Actual source code: hdf5v.c

petsc-3.15.0 2021-04-05
Report Typos and Errors
  1: #include <petsc/private/viewerimpl.h>
  2: #include <petsc/private/viewerhdf5impl.h>
  3: #include <petscviewerhdf5.h>

  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:   case FILE_MODE_UPDATE:
400:   {
401:     PetscBool flg;
402:     PetscTestFile(hdf5->filename, 'r', &flg);
403:     if (flg) PetscStackCallHDF5Return(hdf5->file_id,H5Fopen,(name, H5F_ACC_RDWR, plist_id));
404:     else     PetscStackCallHDF5Return(hdf5->file_id,H5Fcreate,(name, H5F_ACC_EXCL, H5P_DEFAULT, plist_id));
405:     break;
406:   }
407:   case FILE_MODE_WRITE:
408:     PetscStackCallHDF5Return(hdf5->file_id,H5Fcreate,(name, H5F_ACC_TRUNC, H5P_DEFAULT, plist_id));
409:     break;
410:   case FILE_MODE_UNDEFINED:
411:     SETERRQ(PetscObjectComm((PetscObject)viewer),PETSC_ERR_ORDER, "Must call PetscViewerFileSetMode() before PetscViewerFileSetName()");
412:   default:
413:     SETERRQ1(PetscObjectComm((PetscObject)viewer),PETSC_ERR_SUP, "Unsupported file mode %s",PetscFileModes[hdf5->btype]);
414:   }
415:   if (hdf5->file_id < 0) SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_LIB, "H5Fcreate failed for %s", name);
416:   PetscStackCallHDF5(H5Pclose,(plist_id));
417:   return(0);
418: }

420: static PetscErrorCode PetscViewerFileGetName_HDF5(PetscViewer viewer,const char **name)
421: {
422:   PetscViewer_HDF5 *vhdf5 = (PetscViewer_HDF5*)viewer->data;

425:   *name = vhdf5->filename;
426:   return(0);
427: }

429: static PetscErrorCode PetscViewerSetUp_HDF5(PetscViewer viewer)
430: {
431:   /*
432:   PetscViewer_HDF5 *hdf5 = (PetscViewer_HDF5*) viewer->data;
433:   PetscErrorCode   ierr;
434:   */

437:   return(0);
438: }

440: /*MC
441:    PETSCVIEWERHDF5 - A viewer that writes to an HDF5 file


444: .seealso:  PetscViewerHDF5Open(), PetscViewerStringSPrintf(), PetscViewerSocketOpen(), PetscViewerDrawOpen(), PETSCVIEWERSOCKET,
445:            PetscViewerCreate(), PetscViewerASCIIOpen(), PetscViewerBinaryOpen(), PETSCVIEWERBINARY, PETSCVIEWERDRAW, PETSCVIEWERSTRING,
446:            PetscViewerMatlabOpen(), VecView(), DMView(), PetscViewerMatlabPutArray(), PETSCVIEWERASCII, PETSCVIEWERMATLAB,
447:            PetscViewerFileSetName(), PetscViewerFileSetMode(), PetscViewerFormat, PetscViewerType, PetscViewerSetType()

449:   Level: beginner
450: M*/

452: PETSC_EXTERN PetscErrorCode PetscViewerCreate_HDF5(PetscViewer v)
453: {
454:   PetscViewer_HDF5 *hdf5;
455:   PetscErrorCode   ierr;

458:   PetscNewLog(v,&hdf5);

460:   v->data                = (void*) hdf5;
461:   v->ops->destroy        = PetscViewerDestroy_HDF5;
462:   v->ops->setfromoptions = PetscViewerSetFromOptions_HDF5;
463:   v->ops->setup          = PetscViewerSetUp_HDF5;
464:   v->ops->view           = PetscViewerView_HDF5;
465:   v->ops->flush          = NULL;
466:   hdf5->btype            = FILE_MODE_UNDEFINED;
467:   hdf5->filename         = NULL;
468:   hdf5->timestep         = -1;
469:   hdf5->groups           = NULL;

