Actual source code: hdf5v.c

petsc-3.8.3 2017-12-09
Report Typos and Errors
  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;

 19: static PetscErrorCode PetscViewerSetFromOptions_HDF5(PetscOptionItems *PetscOptionsObject,PetscViewer v)
 20: {
 21:   PetscErrorCode   ierr;
 22:   PetscViewer_HDF5 *hdf5 = (PetscViewer_HDF5*)v->data;

 25:   PetscOptionsHead(PetscOptionsObject,"HDF5 PetscViewer Options");
 26:   PetscOptionsBool("-viewer_hdf5_base_dimension2","1d Vectors get 2 dimensions in HDF5","PetscViewerHDF5SetBaseDimension2",hdf5->basedimension2,&hdf5->basedimension2,NULL);
 27:   PetscOptionsBool("-viewer_hdf5_sp_output","Force data to be written in single precision","PetscViewerHDF5SetSPOutput",hdf5->spoutput,&hdf5->spoutput,NULL);
 28:   PetscOptionsTail();
 29:   return(0);
 30: }

 32: static PetscErrorCode PetscViewerFileClose_HDF5(PetscViewer viewer)
 33: {
 34:   PetscViewer_HDF5 *hdf5 = (PetscViewer_HDF5*)viewer->data;
 35:   PetscErrorCode   ierr;

 38:   PetscFree(hdf5->filename);
 39:   if (hdf5->file_id) PetscStackCallHDF5(H5Fclose,(hdf5->file_id));
 40:   return(0);
 41: }

 43: PetscErrorCode PetscViewerDestroy_HDF5(PetscViewer viewer)
 44: {
 45:   PetscViewer_HDF5 *hdf5 = (PetscViewer_HDF5*) viewer->data;
 46:   PetscErrorCode   ierr;

 49:   PetscViewerFileClose_HDF5(viewer);
 50:   while (hdf5->groups) {
 51:     GroupList *tmp = hdf5->groups->next;

 53:     PetscFree(hdf5->groups->name);
 54:     PetscFree(hdf5->groups);
 55:     hdf5->groups = tmp;
 56:   }
 57:   PetscFree(hdf5);
 58:   PetscObjectComposeFunction((PetscObject)viewer,"PetscViewerFileSetName_C",NULL);
 59:   PetscObjectComposeFunction((PetscObject)viewer,"PetscViewerFileGetName_C",NULL);
 60:   PetscObjectComposeFunction((PetscObject)viewer,"PetscViewerFileSetMode_C",NULL);
 61:   return(0);
 62: }

 64: PetscErrorCode  PetscViewerFileSetMode_HDF5(PetscViewer viewer, PetscFileMode type)
 65: {
 66:   PetscViewer_HDF5 *hdf5 = (PetscViewer_HDF5*) viewer->data;

 70:   hdf5->btype = type;
 71:   return(0);
 72: }

 74: PetscErrorCode  PetscViewerHDF5SetBaseDimension2_HDF5(PetscViewer viewer, PetscBool flg)
 75: {
 76:   PetscViewer_HDF5 *hdf5 = (PetscViewer_HDF5*) viewer->data;

 79:   hdf5->basedimension2 = flg;
 80:   return(0);
 81: }

 83: /*@
 84:      PetscViewerHDF5SetBaseDimension2 - Vectors of 1 dimension (i.e. bs/dof is 1) will be saved in the HDF5 file with a
 85:        dimension of 2.

 87:     Logically Collective on PetscViewer

 89:   Input Parameters:
 90: +  viewer - the PetscViewer; if it is not hdf5 then this command is ignored
 91: -  flg - if PETSC_TRUE the vector will always have at least a dimension of 2 even if that first dimension is of size 1

 93:   Options Database:
 94: .  -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


 97:   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
 98:          of one when the dimension is lower. Others think the option is crazy.

100:   Level: intermediate

102: .seealso: PetscViewerFileSetMode(), PetscViewerCreate(), PetscViewerSetType(), PetscViewerBinaryOpen()

104: @*/
105: PetscErrorCode PetscViewerHDF5SetBaseDimension2(PetscViewer viewer,PetscBool flg)
106: {

111:   PetscTryMethod(viewer,"PetscViewerHDF5SetBaseDimension2_C",(PetscViewer,PetscBool),(viewer,flg));
112:   return(0);
113: }

115: /*@
116:      PetscViewerHDF5GetBaseDimension2 - Vectors of 1 dimension (i.e. bs/dof is 1) will be saved in the HDF5 file with a
117:        dimension of 2.

