Actual source code: hdf5v.c

petsc-master 2019-12-03
Report Typos and Errors
  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) && defined(H5_HAVE_PARALLEL)
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 or if built without MPI support\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 and if HDF5 is installed for MPI; 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: #if defined(H5_HAVE_PARALLEL)
332:   PetscViewer_HDF5  *hdf5 = (PetscViewer_HDF5*) viewer->data;
333:   H5FD_mpio_xfer_t  mode;
334: #endif

337: #if !defined(H5_HAVE_PARALLEL)
338:   *flg = PETSC_FALSE;
339: #else
340:   PetscStackCallHDF5(H5Pget_dxpl_mpio,(hdf5->dxpl_id, &mode));
341:   *flg = (mode == H5FD_MPIO_COLLECTIVE) ? PETSC_TRUE : PETSC_FALSE;
342: #endif
343:   return(0);
344: }

346: /*@
347:   PetscViewerHDF5GetCollective - Return flag whether collective MPI-IO transfer mode is used for HDF5 reads and writes.

349:   Not Collective

351:   Input Parameters:
352: . viewer - the HDF5 PetscViewer

354:   Output Parameters:
355: . flg - the flag

357:   Level: intermediate

359:   Notes:
360:   This setting works correctly only since HDF5 1.10.3 and if HDF5 was installed for MPI. For older versions, PETSC_FALSE will be always returned.
361:   For more details, see PetscViewerHDF5SetCollective().

363: .seealso: PetscViewerHDF5SetCollective(), PetscViewerCreate(), PetscViewerSetType(), PetscViewerHDF5Open()

365: @*/
366: PetscErrorCode PetscViewerHDF5GetCollective(PetscViewer viewer,PetscBool *flg)
367: {


374:   PetscUseMethod(viewer,"PetscViewerHDF5GetCollective_C",(PetscViewer,PetscBool*),(viewer,flg));
375:   return(0);
376: }

378: static PetscErrorCode  PetscViewerFileSetName_HDF5(PetscViewer viewer, const char name[])
379: {
380:   PetscViewer_HDF5 *hdf5 = (PetscViewer_HDF5*) viewer->data;
381:   hid_t             plist_id;
382:   PetscErrorCode    ierr;

385:   if (hdf5->file_id) PetscStackCallHDF5(H5Fclose,(hdf5->file_id));
386:   if (hdf5->filename) {PetscFree(hdf5->filename);}
387:   PetscStrallocpy(name, &hdf5->filename);
388:   /* Set up file access property list with parallel I/O access */
389:   PetscStackCallHDF5Return(plist_id,H5Pcreate,(H5P_FILE_ACCESS));
390: #if defined(H5_HAVE_PARALLEL)
391:   PetscStackCallHDF5(H5Pset_fapl_mpio,(plist_id, PetscObjectComm((PetscObject)viewer), MPI_INFO_NULL));
392: #endif
393:   /* Create or open the file collectively */
394:   switch (hdf5->btype) {
395:   case FILE_MODE_READ:
396:     PetscStackCallHDF5Return(hdf5->file_id,H5Fopen,(name, H5F_ACC_RDONLY, plist_id));
397:     break;
398:   case FILE_MODE_APPEND:
399:     PetscStackCallHDF5Return(hdf5->file_id,H5Fopen,(name, H5F_ACC_RDWR, plist_id));
400:     break;
401:   case FILE_MODE_WRITE:
402:     PetscStackCallHDF5Return(hdf5->file_id,H5Fcreate,(name, H5F_ACC_TRUNC, H5P_DEFAULT, plist_id));
403:     break;
404:   default:
405:     SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ORDER, "Must call PetscViewerFileSetMode() before PetscViewerFileSetName()");
406:   }
407:   if (hdf5->file_id < 0) SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_LIB, "H5Fcreate failed for %s", name);
408:   PetscStackCallHDF5(H5Pclose,(plist_id));
409:   return(0);
410: }

412: static PetscErrorCode PetscViewerFileGetName_HDF5(PetscViewer viewer,const char **name)
413: {
414:   PetscViewer_HDF5 *vhdf5 = (PetscViewer_HDF5*)viewer->data;

417:   *name = vhdf5->filename;
418:   return(0);
419: }

421: static PetscErrorCode PetscViewerSetUp_HDF5(PetscViewer viewer)
422: {
423:   /*
424:   PetscViewer_HDF5 *hdf5 = (PetscViewer_HDF5*) viewer->data;
425:   PetscErrorCode   ierr;
426:   */

429:   return(0);
430: }

432: /*MC
433:    PETSCVIEWERHDF5 - A viewer that writes to an HDF5 file


436: .seealso:  PetscViewerHDF5Open(), PetscViewerStringSPrintf(), PetscViewerSocketOpen(), PetscViewerDrawOpen(), PETSCVIEWERSOCKET,
437:            PetscViewerCreate(), PetscViewerASCIIOpen(), PetscViewerBinaryOpen(), PETSCVIEWERBINARY, PETSCVIEWERDRAW, PETSCVIEWERSTRING,
438:            PetscViewerMatlabOpen(), VecView(), DMView(), PetscViewerMatlabPutArray(), PETSCVIEWERASCII, PETSCVIEWERMATLAB,
439:            PetscViewerFileSetName(), PetscViewerFileSetMode(), PetscViewerFormat, PetscViewerType, PetscViewerSetType()

