Actual source code: hdf5v.c
petsc-3.7.5 2017-01-01
1: #include <petsc/private/viewerimpl.h> /*I "petscsys.h" I*/
2: #include <petscviewerhdf5.h> /*I "petscviewerhdf5.h" I*/
4: typedef struct GroupList {
5: const char *name;
6: struct GroupList *next;
7: } GroupList;
9: typedef struct {
10: char *filename;
11: PetscFileMode btype;
12: hid_t file_id;
13: PetscInt timestep;
14: GroupList *groups;
15: PetscBool basedimension2; /* save vectors and DMDA vectors with a dimension of at least 2 even if the bs/dof is 1 */
16: PetscBool spoutput; /* write data in single precision even if PETSc is compiled with double precision PetscReal */
17: } PetscViewer_HDF5;
21: static PetscErrorCode PetscViewerSetFromOptions_HDF5(PetscOptionItems *PetscOptionsObject,PetscViewer v)
22: {
23: PetscErrorCode ierr;
24: PetscViewer_HDF5 *hdf5 = (PetscViewer_HDF5*)v->data;
27: PetscOptionsHead(PetscOptionsObject,"HDF5 PetscViewer Options");
28: PetscOptionsBool("-viewer_hdf5_base_dimension2","1d Vectors get 2 dimensions in HDF5","PetscViewerHDF5SetBaseDimension2",hdf5->basedimension2,&hdf5->basedimension2,NULL);
29: PetscOptionsBool("-viewer_hdf5_sp_output","Force data to be written in single precision","PetscViewerHDF5SetSPOutput",hdf5->spoutput,&hdf5->spoutput,NULL);
30: PetscOptionsTail();
31: return(0);
32: }
36: static PetscErrorCode PetscViewerFileClose_HDF5(PetscViewer viewer)
37: {
38: PetscViewer_HDF5 *hdf5 = (PetscViewer_HDF5*)viewer->data;
39: PetscErrorCode ierr;
42: PetscFree(hdf5->filename);
43: if (hdf5->file_id) PetscStackCallHDF5(H5Fclose,(hdf5->file_id));
44: return(0);
45: }
49: PetscErrorCode PetscViewerDestroy_HDF5(PetscViewer viewer)
50: {
51: PetscViewer_HDF5 *hdf5 = (PetscViewer_HDF5*) viewer->data;
52: PetscErrorCode ierr;
55: PetscViewerFileClose_HDF5(viewer);
56: while (hdf5->groups) {
57: GroupList *tmp = hdf5->groups->next;
59: PetscFree(hdf5->groups->name);
60: PetscFree(hdf5->groups);
61: hdf5->groups = tmp;
62: }
63: PetscFree(hdf5);
64: PetscObjectComposeFunction((PetscObject)viewer,"PetscViewerFileSetName_C",NULL);
65: PetscObjectComposeFunction((PetscObject)viewer,"PetscViewerFileSetMode_C",NULL);
66: return(0);
67: }
71: PetscErrorCode PetscViewerFileSetMode_HDF5(PetscViewer viewer, PetscFileMode type)
72: {
73: PetscViewer_HDF5 *hdf5 = (PetscViewer_HDF5*) viewer->data;
77: hdf5->btype = type;
78: return(0);
79: }
83: PetscErrorCode PetscViewerHDF5SetBaseDimension2_HDF5(PetscViewer viewer, PetscBool flg)
84: {
85: PetscViewer_HDF5 *hdf5 = (PetscViewer_HDF5*) viewer->data;
88: hdf5->basedimension2 = flg;
89: return(0);
90: }
94: /*@C
95: PetscViewerHDF5SetBaseDimension2 - Vectors of 1 dimension (i.e. bs/dof is 1) will be saved in the HDF5 file with a
96: dimension of 2.
98: Logically Collective on PetscViewer
100: Input Parameters:
101: + viewer - the PetscViewer; if it is not hdf5 then this command is ignored
102: - flg - if PETSC_TRUE the vector will always have at least a dimension of 2 even if that first dimension is of size 1
104: Options Database:
105: . -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
108: Notes: Setting this option allegedly makes code that reads the HDF5 in easier since they do not have a "special case" of a bs/dof
109: of one when the dimension is lower. Others think the option is crazy.