119:     Logically Collective on PetscViewer

121:   Input Parameter:
122: .  viewer - the PetscViewer, must be of type HDF5

124:   Output Parameter:
125: .  flg - if PETSC_TRUE the vector will always have at least a dimension of 2 even if that first dimension is of size 1

127:   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
128:          of one when the dimension is lower. Others think the option is crazy.

130:   Level: intermediate

132: .seealso: PetscViewerFileSetMode(), PetscViewerCreate(), PetscViewerSetType(), PetscViewerBinaryOpen()

134: @*/
135: PetscErrorCode PetscViewerHDF5GetBaseDimension2(PetscViewer viewer,PetscBool *flg)
136: {
137:   PetscViewer_HDF5 *hdf5 = (PetscViewer_HDF5*) viewer->data;

141:   *flg = hdf5->basedimension2;
142:   return(0);
143: }

145: PetscErrorCode  PetscViewerHDF5SetSPOutput_HDF5(PetscViewer viewer, PetscBool flg)
146: {
147:   PetscViewer_HDF5 *hdf5 = (PetscViewer_HDF5*) viewer->data;

150:   hdf5->spoutput = flg;
151:   return(0);
152: }

154: /*@
155:      PetscViewerHDF5SetSPOutput - Data is written to disk in single precision even if PETSc is
156:        compiled with double precision PetscReal.

158:     Logically Collective on PetscViewer

160:   Input Parameters:
161: +  viewer - the PetscViewer; if it is not hdf5 then this command is ignored
162: -  flg - if PETSC_TRUE the data will be written to disk with single precision

164:   Options Database:
165: .  -viewer_hdf5_sp_output - turns on (true) or off (false) output in single precision


168:   Notes: Setting this option does not make any difference if PETSc is compiled with single precision
169:          in the first place. It does not affect reading datasets (HDF5 handle this internally).

171:   Level: intermediate

173: .seealso: PetscViewerFileSetMode(), PetscViewerCreate(), PetscViewerSetType(), PetscViewerBinaryOpen(),
174:           PetscReal

176: @*/
177: PetscErrorCode PetscViewerHDF5SetSPOutput(PetscViewer viewer,PetscBool flg)
178: {

183:   PetscTryMethod(viewer,"PetscViewerHDF5SetSPOutput_C",(PetscViewer,PetscBool),(viewer,flg));
184:   return(0);
185: }

187: /*@
188:      PetscViewerHDF5GetSPOutput - Data is written to disk in single precision even if PETSc is
189:        compiled with double precision PetscReal.

191:     Logically Collective on PetscViewer

193:   Input Parameter:
194: .  viewer - the PetscViewer, must be of type HDF5

196:   Output Parameter:
197: .  flg - if PETSC_TRUE the data will be written to disk with single precision

199:   Notes: Setting this option does not make any difference if PETSc is compiled with single precision
200:          in the first place. It does not affect reading datasets (HDF5 handle this internally).

202:   Level: intermediate

204: .seealso: PetscViewerFileSetMode(), PetscViewerCreate(), PetscViewerSetType(), PetscViewerBinaryOpen(),
205:           PetscReal

207: @*/
208: PetscErrorCode PetscViewerHDF5GetSPOutput(PetscViewer viewer,PetscBool *flg)
209: {
210:   PetscViewer_HDF5 *hdf5 = (PetscViewer_HDF5*) viewer->data;

214:   *flg = hdf5->spoutput;
215:   return(0);
216: }

218: PetscErrorCode  PetscViewerFileSetName_HDF5(PetscViewer viewer, const char name[])
219: {
220:   PetscViewer_HDF5 *hdf5 = (PetscViewer_HDF5*) viewer->data;
221: #if defined(PETSC_HAVE_H5PSET_FAPL_MPIO)
222:   MPI_Info          info = MPI_INFO_NULL;
223: #endif
224:   hid_t             plist_id;
225:   PetscErrorCode    ierr;