441:   Level: beginner
442: M*/

444: PETSC_EXTERN PetscErrorCode PetscViewerCreate_HDF5(PetscViewer v)
445: {
446:   PetscViewer_HDF5 *hdf5;
447:   PetscErrorCode   ierr;

450:   PetscNewLog(v,&hdf5);

452:   v->data                = (void*) hdf5;
453:   v->ops->destroy        = PetscViewerDestroy_HDF5;
454:   v->ops->setfromoptions = PetscViewerSetFromOptions_HDF5;
455:   v->ops->setup          = PetscViewerSetUp_HDF5;
456:   v->ops->view           = PetscViewerView_HDF5;
457:   v->ops->flush          = 0;
458:   hdf5->btype            = (PetscFileMode) -1;
459:   hdf5->filename         = 0;
460:   hdf5->timestep         = -1;
461:   hdf5->groups           = NULL;

463:   PetscStackCallHDF5Return(hdf5->dxpl_id,H5Pcreate,(H5P_DATASET_XFER));

465:   PetscObjectComposeFunction((PetscObject)v,"PetscViewerFileSetName_C",PetscViewerFileSetName_HDF5);
466:   PetscObjectComposeFunction((PetscObject)v,"PetscViewerFileGetName_C",PetscViewerFileGetName_HDF5);
467:   PetscObjectComposeFunction((PetscObject)v,"PetscViewerFileSetMode_C",PetscViewerFileSetMode_HDF5);
468:   PetscObjectComposeFunction((PetscObject)v,"PetscViewerFileGetMode_C",PetscViewerFileGetMode_HDF5);
469:   PetscObjectComposeFunction((PetscObject)v,"PetscViewerHDF5SetBaseDimension2_C",PetscViewerHDF5SetBaseDimension2_HDF5);
470:   PetscObjectComposeFunction((PetscObject)v,"PetscViewerHDF5SetSPOutput_C",PetscViewerHDF5SetSPOutput_HDF5);
471:   PetscObjectComposeFunction((PetscObject)v,"PetscViewerHDF5SetCollective_C",PetscViewerHDF5SetCollective_HDF5);
472:   PetscObjectComposeFunction((PetscObject)v,"PetscViewerHDF5GetCollective_C",PetscViewerHDF5GetCollective_HDF5);
473:   return(0);
474: }

476: /*@C
477:    PetscViewerHDF5Open - Opens a file for HDF5 input/output.

479:    Collective

481:    Input Parameters:
482: +  comm - MPI communicator
483: .  name - name of file
484: -  type - type of file
485: $    FILE_MODE_WRITE - create new file for binary output
486: $    FILE_MODE_READ - open existing file for binary input
487: $    FILE_MODE_APPEND - open existing file for binary output

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

492:   Options Database:
493: +  -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
494: -  -viewer_hdf5_sp_output - forces (if true) the viewer to write data in single precision independent on the precision of PetscReal

496:    Level: beginner

498:    Note:
499:    This PetscViewer should be destroyed with PetscViewerDestroy().


502: .seealso: PetscViewerASCIIOpen(), PetscViewerPushFormat(), PetscViewerDestroy(), PetscViewerHDF5SetBaseDimension2(),
503:           PetscViewerHDF5SetSPOutput(), PetscViewerHDF5GetBaseDimension2(), VecView(), MatView(), VecLoad(),
504:           MatLoad(), PetscFileMode, PetscViewer, PetscViewerSetType(), PetscViewerFileSetMode(), PetscViewerFileSetName()
505: @*/
506: PetscErrorCode  PetscViewerHDF5Open(MPI_Comm comm, const char name[], PetscFileMode type, PetscViewer *hdf5v)
507: {

511:   PetscViewerCreate(comm, hdf5v);
512:   PetscViewerSetType(*hdf5v, PETSCVIEWERHDF5);
513:   PetscViewerFileSetMode(*hdf5v, type);
514:   PetscViewerFileSetName(*hdf5v, name);
515:   PetscViewerSetFromOptions(*hdf5v);
516:   return(0);
517: }

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

522:   Not collective

524:   Input Parameter:
525: . viewer - the PetscViewer

527:   Output Parameter:
528: . file_id - The file id

530:   Level: intermediate

532: .seealso: PetscViewerHDF5Open()
533: @*/
534: PetscErrorCode  PetscViewerHDF5GetFileId(PetscViewer viewer, hid_t *file_id)
535: {
536:   PetscViewer_HDF5 *hdf5 = (PetscViewer_HDF5*) viewer->data;

540:   if (file_id) *file_id = hdf5->file_id;
541:   return(0);
542: }

544: /*@C
545:   PetscViewerHDF5PushGroup - Set the current HDF5 group for output

547:   Not collective

549:   Input Parameters:
550: + viewer - the PetscViewer
551: - name - The group name

553:   Level: intermediate

555:   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 "/".