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

473:   PetscObjectComposeFunction((PetscObject)v,"PetscViewerFileSetName_C",PetscViewerFileSetName_HDF5);
474:   PetscObjectComposeFunction((PetscObject)v,"PetscViewerFileGetName_C",PetscViewerFileGetName_HDF5);
475:   PetscObjectComposeFunction((PetscObject)v,"PetscViewerFileSetMode_C",PetscViewerFileSetMode_HDF5);
476:   PetscObjectComposeFunction((PetscObject)v,"PetscViewerFileGetMode_C",PetscViewerFileGetMode_HDF5);
477:   PetscObjectComposeFunction((PetscObject)v,"PetscViewerHDF5SetBaseDimension2_C",PetscViewerHDF5SetBaseDimension2_HDF5);
478:   PetscObjectComposeFunction((PetscObject)v,"PetscViewerHDF5SetSPOutput_C",PetscViewerHDF5SetSPOutput_HDF5);
479:   PetscObjectComposeFunction((PetscObject)v,"PetscViewerHDF5SetCollective_C",PetscViewerHDF5SetCollective_HDF5);
480:   PetscObjectComposeFunction((PetscObject)v,"PetscViewerHDF5GetCollective_C",PetscViewerHDF5GetCollective_HDF5);
481:   return(0);
482: }

484: /*@C
485:    PetscViewerHDF5Open - Opens a file for HDF5 input/output.

487:    Collective

489:    Input Parameters:
490: +  comm - MPI communicator
491: .  name - name of file
492: -  type - type of file

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

497:   Options Database:
498: +  -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
499: -  -viewer_hdf5_sp_output - forces (if true) the viewer to write data in single precision independent on the precision of PetscReal

501:    Level: beginner

503:    Notes:
504:    Reading is always available, regardless of the mode. Available modes are
505: +  FILE_MODE_READ - open existing HDF5 file for read only access, fail if file does not exist [H5Fopen() with H5F_ACC_RDONLY]
506: .  FILE_MODE_WRITE - if file exists, fully overwrite it, else create new HDF5 file [H5FcreateH5Fcreate() with H5F_ACC_TRUNC]
507: .  FILE_MODE_APPEND - if file exists, keep existing contents [H5Fopen() with H5F_ACC_RDWR], else create new HDF5 file [H5FcreateH5Fcreate() with H5F_ACC_EXCL]
508: -  FILE_MODE_UPDATE - same as FILE_MODE_APPEND

510:    In case of FILE_MODE_APPEND / FILE_MODE_UPDATE, any stored object (dataset, attribute) can be selectively ovewritten if the same fully qualified name (/group/path/to/object) is specified.

512:    This PetscViewer should be destroyed with PetscViewerDestroy().


515: .seealso: PetscViewerASCIIOpen(), PetscViewerPushFormat(), PetscViewerDestroy(), PetscViewerHDF5SetBaseDimension2(),
516:           PetscViewerHDF5SetSPOutput(), PetscViewerHDF5GetBaseDimension2(), VecView(), MatView(), VecLoad(),
517:           MatLoad(), PetscFileMode, PetscViewer, PetscViewerSetType(), PetscViewerFileSetMode(), PetscViewerFileSetName()
518: @*/
519: PetscErrorCode  PetscViewerHDF5Open(MPI_Comm comm, const char name[], PetscFileMode type, PetscViewer *hdf5v)
520: {

524:   PetscViewerCreate(comm, hdf5v);
525:   PetscViewerSetType(*hdf5v, PETSCVIEWERHDF5);
526:   PetscViewerFileSetMode(*hdf5v, type);
527:   PetscViewerFileSetName(*hdf5v, name);
528:   PetscViewerSetFromOptions(*hdf5v);
529:   return(0);
530: }