111: Level: intermediate
113: .seealso: PetscViewerFileSetMode(), PetscViewerCreate(), PetscViewerSetType(), PetscViewerBinaryOpen()
115: @*/
116: PetscErrorCode PetscViewerHDF5SetBaseDimension2(PetscViewer viewer,PetscBool flg)
117: {
122: PetscTryMethod(viewer,"PetscViewerHDF5SetBaseDimension2_C",(PetscViewer,PetscBool),(viewer,flg));
123: return(0);
124: }
128: /*@C
129: PetscViewerHDF5GetBaseDimension2 - Vectors of 1 dimension (i.e. bs/dof is 1) will be saved in the HDF5 file with a
130: dimension of 2.
132: Logically Collective on PetscViewer
134: Input Parameter:
135: . viewer - the PetscViewer, must be of type HDF5
137: Output Parameter:
138: . flg - if PETSC_TRUE the vector will always have at least a dimension of 2 even if that first dimension is of size 1
140: Notes: Setting this option allegedly makes code that reads the HDF5 in easier since they do not have a "special case" of a bs/dof
141: of one when the dimension is lower. Others think the option is crazy.
143: Level: intermediate
145: .seealso: PetscViewerFileSetMode(), PetscViewerCreate(), PetscViewerSetType(), PetscViewerBinaryOpen()
147: @*/
148: PetscErrorCode PetscViewerHDF5GetBaseDimension2(PetscViewer viewer,PetscBool *flg)
149: {
150: PetscViewer_HDF5 *hdf5 = (PetscViewer_HDF5*) viewer->data;
154: *flg = hdf5->basedimension2;
155: return(0);
156: }
160: PetscErrorCode PetscViewerHDF5SetSPOutput_HDF5(PetscViewer viewer, PetscBool flg)
161: {
162: PetscViewer_HDF5 *hdf5 = (PetscViewer_HDF5*) viewer->data;
165: hdf5->spoutput = flg;
166: return(0);
167: }
171: /*@C
172: PetscViewerHDF5SetSPOutput - Data is written to disk in single precision even if PETSc is
173: compiled with double precision PetscReal.
175: Logically Collective on PetscViewer
177: Input Parameters:
178: + viewer - the PetscViewer; if it is not hdf5 then this command is ignored
179: - flg - if PETSC_TRUE the data will be written to disk with single precision
181: Options Database:
182: . -viewer_hdf5_sp_output - turns on (true) or off (false) output in single precision
185: Notes: Setting this option does not make any difference if PETSc is compiled with single precision
186: in the first place. It does not affect reading datasets (HDF5 handle this internally).
188: Level: intermediate
190: .seealso: PetscViewerFileSetMode(), PetscViewerCreate(), PetscViewerSetType(), PetscViewerBinaryOpen(),
191: PetscReal
193: @*/
194: PetscErrorCode PetscViewerHDF5SetSPOutput(PetscViewer viewer,PetscBool flg)
195: {
200: PetscTryMethod(viewer,"PetscViewerHDF5SetSPOutput_C",(PetscViewer,PetscBool),(viewer,flg));
201: return(0);
202: }
206: /*@C
207: PetscViewerHDF5GetSPOutput - Data is written to disk in single precision even if PETSc is
208: compiled with double precision PetscReal.
210: Logically Collective on PetscViewer
212: Input Parameter:
213: . viewer - the PetscViewer, must be of type HDF5
215: Output Parameter:
216: . flg - if PETSC_TRUE the data will be written to disk with single precision
218: Notes: Setting this option does not make any difference if PETSc is compiled with single precision
219: in the first place. It does not affect reading datasets (HDF5 handle this internally).