557: .seealso: PetscViewerHDF5Open(),PetscViewerHDF5PopGroup(),PetscViewerHDF5GetGroup(),PetscViewerHDF5OpenGroup()
558: @*/
559: PetscErrorCode  PetscViewerHDF5PushGroup(PetscViewer viewer, const char name[])
560: {
561:   PetscViewer_HDF5 *hdf5 = (PetscViewer_HDF5*) viewer->data;
562:   PetscViewerHDF5GroupList *groupNode;
563:   PetscErrorCode   ierr;

568:   if (name && name[0]) {
569:      size_t i,len;
570:      PetscStrlen(name, &len);
571:      for (i=0; i<len; i++) if (name[i] != '/') break;
572:      if (i == len) name = NULL;
573:   } else name = NULL;
574:   PetscNew(&groupNode);
575:   PetscStrallocpy(name, (char**) &groupNode->name);
576:   groupNode->next = hdf5->groups;
577:   hdf5->groups    = groupNode;
578:   return(0);
579: }

581: /*@
582:   PetscViewerHDF5PopGroup - Return the current HDF5 group for output to the previous value

584:   Not collective

586:   Input Parameter:
587: . viewer - the PetscViewer

589:   Level: intermediate

591: .seealso: PetscViewerHDF5Open(),PetscViewerHDF5PushGroup(),PetscViewerHDF5GetGroup(),PetscViewerHDF5OpenGroup()
592: @*/
593: PetscErrorCode  PetscViewerHDF5PopGroup(PetscViewer viewer)
594: {
595:   PetscViewer_HDF5 *hdf5 = (PetscViewer_HDF5*) viewer->data;
596:   PetscViewerHDF5GroupList *groupNode;
597:   PetscErrorCode   ierr;

601:   if (!hdf5->groups) SETERRQ(PetscObjectComm((PetscObject)viewer), PETSC_ERR_ARG_WRONGSTATE, "HDF5 group stack is empty, cannot pop");
602:   groupNode    = hdf5->groups;
603:   hdf5->groups = hdf5->groups->next;
604:   PetscFree(groupNode->name);
605:   PetscFree(groupNode);
606:   return(0);
607: }

609: /*@C
610:   PetscViewerHDF5GetGroup - Get the current HDF5 group name (full path), set with PetscViewerHDF5PushGroup()/PetscViewerHDF5PopGroup().
611:   If none has been assigned, returns NULL.

613:   Not collective

615:   Input Parameter:
616: . viewer - the PetscViewer

618:   Output Parameter:
619: . name - The group name

621:   Level: intermediate

623: .seealso: PetscViewerHDF5Open(),PetscViewerHDF5PushGroup(),PetscViewerHDF5PopGroup(),PetscViewerHDF5OpenGroup()
624: @*/
625: PetscErrorCode  PetscViewerHDF5GetGroup(PetscViewer viewer, const char *name[])
626: {
627:   PetscViewer_HDF5 *hdf5 = (PetscViewer_HDF5 *) viewer->data;

632:   if (hdf5->groups) *name = hdf5->groups->name;
633:   else *name = NULL;
634:   return(0);
635: }

637: /*@
638:   PetscViewerHDF5OpenGroup - Open the HDF5 group with the name (full path) returned by PetscViewerHDF5GetGroup(),
639:   and return this group's ID and file ID.
640:   If PetscViewerHDF5GetGroup() yields NULL, then group ID is file ID.

642:   Not collective

644:   Input Parameter:
645: . viewer - the PetscViewer

647:   Output Parameter:
648: + fileId - The HDF5 file ID
649: - groupId - The HDF5 group ID

651:   Notes:
652:   If the viewer is writable, the group is created if it doesn't exist yet.

654:   Level: intermediate

656: .seealso: PetscViewerHDF5Open(),PetscViewerHDF5PushGroup(),PetscViewerHDF5PopGroup(),PetscViewerHDF5GetGroup()
657: @*/
658: PetscErrorCode PetscViewerHDF5OpenGroup(PetscViewer viewer, hid_t *fileId, hid_t *groupId)
659: {
660:   hid_t          file_id;
661:   H5O_type_t     type;
662:   const char     *groupName = NULL;
663:   PetscBool      create;

667:   PetscViewerWritable(viewer, &create);
668:   PetscViewerHDF5GetFileId(viewer, &file_id);
669:   PetscViewerHDF5GetGroup(viewer, &groupName);
670:   PetscViewerHDF5Traverse_Internal(viewer, groupName, create, NULL, &type);
671:   if (type != H5O_TYPE_GROUP) SETERRQ1(PetscObjectComm((PetscObject)viewer), PETSC_ERR_FILE_UNEXPECTED, "Path %s resolves to something which is not a group", groupName);
672:   PetscStackCallHDF5Return(*groupId,H5Gopen2,(file_id, groupName ? groupName : "/", H5P_DEFAULT));
673:   *fileId  = file_id;
674:   return(0);
675: }

677: /*@
678:   PetscViewerHDF5IncrementTimestep - Increments the current timestep for the HDF5 output. Fields are stacked in time.

680:   Not collective

682:   Input Parameter:
683: . viewer - the PetscViewer

685:   Level: intermediate

687: .seealso: PetscViewerHDF5Open(), PetscViewerHDF5SetTimestep(), PetscViewerHDF5GetTimestep()
688: @*/
689: PetscErrorCode PetscViewerHDF5IncrementTimestep(PetscViewer viewer)
690: {
691:   PetscViewer_HDF5 *hdf5 = (PetscViewer_HDF5*) viewer->data;

695:   ++hdf5->timestep;
696:   return(0);
697: }

699: /*@
700:   PetscViewerHDF5SetTimestep - Set the current timestep for the HDF5 output. Fields are stacked in time. A timestep
701:   of -1 disables blocking with timesteps.

