Actual source code: hdf5v.c
petsc-3.12.2 2019-11-22
1: #include <petsc/private/viewerimpl.h>
2: #include <petsc/private/viewerhdf5impl.h>
3: #include <petscviewerhdf5.h> /*I "petscviewerhdf5.h" I*/
5: static PetscErrorCode PetscViewerHDF5Traverse_Internal(PetscViewer, const char[], PetscBool, PetscBool*, H5O_type_t*);
6: static PetscErrorCode PetscViewerHDF5HasAttribute_Internal(PetscViewer, const char[], const char[], PetscBool*);
8: static PetscErrorCode PetscViewerHDF5GetAbsolutePath_Internal(PetscViewer viewer, const char objname[], char **fullpath)
9: {
10: const char *group;
11: char buf[PETSC_MAX_PATH_LEN]="";
15: PetscViewerHDF5GetGroup(viewer, &group);
16: PetscStrcat(buf, group);
17: PetscStrcat(buf, "/");
18: PetscStrcat(buf, objname);
19: PetscStrallocpy(buf, fullpath);
20: return(0);
21: }
23: static PetscErrorCode PetscViewerHDF5CheckNamedObject_Internal(PetscViewer viewer, PetscObject obj)
24: {
25: PetscBool has;
26: const char *group;
30: if (!obj->name) SETERRQ(PetscObjectComm((PetscObject)viewer), PETSC_ERR_ARG_WRONG, "Object must be named");
31: PetscViewerHDF5HasObject(viewer, obj, &has);
32: if (!has) {
33: PetscViewerHDF5GetGroup(viewer, &group);
34: SETERRQ2(PetscObjectComm((PetscObject)viewer), PETSC_ERR_FILE_UNEXPECTED, "Object (dataset) %s not stored in group %s", obj->name, group);
35: }
36: return(0);
37: }
39: static PetscErrorCode PetscViewerSetFromOptions_HDF5(PetscOptionItems *PetscOptionsObject,PetscViewer v)
40: {
41: PetscErrorCode ierr;
42: PetscBool flg = PETSC_FALSE, set;
43: PetscViewer_HDF5 *hdf5 = (PetscViewer_HDF5*)v->data;
46: PetscOptionsHead(PetscOptionsObject,"HDF5 PetscViewer Options");
47: PetscOptionsBool("-viewer_hdf5_base_dimension2","1d Vectors get 2 dimensions in HDF5","PetscViewerHDF5SetBaseDimension2",hdf5->basedimension2,&hdf5->basedimension2,NULL);
48: PetscOptionsBool("-viewer_hdf5_sp_output","Force data to be written in single precision","PetscViewerHDF5SetSPOutput",hdf5->spoutput,&hdf5->spoutput,NULL);
49: PetscOptionsBool("-viewer_hdf5_collective","Enable collective transfer mode","PetscViewerHDF5SetCollective",flg,&flg,&set);
50: if (set) {PetscViewerHDF5SetCollective(v,flg);}
51: PetscOptionsTail();
52: return(0);
53: }
55: static PetscErrorCode PetscViewerView_HDF5(PetscViewer v,PetscViewer viewer)
56: {
57: PetscViewer_HDF5 *hdf5 = (PetscViewer_HDF5*)v->data;
58: PetscBool flg;
59: PetscErrorCode ierr;
62: if (hdf5->filename) {
63: PetscViewerASCIIPrintf(viewer,"Filename: %s\n",hdf5->filename);
64: }
65: PetscViewerASCIIPrintf(viewer,"Vectors with blocksize 1 saved as 2D datasets: %s\n",PetscBools[hdf5->basedimension2]);
66: PetscViewerASCIIPrintf(viewer,"Enforce single precision storage: %s\n",PetscBools[hdf5->spoutput]);
67: PetscViewerHDF5GetCollective(v,&flg);
68: PetscViewerASCIIPrintf(viewer,"MPI-IO transfer mode: %s\n",flg ? "collective" : "independent");
69: return(0);
70: }
72: static PetscErrorCode PetscViewerFileClose_HDF5(PetscViewer viewer)
73: {
74: PetscViewer_HDF5 *hdf5 = (PetscViewer_HDF5*)viewer->data;
75: PetscErrorCode ierr;
78: PetscFree(hdf5->filename);
79: if (hdf5->file_id) PetscStackCallHDF5(H5Fclose,(hdf5->file_id));
80: return(0);
81: }
83: static PetscErrorCode PetscViewerDestroy_HDF5(PetscViewer viewer)
84: {
85: PetscViewer_HDF5 *hdf5 = (PetscViewer_HDF5*) viewer->data;
86: PetscErrorCode ierr;
89: PetscStackCallHDF5(H5Pclose,(hdf5->dxpl_id));
90: PetscViewerFileClose_HDF5(viewer);
91: while (hdf5->groups) {
92: PetscViewerHDF5GroupList *tmp = hdf5->groups->next;
94: PetscFree(hdf5->groups->name);
95: PetscFree(hdf5->groups);
96: hdf5->groups = tmp;
97: }
98: PetscFree(hdf5);
99: PetscObjectComposeFunction((PetscObject)viewer,"PetscViewerFileSetName_C",NULL);
100: PetscObjectComposeFunction((PetscObject)viewer,"PetscViewerFileGetName_C",NULL);
101: PetscObjectComposeFunction((PetscObject)viewer,"PetscViewerFileSetMode_C",NULL);
102: PetscObjectComposeFunction((PetscObject)viewer,"PetscViewerHDF5SetBaseDimension2_C",NULL);
103: PetscObjectComposeFunction((PetscObject)viewer,"PetscViewerHDF5SetSPOutput_C",NULL);
104: return(0);
105: }
107: static PetscErrorCode PetscViewerFileSetMode_HDF5(PetscViewer viewer, PetscFileMode type)
108: {
109: PetscViewer_HDF5 *hdf5 = (PetscViewer_HDF5*) viewer->data;
112: hdf5->btype = type;
113: return(0);
114: }
116: static PetscErrorCode PetscViewerFileGetMode_HDF5(PetscViewer viewer, PetscFileMode *type)
117: {
118: PetscViewer_HDF5 *hdf5 = (PetscViewer_HDF5*) viewer->data;
121: *type = hdf5->btype;
122: return(0);
123: }
125: static PetscErrorCode PetscViewerHDF5SetBaseDimension2_HDF5(PetscViewer viewer, PetscBool flg)
126: {
127: PetscViewer_HDF5 *hdf5 = (PetscViewer_HDF5*) viewer->data;
130: hdf5->basedimension2 = flg;
131: return(0);
132: }
134: /*@
135: PetscViewerHDF5SetBaseDimension2 - Vectors of 1 dimension (i.e. bs/dof is 1) will be saved in the HDF5 file with a
136: dimension of 2.