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

535:   Not collective

537:   Input Parameter:
538: . viewer - the PetscViewer

540:   Output Parameter:
541: . file_id - The file id

543:   Level: intermediate

545: .seealso: PetscViewerHDF5Open()
546: @*/
547: PetscErrorCode  PetscViewerHDF5GetFileId(PetscViewer viewer, hid_t *file_id)
548: {
549:   PetscViewer_HDF5 *hdf5 = (PetscViewer_HDF5*) viewer->data;

553:   if (file_id) *file_id = hdf5->file_id;
554:   return(0);
555: }

557: /*@C
558:   PetscViewerHDF5PushGroup - Set the current HDF5 group for output

560:   Not collective

562:   Input Parameters:
563: + viewer - the PetscViewer
564: - name - The group name

566:   Level: intermediate

568:   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 "/".

570: .seealso: PetscViewerHDF5Open(),PetscViewerHDF5PopGroup(),PetscViewerHDF5GetGroup(),PetscViewerHDF5OpenGroup()
571: @*/
572: PetscErrorCode  PetscViewerHDF5PushGroup(PetscViewer viewer, const char name[])
573: {
574:   PetscViewer_HDF5 *hdf5 = (PetscViewer_HDF5*) viewer->data;
575:   PetscViewerHDF5GroupList *groupNode;
576:   PetscErrorCode   ierr;

581:   if (name && name[0]) {
582:      size_t i,len;
583:      PetscStrlen(name, &len);
584:      for (i=0; i<len; i++) if (name[i] != '/') break;
585:      if (i == len) name = NULL;
586:   } else name = NULL;
587:   PetscNew(&groupNode);
588:   PetscStrallocpy(name, (char**) &groupNode->name);
589:   groupNode->next = hdf5->groups;
590:   hdf5->groups    = groupNode;
591:   return(0);
592: }

594: /*@
595:   PetscViewerHDF5PopGroup - Return the current HDF5 group for output to the previous value

597:   Not collective

599:   Input Parameter:
600: . viewer - the PetscViewer

602:   Level: intermediate

604: .seealso: PetscViewerHDF5Open(),PetscViewerHDF5PushGroup(),PetscViewerHDF5GetGroup(),PetscViewerHDF5OpenGroup()
605: @*/
606: PetscErrorCode  PetscViewerHDF5PopGroup(PetscViewer viewer)
607: {
608:   PetscViewer_HDF5 *hdf5 = (PetscViewer_HDF5*) viewer->data;
609:   PetscViewerHDF5GroupList *groupNode;
610:   PetscErrorCode   ierr;

614:   if (!hdf5->groups) SETERRQ(PetscObjectComm((PetscObject)viewer), PETSC_ERR_ARG_WRONGSTATE, "HDF5 group stack is empty, cannot pop");
615:   groupNode    = hdf5->groups;
616:   hdf5->groups = hdf5->groups->next;
617:   PetscFree(groupNode->name);
618:   PetscFree(groupNode);
619:   return(0);
620: }

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

626:   Not collective

628:   Input Parameter:
629: . viewer - the PetscViewer

631:   Output Parameter:
632: . name - The group name

634:   Level: intermediate

636: .seealso: PetscViewerHDF5Open(),PetscViewerHDF5PushGroup(),PetscViewerHDF5PopGroup(),PetscViewerHDF5OpenGroup()
637: @*/
638: PetscErrorCode  PetscViewerHDF5GetGroup(PetscViewer viewer, const char *name[])
639: {
640:   PetscViewer_HDF5 *hdf5 = (PetscViewer_HDF5 *) viewer->data;

645:   if (hdf5->groups) *name = hdf5->groups->name;
646:   else *name = NULL;
647:   return(0);
648: }

650: /*@
651:   PetscViewerHDF5OpenGroup - Open the HDF5 group with the name (full path) returned by PetscViewerHDF5GetGroup(),
652:   and return this group's ID and file ID.
653:   If PetscViewerHDF5GetGroup() yields NULL, then group ID is file ID.