703:   Not collective

705:   Input Parameters:
706: + viewer - the PetscViewer
707: - timestep - The timestep number

709:   Level: intermediate

711: .seealso: PetscViewerHDF5Open(), PetscViewerHDF5IncrementTimestep(), PetscViewerHDF5GetTimestep()
712: @*/
713: PetscErrorCode  PetscViewerHDF5SetTimestep(PetscViewer viewer, PetscInt timestep)
714: {
715:   PetscViewer_HDF5 *hdf5 = (PetscViewer_HDF5*) viewer->data;

719:   hdf5->timestep = timestep;
720:   return(0);
721: }

723: /*@
724:   PetscViewerHDF5GetTimestep - Get the current timestep for the HDF5 output. Fields are stacked in time.

726:   Not collective

728:   Input Parameter:
729: . viewer - the PetscViewer

731:   Output Parameter:
732: . timestep - The timestep number

734:   Level: intermediate

736: .seealso: PetscViewerHDF5Open(), PetscViewerHDF5IncrementTimestep(), PetscViewerHDF5SetTimestep()
737: @*/
738: PetscErrorCode  PetscViewerHDF5GetTimestep(PetscViewer viewer, PetscInt *timestep)
739: {
740:   PetscViewer_HDF5 *hdf5 = (PetscViewer_HDF5*) viewer->data;

745:   *timestep = hdf5->timestep;
746:   return(0);
747: }

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

752:   Not collective

754:   Input Parameter:
755: . ptype - the PETSc datatype name (for example PETSC_DOUBLE)

757:   Output Parameter:
758: . mtype - the MPI datatype (for example MPI_DOUBLE, ...)

760:   Level: advanced

762: .seealso: PetscDataType, PetscHDF5DataTypeToPetscDataType()
763: @*/
764: PetscErrorCode PetscDataTypeToHDF5DataType(PetscDataType ptype, hid_t *htype)
765: {
767:   if (ptype == PETSC_INT)
768: #if defined(PETSC_USE_64BIT_INDICES)
769:                                        *htype = H5T_NATIVE_LLONG;
770: #else
771:                                        *htype = H5T_NATIVE_INT;
772: #endif
773:   else if (ptype == PETSC_DOUBLE)      *htype = H5T_NATIVE_DOUBLE;
774:   else if (ptype == PETSC_LONG)        *htype = H5T_NATIVE_LONG;
775:   else if (ptype == PETSC_SHORT)       *htype = H5T_NATIVE_SHORT;
776:   else if (ptype == PETSC_ENUM)        *htype = H5T_NATIVE_INT;
777:   else if (ptype == PETSC_BOOL)        *htype = H5T_NATIVE_INT;
778:   else if (ptype == PETSC_FLOAT)       *htype = H5T_NATIVE_FLOAT;
779:   else if (ptype == PETSC_CHAR)        *htype = H5T_NATIVE_CHAR;
780:   else if (ptype == PETSC_BIT_LOGICAL) *htype = H5T_NATIVE_UCHAR;
781:   else if (ptype == PETSC_STRING)      *htype = H5Tcopy(H5T_C_S1);
782:   else SETERRQ(PETSC_COMM_SELF, PETSC_ERR_ARG_OUTOFRANGE, "Unsupported PETSc datatype");
783:   return(0);
784: }

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

789:   Not collective

791:   Input Parameter:
792: . htype - the HDF5 datatype (for example H5T_NATIVE_DOUBLE, ...)

794:   Output Parameter:
795: . ptype - the PETSc datatype name (for example PETSC_DOUBLE)

797:   Level: advanced

799: .seealso: PetscDataType, PetscHDF5DataTypeToPetscDataType()
800: @*/
801: PetscErrorCode PetscHDF5DataTypeToPetscDataType(hid_t htype, PetscDataType *ptype)
802: {
804: #if defined(PETSC_USE_64BIT_INDICES)
805:   if      (htype == H5T_NATIVE_INT)    *ptype = PETSC_LONG;
806:   else if (htype == H5T_NATIVE_LLONG)  *ptype = PETSC_INT;
807: #else
808:   if      (htype == H5T_NATIVE_INT)    *ptype = PETSC_INT;
809: #endif
810:   else if (htype == H5T_NATIVE_DOUBLE) *ptype = PETSC_DOUBLE;
811:   else if (htype == H5T_NATIVE_LONG)   *ptype = PETSC_LONG;
812:   else if (htype == H5T_NATIVE_SHORT)  *ptype = PETSC_SHORT;
813:   else if (htype == H5T_NATIVE_FLOAT)  *ptype = PETSC_FLOAT;
814:   else if (htype == H5T_NATIVE_CHAR)   *ptype = PETSC_CHAR;
815:   else if (htype == H5T_NATIVE_UCHAR)  *ptype = PETSC_CHAR;
816:   else if (htype == H5T_C_S1)          *ptype = PETSC_STRING;
817:   else SETERRQ(PETSC_COMM_SELF, PETSC_ERR_ARG_OUTOFRANGE, "Unsupported HDF5 datatype");
818:   return(0);
819: }

821: /*@C
822:  PetscViewerHDF5WriteAttribute - Write an attribute

824:   Input Parameters:
825: + viewer - The HDF5 viewer
826: . dataset - The parent dataset name, relative to the current group. NULL means a group-wise attribute.
827: . name   - The attribute name
828: . datatype - The attribute type
829: - value    - The attribute value