138: Logically Collective on PetscViewer
140: Input Parameters:
141: + viewer - the PetscViewer; if it is not hdf5 then this command is ignored
142: - flg - if PETSC_TRUE the vector will always have at least a dimension of 2 even if that first dimension is of size 1
144: Options Database:
145: . -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
148: Notes:
149: Setting this option allegedly makes code that reads the HDF5 in easier since they do not have a "special case" of a bs/dof
150: of one when the dimension is lower. Others think the option is crazy.
152: Level: intermediate
154: .seealso: PetscViewerFileSetMode(), PetscViewerCreate(), PetscViewerSetType(), PetscViewerBinaryOpen()
156: @*/
157: PetscErrorCode PetscViewerHDF5SetBaseDimension2(PetscViewer viewer,PetscBool flg)
158: {
163: PetscTryMethod(viewer,"PetscViewerHDF5SetBaseDimension2_C",(PetscViewer,PetscBool),(viewer,flg));
164: return(0);
165: }
167: /*@
168: PetscViewerHDF5GetBaseDimension2 - Vectors of 1 dimension (i.e. bs/dof is 1) will be saved in the HDF5 file with a
169: dimension of 2.
171: Logically Collective on PetscViewer
173: Input Parameter:
174: . viewer - the PetscViewer, must be of type HDF5
176: Output Parameter:
177: . flg - if PETSC_TRUE the vector will always have at least a dimension of 2 even if that first dimension is of size 1
179: Notes:
180: Setting this option allegedly makes code that reads the HDF5 in easier since they do not have a "special case" of a bs/dof
181: of one when the dimension is lower. Others think the option is crazy.
183: Level: intermediate
185: .seealso: PetscViewerFileSetMode(), PetscViewerCreate(), PetscViewerSetType(), PetscViewerBinaryOpen()
187: @*/
188: PetscErrorCode PetscViewerHDF5GetBaseDimension2(PetscViewer viewer,PetscBool *flg)
189: {
190: PetscViewer_HDF5 *hdf5 = (PetscViewer_HDF5*) viewer->data;
194: *flg = hdf5->basedimension2;
195: return(0);
196: }
198: static PetscErrorCode PetscViewerHDF5SetSPOutput_HDF5(PetscViewer viewer, PetscBool flg)
199: {
200: PetscViewer_HDF5 *hdf5 = (PetscViewer_HDF5*) viewer->data;
203: hdf5->spoutput = flg;
204: return(0);
205: }
207: /*@
208: PetscViewerHDF5SetSPOutput - Data is written to disk in single precision even if PETSc is
209: compiled with double precision PetscReal.
211: Logically Collective on PetscViewer
213: Input Parameters:
214: + viewer - the PetscViewer; if it is not hdf5 then this command is ignored
215: - flg - if PETSC_TRUE the data will be written to disk with single precision
217: Options Database:
218: . -viewer_hdf5_sp_output - turns on (true) or off (false) output in single precision
221: Notes:
222: Setting this option does not make any difference if PETSc is compiled with single precision
223: in the first place. It does not affect reading datasets (HDF5 handle this internally).
225: Level: intermediate
227: .seealso: PetscViewerFileSetMode(), PetscViewerCreate(), PetscViewerSetType(), PetscViewerBinaryOpen(),
228: PetscReal
230: @*/
231: PetscErrorCode PetscViewerHDF5SetSPOutput(PetscViewer viewer,PetscBool flg)
232: {
237: PetscTryMethod(viewer,"PetscViewerHDF5SetSPOutput_C",(PetscViewer,PetscBool),(viewer,flg));
238: return(0);
239: }
241: /*@
242: PetscViewerHDF5GetSPOutput - Data is written to disk in single precision even if PETSc is
243: compiled with double precision PetscReal.
245: Logically Collective on PetscViewer
247: Input Parameter:
248: . viewer - the PetscViewer, must be of type HDF5
250: Output Parameter:
251: . flg - if PETSC_TRUE the data will be written to disk with single precision
253: Notes:
254: Setting this option does not make any difference if PETSc is compiled with single precision
255: in the first place. It does not affect reading datasets (HDF5 handle this internally).
257: Level: intermediate
259: .seealso: PetscViewerFileSetMode(), PetscViewerCreate(), PetscViewerSetType(), PetscViewerBinaryOpen(),
260: PetscReal
262: @*/
263: PetscErrorCode PetscViewerHDF5GetSPOutput(PetscViewer viewer,PetscBool *flg)
264: {
265: PetscViewer_HDF5 *hdf5 = (PetscViewer_HDF5*) viewer->data;
269: *flg = hdf5->spoutput;
270: return(0);
271: }
273: static PetscErrorCode PetscViewerHDF5SetCollective_HDF5(PetscViewer viewer, PetscBool flg)
274: {
276: /* H5FD_MPIO_COLLECTIVE is wrong in hdf5 1.10.2, and is the same as H5FD_MPIO_INDEPENDENT in earlier versions
277: - see e.g. https://gitlab.cosma.dur.ac.uk/swift/swiftsim/issues/431 */
278: #if H5_VERSION_GE(1,10,3)
279: {
280: PetscViewer_HDF5 *hdf5 = (PetscViewer_HDF5*) viewer->data;
281: PetscStackCallHDF5(H5Pset_dxpl_mpio,(hdf5->dxpl_id, flg ? H5FD_MPIO_COLLECTIVE : H5FD_MPIO_INDEPENDENT));
282: }
283: #else
284: if (flg) {
286: PetscPrintf(PetscObjectComm((PetscObject)viewer), "Warning: PetscViewerHDF5SetCollective(viewer,PETSC_TRUE) is ignored for HDF5 versions prior to 1.10.3\n");
287: }
288: #endif
289: return(0);
290: }
292: /*@
293: PetscViewerHDF5SetCollective - Use collective MPI-IO transfer mode for HDF5 reads and writes.
295: Logically Collective; flg must contain common value
297: Input Parameters:
298: + viewer - the PetscViewer; if it is not hdf5 then this command is ignored
299: - flg - PETSC_TRUE for collective mode; PETSC_FALSE for independent mode (default)
301: Options Database:
302: . -viewer_hdf5_collective - turns on (true) or off (false) collective transfers
304: Notes:
305: Collective mode gives the MPI-IO layer underneath HDF5 a chance to do some additional collective optimizations and hence can perform better.
306: However, this works correctly only since HDF5 1.10.3; hence, we ignore this setting for older versions.
308: Developer notes:
309: In the HDF5 layer, PETSC_TRUE / PETSC_FALSE means H5Pset_dxpl_mpio() is called with H5FD_MPIO_COLLECTIVE / H5FD_MPIO_INDEPENDENT, respectively.
310: This in turn means use of MPI_File_{read,write}_all / MPI_File_{read,write} in the MPI-IO layer, respectively.
311: See HDF5 documentation and MPI-IO documentation for details.