228:   if (hdf5->file_id) PetscStackCallHDF5(H5Fclose,(hdf5->file_id));
229:   if (hdf5->filename) {PetscFree(hdf5->filename);}
230:   PetscStrallocpy(name, &hdf5->filename);
231:   /* Set up file access property list with parallel I/O access */
232:   PetscStackCallHDF5Return(plist_id,H5Pcreate,(H5P_FILE_ACCESS));
233: #if defined(PETSC_HAVE_H5PSET_FAPL_MPIO)
234:   PetscStackCallHDF5(H5Pset_fapl_mpio,(plist_id, PetscObjectComm((PetscObject)viewer), info));
235: #endif
236:   /* Create or open the file collectively */
237:   switch (hdf5->btype) {
238:   case FILE_MODE_READ:
239:     PetscStackCallHDF5Return(hdf5->file_id,H5Fopen,(name, H5F_ACC_RDONLY, plist_id));
240:     break;
241:   case FILE_MODE_APPEND:
242:     PetscStackCallHDF5Return(hdf5->file_id,H5Fopen,(name, H5F_ACC_RDWR, plist_id));
243:     break;
244:   case FILE_MODE_WRITE:
245:     PetscStackCallHDF5Return(hdf5->file_id,H5Fcreate,(name, H5F_ACC_TRUNC, H5P_DEFAULT, plist_id));
246:     break;
247:   default:
248:     SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ORDER, "Must call PetscViewerFileSetMode() before PetscViewerFileSetName()");
249:   }
250:   if (hdf5->file_id < 0) SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_LIB, "H5Fcreate failed for %s", name);
251:   PetscStackCallHDF5(H5Pclose,(plist_id));
252:   return(0);
253: }

255: static PetscErrorCode PetscViewerFileGetName_HDF5(PetscViewer viewer,const char **name)
256: {
257:   PetscViewer_HDF5 *vhdf5 = (PetscViewer_HDF5*)viewer->data;

260:   *name = vhdf5->filename;
261:   return(0);
262: }

264: /*MC
265:    PETSCVIEWERHDF5 - A viewer that writes to an HDF5 file


268: .seealso:  PetscViewerHDF5Open(), PetscViewerStringSPrintf(), PetscViewerSocketOpen(), PetscViewerDrawOpen(), PETSCVIEWERSOCKET,
269:            PetscViewerCreate(), PetscViewerASCIIOpen(), PetscViewerBinaryOpen(), PETSCVIEWERBINARY, PETSCVIEWERDRAW, PETSCVIEWERSTRING,
270:            PetscViewerMatlabOpen(), VecView(), DMView(), PetscViewerMatlabPutArray(), PETSCVIEWERASCII, PETSCVIEWERMATLAB,
271:            PetscViewerFileSetName(), PetscViewerFileSetMode(), PetscViewerFormat, PetscViewerType, PetscViewerSetType()

273:   Level: beginner
274: M*/

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,"PetscViewerFileGetName_C",PetscViewerFileGetName_HDF5);
295:   PetscObjectComposeFunction((PetscObject)v,"PetscViewerFileSetMode_C",PetscViewerFileSetMode_HDF5);
296:   PetscObjectComposeFunction((PetscObject)v,"PetscViewerHDF5SetBaseDimension2_C",PetscViewerHDF5SetBaseDimension2_HDF5);
297:   PetscObjectComposeFunction((PetscObject)v,"PetscViewerHDF5SetSPOutput_C",PetscViewerHDF5SetSPOutput_HDF5);
298:   return(0);
299: }

301: /*@C
302:    PetscViewerHDF5Open - Opens a file for HDF5 input/output.

304:    Collective on MPI_Comm

306:    Input Parameters:
307: +  comm - MPI communicator
308: .  name - name of file
309: -  type - type of file
310: $    FILE_MODE_WRITE - create new file for binary output
311: $    FILE_MODE_READ - open existing file for binary input
312: $    FILE_MODE_APPEND - open existing file for binary output

314:    Output Parameter:
315: .  hdf5v - PetscViewer for HDF5 input/output to use with the specified file

317:   Options Database:
318: .  -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
319: .  -viewer_hdf5_sp_output - forces (if true) the viewer to write data in single precision independent on the precision of PetscReal

321:    Level: beginner

323:    Note:
324:    This PetscViewer should be destroyed with PetscViewerDestroy().