655:   Not collective

657:   Input Parameter:
658: . viewer - the PetscViewer

660:   Output Parameter:
661: + fileId - The HDF5 file ID
662: - groupId - The HDF5 group ID

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

667:   Level: intermediate

669: .seealso: PetscViewerHDF5Open(),PetscViewerHDF5PushGroup(),PetscViewerHDF5PopGroup(),PetscViewerHDF5GetGroup()
670: @*/
671: PetscErrorCode PetscViewerHDF5OpenGroup(PetscViewer viewer, hid_t *fileId, hid_t *groupId)
672: {
673:   hid_t          file_id;
674:   H5O_type_t     type;
675:   const char     *groupName = NULL;
676:   PetscBool      create;

680:   PetscViewerWritable(viewer, &create);
681:   PetscViewerHDF5GetFileId(viewer, &file_id);
682:   PetscViewerHDF5GetGroup(viewer, &groupName);
683:   PetscViewerHDF5Traverse_Internal(viewer, groupName, create, NULL, &type);
684:   if (type != H5O_TYPE_GROUP) SETERRQ1(PetscObjectComm((PetscObject)viewer), PETSC_ERR_FILE_UNEXPECTED, "Path %s resolves to something which is not a group", groupName);
685:   PetscStackCallHDF5Return(*groupId,H5Gopen2,(file_id, groupName ? groupName : "/", H5P_DEFAULT));
686:   *fileId  = file_id;
687:   return(0);
688: }

690: /*@
691:   PetscViewerHDF5IncrementTimestep - Increments the current timestep for the HDF5 output. Fields are stacked in time.

693:   Not collective

695:   Input Parameter:
696: . viewer - the PetscViewer

698:   Level: intermediate

700: .seealso: PetscViewerHDF5Open(), PetscViewerHDF5SetTimestep(), PetscViewerHDF5GetTimestep()
701: @*/
702: PetscErrorCode PetscViewerHDF5IncrementTimestep(PetscViewer viewer)
703: {
704:   PetscViewer_HDF5 *hdf5 = (PetscViewer_HDF5*) viewer->data;

708:   ++hdf5->timestep;
709:   return(0);
710: }

712: /*@
713:   PetscViewerHDF5SetTimestep - Set the current timestep for the HDF5 output. Fields are stacked in time. A timestep
714:   of -1 disables blocking with timesteps.

716:   Not collective

718:   Input Parameters:
719: + viewer - the PetscViewer
720: - timestep - The timestep number

722:   Level: intermediate

724: .seealso: PetscViewerHDF5Open(), PetscViewerHDF5IncrementTimestep(), PetscViewerHDF5GetTimestep()
725: @*/
726: PetscErrorCode  PetscViewerHDF5SetTimestep(PetscViewer viewer, PetscInt timestep)
727: {
728:   PetscViewer_HDF5 *hdf5 = (PetscViewer_HDF5*) viewer->data;

732:   hdf5->timestep = timestep;
733:   return(0);
734: }

736: /*@
737:   PetscViewerHDF5GetTimestep - Get the current timestep for the HDF5 output. Fields are stacked in time.

739:   Not collective

741:   Input Parameter:
742: . viewer - the PetscViewer

744:   Output Parameter:
745: . timestep - The timestep number

747:   Level: intermediate

749: .seealso: PetscViewerHDF5Open(), PetscViewerHDF5IncrementTimestep(), PetscViewerHDF5SetTimestep()
750: @*/
751: PetscErrorCode  PetscViewerHDF5GetTimestep(PetscViewer viewer, PetscInt *timestep)
752: {
753:   PetscViewer_HDF5 *hdf5 = (PetscViewer_HDF5*) viewer->data;

758:   *timestep = hdf5->timestep;
759:   return(0);
760: }

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

765:   Not collective

767:   Input Parameter:
768: . ptype - the PETSc datatype name (for example PETSC_DOUBLE)

770:   Output Parameter:
771: . mtype - the MPI datatype (for example MPI_DOUBLE, ...)