313: Level: intermediate
315: .seealso: PetscViewerHDF5GetCollective(), PetscViewerCreate(), PetscViewerSetType(), PetscViewerHDF5Open()
317: @*/
318: PetscErrorCode PetscViewerHDF5SetCollective(PetscViewer viewer,PetscBool flg)
319: {
325: PetscTryMethod(viewer,"PetscViewerHDF5SetCollective_C",(PetscViewer,PetscBool),(viewer,flg));
326: return(0);
327: }
329: static PetscErrorCode PetscViewerHDF5GetCollective_HDF5(PetscViewer viewer, PetscBool *flg)
330: {
331: PetscViewer_HDF5 *hdf5 = (PetscViewer_HDF5*) viewer->data;
332: H5FD_mpio_xfer_t mode;
335: PetscStackCallHDF5(H5Pget_dxpl_mpio,(hdf5->dxpl_id, &mode));
336: *flg = (mode == H5FD_MPIO_COLLECTIVE) ? PETSC_TRUE : PETSC_FALSE;
337: return(0);
338: }
340: /*@
341: PetscViewerHDF5GetCollective - Return flag whether collective MPI-IO transfer mode is used for HDF5 reads and writes.
343: Not Collective
345: Input Parameters:
346: . viewer - the HDF5 PetscViewer
348: Output Parameters:
349: . flg - the flag
351: Level: intermediate
353: Notes:
354: This setting works correctly only since HDF5 1.10.3. For older versions, PETSC_FALSE will be always returned.
355: For more details, see PetscViewerHDF5SetCollective().
357: .seealso: PetscViewerHDF5SetCollective(), PetscViewerCreate(), PetscViewerSetType(), PetscViewerHDF5Open()
359: @*/
360: PetscErrorCode PetscViewerHDF5GetCollective(PetscViewer viewer,PetscBool *flg)
361: {
368: PetscUseMethod(viewer,"PetscViewerHDF5GetCollective_C",(PetscViewer,PetscBool*),(viewer,flg));
369: return(0);
370: }
372: static PetscErrorCode PetscViewerFileSetName_HDF5(PetscViewer viewer, const char name[])
373: {
374: PetscViewer_HDF5 *hdf5 = (PetscViewer_HDF5*) viewer->data;
375: hid_t plist_id;
376: PetscErrorCode ierr;
379: if (hdf5->file_id) PetscStackCallHDF5(H5Fclose,(hdf5->file_id));
380: if (hdf5->filename) {PetscFree(hdf5->filename);}
381: PetscStrallocpy(name, &hdf5->filename);
382: /* Set up file access property list with parallel I/O access */
383: PetscStackCallHDF5Return(plist_id,H5Pcreate,(H5P_FILE_ACCESS));
384: PetscStackCallHDF5(H5Pset_fapl_mpio,(plist_id, PetscObjectComm((PetscObject)viewer), MPI_INFO_NULL));
385: /* Create or open the file collectively */
386: switch (hdf5->btype) {
387: case FILE_MODE_READ:
388: PetscStackCallHDF5Return(hdf5->file_id,H5Fopen,(name, H5F_ACC_RDONLY, plist_id));
389: break;
390: case FILE_MODE_APPEND:
391: PetscStackCallHDF5Return(hdf5->file_id,H5Fopen,(name, H5F_ACC_RDWR, plist_id));
392: break;
393: case FILE_MODE_WRITE:
394: PetscStackCallHDF5Return(hdf5->file_id,H5Fcreate,(name, H5F_ACC_TRUNC, H5P_DEFAULT, plist_id));
395: break;
396: default:
397: SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ORDER, "Must call PetscViewerFileSetMode() before PetscViewerFileSetName()");
398: }
399: if (hdf5->file_id < 0) SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_LIB, "H5Fcreate failed for %s", name);
400: PetscStackCallHDF5(H5Pclose,(plist_id));
401: return(0);
402: }
404: static PetscErrorCode PetscViewerFileGetName_HDF5(PetscViewer viewer,const char **name)
405: {
406: PetscViewer_HDF5 *vhdf5 = (PetscViewer_HDF5*)viewer->data;
409: *name = vhdf5->filename;
410: return(0);
411: }
413: static PetscErrorCode PetscViewerSetUp_HDF5(PetscViewer viewer)
414: {
415: /*
416: PetscViewer_HDF5 *hdf5 = (PetscViewer_HDF5*) viewer->data;
417: PetscErrorCode ierr;
418: */
421: return(0);
422: }
424: /*MC
425: PETSCVIEWERHDF5 - A viewer that writes to an HDF5 file
428: .seealso: PetscViewerHDF5Open(), PetscViewerStringSPrintf(), PetscViewerSocketOpen(), PetscViewerDrawOpen(), PETSCVIEWERSOCKET,
429: PetscViewerCreate(), PetscViewerASCIIOpen(), PetscViewerBinaryOpen(), PETSCVIEWERBINARY, PETSCVIEWERDRAW, PETSCVIEWERSTRING,
430: PetscViewerMatlabOpen(), VecView(), DMView(), PetscViewerMatlabPutArray(), PETSCVIEWERASCII, PETSCVIEWERMATLAB,
431: PetscViewerFileSetName(), PetscViewerFileSetMode(), PetscViewerFormat, PetscViewerType, PetscViewerSetType()
433: Level: beginner
434: M*/
436: PETSC_EXTERN PetscErrorCode PetscViewerCreate_HDF5(PetscViewer v)
437: {
438: PetscViewer_HDF5 *hdf5;
439: PetscErrorCode ierr;
442: PetscNewLog(v,&hdf5);
444: v->data = (void*) hdf5;
445: v->ops->destroy = PetscViewerDestroy_HDF5;
446: v->ops->setfromoptions = PetscViewerSetFromOptions_HDF5;
447: v->ops->setup = PetscViewerSetUp_HDF5;
448: v->ops->view = PetscViewerView_HDF5;
449: v->ops->flush = 0;
450: hdf5->btype = (PetscFileMode) -1;
451: hdf5->filename = 0;
452: hdf5->timestep = -1;
453: hdf5->groups = NULL;
455: PetscStackCallHDF5Return(hdf5->dxpl_id,H5Pcreate,(H5P_DATASET_XFER));
457: PetscObjectComposeFunction((PetscObject)v,"PetscViewerFileSetName_C",PetscViewerFileSetName_HDF5);
458: PetscObjectComposeFunction((PetscObject)v,"PetscViewerFileGetName_C",PetscViewerFileGetName_HDF5);
459: PetscObjectComposeFunction((PetscObject)v,"PetscViewerFileSetMode_C",PetscViewerFileSetMode_HDF5);
460: PetscObjectComposeFunction((PetscObject)v,"PetscViewerFileGetMode_C",PetscViewerFileGetMode_HDF5);
461: PetscObjectComposeFunction((PetscObject)v,"PetscViewerHDF5SetBaseDimension2_C",PetscViewerHDF5SetBaseDimension2_HDF5);
462: PetscObjectComposeFunction((PetscObject)v,"PetscViewerHDF5SetSPOutput_C",PetscViewerHDF5SetSPOutput_HDF5);
463: PetscObjectComposeFunction((PetscObject)v,"PetscViewerHDF5SetCollective_C",PetscViewerHDF5SetCollective_HDF5);
464: PetscObjectComposeFunction((PetscObject)v,"PetscViewerHDF5GetCollective_C",PetscViewerHDF5GetCollective_HDF5);
465: return(0);
466: }
468: /*@C
469: PetscViewerHDF5Open - Opens a file for HDF5 input/output.