326:    Concepts: HDF5 files
327:    Concepts: PetscViewerHDF5^creating

329: .seealso: PetscViewerASCIIOpen(), PetscViewerPushFormat(), PetscViewerDestroy(), PetscViewerHDF5SetBaseDimension2(),
330:           PetscViewerHDF5SetSPOutput(), PetscViewerHDF5GetBaseDimension2(), VecView(), MatView(), VecLoad(),
331:           MatLoad(), PetscFileMode, PetscViewer
332: @*/
333: PetscErrorCode  PetscViewerHDF5Open(MPI_Comm comm, const char name[], PetscFileMode type, PetscViewer *hdf5v)
334: {

338:   PetscViewerCreate(comm, hdf5v);
339:   PetscViewerSetType(*hdf5v, PETSCVIEWERHDF5);
340:   PetscViewerFileSetMode(*hdf5v, type);
341:   PetscViewerFileSetName(*hdf5v, name);
342:   return(0);
343: }

345: /*@C
346:   PetscViewerHDF5GetFileId - Retrieve the file id, this file ID then can be used in direct HDF5 calls

348:   Not collective

350:   Input Parameter:
351: . viewer - the PetscViewer

353:   Output Parameter:
354: . file_id - The file id

356:   Level: intermediate

358: .seealso: PetscViewerHDF5Open()
359: @*/
360: PetscErrorCode  PetscViewerHDF5GetFileId(PetscViewer viewer, hid_t *file_id)
361: {
362:   PetscViewer_HDF5 *hdf5 = (PetscViewer_HDF5*) viewer->data;

366:   if (file_id) *file_id = hdf5->file_id;
367:   return(0);
368: }

370: /*@C
371:   PetscViewerHDF5PushGroup - Set the current HDF5 group for output

373:   Not collective

375:   Input Parameters:
376: + viewer - the PetscViewer
377: - name - The group name

379:   Level: intermediate

381: .seealso: PetscViewerHDF5Open(),PetscViewerHDF5PopGroup(),PetscViewerHDF5GetGroup()
382: @*/
383: PetscErrorCode  PetscViewerHDF5PushGroup(PetscViewer viewer, const char *name)
384: {
385:   PetscViewer_HDF5 *hdf5 = (PetscViewer_HDF5*) viewer->data;
386:   GroupList        *groupNode;
387:   PetscErrorCode   ierr;

392:   PetscNew(&groupNode);
393:   PetscStrallocpy(name, (char**) &groupNode->name);

395:   groupNode->next = hdf5->groups;
396:   hdf5->groups    = groupNode;
397:   return(0);
398: }

400: /*@
401:   PetscViewerHDF5PopGroup - Return the current HDF5 group for output to the previous value

403:   Not collective

405:   Input Parameter:
406: . viewer - the PetscViewer

408:   Level: intermediate

410: .seealso: PetscViewerHDF5Open(),PetscViewerHDF5PushGroup(),PetscViewerHDF5GetGroup()
411: @*/
412: PetscErrorCode  PetscViewerHDF5PopGroup(PetscViewer viewer)
413: {
414:   PetscViewer_HDF5 *hdf5 = (PetscViewer_HDF5*) viewer->data;
415:   GroupList        *groupNode;
416:   PetscErrorCode   ierr;

420:   if (!hdf5->groups) SETERRQ(PetscObjectComm((PetscObject)viewer), PETSC_ERR_ARG_WRONGSTATE, "HDF5 group stack is empty, cannot pop");
421:   groupNode    = hdf5->groups;
422:   hdf5->groups = hdf5->groups->next;
423:   PetscFree(groupNode->name);
424:   PetscFree(groupNode);
425:   return(0);
426: }

428: /*@C
429:   PetscViewerHDF5GetGroup - Get the current HDF5 group for output. If none has been assigned, returns NULL.

431:   Not collective

433:   Input Parameter:
434: . viewer - the PetscViewer

436:   Output Parameter:
437: . name - The group name

439:   Level: intermediate

441: .seealso: PetscViewerHDF5Open(),PetscViewerHDF5PushGroup(),PetscViewerHDF5PopGroup()
442: @*/
443: PetscErrorCode  PetscViewerHDF5GetGroup(PetscViewer viewer, const char **name)
444: {
445:   PetscViewer_HDF5 *hdf5 = (PetscViewer_HDF5 *) viewer->data;

450:   if (hdf5->groups) *name = hdf5->groups->name;
451:   else *name = NULL;
452:   return(0);
453: }

455: /*@
456:   PetscViewerHDF5IncrementTimestep - Increments the current timestep for the HDF5 output. Fields are stacked in time.

