has, H5O_type_t *otype)
1400: {
1401: const char rootGroupName[] = "/";
1402: hid_t h5;
1403: PetscBool exists = PETSC_FALSE;
1404: PetscInt i;
1405: int n;
1406: char **hierarchy;
1407: char buf[PETSC_MAX_PATH_LEN] = "";
1409: PetscFunctionBegin;
1411: if (name) PetscAssertPointer(name, 2);
1412: else name = rootGroupName;
1413: if (has) {
1414: PetscAssertPointer(has, 4);
1415: *has = PETSC_FALSE;
1416: }
1417: if (otype) {
1418: PetscAssertPointer(otype, 5);
1419: *otype = H5O_TYPE_UNKNOWN;
1420: }
1421: PetscCall(PetscViewerHDF5GetFileId(viewer, &h5));
1423: /*
1424: Unfortunately, H5Oexists_by_name() fails if any object in hierarchy is missing.
1425: Hence, each of them needs to be tested separately:
1426: 1) whether it's a valid link
1427: 2) whether this link resolves to an object
1428: See H5Oexists_by_name() documentation.
1429: */
1430: PetscCall(PetscStrToArray(name, '/', &n, &hierarchy));
1431: if (!n) {
1432: /* Assume group "/" always exists in accordance with HDF5 >= 1.10.0. See H5Lexists() documentation. */
1433: if (has) *has = PETSC_TRUE;
1434: if (otype) *otype = H5O_TYPE_GROUP;
1435: PetscCall(PetscStrToArrayDestroy(n, hierarchy));
1436: PetscFunctionReturn(PETSC_SUCCESS);
1437: }
1438: for (i = 0; i < n; i++) {
1439: PetscCall(PetscStrlcat(buf, "/", sizeof(buf)));
1440: PetscCall(PetscStrlcat(buf, hierarchy[i], sizeof(buf)));
1441: PetscCall(PetscViewerHDF5Traverse_Inner_Internal(h5, buf, createGroup, &exists));
1442: if (!exists) break;
1443: }
1444: PetscCall(PetscStrToArrayDestroy(n, hierarchy));
1446: /* If the object exists, get its type */
1447: if (exists && otype) {
1448: H5O_info_t info;
1450: /* We could use H5Iget_type() here but that would require opening the object. This way we only need its name. */
1451: PetscCallHDF5(H5Oget_info_by_name, (h5, name, &info, H5P_DEFAULT));
1452: *otype = info.type;
1453: }
1454: if (has) *has = exists;
1455: PetscFunctionReturn(PETSC_SUCCESS);
1456: }
1458: /*@C
1459: PetscViewerHDF5HasGroup - Check whether the current (pushed) group exists in the HDF5 file
1461: Collective
1463: Input Parameters:
1464: + viewer - The `PETSCVIEWERHDF5` viewer
1465: - path - (Optional) The path relative to the pushed group
1467: Output Parameter:
1468: . has - Flag for group existence
1470: Level: advanced
1472: Notes:
1473: If path starts with '/', it is taken as an absolute path overriding currently pushed group, else path is relative to the current pushed group.
1474: `NULL` or empty path means the current pushed group.
1476: If path exists but is not a group, `PETSC_FALSE` is returned.
1478: .seealso: [](sec_viewers), `PETSCVIEWERHDF5`, `PetscViewerHDF5HasAttribute()`, `PetscViewerHDF5HasDataset()`, `PetscViewerHDF5PushGroup()`, `PetscViewerHDF5PopGroup()`, `PetscViewerHDF5GetGroup()`, `PetscViewerHDF5OpenGroup()`
1479: @*/
1480: PetscErrorCode PetscViewerHDF5HasGroup(PetscViewer viewer, const char path[], PetscBool *has)
1481: {
1482: H5O_type_t type;
1483: const char *abspath;
1485: PetscFunctionBegin;
1487: if (path) PetscAssertPointer(path, 2);
1488: PetscAssertPointer(has, 3);
1489: PetscCall(PetscViewerHDF5GetGroup(viewer, path, &abspath));
1490: PetscCall(PetscViewerHDF5Traverse_Internal(viewer, abspath, PETSC_FALSE, NULL, &type));
1491: *has = (PetscBool)(type == H5O_TYPE_GROUP);
1492: PetscCall(PetscFree(abspath));
1493: PetscFunctionReturn(PETSC_SUCCESS);
1494: }
1496: /*@C
1497: PetscViewerHDF5HasDataset - Check whether a given dataset exists in the HDF5 file
1499: Collective
1501: Input Parameters:
1502: + viewer - The `PETSCVIEWERHDF5` viewer
1503: - path - The dataset path
1505: Output Parameter:
1506: . has - Flag whether dataset exists
1508: Level: advanced
1510: Notes:
1511: If path starts with '/', it is taken as an absolute path overriding currently pushed group, else path is relative to the current pushed group.