773:   Level: advanced

775: .seealso: PetscDataType, PetscHDF5DataTypeToPetscDataType()
776: @*/
777: PetscErrorCode PetscDataTypeToHDF5DataType(PetscDataType ptype, hid_t *htype)
778: {
780:   if (ptype == PETSC_INT)
781: #if defined(PETSC_USE_64BIT_INDICES)
782:                                        *htype = H5T_NATIVE_LLONG;
783: #else
784:                                        *htype = H5T_NATIVE_INT;
785: #endif
786:   else if (ptype == PETSC_DOUBLE)      *htype = H5T_NATIVE_DOUBLE;
787:   else if (ptype == PETSC_LONG)        *htype = H5T_NATIVE_LONG;
788:   else if (ptype == PETSC_SHORT)       *htype = H5T_NATIVE_SHORT;
789:   else if (ptype == PETSC_ENUM)        *htype = H5T_NATIVE_INT;
790:   else if (ptype == PETSC_BOOL)        *htype = H5T_NATIVE_INT;
791:   else if (ptype == PETSC_FLOAT)       *htype = H5T_NATIVE_FLOAT;
792:   else if (ptype == PETSC_CHAR)        *htype = H5T_NATIVE_CHAR;
793:   else if (ptype == PETSC_BIT_LOGICAL) *htype = H5T_NATIVE_UCHAR;
794:   else if (ptype == PETSC_STRING)      *htype = H5Tcopy(H5T_C_S1);
795:   else SETERRQ(PETSC_COMM_SELF, PETSC_ERR_ARG_OUTOFRANGE, "Unsupported PETSc datatype");
796:   return(0);
797: }

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

802:   Not collective

804:   Input Parameter:
805: . htype - the HDF5 datatype (for example H5T_NATIVE_DOUBLE, ...)

807:   Output Parameter:
808: . ptype - the PETSc datatype name (for example PETSC_DOUBLE)

810:   Level: advanced

812: .seealso: PetscDataType, PetscHDF5DataTypeToPetscDataType()
813: @*/
814: PetscErrorCode PetscHDF5DataTypeToPetscDataType(hid_t htype, PetscDataType *ptype)
815: {
817: #if defined(PETSC_USE_64BIT_INDICES)
818:   if      (htype == H5T_NATIVE_INT)    *ptype = PETSC_LONG;
819:   else if (htype == H5T_NATIVE_LLONG)  *ptype = PETSC_INT;
820: #else
821:   if      (htype == H5T_NATIVE_INT)    *ptype = PETSC_INT;
822: #endif
823:   else if (htype == H5T_NATIVE_DOUBLE) *ptype = PETSC_DOUBLE;
824:   else if (htype == H5T_NATIVE_LONG)   *ptype = PETSC_LONG;
825:   else if (htype == H5T_NATIVE_SHORT)  *ptype = PETSC_SHORT;
826:   else if (htype == H5T_NATIVE_FLOAT)  *ptype = PETSC_FLOAT;
827:   else if (htype == H5T_NATIVE_CHAR)   *ptype = PETSC_CHAR;
828:   else if (htype == H5T_NATIVE_UCHAR)  *ptype = PETSC_CHAR;
829:   else if (htype == H5T_C_S1)          *ptype = PETSC_STRING;
830:   else SETERRQ(PETSC_COMM_SELF, PETSC_ERR_ARG_OUTOFRANGE, "Unsupported HDF5 datatype");
831:   return(0);
832: }

834: /*@C
835:  PetscViewerHDF5WriteAttribute - Write an attribute

837:   Input Parameters:
838: + viewer - The HDF5 viewer
839: . dataset - The parent dataset name, relative to the current group. NULL means a group-wise attribute.
840: . name   - The attribute name
841: . datatype - The attribute type
842: - value    - The attribute value