831:   Level: advanced

833: .seealso: PetscViewerHDF5Open(), PetscViewerHDF5WriteObjectAttribute(), PetscViewerHDF5ReadAttribute(), PetscViewerHDF5HasAttribute(), PetscViewerHDF5PushGroup(),PetscViewerHDF5PopGroup(),PetscViewerHDF5GetGroup()
834: @*/
835: PetscErrorCode PetscViewerHDF5WriteAttribute(PetscViewer viewer, const char dataset[], const char name[], PetscDataType datatype, const void *value)
836: {
837:   char           *parent;
838:   hid_t          h5, dataspace, obj, attribute, dtype;
839:   PetscBool      has;

847:   PetscViewerHDF5GetAbsolutePath_Internal(viewer, dataset, &parent);
848:   PetscViewerHDF5Traverse_Internal(viewer, parent, PETSC_TRUE, NULL, NULL);
849:   PetscViewerHDF5HasAttribute_Internal(viewer, parent, name, &has);
850:   PetscDataTypeToHDF5DataType(datatype, &dtype);
851:   if (datatype == PETSC_STRING) {
852:     size_t len;
853:     PetscStrlen((const char *) value, &len);
854:     PetscStackCallHDF5(H5Tset_size,(dtype, len+1));
855:   }
856:   PetscViewerHDF5GetFileId(viewer, &h5);
857:   PetscStackCallHDF5Return(dataspace,H5Screate,(H5S_SCALAR));
858:   PetscStackCallHDF5Return(obj,H5Oopen,(h5, parent, H5P_DEFAULT));
859:   if (has) {
860:     PetscStackCallHDF5Return(attribute,H5Aopen_name,(obj, name));
861:   } else {
862:     PetscStackCallHDF5Return(attribute,H5Acreate2,(obj, name, dtype, dataspace, H5P_DEFAULT, H5P_DEFAULT));
863:   }
864:   PetscStackCallHDF5(H5Awrite,(attribute, dtype, value));
865:   if (datatype == PETSC_STRING) PetscStackCallHDF5(H5Tclose,(dtype));
866:   PetscStackCallHDF5(H5Aclose,(attribute));
867:   PetscStackCallHDF5(H5Oclose,(obj));
868:   PetscStackCallHDF5(H5Sclose,(dataspace));
869:   PetscFree(parent);
870:   return(0);
871: }

873: /*@C
874:  PetscViewerHDF5WriteObjectAttribute - Write an attribute to the dataset matching the given PetscObject by name

876:   Input Parameters:
877: + viewer   - The HDF5 viewer
878: . obj      - The object whose name is used to lookup the parent dataset, relative to the current group.
879: . name     - The attribute name
880: . datatype - The attribute type
881: - value    - The attribute value

883:   Notes:
884:   This fails if current_group/object_name doesn't resolve to a dataset (the path doesn't exist or is not a dataset).
885:   You might want to check first if it does using PetscViewerHDF5HasObject().

887:   Level: advanced

889: .seealso: PetscViewerHDF5Open(), PetscViewerHDF5WriteAttribute(), PetscViewerHDF5ReadObjectAttribute(), PetscViewerHDF5HasObjectAttribute(), PetscViewerHDF5HasObject(), PetscViewerHDF5PushGroup(),PetscViewerHDF5PopGroup(),PetscViewerHDF5GetGroup()
890: @*/
891: PetscErrorCode PetscViewerHDF5WriteObjectAttribute(PetscViewer viewer, PetscObject obj, const char name[], PetscDataType datatype, const void *value)
892: {

900:   PetscViewerHDF5CheckNamedObject_Internal(viewer, obj);
901:   PetscViewerHDF5WriteAttribute(viewer, obj->name, name, datatype, value);
902:   return(0);
903: }

905: /*@C
906:  PetscViewerHDF5ReadAttribute - Read an attribute

908:   Input Parameters:
909: + viewer - The HDF5 viewer
910: . dataset - The parent dataset name, relative to the current group. NULL means a group-wise attribute.
911: . name   - The attribute name
912: - datatype - The attribute type

914:   Output Parameter:
915: . value    - The attribute value

917:   Level: advanced

919: .seealso: PetscViewerHDF5Open(), PetscViewerHDF5ReadObjectAttribute(), PetscViewerHDF5WriteAttribute(), PetscViewerHDF5HasAttribute(), PetscViewerHDF5HasObject(), PetscViewerHDF5PushGroup(),PetscViewerHDF5PopGroup(),PetscViewerHDF5GetGroup()
920: @*/
921: PetscErrorCode PetscViewerHDF5ReadAttribute(PetscViewer viewer, const char dataset[], const char name[], PetscDataType datatype, void *value)
922: {
923:   char           *parent;
924:   hid_t          h5, obj, attribute, atype, dtype;
925:   PetscBool      has;

933:   PetscViewerHDF5GetAbsolutePath_Internal(viewer, dataset, &parent);
934:   PetscViewerHDF5Traverse_Internal(viewer, parent, PETSC_FALSE, &has, NULL);
935:   if (has) {PetscViewerHDF5HasAttribute_Internal(viewer, parent, name, &has);}
936:   if (!has) SETERRQ2(PetscObjectComm((PetscObject)viewer), PETSC_ERR_FILE_UNEXPECTED, "Attribute %s/%s does not exist", parent, name);
937:   PetscDataTypeToHDF5DataType(datatype, &dtype);
938:   PetscViewerHDF5GetFileId(viewer, &h5);
939:   PetscStackCallHDF5Return(obj,H5Oopen,(h5, parent, H5P_DEFAULT));
940:   PetscStackCallHDF5Return(attribute,H5Aopen_name,(obj, name));
941:   if (datatype == PETSC_STRING) {
942:     size_t len;
943:     PetscStackCallHDF5Return(atype,H5Aget_type,(attribute));
944:     PetscStackCall("H5Tget_size",len = H5Tget_size(atype));
945:     PetscStackCallHDF5(H5Tclose,(atype));
946:     PetscMalloc((len+1) * sizeof(char *), &value);
947:   }
948:   PetscStackCallHDF5(H5Aread,(attribute, dtype, value));
949:   PetscStackCallHDF5(H5Aclose,(attribute));
950:   /* H5Oclose can be used to close groups, datasets, or committed datatypes */
951:   PetscStackCallHDF5(H5Oclose,(obj));
952:   PetscFree(parent);
953:   return(0);
954: }