221: Level: intermediate
223: .seealso: PetscViewerFileSetMode(), PetscViewerCreate(), PetscViewerSetType(), PetscViewerBinaryOpen(),
224: PetscReal
226: @*/
227: PetscErrorCode PetscViewerHDF5GetSPOutput(PetscViewer viewer,PetscBool *flg)
228: {
229: PetscViewer_HDF5 *hdf5 = (PetscViewer_HDF5*) viewer->data;
233: *flg = hdf5->spoutput;
234: return(0);
235: }
239: PetscErrorCode PetscViewerFileSetName_HDF5(PetscViewer viewer, const char name[])
240: {
241: PetscViewer_HDF5 *hdf5 = (PetscViewer_HDF5*) viewer->data;
242: #if defined(PETSC_HAVE_H5PSET_FAPL_MPIO)
243: MPI_Info info = MPI_INFO_NULL;
244: #endif
245: hid_t plist_id;
246: PetscErrorCode ierr;
249: PetscStrallocpy(name, &hdf5->filename);
250: /* Set up file access property list with parallel I/O access */
251: PetscStackCallHDF5Return(plist_id,H5Pcreate,(H5P_FILE_ACCESS));
252: #if defined(PETSC_HAVE_H5PSET_FAPL_MPIO)
253: PetscStackCallHDF5(H5Pset_fapl_mpio,(plist_id, PetscObjectComm((PetscObject)viewer), info));
254: #endif
255: /* Create or open the file collectively */
256: switch (hdf5->btype) {
257: case FILE_MODE_READ:
258: PetscStackCallHDF5Return(hdf5->file_id,H5Fopen,(name, H5F_ACC_RDONLY, plist_id));
259: break;
260: case FILE_MODE_APPEND:
261: PetscStackCallHDF5Return(hdf5->file_id,H5Fopen,(name, H5F_ACC_RDWR, plist_id));
262: break;
263: case FILE_MODE_WRITE:
264: PetscStackCallHDF5Return(hdf5->file_id,H5Fcreate,(name, H5F_ACC_TRUNC, H5P_DEFAULT, plist_id));
265: break;
266: default:
267: SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ORDER, "Must call PetscViewerFileSetMode() before PetscViewerFileSetName()");
268: }
269: if (hdf5->file_id < 0) SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_LIB, "H5Fcreate failed for %s", name);
270: PetscStackCallHDF5(H5Pclose,(plist_id));
271: return(0);
272: }
276: PETSC_EXTERN PetscErrorCode PetscViewerCreate_HDF5(PetscViewer v)
277: {
278: PetscViewer_HDF5 *hdf5;
279: PetscErrorCode ierr;
282: PetscNewLog(v,&hdf5);
284: v->data = (void*) hdf5;
285: v->ops->destroy = PetscViewerDestroy_HDF5;
286: v->ops->setfromoptions = PetscViewerSetFromOptions_HDF5;
287: v->ops->flush = 0;
288: hdf5->btype = (PetscFileMode) -1;
289: hdf5->filename = 0;
290: hdf5->timestep = -1;
291: hdf5->groups = NULL;
293: PetscObjectComposeFunction((PetscObject)v,"PetscViewerFileSetName_C",PetscViewerFileSetName_HDF5);
294: PetscObjectComposeFunction((PetscObject)v,"PetscViewerFileSetMode_C",PetscViewerFileSetMode_HDF5);
295: PetscObjectComposeFunction((PetscObject)v,"PetscViewerHDF5SetBaseDimension2_C",PetscViewerHDF5SetBaseDimension2_HDF5);
296: PetscObjectComposeFunction((PetscObject)v,"PetscViewerHDF5SetSPOutput_C",PetscViewerHDF5SetSPOutput_HDF5);
297: return(0);
298: }
302: /*@C
303: PetscViewerHDF5Open - Opens a file for HDF5 input/output.
305: Collective on MPI_Comm
307: Input Parameters:
308: + comm - MPI communicator
309: . name - name of file
310: - type - type of file
311: $ FILE_MODE_WRITE - create new file for binary output
312: $ FILE_MODE_READ - open existing file for binary input
313: $ FILE_MODE_APPEND - open existing file for binary output
315: Output Parameter:
316: . hdf5v - PetscViewer for HDF5 input/output to use with the specified file
318: Options Database:
319: . -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
320: . -viewer_hdf5_sp_output - forces (if true) the viewer to write data in single precision independent on the precision of PetscReal
322: Level: beginner
324: Note:
325: This PetscViewer should be destroyed with PetscViewerDestroy().