844:   Level: advanced

846: .seealso: PetscViewerHDF5Open(), PetscViewerHDF5WriteObjectAttribute(), PetscViewerHDF5ReadAttribute(), PetscViewerHDF5HasAttribute(), PetscViewerHDF5PushGroup(),PetscViewerHDF5PopGroup(),PetscViewerHDF5GetGroup()
847: @*/
848: PetscErrorCode PetscViewerHDF5WriteAttribute(PetscViewer viewer, const char dataset[], const char name[], PetscDataType datatype, const void *value)
849: {
850:   char           *parent;
851:   hid_t          h5, dataspace, obj, attribute, dtype;
852:   PetscBool      has;

860:   PetscViewerHDF5GetAbsolutePath_Internal(viewer, dataset, &parent);
861:   PetscViewerHDF5Traverse_Internal(viewer, parent, PETSC_TRUE, NULL, NULL);
862:   PetscViewerHDF5HasAttribute_Internal(viewer, parent, name, &has);
863:   PetscDataTypeToHDF5DataType(datatype, &dtype);
864:   if (datatype == PETSC_STRING) {
865:     size_t len;
866:     PetscStrlen((const char *) value, &len);
867:     PetscStackCallHDF5(H5Tset_size,(dtype, len+1));
868:   }
869:   PetscViewerHDF5GetFileId(viewer, &h5);
870:   PetscStackCallHDF5Return(dataspace,H5Screate,(H5S_SCALAR));
871:   PetscStackCallHDF5Return(obj,H5Oopen,(h5, parent, H5P_DEFAULT));
872:   if (has) {
873:     PetscStackCallHDF5Return(attribute,H5Aopen_name,(obj, name));
874:   } else {
875:     PetscStackCallHDF5Return(attribute,H5Acreate2,(obj, name, dtype, dataspace, H5P_DEFAULT, H5P_DEFAULT));
876:   }
877:   PetscStackCallHDF5(H5Awrite,(attribute, dtype, value));
878:   if (datatype == PETSC_STRING) PetscStackCallHDF5(H5Tclose,(dtype));
879:   PetscStackCallHDF5(H5Aclose,(attribute));
880:   PetscStackCallHDF5(H5Oclose,(obj));
881:   PetscStackCallHDF5(H5Sclose,(dataspace));
882:   PetscFree(parent);
883:   return(0);
884: }

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

889:   Input Parameters:
890: + viewer   - The HDF5 viewer
891: . obj      - The object whose name is used to lookup the parent dataset, relative to the current group.
892: . name     - The attribute name
893: . datatype - The attribute type
894: - value    - The attribute value

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

900:   Level: advanced

902: .seealso: PetscViewerHDF5Open(), PetscViewerHDF5WriteAttribute(), PetscViewerHDF5ReadObjectAttribute(), PetscViewerHDF5HasObjectAttribute(), PetscViewerHDF5HasObject(), PetscViewerHDF5PushGroup(),PetscViewerHDF5PopGroup(),PetscViewerHDF5GetGroup()
903: @*/
904: PetscErrorCode PetscViewerHDF5WriteObjectAttribute(PetscViewer viewer, PetscObject obj, const char name[], PetscDataType datatype, const void *value)
905: {

913:   PetscViewerHDF5CheckNamedObject_Internal(viewer, obj);
914:   PetscViewerHDF5WriteAttribute(viewer, obj->name, name, datatype, value);
915:   return(0);
916: }

918: /*@C
919:  PetscViewerHDF5ReadAttribute - Read an attribute

921:   Input Parameters:
922: + viewer - The HDF5 viewer
923: . dataset - The parent dataset name, relative to the current group. NULL means a group-wise attribute.
924: . name   - The attribute name
925: - datatype - The attribute type

927:   Output Parameter:
928: . value    - The attribute value

930:   Notes: If the datatype is PETSC_STRING one must PetscFree() the obtained value when it is no longer needed.