956: /*@C
957:  PetscViewerHDF5ReadObjectAttribute - Read an attribute from the dataset matching the given PetscObject by name

959:   Input Parameters:
960: + viewer   - The HDF5 viewer
961: . obj      - The object whose name is used to lookup the parent dataset, relative to the current group.
962: . name     - The attribute name
963: - datatype - The attribute type

965:   Output Parameter:
966: . value    - The attribute value

968:   Notes:
969:   This fails if current_group/object_name doesn't resolve to a dataset (the path doesn't exist or is not a dataset).
970:   You might want to check first if it does using PetscViewerHDF5HasObject().

972:   Level: advanced

974: .seealso: PetscViewerHDF5Open(), PetscViewerHDF5ReadAttribute() PetscViewerHDF5WriteObjectAttribute(), PetscViewerHDF5HasObjectAttribute(), PetscViewerHDF5PushGroup(),PetscViewerHDF5PopGroup(),PetscViewerHDF5GetGroup()
975: @*/
976: PetscErrorCode PetscViewerHDF5ReadObjectAttribute(PetscViewer viewer, PetscObject obj, const char name[], PetscDataType datatype, void *value)
977: {

985:   PetscViewerHDF5CheckNamedObject_Internal(viewer, obj);
986:   PetscViewerHDF5ReadAttribute(viewer, obj->name, name, datatype, value);
987:   return(0);
988: }

990: PETSC_STATIC_INLINE PetscErrorCode PetscViewerHDF5Traverse_Inner_Internal(hid_t h5, const char name[], PetscBool createGroup, PetscBool *exists_)
991: {
992:   htri_t exists;
993:   hid_t group;

996:   PetscStackCallHDF5Return(exists,H5Lexists,(h5, name, H5P_DEFAULT));
997:   if (exists) PetscStackCallHDF5Return(exists,H5Oexists_by_name,(h5, name, H5P_DEFAULT));
998:   if (!exists && createGroup) {
999:     PetscStackCallHDF5Return(group,H5Gcreate2,(h5, name, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT));
1000:     PetscStackCallHDF5(H5Gclose,(group));
1001:     exists = PETSC_TRUE;
1002:   }
1003:   *exists_ = (PetscBool) exists;
1004:   return(0);
1005: }

1007: static PetscErrorCode PetscViewerHDF5Traverse_Internal(PetscViewer viewer, const char name[], PetscBool createGroup, PetscBool *has, H5O_type_t *otype)
1008: {
1009:   const char     rootGroupName[] = "/";
1010:   hid_t          h5;
1011:   PetscBool      exists=PETSC_FALSE;
1012:   PetscInt       i;
1013:   int            n;
1014:   char           **hierarchy;
1015:   char           buf[PETSC_MAX_PATH_LEN]="";

1021:   else name = rootGroupName;
1022:   if (has) {
1024:     *has = PETSC_FALSE;
1025:   }
1026:   if (otype) {
1028:     *otype = H5O_TYPE_UNKNOWN;
1029:   }
1030:   PetscViewerHDF5GetFileId(viewer, &h5);

1032:   /*
1033:      Unfortunately, H5Oexists_by_name() fails if any object in hierarchy is missing.
1034:      Hence, each of them needs to be tested separately:
1035:      1) whether it's a valid link
1036:      2) whether this link resolves to an object
1037:      See H5Oexists_by_name() documentation.
1038:   */
1039:   PetscStrToArray(name,'/',&n,&hierarchy);
1040:   if (!n) {
1041:     /*  Assume group "/" always exists in accordance with HDF5 >= 1.10.0. See H5Lexists() documentation. */
1042:     if (has)   *has   = PETSC_TRUE;
1043:     if (otype) *otype = H5O_TYPE_GROUP;
1044:     PetscStrToArrayDestroy(n,hierarchy);
1045:     return(0);
1046:   }
1047:   for (i=0; i<n; i++) {
1048:     PetscStrcat(buf,"/");
1049:     PetscStrcat(buf,hierarchy[i]);
1050:     PetscViewerHDF5Traverse_Inner_Internal(h5, buf, createGroup, &exists);
1051:     if (!exists) break;
1052:   }
1053:   PetscStrToArrayDestroy(n,hierarchy);

1055:   /* If the object exists, get its type */
1056:   if (exists && otype) {
1057:     H5O_info_t info;

1059:     /* We could use H5Iget_type() here but that would require opening the object. This way we only need its name. */
1060:     PetscStackCallHDF5(H5Oget_info_by_name,(h5, name, &info, H5P_DEFAULT));
1061:     *otype = info.type;
1062:   }
1063:   if (has) *has = exists;
1064:   return(0);
1065: }

1067: /*@
1068:  PetscViewerHDF5HasGroup - Check whether the current (pushed) group exists in the HDF5 file

1070:   Input Parameters:
1071: . viewer - The HDF5 viewer

1073:   Output Parameter:
1074: . has    - Flag for group existence

1076:   Notes:
1077:   If the path exists but is not a group, this returns PETSC_FALSE as well.