327: Concepts: HDF5 files
328: Concepts: PetscViewerHDF5^creating
330: .seealso: PetscViewerASCIIOpen(), PetscViewerPushFormat(), PetscViewerDestroy(), PetscViewerHDF5SetBaseDimension2(),
331: PetscViewerHDF5SetSPOutput(), PetscViewerHDF5GetBaseDimension2(), VecView(), MatView(), VecLoad(),
332: MatLoad(), PetscFileMode, PetscViewer
333: @*/
334: PetscErrorCode PetscViewerHDF5Open(MPI_Comm comm, const char name[], PetscFileMode type, PetscViewer *hdf5v)
335: {
339: PetscViewerCreate(comm, hdf5v);
340: PetscViewerSetType(*hdf5v, PETSCVIEWERHDF5);
341: PetscViewerFileSetMode(*hdf5v, type);
342: PetscViewerFileSetName(*hdf5v, name);
343: return(0);
344: }
348: /*@C
349: PetscViewerHDF5GetFileId - Retrieve the file id, this file ID then can be used in direct HDF5 calls
351: Not collective
353: Input Parameter:
354: . viewer - the PetscViewer
356: Output Parameter:
357: . file_id - The file id
359: Level: intermediate
361: .seealso: PetscViewerHDF5Open()
362: @*/
363: PetscErrorCode PetscViewerHDF5GetFileId(PetscViewer viewer, hid_t *file_id)
364: {
365: PetscViewer_HDF5 *hdf5 = (PetscViewer_HDF5*) viewer->data;
369: if (file_id) *file_id = hdf5->file_id;
370: return(0);
371: }
375: /*@C
376: PetscViewerHDF5PushGroup - Set the current HDF5 group for output
378: Not collective
380: Input Parameters:
381: + viewer - the PetscViewer
382: - name - The group name
384: Level: intermediate
386: .seealso: PetscViewerHDF5Open(),PetscViewerHDF5PopGroup(),PetscViewerHDF5GetGroup()
387: @*/
388: PetscErrorCode PetscViewerHDF5PushGroup(PetscViewer viewer, const char *name)
389: {
390: PetscViewer_HDF5 *hdf5 = (PetscViewer_HDF5*) viewer->data;
391: GroupList *groupNode;
392: PetscErrorCode ierr;
397: PetscMalloc(sizeof(GroupList), &groupNode);
398: PetscStrallocpy(name, (char**) &groupNode->name);
400: groupNode->next = hdf5->groups;
401: hdf5->groups = groupNode;
402: return(0);
403: }
407: /*@
408: PetscViewerHDF5PopGroup - Return the current HDF5 group for output to the previous value
410: Not collective
412: Input Parameter:
413: . viewer - the PetscViewer
415: Level: intermediate
417: .seealso: PetscViewerHDF5Open(),PetscViewerHDF5PushGroup(),PetscViewerHDF5GetGroup()
418: @*/
419: PetscErrorCode PetscViewerHDF5PopGroup(PetscViewer viewer)
420: {
421: PetscViewer_HDF5 *hdf5 = (PetscViewer_HDF5*) viewer->data;
422: GroupList *groupNode;
423: PetscErrorCode ierr;
427: if (!hdf5->groups) SETERRQ(PetscObjectComm((PetscObject)viewer), PETSC_ERR_ARG_WRONGSTATE, "HDF5 group stack is empty, cannot pop");
428: groupNode = hdf5->groups;
429: hdf5->groups = hdf5->groups->next;
430: PetscFree(groupNode->name);
431: PetscFree(groupNode);
432: return(0);
433: }
437: /*@C
438: PetscViewerHDF5GetGroup - Get the current HDF5 group for output. If none has been assigned, returns NULL.
440: Not collective
442: Input Parameter:
443: . viewer - the PetscViewer
445: Output Parameter:
446: . name - The group name
448: Level: intermediate
450: .seealso: PetscViewerHDF5Open(),PetscViewerHDF5PushGroup(),PetscViewerHDF5PopGroup()
451: @*/
452: PetscErrorCode PetscViewerHDF5GetGroup(PetscViewer viewer, const char **name)
453: {
454: PetscViewer_HDF5 *hdf5 = (PetscViewer_HDF5 *) viewer->data;
459: if (hdf5->groups) *name = hdf5->groups->name;
460: else *name = NULL;
461: return(0);
462: }
466: /*@
467: PetscViewerHDF5IncrementTimestep - Increments the current timestep for the HDF5 output. Fields are stacked in time.