932:   Level: advanced

934: .seealso: PetscViewerHDF5Open(), PetscViewerHDF5ReadObjectAttribute(), PetscViewerHDF5WriteAttribute(), PetscViewerHDF5HasAttribute(), PetscViewerHDF5HasObject(), PetscViewerHDF5PushGroup(),PetscViewerHDF5PopGroup(),PetscViewerHDF5GetGroup()
935: @*/
936: PetscErrorCode PetscViewerHDF5ReadAttribute(PetscViewer viewer, const char dataset[], const char name[], PetscDataType datatype, void *value)
937: {
938:   char           *parent;
939:   hid_t          h5, obj, attribute, atype, dtype;
940:   PetscBool      has;

948:   PetscViewerHDF5GetAbsolutePath_Internal(viewer, dataset, &parent);
949:   PetscViewerHDF5Traverse_Internal(viewer, parent, PETSC_FALSE, &has, NULL);
950:   if (has) {PetscViewerHDF5HasAttribute_Internal(viewer, parent, name, &has);}
951:   if (!has) SETERRQ2(PetscObjectComm((PetscObject)viewer), PETSC_ERR_FILE_UNEXPECTED, "Attribute %s/%s does not exist", parent, name);
952:   PetscDataTypeToHDF5DataType(datatype, &dtype);
953:   PetscViewerHDF5GetFileId(viewer, &h5);
954:   PetscStackCallHDF5Return(obj,H5Oopen,(h5, parent, H5P_DEFAULT));
955:   PetscStackCallHDF5Return(attribute,H5Aopen_name,(obj, name));
956:   if (datatype == PETSC_STRING) {
957:     size_t len;
958:     PetscStackCallHDF5Return(atype,H5Aget_type,(attribute));
959:     PetscStackCall("H5Tget_size",len = H5Tget_size(atype));
960:     PetscMalloc((len+1) * sizeof(char), value);
961:     PetscStackCallHDF5(H5Tset_size,(dtype, len+1));
962:     PetscStackCallHDF5(H5Aread,(attribute, dtype, *(char**)value));
963:   } else {
964:     PetscStackCallHDF5(H5Aread,(attribute, dtype, value));
965:   }
966:   PetscStackCallHDF5(H5Aclose,(attribute));
967:   /* H5Oclose can be used to close groups, datasets, or committed datatypes */
968:   PetscStackCallHDF5(H5Oclose,(obj));
969:   PetscFree(parent);
970:   return(0);
971: }

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

976:   Input Parameters:
977: + viewer   - The HDF5 viewer
978: . obj      - The object whose name is used to lookup the parent dataset, relative to the current group.
979: . name     - The attribute name
980: - datatype - The attribute type

982:   Output Parameter:
983: . value    - The attribute value

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

989:   Level: advanced

991: .seealso: PetscViewerHDF5Open(), PetscViewerHDF5ReadAttribute() PetscViewerHDF5WriteObjectAttribute(), PetscViewerHDF5HasObjectAttribute(), PetscViewerHDF5PushGroup(),PetscViewerHDF5PopGroup(),PetscViewerHDF5GetGroup()
992: @*/
993: PetscErrorCode PetscViewerHDF5ReadObjectAttribute(PetscViewer viewer, PetscObject obj, const char name[], PetscDataType datatype, void *value)
994: {

1002:   PetscViewerHDF5CheckNamedObject_Internal(viewer, obj);
1003:   PetscViewerHDF5ReadAttribute(viewer, obj->name, name, datatype, value);
1004:   return(0);
1005: }

1007: PETSC_STATIC_INLINE PetscErrorCode PetscViewerHDF5Traverse_Inner_Internal(hid_t h5, const char name[], PetscBool createGroup, PetscBool *exists_)
1008: {
1009:   htri_t exists;
1010:   hid_t group;