458:   Not collective

460:   Input Parameter:
461: . viewer - the PetscViewer

463:   Level: intermediate

465: .seealso: PetscViewerHDF5Open(), PetscViewerHDF5SetTimestep(), PetscViewerHDF5GetTimestep()
466: @*/
467: PetscErrorCode PetscViewerHDF5IncrementTimestep(PetscViewer viewer)
468: {
469:   PetscViewer_HDF5 *hdf5 = (PetscViewer_HDF5*) viewer->data;

473:   ++hdf5->timestep;
474:   return(0);
475: }

477: /*@
478:   PetscViewerHDF5SetTimestep - Set the current timestep for the HDF5 output. Fields are stacked in time. A timestep
479:   of -1 disables blocking with timesteps.

481:   Not collective

483:   Input Parameters:
484: + viewer - the PetscViewer
485: - timestep - The timestep number

487:   Level: intermediate

489: .seealso: PetscViewerHDF5Open(), PetscViewerHDF5IncrementTimestep(), PetscViewerHDF5GetTimestep()
490: @*/
491: PetscErrorCode  PetscViewerHDF5SetTimestep(PetscViewer viewer, PetscInt timestep)
492: {
493:   PetscViewer_HDF5 *hdf5 = (PetscViewer_HDF5*) viewer->data;

497:   hdf5->timestep = timestep;
498:   return(0);
499: }

501: /*@
502:   PetscViewerHDF5GetTimestep - Get the current timestep for the HDF5 output. Fields are stacked in time.

504:   Not collective

506:   Input Parameter:
507: . viewer - the PetscViewer

509:   Output Parameter:
510: . timestep - The timestep number

512:   Level: intermediate

514: .seealso: PetscViewerHDF5Open(), PetscViewerHDF5IncrementTimestep(), PetscViewerHDF5SetTimestep()
515: @*/
516: PetscErrorCode  PetscViewerHDF5GetTimestep(PetscViewer viewer, PetscInt *timestep)
517: {
518:   PetscViewer_HDF5 *hdf5 = (PetscViewer_HDF5*) viewer->data;

523:   *timestep = hdf5->timestep;
524:   return(0);
525: }

527: /*@C
528:   PetscDataTypeToHDF5DataType - Converts the PETSc name of a datatype to its HDF5 name.

530:   Not collective

532:   Input Parameter:
533: . ptype - the PETSc datatype name (for example PETSC_DOUBLE)

535:   Output Parameter:
536: . mtype - the MPI datatype (for example MPI_DOUBLE, ...)

538:   Level: advanced

540: .seealso: PetscDataType, PetscHDF5DataTypeToPetscDataType()
541: @*/
542: PetscErrorCode PetscDataTypeToHDF5DataType(PetscDataType ptype, hid_t *htype)
543: {
545:   if (ptype == PETSC_INT)
546: #if defined(PETSC_USE_64BIT_INDICES)
547:                                        *htype = H5T_NATIVE_LLONG;
548: #else
549:                                        *htype = H5T_NATIVE_INT;
550: #endif
551:   else if (ptype == PETSC_DOUBLE)      *htype = H5T_NATIVE_DOUBLE;
552:   else if (ptype == PETSC_LONG)        *htype = H5T_NATIVE_LONG;
553:   else if (ptype == PETSC_SHORT)       *htype = H5T_NATIVE_SHORT;
554:   else if (ptype == PETSC_ENUM)        *htype = H5T_NATIVE_DOUBLE;
555:   else if (ptype == PETSC_BOOL)        *htype = H5T_NATIVE_DOUBLE;
556:   else if (ptype == PETSC_FLOAT)       *htype = H5T_NATIVE_FLOAT;
557:   else if (ptype == PETSC_CHAR)        *htype = H5T_NATIVE_CHAR;
558:   else if (ptype == PETSC_BIT_LOGICAL) *htype = H5T_NATIVE_UCHAR;
559:   else if (ptype == PETSC_STRING)      *htype = H5Tcopy(H5T_C_S1);
560:   else SETERRQ(PETSC_COMM_SELF, PETSC_ERR_ARG_OUTOFRANGE, "Unsupported PETSc datatype");
561:   return(0);
562: }

564: /*@C
565:   PetscHDF5DataTypeToPetscDataType - Finds the PETSc name of a datatype from its HDF5 name

567:   Not collective

569:   Input Parameter:
570: . htype - the HDF5 datatype (for example H5T_NATIVE_DOUBLE, ...)