1513: If `path` is `NULL` or empty, has is set to `PETSC_FALSE`.
1515: If `path` exists but is not a dataset, has is set to `PETSC_FALSE` as well.
1517: .seealso: [](sec_viewers), `PETSCVIEWERHDF5`, `PetscViewerHDF5HasObject()`, `PetscViewerHDF5HasAttribute()`, `PetscViewerHDF5HasGroup()`, `PetscViewerHDF5PushGroup()`, `PetscViewerHDF5PopGroup()`, `PetscViewerHDF5GetGroup()`
1518: @*/
1519: PetscErrorCode PetscViewerHDF5HasDataset(PetscViewer viewer, const char path[], PetscBool *has)
1520: {
1521: H5O_type_t type;
1522: const char *abspath;
1524: PetscFunctionBegin;
1526: if (path) PetscAssertPointer(path, 2);
1527: PetscAssertPointer(has, 3);
1528: PetscCall(PetscViewerHDF5GetGroup(viewer, path, &abspath));
1529: PetscCall(PetscViewerHDF5Traverse_Internal(viewer, abspath, PETSC_FALSE, NULL, &type));
1530: *has = (PetscBool)(type == H5O_TYPE_DATASET);
1531: PetscCall(PetscFree(abspath));
1532: PetscFunctionReturn(PETSC_SUCCESS);
1533: }
1535: /*@
1536: PetscViewerHDF5HasObject - Check whether a dataset with the same name as given object exists in the HDF5 file under current group
1538: Collective
1540: Input Parameters:
1541: + viewer - The `PETSCVIEWERHDF5` viewer
1542: - obj - The named object
1544: Output Parameter:
1545: . has - Flag for dataset existence
1547: Level: advanced
1549: Notes:
1550: If the object is unnamed, an error occurs.
1552: If the path current_group/object_name exists but is not a dataset, has is set to `PETSC_FALSE` as well.
1554: .seealso: [](sec_viewers), `PETSCVIEWERHDF5`, `PetscViewerHDF5Open()`, `PetscViewerHDF5HasDataset()`, `PetscViewerHDF5HasAttribute()`, `PetscViewerHDF5PushGroup()`, `PetscViewerHDF5PopGroup()`, `PetscViewerHDF5GetGroup()`
1555: @*/
1556: PetscErrorCode PetscViewerHDF5HasObject(PetscViewer viewer, PetscObject obj, PetscBool *has)
1557: {
1558: size_t len;
1560: PetscFunctionBegin;
1563: PetscAssertPointer(has, 3);
1564: PetscCall(PetscStrlen(obj->name, &len));
1565: PetscCheck(len, PetscObjectComm((PetscObject)viewer), PETSC_ERR_ARG_WRONG, "Object must be named");
1566: PetscCall(PetscViewerHDF5HasDataset(viewer, obj->name, has));
1567: PetscFunctionReturn(PETSC_SUCCESS);
1568: }
1570: /*@C
1571: PetscViewerHDF5HasAttribute - Check whether an attribute exists
1573: Collective
1575: Input Parameters:
1576: + viewer - The `PETSCVIEWERHDF5` viewer
1577: . parent - The parent dataset/group name
1578: - name - The attribute name
1580: Output Parameter:
1581: . has - Flag for attribute existence
1583: Level: advanced
1585: Note:
1586: If parent starts with '/', it is taken as an absolute path overriding currently pushed group, else parent is relative to the current pushed group. `NULL` means the current pushed group.