1079:   Level: advanced

1081: .seealso: PetscViewerHDF5Open(), PetscViewerHDF5PushGroup(), PetscViewerHDF5PopGroup(), PetscViewerHDF5OpenGroup()
1082: @*/
1083: PetscErrorCode PetscViewerHDF5HasGroup(PetscViewer viewer, PetscBool *has)
1084: {
1085:   H5O_type_t type;
1086:   const char *name;

1092:   PetscViewerHDF5GetGroup(viewer, &name);
1093:   PetscViewerHDF5Traverse_Internal(viewer, name, PETSC_FALSE, has, &type);
1094:   *has = (type == H5O_TYPE_GROUP) ? PETSC_TRUE : PETSC_FALSE;
1095:   return(0);
1096: }

1098: /*@
1099:  PetscViewerHDF5HasObject - Check whether a dataset with the same name as given object exists in the HDF5 file under current group

1101:   Input Parameters:
1102: + viewer - The HDF5 viewer
1103: - obj    - The named object

1105:   Output Parameter:
1106: . has    - Flag for dataset existence; PETSC_FALSE for unnamed object

1108:   Notes:
1109:   If the path exists but is not a dataset, this returns PETSC_FALSE as well.

1111:   Level: advanced

1113: .seealso: PetscViewerHDF5Open(), PetscViewerHDF5HasAttribute(), PetscViewerHDF5PushGroup(),PetscViewerHDF5PopGroup(),PetscViewerHDF5GetGroup()
1114: @*/
1115: PetscErrorCode PetscViewerHDF5HasObject(PetscViewer viewer, PetscObject obj, PetscBool *has)
1116: {
1117:   H5O_type_t type;
1118:   char *path;

1125:   *has = PETSC_FALSE;
1126:   if (!obj->name) return(0);
1127:   PetscViewerHDF5GetAbsolutePath_Internal(viewer, obj->name, &path);
1128:   PetscViewerHDF5Traverse_Internal(viewer, path, PETSC_FALSE, has, &type);
1129:   *has = (type == H5O_TYPE_DATASET) ? PETSC_TRUE : PETSC_FALSE;
1130:   PetscFree(path);
1131:   return(0);
1132: }

1134: /*@C
1135:  PetscViewerHDF5HasAttribute - Check whether an attribute exists

1137:   Input Parameters:
1138: + viewer - The HDF5 viewer
1139: . dataset - The parent dataset name, relative to the current group. NULL means a group-wise attribute.
1140: - name   - The attribute name

1142:   Output Parameter:
1143: . has    - Flag for attribute existence

1145:   Level: advanced

1147: .seealso: PetscViewerHDF5Open(), PetscViewerHDF5HasObjectAttribute(), PetscViewerHDF5WriteAttribute(), PetscViewerHDF5ReadAttribute(), PetscViewerHDF5PushGroup(),PetscViewerHDF5PopGroup(),PetscViewerHDF5GetGroup()
1148: @*/
1149: PetscErrorCode PetscViewerHDF5HasAttribute(PetscViewer viewer, const char dataset[], const char name[], PetscBool *has)
1150: {
1151:   char           *parent;

1159:   PetscViewerHDF5GetAbsolutePath_Internal(viewer, dataset, &parent);
1160:   PetscViewerHDF5Traverse_Internal(viewer, parent, PETSC_FALSE, has, NULL);
1161:   if (*has) {PetscViewerHDF5HasAttribute_Internal(viewer, parent, name, has);}
1162:   PetscFree(parent);
1163:   return(0);
1164: }

1166: /*@C
1167:  PetscViewerHDF5HasObjectAttribute - Check whether an attribute is attached to the dataset matching the given PetscObject by name

1169:   Input Parameters:
1170: + viewer - The HDF5 viewer
1171: . obj    - The object whose name is used to lookup the parent dataset, relative to the current group.
1172: - name   - The attribute name

1174:   Output Parameter:
1175: . has    - Flag for attribute existence

1177:   Notes:
1178:   This fails if current_group/object_name doesn't resolve to a dataset (the path doesn't exist or is not a dataset).
1179:   You might want to check first if it does using PetscViewerHDF5HasObject().

1181:   Level: advanced

1183: .seealso: PetscViewerHDF5Open(), PetscViewerHDF5HasAttribute(), PetscViewerHDF5WriteObjectAttribute(), PetscViewerHDF5ReadObjectAttribute(), PetscViewerHDF5HasObject(), PetscViewerHDF5PushGroup(),PetscViewerHDF5PopGroup(),PetscViewerHDF5GetGroup()
1184: @*/
1185: PetscErrorCode PetscViewerHDF5HasObjectAttribute(PetscViewer viewer, PetscObject obj, const char name[], PetscBool *has)
1186: {

1194:   PetscViewerHDF5CheckNamedObject_Internal(viewer, obj);
1195:   PetscViewerHDF5HasAttribute(viewer, obj->name, name, has);
1196:   return(0);
1197: }

1199: static PetscErrorCode PetscViewerHDF5HasAttribute_Internal(PetscViewer viewer, const char parent[], const char name[], PetscBool *has)
1200: {
1201:   hid_t          h5;
1202:   htri_t         hhas;