572:   Output Parameter:
573: . ptype - the PETSc datatype name (for example PETSC_DOUBLE)

575:   Level: advanced

577: .seealso: PetscDataType, PetscHDF5DataTypeToPetscDataType()
578: @*/
579: PetscErrorCode PetscHDF5DataTypeToPetscDataType(hid_t htype, PetscDataType *ptype)
580: {
582: #if defined(PETSC_USE_64BIT_INDICES)
583:   if      (htype == H5T_NATIVE_INT)    *ptype = PETSC_LONG;
584:   else if (htype == H5T_NATIVE_LLONG)  *ptype = PETSC_INT;
585: #else
586:   if      (htype == H5T_NATIVE_INT)    *ptype = PETSC_INT;
587: #endif
588:   else if (htype == H5T_NATIVE_DOUBLE) *ptype = PETSC_DOUBLE;
589:   else if (htype == H5T_NATIVE_LONG)   *ptype = PETSC_LONG;
590:   else if (htype == H5T_NATIVE_SHORT)  *ptype = PETSC_SHORT;
591:   else if (htype == H5T_NATIVE_FLOAT)  *ptype = PETSC_FLOAT;
592:   else if (htype == H5T_NATIVE_CHAR)   *ptype = PETSC_CHAR;
593:   else if (htype == H5T_NATIVE_UCHAR)  *ptype = PETSC_CHAR;
594:   else if (htype == H5T_C_S1)          *ptype = PETSC_STRING;
595:   else SETERRQ(PETSC_COMM_SELF, PETSC_ERR_ARG_OUTOFRANGE, "Unsupported HDF5 datatype");
596:   return(0);
597: }

599: /*@C
600:  PetscViewerHDF5WriteAttribute - Write a scalar attribute

602:   Input Parameters:
603: + viewer - The HDF5 viewer
604: . parent - The parent name
605: . name   - The attribute name
606: . datatype - The attribute type
607: - value    - The attribute value

609:   Level: advanced

611: .seealso: PetscViewerHDF5Open(), PetscViewerHDF5ReadAttribute(), PetscViewerHDF5HasAttribute()
612: @*/
613: PetscErrorCode PetscViewerHDF5WriteAttribute(PetscViewer viewer, const char parent[], const char name[], PetscDataType datatype, const void *value)
614: {
615:   hid_t          h5, dataspace, dataset, attribute, dtype;

623:   PetscDataTypeToHDF5DataType(datatype, &dtype);
624:   if (datatype == PETSC_STRING) {
625:     size_t len;
626:     PetscStrlen((const char *) value, &len);
627:     PetscStackCallHDF5(H5Tset_size,(dtype, len+1));
628:   }
629:   PetscViewerHDF5GetFileId(viewer, &h5);
630:   PetscStackCallHDF5Return(dataspace,H5Screate,(H5S_SCALAR));
631: #if (H5_VERS_MAJOR * 10000 + H5_VERS_MINOR * 100 + H5_VERS_RELEASE >= 10800)
632:   PetscStackCallHDF5Return(dataset,H5Dopen2,(h5, parent, H5P_DEFAULT));
633:   PetscStackCallHDF5Return(attribute,H5Acreate2,(dataset, name, dtype, dataspace, H5P_DEFAULT, H5P_DEFAULT));
634: #else
635:   PetscStackCallHDF5Return(dataset,H5Dopen,(h5, parent));
636:   PetscStackCallHDF5Return(attribute,H5Acreate,(dataset, name, dtype, dataspace, H5P_DEFAULT));
637: #endif
638:   PetscStackCallHDF5(H5Awrite,(attribute, dtype, value));
639:   if (datatype == PETSC_STRING) PetscStackCallHDF5(H5Tclose,(dtype));
640:   PetscStackCallHDF5(H5Aclose,(attribute));
641:   PetscStackCallHDF5(H5Dclose,(dataset));
642:   PetscStackCallHDF5(H5Sclose,(dataspace));
643:   return(0);
644: }

646: /*@C
647:  PetscViewerHDF5ReadAttribute - Read a scalar attribute

649:   Input Parameters:
650: + viewer - The HDF5 viewer
651: . parent - The parent name
652: . name   - The attribute name
653: - datatype - The attribute type

655:   Output Parameter:
656: . value    - The attribute value

658:   Level: advanced

660: .seealso: PetscViewerHDF5Open(), PetscViewerHDF5WriteAttribute(), PetscViewerHDF5HasAttribute()
661: @*/
662: PetscErrorCode PetscViewerHDF5ReadAttribute(PetscViewer viewer, const char parent[], const char name[], PetscDataType datatype, void *value)
663: {
664:   hid_t          h5, dataspace, dataset, attribute, dtype;