1588: .seealso: [](sec_viewers), `PETSCVIEWERHDF5`, `PetscViewerHDF5Open()`, `PetscViewerHDF5HasObjectAttribute()`, `PetscViewerHDF5WriteAttribute()`, `PetscViewerHDF5ReadAttribute()`, `PetscViewerHDF5PushGroup()`, `PetscViewerHDF5PopGroup()`, `PetscViewerHDF5GetGroup()`
1589: @*/
1590: PetscErrorCode PetscViewerHDF5HasAttribute(PetscViewer viewer, const char parent[], const char name[], PetscBool *has)
1591: {
1592: const char *parentAbsPath;
1594: PetscFunctionBegin;
1596: if (parent) PetscAssertPointer(parent, 2);
1597: PetscAssertPointer(name, 3);
1598: PetscAssertPointer(has, 4);
1599: PetscCall(PetscViewerHDF5GetGroup(viewer, parent, &parentAbsPath));
1600: PetscCall(PetscViewerHDF5Traverse_Internal(viewer, parentAbsPath, PETSC_FALSE, has, NULL));
1601: if (*has) PetscCall(PetscViewerHDF5HasAttribute_Internal(viewer, parentAbsPath, name, has));
1602: PetscCall(PetscFree(parentAbsPath));
1603: PetscFunctionReturn(PETSC_SUCCESS);
1604: }
1606: /*@C
1607: PetscViewerHDF5HasObjectAttribute - Check whether an attribute is attached to the dataset matching the given `PetscObject` by name
1609: Collective
1611: Input Parameters:
1612: + viewer - The `PETSCVIEWERHDF5` viewer
1613: . obj - The object whose name is used to lookup the parent dataset, relative to the current group.
1614: - name - The attribute name
1616: Output Parameter:
1617: . has - Flag for attribute existence
1619: Level: advanced
1621: Note:
1622: This fails if current_group/object_name doesn't resolve to a dataset (the path doesn't exist or is not a dataset).
1623: You might want to check first if it does using `PetscViewerHDF5HasObject()`.
1625: .seealso: [](sec_viewers), `PETSCVIEWERHDF5`, `PetscViewerHDF5Open()`, `PetscViewerHDF5HasAttribute()`, `PetscViewerHDF5WriteObjectAttribute()`, `PetscViewerHDF5ReadObjectAttribute()`, `PetscViewerHDF5HasObject()`, `PetscViewerHDF5PushGroup()`, `PetscViewerHDF5PopGroup()`, `PetscViewerHDF5GetGroup()`
1626: @*/
1627: PetscErrorCode PetscViewerHDF5HasObjectAttribute(PetscViewer viewer, PetscObject obj, const char name[], PetscBool *has)
1628: {
1629: PetscFunctionBegin;
1632: PetscAssertPointer(name, 3);
1633: PetscAssertPointer(has, 4);
1634: PetscCall(PetscViewerHDF5CheckNamedObject_Internal(viewer, obj));
1635: PetscCall(PetscViewerHDF5HasAttribute(viewer, obj->name, name, has));
1636: PetscFunctionReturn(PETSC_SUCCESS);
1637: }
1639: static PetscErrorCode PetscViewerHDF5HasAttribute_Internal(PetscViewer viewer, const char parent[], const char name[], PetscBool *has)
1640: {
1641: hid_t h5;
1642: htri_t hhas;
1644: PetscFunctionBegin;
1645: PetscCall(PetscViewerHDF5GetFileId(viewer, &h5));
1646: PetscCallHDF5Return(hhas, H5Aexists_by_name, (h5, parent, name, H5P_DEFAULT));
1647: *has = hhas ? PETSC_TRUE : PETSC_FALSE;
1648: PetscFunctionReturn(PETSC_SUCCESS);
1649: }
1651: /*
1652: The variable Petsc_Viewer_HDF5_keyval is used to indicate an MPI attribute that
1653: is attached to a communicator, in this case the attribute is a PetscViewer.
1654: */
1655: PetscMPIInt Petsc_Viewer_HDF5_keyval = MPI_KEYVAL_INVALID;
1657: /*@C
1658: PETSC_VIEWER_HDF5_ - Creates an `PETSCVIEWERHDF5` `PetscViewer` shared by all processors in a communicator.