471: Collective
473: Input Parameters:
474: + comm - MPI communicator
475: . name - name of file
476: - type - type of file
477: $ FILE_MODE_WRITE - create new file for binary output
478: $ FILE_MODE_READ - open existing file for binary input
479: $ FILE_MODE_APPEND - open existing file for binary output
481: Output Parameter:
482: . hdf5v - PetscViewer for HDF5 input/output to use with the specified file
484: Options Database:
485: + -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
486: - -viewer_hdf5_sp_output - forces (if true) the viewer to write data in single precision independent on the precision of PetscReal
488: Level: beginner
490: Note:
491: This PetscViewer should be destroyed with PetscViewerDestroy().
494: .seealso: PetscViewerASCIIOpen(), PetscViewerPushFormat(), PetscViewerDestroy(), PetscViewerHDF5SetBaseDimension2(),
495: PetscViewerHDF5SetSPOutput(), PetscViewerHDF5GetBaseDimension2(), VecView(), MatView(), VecLoad(),
496: MatLoad(), PetscFileMode, PetscViewer, PetscViewerSetType(), PetscViewerFileSetMode(), PetscViewerFileSetName()
497: @*/
498: PetscErrorCode PetscViewerHDF5Open(MPI_Comm comm, const char name[], PetscFileMode type, PetscViewer *hdf5v)
499: {
503: PetscViewerCreate(comm, hdf5v);
504: PetscViewerSetType(*hdf5v, PETSCVIEWERHDF5);
505: PetscViewerFileSetMode(*hdf5v, type);
506: PetscViewerFileSetName(*hdf5v, name);
507: PetscViewerSetFromOptions(*hdf5v);
508: return(0);
509: }
511: /*@C
512: PetscViewerHDF5GetFileId - Retrieve the file id, this file ID then can be used in direct HDF5 calls
514: Not collective
516: Input Parameter:
517: . viewer - the PetscViewer
519: Output Parameter:
520: . file_id - The file id
522: Level: intermediate
524: .seealso: PetscViewerHDF5Open()
525: @*/
526: PetscErrorCode PetscViewerHDF5GetFileId(PetscViewer viewer, hid_t *file_id)
527: {
528: PetscViewer_HDF5 *hdf5 = (PetscViewer_HDF5*) viewer->data;
532: if (file_id) *file_id = hdf5->file_id;
533: return(0);
534: }
536: /*@C
537: PetscViewerHDF5PushGroup - Set the current HDF5 group for output
539: Not collective
541: Input Parameters:
542: + viewer - the PetscViewer
543: - name - The group name
545: Level: intermediate
547: Note: The group name being NULL, empty string, or a sequence of all slashes (e.g. "///") is always internally stored as NULL and interpreted as "/".
549: .seealso: PetscViewerHDF5Open(),PetscViewerHDF5PopGroup(),PetscViewerHDF5GetGroup(),PetscViewerHDF5OpenGroup()
550: @*/
551: PetscErrorCode PetscViewerHDF5PushGroup(PetscViewer viewer, const char name[])
552: {
553: PetscViewer_HDF5 *hdf5 = (PetscViewer_HDF5*) viewer->data;
554: PetscViewerHDF5GroupList *groupNode;
555: PetscErrorCode ierr;
560: if (name && name[0]) {
561: size_t i,len;
562: PetscStrlen(name, &len);
563: for (i=0; i<len; i++) if (name[i] != '/') break;
564: if (i == len) name = NULL;
565: } else name = NULL;
566: PetscNew(&groupNode);
567: PetscStrallocpy(name, (char**) &groupNode->name);
568: groupNode->next = hdf5->groups;
569: hdf5->groups = groupNode;
570: return(0);
571: }
573: /*@
574: PetscViewerHDF5PopGroup - Return the current HDF5 group for output to the previous value
576: Not collective
578: Input Parameter:
579: . viewer - the PetscViewer
581: Level: intermediate
583: .seealso: PetscViewerHDF5Open(),PetscViewerHDF5PushGroup(),PetscViewerHDF5GetGroup(),PetscViewerHDF5OpenGroup()
584: @*/
585: PetscErrorCode PetscViewerHDF5PopGroup(PetscViewer viewer)
586: {
587: PetscViewer_HDF5 *hdf5 = (PetscViewer_HDF5*) viewer->data;
588: PetscViewerHDF5GroupList *groupNode;
589: PetscErrorCode ierr;
593: if (!hdf5->groups) SETERRQ(PetscObjectComm((PetscObject)viewer), PETSC_ERR_ARG_WRONGSTATE, "HDF5 group stack is empty, cannot pop");
594: groupNode = hdf5->groups;
595: hdf5->groups = hdf5->groups->next;
596: PetscFree(groupNode->name);
597: PetscFree(groupNode);
598: return(0);
599: }
601: /*@C
602: PetscViewerHDF5GetGroup - Get the current HDF5 group name (full path), set with PetscViewerHDF5PushGroup()/PetscViewerHDF5PopGroup().
603: If none has been assigned, returns NULL.
605: Not collective
607: Input Parameter:
608: . viewer - the PetscViewer
610: Output Parameter:
611: . name - The group name
613: Level: intermediate
615: .seealso: PetscViewerHDF5Open(),PetscViewerHDF5PushGroup(),PetscViewerHDF5PopGroup(),PetscViewerHDF5OpenGroup()
616: @*/
617: PetscErrorCode PetscViewerHDF5GetGroup(PetscViewer viewer, const char *name[])
618: {
619: PetscViewer_HDF5 *hdf5 = (PetscViewer_HDF5 *) viewer->data;
624: if (hdf5->groups) *name = hdf5->groups->name;
625: else *name = NULL;
626: return(0);
627: }
629: /*@
630: PetscViewerHDF5OpenGroup - Open the HDF5 group with the name (full path) returned by PetscViewerHDF5GetGroup(),
631: and return this group's ID and file ID.
632: If PetscViewerHDF5GetGroup() yields NULL, then group ID is file ID.
634: Not collective
636: Input Parameter:
637: . viewer - the PetscViewer
639: Output Parameter:
640: + fileId - The HDF5 file ID
641: - groupId - The HDF5 group ID
643: Notes:
644: If the viewer is writable, the group is created if it doesn't exist yet.