672:   PetscDataTypeToHDF5DataType(datatype, &dtype);
673:   PetscViewerHDF5GetFileId(viewer, &h5);
674:   PetscStackCallHDF5Return(dataspace,H5Screate,(H5S_SCALAR));
675: #if (H5_VERS_MAJOR * 10000 + H5_VERS_MINOR * 100 + H5_VERS_RELEASE >= 10800)
676:   PetscStackCallHDF5Return(dataset,H5Dopen2,(h5, parent, H5P_DEFAULT));
677: #else
678:   PetscStackCallHDF5Return(dataset,H5Dopen,(h5, parent));
679: #endif
680:   PetscStackCallHDF5Return(attribute,H5Aopen_name,(dataset, name));
681:   PetscStackCallHDF5(H5Aread,(attribute, dtype, value));
682:   PetscStackCallHDF5(H5Aclose,(attribute));
683:   PetscStackCallHDF5(H5Dclose,(dataset));
684:   PetscStackCallHDF5(H5Sclose,(dataspace));
685:   return(0);
686: }

688: static PetscErrorCode PetscViewerHDF5HasObject(PetscViewer viewer, const char name[], H5O_type_t otype, PetscBool *has)
689: {
690:   hid_t          h5;

697:   *has = PETSC_FALSE;
698:   PetscViewerHDF5GetFileId(viewer, &h5);
699:   if (H5Lexists(h5, name, H5P_DEFAULT)) {
700:     H5O_info_t info;
701:     hid_t      obj;

703:     PetscStackCallHDF5Return(obj,H5Oopen,(h5, name, H5P_DEFAULT));
704:     PetscStackCallHDF5(H5Oget_info,(obj, &info));
705:     if (otype == info.type) *has = PETSC_TRUE;
706:     PetscStackCallHDF5(H5Oclose,(obj));
707:   }
708:   return(0);
709: }

711: /*@C
712:  PetscViewerHDF5HasAttribute - Check whether a scalar attribute exists

714:   Input Parameters:
715: + viewer - The HDF5 viewer
716: . parent - The parent name
717: - name   - The attribute name

719:   Output Parameter:
720: . has    - Flag for attribute existence

722:   Level: advanced

724: .seealso: PetscViewerHDF5Open(), PetscViewerHDF5WriteAttribute(), PetscViewerHDF5ReadAttribute()
725: @*/
726: PetscErrorCode PetscViewerHDF5HasAttribute(PetscViewer viewer, const char parent[], const char name[], PetscBool *has)
727: {
728:   hid_t          h5, dataset;
729:   htri_t         hhas;
730:   PetscBool      exists;

738:   *has = PETSC_FALSE;
739:   PetscViewerHDF5GetFileId(viewer, &h5);
740:   PetscViewerHDF5HasObject(viewer, parent, H5O_TYPE_DATASET, &exists);
741:   if (exists) {
742: #if (H5_VERS_MAJOR * 10000 + H5_VERS_MINOR * 100 + H5_VERS_RELEASE >= 10800)
743:     PetscStackCall("H5Dopen2",dataset = H5Dopen2(h5, parent, H5P_DEFAULT));
744: #else
745:     PetscStackCall("H5Dopen",dataset = H5Dopen(h5, parent));
746: #endif
747:     if (dataset < 0) return(0);
748:     PetscStackCall("H5Aexists",hhas = H5Aexists(dataset, name));
749:     if (hhas < 0) {
750:       PetscStackCallHDF5(H5Dclose,(dataset));
751:       return(0);
752:     }
753:     PetscStackCallHDF5(H5Dclose,(dataset));
754:     *has = hhas ? PETSC_TRUE : PETSC_FALSE;
755:   }
756:   return(0);
757: }

759: /*
760:   The variable Petsc_Viewer_HDF5_keyval is used to indicate an MPI attribute that
761:   is attached to a communicator, in this case the attribute is a PetscViewer.
762: */
763: PetscMPIInt Petsc_Viewer_HDF5_keyval = MPI_KEYVAL_INVALID;

765: /*@C
766:   PETSC_VIEWER_HDF5_ - Creates an HDF5 PetscViewer shared by all processors in a communicator.