469: Not collective
471: Input Parameter:
472: . viewer - the PetscViewer
474: Level: intermediate
476: .seealso: PetscViewerHDF5Open(), PetscViewerHDF5SetTimestep(), PetscViewerHDF5GetTimestep()
477: @*/
478: PetscErrorCode PetscViewerHDF5IncrementTimestep(PetscViewer viewer)
479: {
480: PetscViewer_HDF5 *hdf5 = (PetscViewer_HDF5*) viewer->data;
484: ++hdf5->timestep;
485: return(0);
486: }
490: /*@
491: PetscViewerHDF5SetTimestep - Set the current timestep for the HDF5 output. Fields are stacked in time. A timestep
492: of -1 disables blocking with timesteps.
494: Not collective
496: Input Parameters:
497: + viewer - the PetscViewer
498: - timestep - The timestep number
500: Level: intermediate
502: .seealso: PetscViewerHDF5Open(), PetscViewerHDF5IncrementTimestep(), PetscViewerHDF5GetTimestep()
503: @*/
504: PetscErrorCode PetscViewerHDF5SetTimestep(PetscViewer viewer, PetscInt timestep)
505: {
506: PetscViewer_HDF5 *hdf5 = (PetscViewer_HDF5*) viewer->data;
510: hdf5->timestep = timestep;
511: return(0);
512: }
516: /*@
517: PetscViewerHDF5GetTimestep - Get the current timestep for the HDF5 output. Fields are stacked in time.
519: Not collective
521: Input Parameter:
522: . viewer - the PetscViewer
524: Output Parameter:
525: . timestep - The timestep number
527: Level: intermediate
529: .seealso: PetscViewerHDF5Open(), PetscViewerHDF5IncrementTimestep(), PetscViewerHDF5SetTimestep()
530: @*/
531: PetscErrorCode PetscViewerHDF5GetTimestep(PetscViewer viewer, PetscInt *timestep)
532: {
533: PetscViewer_HDF5 *hdf5 = (PetscViewer_HDF5*) viewer->data;
538: *timestep = hdf5->timestep;
539: return(0);
540: }
544: /*@C
545: PetscDataTypeToHDF5DataType - Converts the PETSc name of a datatype to its HDF5 name.
547: Not collective
549: Input Parameter:
550: . ptype - the PETSc datatype name (for example PETSC_DOUBLE)
552: Output Parameter:
553: . mtype - the MPI datatype (for example MPI_DOUBLE, ...)
555: Level: advanced
557: .seealso: PetscDataType, PetscHDF5DataTypeToPetscDataType()
558: @*/
559: PetscErrorCode PetscDataTypeToHDF5DataType(PetscDataType ptype, hid_t *htype)
560: {
562: if (ptype == PETSC_INT)
563: #if defined(PETSC_USE_64BIT_INDICES)
564: *htype = H5T_NATIVE_LLONG;
565: #else
566: *htype = H5T_NATIVE_INT;
567: #endif
568: else if (ptype == PETSC_DOUBLE) *htype = H5T_NATIVE_DOUBLE;
569: else if (ptype == PETSC_LONG) *htype = H5T_NATIVE_LONG;
570: else if (ptype == PETSC_SHORT) *htype = H5T_NATIVE_SHORT;
571: else if (ptype == PETSC_ENUM) *htype = H5T_NATIVE_DOUBLE;
572: else if (ptype == PETSC_BOOL) *htype = H5T_NATIVE_DOUBLE;
573: else if (ptype == PETSC_FLOAT) *htype = H5T_NATIVE_FLOAT;
574: else if (ptype == PETSC_CHAR) *htype = H5T_NATIVE_CHAR;
575: else if (ptype == PETSC_BIT_LOGICAL) *htype = H5T_NATIVE_UCHAR;
576: else if (ptype == PETSC_STRING) *htype = H5Tcopy(H5T_C_S1);
577: else SETERRQ(PETSC_COMM_SELF, PETSC_ERR_ARG_OUTOFRANGE, "Unsupported PETSc datatype");
578: return(0);
579: }
583: /*@C
584: PetscHDF5DataTypeToPetscDataType - Finds the PETSc name of a datatype from its HDF5 name
586: Not collective
588: Input Parameter:
589: . htype - the HDF5 datatype (for example H5T_NATIVE_DOUBLE, ...)