646: Level: intermediate
648: .seealso: PetscViewerHDF5Open(),PetscViewerHDF5PushGroup(),PetscViewerHDF5PopGroup(),PetscViewerHDF5GetGroup()
649: @*/
650: PetscErrorCode PetscViewerHDF5OpenGroup(PetscViewer viewer, hid_t *fileId, hid_t *groupId)
651: {
652: hid_t file_id;
653: H5O_type_t type;
654: const char *groupName = NULL;
655: PetscBool create;
659: PetscViewerWritable(viewer, &create);
660: PetscViewerHDF5GetFileId(viewer, &file_id);
661: PetscViewerHDF5GetGroup(viewer, &groupName);
662: PetscViewerHDF5Traverse_Internal(viewer, groupName, create, NULL, &type);
663: if (type != H5O_TYPE_GROUP) SETERRQ1(PetscObjectComm((PetscObject)viewer), PETSC_ERR_FILE_UNEXPECTED, "Path %s resolves to something which is not a group", groupName);
664: PetscStackCallHDF5Return(*groupId,H5Gopen2,(file_id, groupName ? groupName : "/", H5P_DEFAULT));
665: *fileId = file_id;
666: return(0);
667: }
669: /*@
670: PetscViewerHDF5IncrementTimestep - Increments the current timestep for the HDF5 output. Fields are stacked in time.
672: Not collective
674: Input Parameter:
675: . viewer - the PetscViewer
677: Level: intermediate
679: .seealso: PetscViewerHDF5Open(), PetscViewerHDF5SetTimestep(), PetscViewerHDF5GetTimestep()
680: @*/
681: PetscErrorCode PetscViewerHDF5IncrementTimestep(PetscViewer viewer)
682: {
683: PetscViewer_HDF5 *hdf5 = (PetscViewer_HDF5*) viewer->data;
687: ++hdf5->timestep;
688: return(0);
689: }
691: /*@
692: PetscViewerHDF5SetTimestep - Set the current timestep for the HDF5 output. Fields are stacked in time. A timestep
693: of -1 disables blocking with timesteps.
695: Not collective
697: Input Parameters:
698: + viewer - the PetscViewer
699: - timestep - The timestep number
701: Level: intermediate
703: .seealso: PetscViewerHDF5Open(), PetscViewerHDF5IncrementTimestep(), PetscViewerHDF5GetTimestep()
704: @*/
705: PetscErrorCode PetscViewerHDF5SetTimestep(PetscViewer viewer, PetscInt timestep)
706: {
707: PetscViewer_HDF5 *hdf5 = (PetscViewer_HDF5*) viewer->data;
711: hdf5->timestep = timestep;
712: return(0);
713: }
715: /*@
716: PetscViewerHDF5GetTimestep - Get the current timestep for the HDF5 output. Fields are stacked in time.
718: Not collective
720: Input Parameter:
721: . viewer - the PetscViewer
723: Output Parameter:
724: . timestep - The timestep number
726: Level: intermediate
728: .seealso: PetscViewerHDF5Open(), PetscViewerHDF5IncrementTimestep(), PetscViewerHDF5SetTimestep()
729: @*/
730: PetscErrorCode PetscViewerHDF5GetTimestep(PetscViewer viewer, PetscInt *timestep)
731: {
732: PetscViewer_HDF5 *hdf5 = (PetscViewer_HDF5*) viewer->data;
737: *timestep = hdf5->timestep;
738: return(0);
739: }
741: /*@C
742: PetscDataTypeToHDF5DataType - Converts the PETSc name of a datatype to its HDF5 name.
744: Not collective
746: Input Parameter:
747: . ptype - the PETSc datatype name (for example PETSC_DOUBLE)
749: Output Parameter:
750: . mtype - the MPI datatype (for example MPI_DOUBLE, ...)
752: Level: advanced
754: .seealso: PetscDataType, PetscHDF5DataTypeToPetscDataType()
755: @*/
756: PetscErrorCode PetscDataTypeToHDF5DataType(PetscDataType ptype, hid_t *htype)
757: {
759: if (ptype == PETSC_INT)
760: #if defined(PETSC_USE_64BIT_INDICES)
761: *htype = H5T_NATIVE_LLONG;
762: #else
763: *htype = H5T_NATIVE_INT;
764: #endif
765: else if (ptype == PETSC_DOUBLE) *htype = H5T_NATIVE_DOUBLE;
766: else if (ptype == PETSC_LONG) *htype = H5T_NATIVE_LONG;
767: else if (ptype == PETSC_SHORT) *htype = H5T_NATIVE_SHORT;
768: else if (ptype == PETSC_ENUM) *htype = H5T_NATIVE_INT;
769: else if (ptype == PETSC_BOOL) *htype = H5T_NATIVE_INT;
770: else if (ptype == PETSC_FLOAT) *htype = H5T_NATIVE_FLOAT;
771: else if (ptype == PETSC_CHAR) *htype = H5T_NATIVE_CHAR;
772: else if (ptype == PETSC_BIT_LOGICAL) *htype = H5T_NATIVE_UCHAR;
773: else if (ptype == PETSC_STRING) *htype = H5Tcopy(H5T_C_S1);
774: else SETERRQ(PETSC_COMM_SELF, PETSC_ERR_ARG_OUTOFRANGE, "Unsupported PETSc datatype");
775: return(0);
776: }
778: /*@C
779: PetscHDF5DataTypeToPetscDataType - Finds the PETSc name of a datatype from its HDF5 name
781: Not collective
783: Input Parameter:
784: . htype - the HDF5 datatype (for example H5T_NATIVE_DOUBLE, ...)
786: Output Parameter:
787: . ptype - the PETSc datatype name (for example PETSC_DOUBLE)
789: Level: advanced
791: .seealso: PetscDataType, PetscHDF5DataTypeToPetscDataType()
792: @*/
793: PetscErrorCode PetscHDF5DataTypeToPetscDataType(hid_t htype, PetscDataType *ptype)
794: {
796: #if defined(PETSC_USE_64BIT_INDICES)
797: if (htype == H5T_NATIVE_INT) *ptype = PETSC_LONG;
798: else if (htype == H5T_NATIVE_LLONG) *ptype = PETSC_INT;
799: #else
800: if (htype == H5T_NATIVE_INT) *ptype = PETSC_INT;
801: #endif
802: else if (htype == H5T_NATIVE_DOUBLE) *ptype = PETSC_DOUBLE;
803: else if (htype == H5T_NATIVE_LONG) *ptype = PETSC_LONG;
804: else if (htype == H5T_NATIVE_SHORT) *ptype = PETSC_SHORT;
805: else if (htype == H5T_NATIVE_FLOAT) *ptype = PETSC_FLOAT;
806: else if (htype == H5T_NATIVE_CHAR) *ptype = PETSC_CHAR;
807: else if (htype == H5T_NATIVE_UCHAR) *ptype = PETSC_CHAR;
808: else if (htype == H5T_C_S1) *ptype = PETSC_STRING;
809: else SETERRQ(PETSC_COMM_SELF, PETSC_ERR_ARG_OUTOFRANGE, "Unsupported HDF5 datatype");
810: return(0);
811: }
813: /*@C
814: PetscViewerHDF5WriteAttribute - Write an attribute
816: Input Parameters:
817: + viewer - The HDF5 viewer
818: . dataset - The parent dataset name, relative to the current group. NULL means a group-wise attribute.