1206:   PetscViewerHDF5GetFileId(viewer, &h5);
1207:   PetscStackCallHDF5Return(hhas,H5Aexists_by_name,(h5, parent, name, H5P_DEFAULT));
1208:   *has = hhas ? PETSC_TRUE : PETSC_FALSE;
1209:   return(0);
1210: }

1212: /*
1213:   The variable Petsc_Viewer_HDF5_keyval is used to indicate an MPI attribute that
1214:   is attached to a communicator, in this case the attribute is a PetscViewer.
1215: */
1216: PetscMPIInt Petsc_Viewer_HDF5_keyval = MPI_KEYVAL_INVALID;

1218: /*@C
1219:   PETSC_VIEWER_HDF5_ - Creates an HDF5 PetscViewer shared by all processors in a communicator.

1221:   Collective

1223:   Input Parameter:
1224: . comm - the MPI communicator to share the HDF5 PetscViewer

1226:   Level: intermediate

1228:   Options Database Keys:
1229: . -viewer_hdf5_filename <name>

1231:   Environmental variables:
1232: . PETSC_VIEWER_HDF5_FILENAME

1234:   Notes:
1235:   Unlike almost all other PETSc routines, PETSC_VIEWER_HDF5_ does not return
1236:   an error code.  The HDF5 PetscViewer is usually used in the form
1237: $       XXXView(XXX object, PETSC_VIEWER_HDF5_(comm));

1239: .seealso: PetscViewerHDF5Open(), PetscViewerCreate(), PetscViewerDestroy()
1240: @*/
1241: PetscViewer PETSC_VIEWER_HDF5_(MPI_Comm comm)
1242: {
1244:   PetscBool      flg;
1245:   PetscViewer    viewer;
1246:   char           fname[PETSC_MAX_PATH_LEN];
1247:   MPI_Comm       ncomm;

1250:   PetscCommDuplicate(comm,&ncomm,NULL);if (ierr) {PetscError(PETSC_COMM_SELF,__LINE__,"PETSC_VIEWER_HDF5_",__FILE__,PETSC_ERR_PLIB,PETSC_ERROR_INITIAL," ");return(0);}
1251:   if (Petsc_Viewer_HDF5_keyval == MPI_KEYVAL_INVALID) {
1252:     MPI_Comm_create_keyval(MPI_COMM_NULL_COPY_FN,MPI_COMM_NULL_DELETE_FN,&Petsc_Viewer_HDF5_keyval,0);
1253:     if (ierr) {PetscError(PETSC_COMM_SELF,__LINE__,"PETSC_VIEWER_HDF5_",__FILE__,PETSC_ERR_PLIB,PETSC_ERROR_INITIAL," ");return(0);}
1254:   }
1255:   MPI_Comm_get_attr(ncomm,Petsc_Viewer_HDF5_keyval,(void**)&viewer,(int*)&flg);
1256:   if (ierr) {PetscError(PETSC_COMM_SELF,__LINE__,"PETSC_VIEWER_HDF5_",__FILE__,PETSC_ERR_PLIB,PETSC_ERROR_INITIAL," ");return(0);}
1257:   if (!flg) { /* PetscViewer not yet created */
1258:     PetscOptionsGetenv(ncomm,"PETSC_VIEWER_HDF5_FILENAME",fname,PETSC_MAX_PATH_LEN,&flg);
1259:     if (ierr) {PetscError(PETSC_COMM_SELF,__LINE__,"PETSC_VIEWER_HDF5_",__FILE__,PETSC_ERR_PLIB,PETSC_ERROR_INITIAL," ");return(0);}
1260:     if (!flg) {
1261:       PetscStrcpy(fname,"output.h5");
1262:       if (ierr) {PetscError(PETSC_COMM_SELF,__LINE__,"PETSC_VIEWER_HDF5_",__FILE__,PETSC_ERR_PLIB,PETSC_ERROR_INITIAL," ");return(0);}
1263:     }
1264:     PetscViewerHDF5Open(ncomm,fname,FILE_MODE_WRITE,&viewer);
1265:     if (ierr) {PetscError(PETSC_COMM_SELF,__LINE__,"PETSC_VIEWER_HDF5_",__FILE__,PETSC_ERR_PLIB,PETSC_ERROR_INITIAL," ");return(0);}
1266:     PetscObjectRegisterDestroy((PetscObject)viewer);
1267:     if (ierr) {PetscError(PETSC_COMM_SELF,__LINE__,"PETSC_VIEWER_HDF5_",__FILE__,PETSC_ERR_PLIB,PETSC_ERROR_INITIAL," ");return(0);}
1268:     MPI_Comm_set_attr(ncomm,Petsc_Viewer_HDF5_keyval,(void*)viewer);
1269:     if (ierr) {PetscError(PETSC_COMM_SELF,__LINE__,"PETSC_VIEWER_HDF5_",__FILE__,PETSC_ERR_PLIB,PETSC_ERROR_INITIAL," ");return(0);}
1270:   }
1271:   PetscCommDestroy(&ncomm);
1272:   if (ierr) {PetscError(PETSC_COMM_SELF,__LINE__,"PETSC_VIEWER_HDF5_",__FILE__,PETSC_ERR_PLIB,PETSC_ERROR_INITIAL," ");return(0);}
1273:   PetscFunctionReturn(viewer);
1274: }