591: Output Parameter:
592: . ptype - the PETSc datatype name (for example PETSC_DOUBLE)
594: Level: advanced
596: .seealso: PetscDataType, PetscHDF5DataTypeToPetscDataType()
597: @*/
598: PetscErrorCode PetscHDF5DataTypeToPetscDataType(hid_t htype, PetscDataType *ptype)
599: {
601: #if defined(PETSC_USE_64BIT_INDICES)
602: if (htype == H5T_NATIVE_INT) *ptype = PETSC_LONG;
603: else if (htype == H5T_NATIVE_LLONG) *ptype = PETSC_INT;
604: #else
605: if (htype == H5T_NATIVE_INT) *ptype = PETSC_INT;
606: #endif
607: else if (htype == H5T_NATIVE_DOUBLE) *ptype = PETSC_DOUBLE;
608: else if (htype == H5T_NATIVE_LONG) *ptype = PETSC_LONG;
609: else if (htype == H5T_NATIVE_SHORT) *ptype = PETSC_SHORT;
610: else if (htype == H5T_NATIVE_FLOAT) *ptype = PETSC_FLOAT;
611: else if (htype == H5T_NATIVE_CHAR) *ptype = PETSC_CHAR;
612: else if (htype == H5T_NATIVE_UCHAR) *ptype = PETSC_CHAR;
613: else if (htype == H5T_C_S1) *ptype = PETSC_STRING;
614: else SETERRQ(PETSC_COMM_SELF, PETSC_ERR_ARG_OUTOFRANGE, "Unsupported HDF5 datatype");
615: return(0);
616: }
620: /*@
621: PetscViewerHDF5WriteAttribute - Write a scalar attribute
623: Input Parameters:
624: + viewer - The HDF5 viewer
625: . parent - The parent name
626: . name - The attribute name
627: . datatype - The attribute type
628: - value - The attribute value
630: Level: advanced
632: .seealso: PetscViewerHDF5Open(), PetscViewerHDF5ReadAttribute(), PetscViewerHDF5HasAttribute()
633: @*/
634: PetscErrorCode PetscViewerHDF5WriteAttribute(PetscViewer viewer, const char parent[], const char name[], PetscDataType datatype, const void *value)
635: {
636: hid_t h5, dataspace, dataset, attribute, dtype;
644: PetscDataTypeToHDF5DataType(datatype, &dtype);
645: if (datatype == PETSC_STRING) {
646: size_t len;
647: PetscStrlen((const char *) value, &len);
648: PetscStackCallHDF5(H5Tset_size,(dtype, len+1));
649: }
650: PetscViewerHDF5GetFileId(viewer, &h5);
651: PetscStackCallHDF5Return(dataspace,H5Screate,(H5S_SCALAR));
652: #if (H5_VERS_MAJOR * 10000 + H5_VERS_MINOR * 100 + H5_VERS_RELEASE >= 10800)
653: PetscStackCallHDF5Return(dataset,H5Dopen2,(h5, parent, H5P_DEFAULT));
654: PetscStackCallHDF5Return(attribute,H5Acreate2,(dataset, name, dtype, dataspace, H5P_DEFAULT, H5P_DEFAULT));
655: #else
656: PetscStackCallHDF5Return(dataset,H5Dopen,(h5, parent));
657: PetscStackCallHDF5Return(attribute,H5Acreate,(dataset, name, dtype, dataspace, H5P_DEFAULT));
658: #endif
659: PetscStackCallHDF5(H5Awrite,(attribute, dtype, value));
660: if (datatype == PETSC_STRING) PetscStackCallHDF5(H5Tclose,(dtype));
661: PetscStackCallHDF5(H5Aclose,(attribute));
662: PetscStackCallHDF5(H5Dclose,(dataset));
663: PetscStackCallHDF5(H5Sclose,(dataspace));
664: return(0);
665: }
669: /*@
670: PetscViewerHDF5ReadAttribute - Read a scalar attribute
672: Input Parameters:
673: + viewer - The HDF5 viewer
674: . parent - The parent name
675: . name - The attribute name
676: - datatype - The attribute type
678: Output Parameter:
679: . value - The attribute value
681: Level: advanced
683: .seealso: PetscViewerHDF5Open(), PetscViewerHDF5WriteAttribute(), PetscViewerHDF5HasAttribute()