819: . name - The attribute name
820: . datatype - The attribute type
821: - value - The attribute value
823: Level: advanced
825: .seealso: PetscViewerHDF5Open(), PetscViewerHDF5WriteObjectAttribute(), PetscViewerHDF5ReadAttribute(), PetscViewerHDF5HasAttribute(), PetscViewerHDF5PushGroup(),PetscViewerHDF5PopGroup(),PetscViewerHDF5GetGroup()
826: @*/
827: PetscErrorCode PetscViewerHDF5WriteAttribute(PetscViewer viewer, const char dataset[], const char name[], PetscDataType datatype, const void *value)
828: {
829: char *parent;
830: hid_t h5, dataspace, obj, attribute, dtype;
831: PetscBool has;
839: PetscViewerHDF5GetAbsolutePath_Internal(viewer, dataset, &parent);
840: PetscViewerHDF5Traverse_Internal(viewer, parent, PETSC_TRUE, NULL, NULL);
841: PetscViewerHDF5HasAttribute_Internal(viewer, parent, name, &has);
842: PetscDataTypeToHDF5DataType(datatype, &dtype);
843: if (datatype == PETSC_STRING) {
844: size_t len;
845: PetscStrlen((const char *) value, &len);
846: PetscStackCallHDF5(H5Tset_size,(dtype, len+1));
847: }
848: PetscViewerHDF5GetFileId(viewer, &h5);
849: PetscStackCallHDF5Return(dataspace,H5Screate,(H5S_SCALAR));
850: PetscStackCallHDF5Return(obj,H5Oopen,(h5, parent, H5P_DEFAULT));
851: if (has) {
852: PetscStackCallHDF5Return(attribute,H5Aopen_name,(obj, name));
853: } else {
854: PetscStackCallHDF5Return(attribute,H5Acreate2,(obj, name, dtype, dataspace, H5P_DEFAULT, H5P_DEFAULT));
855: }
856: PetscStackCallHDF5(H5Awrite,(attribute, dtype, value));
857: if (datatype == PETSC_STRING) PetscStackCallHDF5(H5Tclose,(dtype));
858: PetscStackCallHDF5(H5Aclose,(attribute));
859: PetscStackCallHDF5(H5Oclose,(obj));
860: PetscStackCallHDF5(H5Sclose,(dataspace));
861: PetscFree(parent);
862: return(0);
863: }
865: /*@C
866: PetscViewerHDF5WriteObjectAttribute - Write an attribute to the dataset matching the given PetscObject by name
868: Input Parameters:
869: + viewer - The HDF5 viewer
870: . obj - The object whose name is used to lookup the parent dataset, relative to the current group.
871: . name - The attribute name
872: . datatype - The attribute type
873: - value - The attribute value
875: Notes:
876: This fails if current_group/object_name doesn't resolve to a dataset (the path doesn't exist or is not a dataset).
877: You might want to check first if it does using PetscViewerHDF5HasObject().
879: Level: advanced
881: .seealso: PetscViewerHDF5Open(), PetscViewerHDF5WriteAttribute(), PetscViewerHDF5ReadObjectAttribute(), PetscViewerHDF5HasObjectAttribute(), PetscViewerHDF5HasObject(), PetscViewerHDF5PushGroup(),PetscViewerHDF5PopGroup(),PetscViewerHDF5GetGroup()
882: @*/
883: PetscErrorCode PetscViewerHDF5WriteObjectAttribute(PetscViewer viewer, PetscObject obj, const char name[], PetscDataType datatype, const void *value)
884: {
892: PetscViewerHDF5CheckNamedObject_Internal(viewer, obj);
893: PetscViewerHDF5WriteAttribute(viewer, obj->name, name, datatype, value);
894: return(0);
895: }
897: /*@C
898: PetscViewerHDF5ReadAttribute - Read an attribute
900: Input Parameters:
901: + viewer - The HDF5 viewer
902: . dataset - The parent dataset name, relative to the current group. NULL means a group-wise attribute.
903: . name - The attribute name
904: - datatype - The attribute type
906: Output Parameter:
907: . value - The attribute value
909: Level: advanced
911: .seealso: PetscViewerHDF5Open(), PetscViewerHDF5ReadObjectAttribute(), PetscViewerHDF5WriteAttribute(), PetscViewerHDF5HasAttribute(), PetscViewerHDF5HasObject(), PetscViewerHDF5PushGroup(),PetscViewerHDF5PopGroup(),PetscViewerHDF5GetGroup()
912: @*/
913: PetscErrorCode PetscViewerHDF5ReadAttribute(PetscViewer viewer, const char dataset[], const char name[], PetscDataType datatype, void *value)
914: {
915: char *parent;
916: hid_t h5, obj, attribute, atype, dtype;
917: PetscBool has;
925: PetscViewerHDF5GetAbsolutePath_Internal(viewer, dataset, &parent);
926: PetscViewerHDF5Traverse_Internal(viewer, parent, PETSC_FALSE, &has, NULL);
927: if (has) {PetscViewerHDF5HasAttribute_Internal(viewer, parent, name, &has);}
928: if (!has) SETERRQ2(PetscObjectComm((PetscObject)viewer), PETSC_ERR_FILE_UNEXPECTED, "Attribute %s/%s does not exist", parent, name);
929: PetscDataTypeToHDF5DataType(datatype, &dtype);
930: PetscViewerHDF5GetFileId(viewer, &h5);
931: PetscStackCallHDF5Return(obj,H5Oopen,(h5, parent, H5P_DEFAULT));
932: PetscStackCallHDF5Return(attribute,H5Aopen_name,(obj, name));
933: if (datatype == PETSC_STRING) {
934: size_t len;
935: PetscStackCallHDF5Return(atype,H5Aget_type,(attribute));
936: PetscStackCall("H5Tget_size",len = H5Tget_size(atype));
937: PetscStackCallHDF5(H5Tclose,(atype));
938: PetscMalloc((len+1) * sizeof(char *), &value);
939: }
940: PetscStackCallHDF5(H5Aread,(attribute, dtype, value));
941: PetscStackCallHDF5(H5Aclose,(attribute));
942: /* H5Oclose can be used to close groups, datasets, or committed datatypes */
943: PetscStackCallHDF5(H5Oclose,(obj));
944: PetscFree(parent);
945: return(0);
946: }
948: /*@C
949: PetscViewerHDF5ReadObjectAttribute - Read an attribute from the dataset matching the given PetscObject by name
951: Input Parameters:
952: + viewer - The HDF5 viewer
953: . obj - The object whose name is used to lookup the parent dataset, relative to the current group.
954: . name - The attribute name
955: - datatype - The attribute type
957: Output Parameter:
958: . value - The attribute value
960: Notes:
961: This fails if current_group/object_name doesn't resolve to a dataset (the path doesn't exist or is not a dataset).
962: You might want to check first if it does using PetscViewerHDF5HasObject().