768:   Collective on MPI_Comm

770:   Input Parameter:
771: . comm - the MPI communicator to share the HDF5 PetscViewer

773:   Level: intermediate

775:   Options Database Keys:
776: . -viewer_hdf5_filename <name>

778:   Environmental variables:
779: . PETSC_VIEWER_HDF5_FILENAME

781:   Notes:
782:   Unlike almost all other PETSc routines, PETSC_VIEWER_HDF5_ does not return
783:   an error code.  The HDF5 PetscViewer is usually used in the form
784: $       XXXView(XXX object, PETSC_VIEWER_HDF5_(comm));

786: .seealso: PetscViewerHDF5Open(), PetscViewerCreate(), PetscViewerDestroy()
787: @*/
788: PetscViewer PETSC_VIEWER_HDF5_(MPI_Comm comm)
789: {
791:   PetscBool      flg;
792:   PetscViewer    viewer;
793:   char           fname[PETSC_MAX_PATH_LEN];
794:   MPI_Comm       ncomm;

797:   PetscCommDuplicate(comm,&ncomm,NULL);if (ierr) {PetscError(PETSC_COMM_SELF,__LINE__,"PETSC_VIEWER_HDF5_",__FILE__,PETSC_ERR_PLIB,PETSC_ERROR_INITIAL," ");return(0);}
798:   if (Petsc_Viewer_HDF5_keyval == MPI_KEYVAL_INVALID) {
799:     MPI_Keyval_create(MPI_NULL_COPY_FN,MPI_NULL_DELETE_FN,&Petsc_Viewer_HDF5_keyval,0);
800:     if (ierr) {PetscError(PETSC_COMM_SELF,__LINE__,"PETSC_VIEWER_HDF5_",__FILE__,PETSC_ERR_PLIB,PETSC_ERROR_INITIAL," ");return(0);}
801:   }
802:   MPI_Attr_get(ncomm,Petsc_Viewer_HDF5_keyval,(void**)&viewer,(int*)&flg);
803:   if (ierr) {PetscError(PETSC_COMM_SELF,__LINE__,"PETSC_VIEWER_HDF5_",__FILE__,PETSC_ERR_PLIB,PETSC_ERROR_INITIAL," ");return(0);}
804:   if (!flg) { /* PetscViewer not yet created */
805:     PetscOptionsGetenv(ncomm,"PETSC_VIEWER_HDF5_FILENAME",fname,PETSC_MAX_PATH_LEN,&flg);
806:     if (ierr) {PetscError(PETSC_COMM_SELF,__LINE__,"PETSC_VIEWER_HDF5_",__FILE__,PETSC_ERR_PLIB,PETSC_ERROR_INITIAL," ");return(0);}
807:     if (!flg) {
808:       PetscStrcpy(fname,"output.h5");
809:       if (ierr) {PetscError(PETSC_COMM_SELF,__LINE__,"PETSC_VIEWER_HDF5_",__FILE__,PETSC_ERR_PLIB,PETSC_ERROR_INITIAL," ");return(0);}
810:     }
811:     PetscViewerHDF5Open(ncomm,fname,FILE_MODE_WRITE,&viewer);
812:     if (ierr) {PetscError(PETSC_COMM_SELF,__LINE__,"PETSC_VIEWER_HDF5_",__FILE__,PETSC_ERR_PLIB,PETSC_ERROR_INITIAL," ");return(0);}
813:     PetscObjectRegisterDestroy((PetscObject)viewer);
814:     if (ierr) {PetscError(PETSC_COMM_SELF,__LINE__,"PETSC_VIEWER_HDF5_",__FILE__,PETSC_ERR_PLIB,PETSC_ERROR_INITIAL," ");return(0);}
815:     MPI_Attr_put(ncomm,Petsc_Viewer_HDF5_keyval,(void*)viewer);
816:     if (ierr) {PetscError(PETSC_COMM_SELF,__LINE__,"PETSC_VIEWER_HDF5_",__FILE__,PETSC_ERR_PLIB,PETSC_ERROR_INITIAL," ");return(0);}
817:   }
818:   PetscCommDestroy(&ncomm);
819:   if (ierr) {PetscError(PETSC_COMM_SELF,__LINE__,"PETSC_VIEWER_HDF5_",__FILE__,PETSC_ERR_PLIB,PETSC_ERROR_INITIAL," ");return(0);}
820:   PetscFunctionReturn(viewer);
821: }