684: @*/
685: PetscErrorCode PetscViewerHDF5ReadAttribute(PetscViewer viewer, const char parent[], const char name[], PetscDataType datatype, void *value)
686: {
687: hid_t h5, dataspace, dataset, attribute, dtype;
695: PetscDataTypeToHDF5DataType(datatype, &dtype);
696: PetscViewerHDF5GetFileId(viewer, &h5);
697: PetscStackCallHDF5Return(dataspace,H5Screate,(H5S_SCALAR));
698: #if (H5_VERS_MAJOR * 10000 + H5_VERS_MINOR * 100 + H5_VERS_RELEASE >= 10800)
699: PetscStackCallHDF5Return(dataset,H5Dopen2,(h5, parent, H5P_DEFAULT));
700: #else
701: PetscStackCallHDF5Return(dataset,H5Dopen,(h5, parent));
702: #endif
703: PetscStackCallHDF5Return(attribute,H5Aopen_name,(dataset, name));
704: PetscStackCallHDF5(H5Aread,(attribute, dtype, value));
705: PetscStackCallHDF5(H5Aclose,(attribute));
706: PetscStackCallHDF5(H5Dclose,(dataset));
707: PetscStackCallHDF5(H5Sclose,(dataspace));
708: return(0);
709: }
713: static PetscErrorCode PetscViewerHDF5HasObject(PetscViewer viewer, const char name[], H5O_type_t otype, PetscBool *has)
714: {
715: hid_t h5;
722: *has = PETSC_FALSE;
723: PetscViewerHDF5GetFileId(viewer, &h5);
724: if (H5Lexists(h5, name, H5P_DEFAULT)) {
725: H5O_info_t info;
726: hid_t obj;
728: PetscStackCallHDF5Return(obj,H5Oopen,(h5, name, H5P_DEFAULT));
729: PetscStackCallHDF5(H5Oget_info,(obj, &info));
730: if (otype == info.type) *has = PETSC_TRUE;
731: PetscStackCallHDF5(H5Oclose,(obj));
732: }
733: return(0);
734: }
738: /*@
739: PetscViewerHDF5HasAttribute - Check whether a scalar attribute exists
741: Input Parameters:
742: + viewer - The HDF5 viewer
743: . parent - The parent name
744: - name - The attribute name
746: Output Parameter:
747: . has - Flag for attribute existence
749: Level: advanced
751: .seealso: PetscViewerHDF5Open(), PetscViewerHDF5WriteAttribute(), PetscViewerHDF5ReadAttribute()
752: @*/
753: PetscErrorCode PetscViewerHDF5HasAttribute(PetscViewer viewer, const char parent[], const char name[], PetscBool *has)
754: {
755: hid_t h5, dataset;
756: htri_t hhas;
757: PetscBool exists;
765: *has = PETSC_FALSE;
766: PetscViewerHDF5GetFileId(viewer, &h5);
767: PetscViewerHDF5HasObject(viewer, parent, H5O_TYPE_DATASET, &exists);
768: if (exists) {
769: #if (H5_VERS_MAJOR * 10000 + H5_VERS_MINOR * 100 + H5_VERS_RELEASE >= 10800)
770: PetscStackCall("H5Dopen2",dataset = H5Dopen2(h5, parent, H5P_DEFAULT));
771: #else
772: PetscStackCall("H5Dopen",dataset = H5Dopen(h5, parent));
773: #endif
774: if (dataset < 0) return(0);
775: PetscStackCall("H5Aexists",hhas = H5Aexists(dataset, name));
776: if (hhas < 0) {
777: PetscStackCallHDF5(H5Dclose,(dataset));
778: return(0);
779: }
780: PetscStackCallHDF5(H5Dclose,(dataset));
781: *has = hhas ? PETSC_TRUE : PETSC_FALSE;
782: }
783: return(0);
784: }
786: /*
787: The variable Petsc_Viewer_HDF5_keyval is used to indicate an MPI attribute that
788: is attached to a communicator, in this case the attribute is a PetscViewer.
789: */
790: static int Petsc_Viewer_HDF5_keyval = MPI_KEYVAL_INVALID;
794: /*@C
795: PETSC_VIEWER_HDF5_ - Creates an HDF5 PetscViewer shared by all processors in a communicator.