964: Level: advanced
966: .seealso: PetscViewerHDF5Open(), PetscViewerHDF5ReadAttribute() PetscViewerHDF5WriteObjectAttribute(), PetscViewerHDF5HasObjectAttribute(), PetscViewerHDF5PushGroup(),PetscViewerHDF5PopGroup(),PetscViewerHDF5GetGroup()
967: @*/
968: PetscErrorCode PetscViewerHDF5ReadObjectAttribute(PetscViewer viewer, PetscObject obj, const char name[], PetscDataType datatype, void *value)
969: {
977: PetscViewerHDF5CheckNamedObject_Internal(viewer, obj);
978: PetscViewerHDF5ReadAttribute(viewer, obj->name, name, datatype, value);
979: return(0);
980: }
982: PETSC_STATIC_INLINE PetscErrorCode PetscViewerHDF5Traverse_Inner_Internal(hid_t h5, const char name[], PetscBool createGroup, PetscBool *exists_)
983: {
984: htri_t exists;
985: hid_t group;
988: PetscStackCallHDF5Return(exists,H5Lexists,(h5, name, H5P_DEFAULT));
989: if (exists) PetscStackCallHDF5Return(exists,H5Oexists_by_name,(h5, name, H5P_DEFAULT));
990: if (!exists && createGroup) {
991: PetscStackCallHDF5Return(group,H5Gcreate2,(h5, name, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT));
992: PetscStackCallHDF5(H5Gclose,(group));
993: exists = PETSC_TRUE;
994: }
995: *exists_ = (PetscBool) exists;
996: return(0);
997: }
999: static PetscErrorCode PetscViewerHDF5Traverse_Internal(PetscViewer viewer, const char name[], PetscBool createGroup, PetscBool *has, H5O_type_t *otype)
1000: {
1001: const char rootGroupName[] = "/";
1002: hid_t h5;
1003: PetscBool exists=PETSC_FALSE;
1004: PetscInt i;
1005: int n;
1006: char **hierarchy;
1007: char buf[PETSC_MAX_PATH_LEN]="";
1013: else name = rootGroupName;
1014: if (has) {
1016: *has = PETSC_FALSE;
1017: }
1018: if (otype) {
1020: *otype = H5O_TYPE_UNKNOWN;
1021: }
1022: PetscViewerHDF5GetFileId(viewer, &h5);
1024: /*
1025: Unfortunately, H5Oexists_by_name() fails if any object in hierarchy is missing.
1026: Hence, each of them needs to be tested separately:
1027: 1) whether it's a valid link
1028: 2) whether this link resolves to an object
1029: See H5Oexists_by_name() documentation.
1030: */
1031: PetscStrToArray(name,'/',&n,&hierarchy);
1032: if (!n) {
1033: /* Assume group "/" always exists in accordance with HDF5 >= 1.10.0. See H5Lexists() documentation. */
1034: if (has) *has = PETSC_TRUE;
1035: if (otype) *otype = H5O_TYPE_GROUP;
1036: PetscStrToArrayDestroy(n,hierarchy);
1037: return(0);
1038: }
1039: for (i=0; i<n; i++) {
1040: PetscStrcat(buf,"/");
1041: PetscStrcat(buf,hierarchy[i]);
1042: PetscViewerHDF5Traverse_Inner_Internal(h5, buf, createGroup, &exists);
1043: if (!exists) break;
1044: }
1045: PetscStrToArrayDestroy(n,hierarchy);
1047: /* If the object exists, get its type */
1048: if (exists && otype) {
1049: H5O_info_t info;
1051: /* We could use H5Iget_type() here but that would require opening the object. This way we only need its name. */
1052: PetscStackCallHDF5(H5Oget_info_by_name,(h5, name, &info, H5P_DEFAULT));
1053: *otype = info.type;
1054: }
1055: if (has) *has = exists;
1056: return(0);
1057: }
1059: /*@
1060: PetscViewerHDF5HasGroup - Check whether the current (pushed) group exists in the HDF5 file
1062: Input Parameters:
1063: . viewer - The HDF5 viewer
1065: Output Parameter:
1066: . has - Flag for group existence
1068: Notes:
1069: If the path exists but is not a group, this returns PETSC_FALSE as well.
1071: Level: advanced
1073: .seealso: PetscViewerHDF5Open(), PetscViewerHDF5PushGroup(), PetscViewerHDF5PopGroup(), PetscViewerHDF5OpenGroup()
1074: @*/
1075: PetscErrorCode PetscViewerHDF5HasGroup(PetscViewer viewer, PetscBool *has)
1076: {
1077: H5O_type_t type;
1078: const char *name;
1084: PetscViewerHDF5GetGroup(viewer, &name);
1085: PetscViewerHDF5Traverse_Internal(viewer, name, PETSC_FALSE, has, &type);
1086: *has = (type == H5O_TYPE_GROUP) ? PETSC_TRUE : PETSC_FALSE;
1087: return(0);
1088: }
1090: /*@
1091: PetscViewerHDF5HasObject - Check whether a dataset with the same name as given object exists in the HDF5 file under current group
1093: Input Parameters:
1094: + viewer - The HDF5 viewer
1095: - obj - The named object
1097: Output Parameter:
1098: . has - Flag for dataset existence; PETSC_FALSE for unnamed object
1100: Notes:
1101: If the path exists but is not a dataset, this returns PETSC_FALSE as well.
1103: Level: advanced
1105: .seealso: PetscViewerHDF5Open(), PetscViewerHDF5HasAttribute(), PetscViewerHDF5PushGroup(),PetscViewerHDF5PopGroup(),PetscViewerHDF5GetGroup()
1106: @*/
1107: PetscErrorCode PetscViewerHDF5HasObject(PetscViewer viewer, PetscObject obj, PetscBool *has)
1108: {
1109: H5O_type_t type;
1110: char *path;
1117: *has = PETSC_FALSE;
1118: if (!obj->name) return(0);
1119: PetscViewerHDF5GetAbsolutePath_Internal(viewer, obj->name, &path);
1120: PetscViewerHDF5Traverse_Internal(viewer, path, PETSC_FALSE, has, &type);
1121: *has = (type == H5O_TYPE_DATASET) ? PETSC_TRUE : PETSC_FALSE;
1122: PetscFree(path);
1123: return(0);
1124: }
1126: /*@C
1127: PetscViewerHDF5HasAttribute - Check whether an attribute exists
1129: Input Parameters:
1130: + viewer - The HDF5 viewer
1131: . dataset - The parent dataset name, relative to the current group. NULL means a group-wise attribute.
1132: - name - The attribute name
1134: Output Parameter:
1135: . has - Flag for attribute existence
1137: Level: advanced
1139: .seealso: PetscViewerHDF5Open(), PetscViewerHDF5HasObjectAttribute(), PetscViewerHDF5WriteAttribute(), PetscViewerHDF5ReadAttribute(), PetscViewerHDF5PushGroup(),PetscViewerHDF5PopGroup(),PetscViewerHDF5GetGroup()
1140: @*/
1141: PetscErrorCode PetscViewerHDF5HasAttribute(PetscViewer viewer, const char dataset[], const char name[], PetscBool *has)
1142: {
1143: char *parent;
1151: PetscViewerHDF5GetAbsolutePath_Internal(viewer, dataset, &parent);
1152: PetscViewerHDF5Traverse_Internal(viewer, parent, PETSC_FALSE, has, NULL);
1153: if (*has) {PetscViewerHDF5HasAttribute_Internal(viewer, parent, name, has);}
1154: PetscFree(parent);
1155: return(0);
1156: }
1158: /*@C
1159: PetscViewerHDF5HasObjectAttribute - Check whether an attribute is attached to the dataset matching the given PetscObject by name
1161: Input Parameters:
1162: + viewer - The HDF5 viewer
1163: . obj - The object whose name is used to lookup the parent dataset, relative to the current group.