1660: Collective
1662: Input Parameter:
1663: . comm - the MPI communicator to share the `PETSCVIEWERHDF5` `PetscViewer`
1665: Options Database Key:
1666: . -viewer_hdf5_filename <name> - name of the HDF5 file
1668: Environmental variable:
1669: . `PETSC_VIEWER_HDF5_FILENAME` - name of the HDF5 file
1671: Level: intermediate
1673: Note:
1674: Unlike almost all other PETSc routines, `PETSC_VIEWER_HDF5_()` does not return
1675: an error code. The HDF5 `PetscViewer` is usually used in the form
1676: .vb
1677: XXXView(XXX object, PETSC_VIEWER_HDF5_(comm));
1678: .ve
1680: .seealso: [](sec_viewers), `PETSCVIEWERHDF5`, `PetscViewerHDF5Open()`, `PetscViewerCreate()`, `PetscViewerDestroy()`
1681: @*/
1682: PetscViewer PETSC_VIEWER_HDF5_(MPI_Comm comm)
1683: {
1684: PetscErrorCode ierr;
1685: PetscMPIInt mpi_ierr;
1686: PetscBool flg;
1687: PetscMPIInt iflg;
1688: PetscViewer viewer;
1689: char fname[PETSC_MAX_PATH_LEN];
1690: MPI_Comm ncomm;
1692: PetscFunctionBegin;
1693: ierr = PetscCommDuplicate(comm, &ncomm, NULL);
1694: if (ierr) {
1695: ierr = PetscError(PETSC_COMM_SELF, __LINE__, "PETSC_VIEWER_HDF5_", __FILE__, PETSC_ERR_PLIB, PETSC_ERROR_INITIAL, " ");
1696: PetscFunctionReturn(NULL);
1697: }
1698: if (Petsc_Viewer_HDF5_keyval == MPI_KEYVAL_INVALID) {
1699: mpi_ierr = MPI_Comm_create_keyval(MPI_COMM_NULL_COPY_FN, MPI_COMM_NULL_DELETE_FN, &Petsc_Viewer_HDF5_keyval, NULL);
1700: if (mpi_ierr) {
1701: ierr = PetscError(PETSC_COMM_SELF, __LINE__, "PETSC_VIEWER_HDF5_", __FILE__, PETSC_ERR_PLIB, PETSC_ERROR_INITIAL, " ");
1702: PetscFunctionReturn(NULL);
1703: }
1704: }
1705: mpi_ierr = MPI_Comm_get_attr(ncomm, Petsc_Viewer_HDF5_keyval, (void **)&viewer, &iflg);
1706: if (mpi_ierr) {
1707: ierr = PetscError(PETSC_COMM_SELF, __LINE__, "PETSC_VIEWER_HDF5_", __FILE__, PETSC_ERR_PLIB, PETSC_ERROR_INITIAL, " ");
1708: PetscFunctionReturn(NULL);
1709: }
1710: if (!iflg) { /* PetscViewer not yet created */
1711: ierr = PetscOptionsGetenv(ncomm, "PETSC_VIEWER_HDF5_FILENAME", fname, PETSC_MAX_PATH_LEN, &flg);
1712: if (ierr) {
1713: ierr = PetscError(PETSC_COMM_SELF, __LINE__, "PETSC_VIEWER_HDF5_", __FILE__, PETSC_ERR_PLIB, PETSC_ERROR_REPEAT, " ");
1714: PetscFunctionReturn(NULL);
1715: }
1716: if (!flg) {
1717: ierr = PetscStrncpy(fname, "output.h5", sizeof(fname));
1718: if (ierr) {
1719: ierr = PetscError(PETSC_COMM_SELF, __LINE__, "PETSC_VIEWER_HDF5_", __FILE__, PETSC_ERR_PLIB, PETSC_ERROR_REPEAT, " ");
1720: PetscFunctionReturn(NULL);
1721: }
1722: }
1723: ierr = PetscViewerHDF5Open(ncomm, fname, FILE_MODE_WRITE, &viewer);
1724: if (ierr) {
1725: ierr = PetscError(PETSC_COMM_SELF, __LINE__, "PETSC_VIEWER_HDF5_", __FILE__, PETSC_ERR_PLIB, PETSC_ERROR_REPEAT, " ");
1726: PetscFunctionReturn(NULL);
1727: }
1728: ierr = PetscObjectRegisterDestroy((PetscObject)viewer);
1729: if (ierr) {
1730: ierr = PetscError(PETSC_COMM_SELF, __LINE__, "PETSC_VIEWER_HDF5_", __FILE__, PETSC_ERR_PLIB, PETSC_ERROR_REPEAT, " ");
1731: PetscFunctionReturn(NULL);
1732: }
1733: mpi_ierr = MPI_Comm_set_attr(ncomm, Petsc_Viewer_HDF5_keyval, (void *)viewer);
1734: if (mpi_ierr) {
1735: ierr = PetscError(PETSC_COMM_SELF, __LINE__, "PETSC_VIEWER_HDF5_", __FILE__, PETSC_ERR_PLIB, PETSC_ERROR_INITIAL, " ");
1736: PetscFunctionReturn(NULL);
1737: }
1738: }
1739: ierr = PetscCommDestroy(&ncomm);
1740: if (ierr) {
1741: ierr = PetscError(PETSC_COMM_SELF, __LINE__, "PETSC_VIEWER_HDF5_", __FILE__, PETSC_ERR_PLIB, PETSC_ERROR_REPEAT, " ");
1742: PetscFunctionReturn(NULL);
1743: }
1744: PetscFunctionReturn(viewer);
1745: }