797: Collective on MPI_Comm
799: Input Parameter:
800: . comm - the MPI communicator to share the HDF5 PetscViewer
802: Level: intermediate
804: Options Database Keys:
805: . -viewer_hdf5_filename <name>
807: Environmental variables:
808: . PETSC_VIEWER_HDF5_FILENAME
810: Notes:
811: Unlike almost all other PETSc routines, PETSC_VIEWER_HDF5_ does not return
812: an error code. The HDF5 PetscViewer is usually used in the form
813: $ XXXView(XXX object, PETSC_VIEWER_HDF5_(comm));
815: .seealso: PetscViewerHDF5Open(), PetscViewerCreate(), PetscViewerDestroy()
816: @*/
817: PetscViewer PETSC_VIEWER_HDF5_(MPI_Comm comm)
818: {
820: PetscBool flg;
821: PetscViewer viewer;
822: char fname[PETSC_MAX_PATH_LEN];
823: MPI_Comm ncomm;
826: PetscCommDuplicate(comm,&ncomm,NULL);if (ierr) {PetscError(PETSC_COMM_SELF,__LINE__,"PETSC_VIEWER_HDF5_",__FILE__,PETSC_ERR_PLIB,PETSC_ERROR_INITIAL," ");return(0);}
827: if (Petsc_Viewer_HDF5_keyval == MPI_KEYVAL_INVALID) {
828: MPI_Keyval_create(MPI_NULL_COPY_FN,MPI_NULL_DELETE_FN,&Petsc_Viewer_HDF5_keyval,0);
829: if (ierr) {PetscError(PETSC_COMM_SELF,__LINE__,"PETSC_VIEWER_HDF5_",__FILE__,PETSC_ERR_PLIB,PETSC_ERROR_INITIAL," ");return(0);}
830: }
831: MPI_Attr_get(ncomm,Petsc_Viewer_HDF5_keyval,(void**)&viewer,(int*)&flg);
832: if (ierr) {PetscError(PETSC_COMM_SELF,__LINE__,"PETSC_VIEWER_HDF5_",__FILE__,PETSC_ERR_PLIB,PETSC_ERROR_INITIAL," ");return(0);}
833: if (!flg) { /* PetscViewer not yet created */
834: PetscOptionsGetenv(ncomm,"PETSC_VIEWER_HDF5_FILENAME",fname,PETSC_MAX_PATH_LEN,&flg);
835: if (ierr) {PetscError(PETSC_COMM_SELF,__LINE__,"PETSC_VIEWER_HDF5_",__FILE__,PETSC_ERR_PLIB,PETSC_ERROR_INITIAL," ");return(0);}
836: if (!flg) {
837: PetscStrcpy(fname,"output.h5");
838: if (ierr) {PetscError(PETSC_COMM_SELF,__LINE__,"PETSC_VIEWER_HDF5_",__FILE__,PETSC_ERR_PLIB,PETSC_ERROR_INITIAL," ");return(0);}
839: }
840: PetscViewerHDF5Open(ncomm,fname,FILE_MODE_WRITE,&viewer);
841: if (ierr) {PetscError(PETSC_COMM_SELF,__LINE__,"PETSC_VIEWER_HDF5_",__FILE__,PETSC_ERR_PLIB,PETSC_ERROR_INITIAL," ");return(0);}
842: PetscObjectRegisterDestroy((PetscObject)viewer);
843: if (ierr) {PetscError(PETSC_COMM_SELF,__LINE__,"PETSC_VIEWER_HDF5_",__FILE__,PETSC_ERR_PLIB,PETSC_ERROR_INITIAL," ");return(0);}
844: MPI_Attr_put(ncomm,Petsc_Viewer_HDF5_keyval,(void*)viewer);
845: if (ierr) {PetscError(PETSC_COMM_SELF,__LINE__,"PETSC_VIEWER_HDF5_",__FILE__,PETSC_ERR_PLIB,PETSC_ERROR_INITIAL," ");return(0);}
846: }
847: PetscCommDestroy(&ncomm);
848: if (ierr) {PetscError(PETSC_COMM_SELF,__LINE__,"PETSC_VIEWER_HDF5_",__FILE__,PETSC_ERR_PLIB,PETSC_ERROR_INITIAL," ");return(0);}
849: PetscFunctionReturn(viewer);
850: }