1164: - name - The attribute name
1166: Output Parameter:
1167: . has - Flag for attribute existence
1169: Notes:
1170: This fails if current_group/object_name doesn't resolve to a dataset (the path doesn't exist or is not a dataset).
1171: You might want to check first if it does using PetscViewerHDF5HasObject().
1173: Level: advanced
1175: .seealso: PetscViewerHDF5Open(), PetscViewerHDF5HasAttribute(), PetscViewerHDF5WriteObjectAttribute(), PetscViewerHDF5ReadObjectAttribute(), PetscViewerHDF5HasObject(), PetscViewerHDF5PushGroup(),PetscViewerHDF5PopGroup(),PetscViewerHDF5GetGroup()
1176: @*/
1177: PetscErrorCode PetscViewerHDF5HasObjectAttribute(PetscViewer viewer, PetscObject obj, const char name[], PetscBool *has)
1178: {
1186: PetscViewerHDF5CheckNamedObject_Internal(viewer, obj);
1187: PetscViewerHDF5HasAttribute(viewer, obj->name, name, has);
1188: return(0);
1189: }
1191: static PetscErrorCode PetscViewerHDF5HasAttribute_Internal(PetscViewer viewer, const char parent[], const char name[], PetscBool *has)
1192: {
1193: hid_t h5;
1194: htri_t hhas;
1198: PetscViewerHDF5GetFileId(viewer, &h5);
1199: PetscStackCallHDF5Return(hhas,H5Aexists_by_name,(h5, parent, name, H5P_DEFAULT));
1200: *has = hhas ? PETSC_TRUE : PETSC_FALSE;
1201: return(0);
1202: }
1204: /*
1205: The variable Petsc_Viewer_HDF5_keyval is used to indicate an MPI attribute that
1206: is attached to a communicator, in this case the attribute is a PetscViewer.
1207: */
1208: PetscMPIInt Petsc_Viewer_HDF5_keyval = MPI_KEYVAL_INVALID;
1210: /*@C
1211: PETSC_VIEWER_HDF5_ - Creates an HDF5 PetscViewer shared by all processors in a communicator.
1213: Collective
1215: Input Parameter:
1216: . comm - the MPI communicator to share the HDF5 PetscViewer
1218: Level: intermediate
1220: Options Database Keys:
1221: . -viewer_hdf5_filename <name>
1223: Environmental variables:
1224: . PETSC_VIEWER_HDF5_FILENAME
1226: Notes:
1227: Unlike almost all other PETSc routines, PETSC_VIEWER_HDF5_ does not return
1228: an error code. The HDF5 PetscViewer is usually used in the form
1229: $ XXXView(XXX object, PETSC_VIEWER_HDF5_(comm));
1231: .seealso: PetscViewerHDF5Open(), PetscViewerCreate(), PetscViewerDestroy()
1232: @*/
1233: PetscViewer PETSC_VIEWER_HDF5_(MPI_Comm comm)
1234: {
1236: PetscBool flg;
1237: PetscViewer viewer;
1238: char fname[PETSC_MAX_PATH_LEN];
1239: MPI_Comm ncomm;
1242: PetscCommDuplicate(comm,&ncomm,NULL);if (ierr) {PetscError(PETSC_COMM_SELF,__LINE__,"PETSC_VIEWER_HDF5_",__FILE__,PETSC_ERR_PLIB,PETSC_ERROR_INITIAL," ");return(0);}
1243: if (Petsc_Viewer_HDF5_keyval == MPI_KEYVAL_INVALID) {
1244: MPI_Comm_create_keyval(MPI_COMM_NULL_COPY_FN,MPI_COMM_NULL_DELETE_FN,&Petsc_Viewer_HDF5_keyval,0);
1245: if (ierr) {PetscError(PETSC_COMM_SELF,__LINE__,"PETSC_VIEWER_HDF5_",__FILE__,PETSC_ERR_PLIB,PETSC_ERROR_INITIAL," ");return(0);}
1246: }
1247: MPI_Comm_get_attr(ncomm,Petsc_Viewer_HDF5_keyval,(void**)&viewer,(int*)&flg);
1248: if (ierr) {PetscError(PETSC_COMM_SELF,__LINE__,"PETSC_VIEWER_HDF5_",__FILE__,PETSC_ERR_PLIB,PETSC_ERROR_INITIAL," ");return(0);}
1249: if (!flg) { /* PetscViewer not yet created */
1250: PetscOptionsGetenv(ncomm,"PETSC_VIEWER_HDF5_FILENAME",fname,PETSC_MAX_PATH_LEN,&flg);
1251: if (ierr) {PetscError(PETSC_COMM_SELF,__LINE__,"PETSC_VIEWER_HDF5_",__FILE__,PETSC_ERR_PLIB,PETSC_ERROR_INITIAL," ");return(0);}
1252: if (!flg) {
1253: PetscStrcpy(fname,"output.h5");
1254: if (ierr) {PetscError(PETSC_COMM_SELF,__LINE__,"PETSC_VIEWER_HDF5_",__FILE__,PETSC_ERR_PLIB,PETSC_ERROR_INITIAL," ");return(0);}
1255: }
1256: PetscViewerHDF5Open(ncomm,fname,FILE_MODE_WRITE,&viewer);
1257: if (ierr) {PetscError(PETSC_COMM_SELF,__LINE__,"PETSC_VIEWER_HDF5_",__FILE__,PETSC_ERR_PLIB,PETSC_ERROR_INITIAL," ");return(0);}
1258: PetscObjectRegisterDestroy((PetscObject)viewer);
1259: if (ierr) {PetscError(PETSC_COMM_SELF,__LINE__,"PETSC_VIEWER_HDF5_",__FILE__,PETSC_ERR_PLIB,PETSC_ERROR_INITIAL," ");return(0);}
1260: MPI_Comm_set_attr(ncomm,Petsc_Viewer_HDF5_keyval,(void*)viewer);
1261: if (ierr) {PetscError(PETSC_COMM_SELF,__LINE__,"PETSC_VIEWER_HDF5_",__FILE__,PETSC_ERR_PLIB,PETSC_ERROR_INITIAL," ");return(0);}
1262: }
1263: PetscCommDestroy(&ncomm);
1264: if (ierr) {PetscError(PETSC_COMM_SELF,__LINE__,"PETSC_VIEWER_HDF5_",__FILE__,PETSC_ERR_PLIB,PETSC_ERROR_INITIAL," ");return(0);}
1265: PetscFunctionReturn(viewer);
1266: }