1013:   PetscStackCallHDF5Return(exists,H5Lexists,(h5, name, H5P_DEFAULT));
1014:   if (exists) PetscStackCallHDF5Return(exists,H5Oexists_by_name,(h5, name, H5P_DEFAULT));
1015:   if (!exists && createGroup) {
1016:     PetscStackCallHDF5Return(group,H5Gcreate2,(h5, name, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT));
1017:     PetscStackCallHDF5(H5Gclose,(group));
1018:     exists = PETSC_TRUE;
1019:   }
1020:   *exists_ = (PetscBool) exists;
1021:   return(0);
1022: }

1024: static PetscErrorCode PetscViewerHDF5Traverse_Internal(PetscViewer viewer, const char name[], PetscBool createGroup, PetscBool *has, H5O_type_t *otype)
1025: {
1026:   const char     rootGroupName[] = "/";
1027:   hid_t          h5;
1028:   PetscBool      exists=PETSC_FALSE;
1029:   PetscInt       i;
1030:   int            n;
1031:   char           **hierarchy;
1032:   char           buf[PETSC_MAX_PATH_LEN]="";

1038:   else name = rootGroupName;
1039:   if (has) {
1041:     *has = PETSC_FALSE;
1042:   }
1043:   if (otype) {
1045:     *otype = H5O_TYPE_UNKNOWN;
1046:   }
1047:   PetscViewerHDF5GetFileId(viewer, &h5);

1049:   /*
1050:      Unfortunately, H5Oexists_by_name() fails if any object in hierarchy is missing.
1051:      Hence, each of them needs to be tested separately:
1052:      1) whether it's a valid link
1053:      2) whether this link resolves to an object
1054:      See H5Oexists_by_name() documentation.
1055:   */
1056:   PetscStrToArray(name,'/',&n,&hierarchy);
1057:   if (!n) {
1058:     /*  Assume group "/" always exists in accordance with HDF5 >= 1.10.0. See H5Lexists() documentation. */
1059:     if (has)   *has   = PETSC_TRUE;
1060:     if (otype) *otype = H5O_TYPE_GROUP;
1061:     PetscStrToArrayDestroy(n,hierarchy);
1062:     return(0);
1063:   }
1064:   for (i=0; i<n; i++) {
1065:     PetscStrcat(buf,"/");
1066:     PetscStrcat(buf,hierarchy[i]);
1067:     PetscViewerHDF5Traverse_Inner_Internal(h5, buf, createGroup, &exists);
1068:     if (!exists) break;
1069:   }
1070:   PetscStrToArrayDestroy(n,hierarchy);

1072:   /* If the object exists, get its type */
1073:   if (exists && otype) {
1074:     H5O_info_t info;

1076:     /* We could use H5Iget_type() here but that would require opening the object. This way we only need its name. */
1077:     PetscStackCallHDF5(H5Oget_info_by_name,(h5, name, &info, H5P_DEFAULT));
1078:     *otype = info.type;
1079:   }
1080:   if (has) *has = exists;
1081:   return(0);
1082: }

1084: /*@
1085:  PetscViewerHDF5HasGroup - Check whether the current (pushed) group exists in the HDF5 file

1087:   Input Parameters:
1088: . viewer - The HDF5 viewer

1090:   Output Parameter:
1091: . has    - Flag for group existence

1093:   Notes:
1094:   If the path exists but is not a group, this returns PETSC_FALSE as well.

1096:   Level: advanced

1098: .seealso: PetscViewerHDF5Open(), PetscViewerHDF5PushGroup(), PetscViewerHDF5PopGroup(), PetscViewerHDF5OpenGroup()
1099: @*/
1100: PetscErrorCode PetscViewerHDF5HasGroup(PetscViewer viewer, PetscBool *has)
1101: {
1102:   H5O_type_t type;
1103:   const char *name;

1109:   PetscViewerHDF5GetGroup(viewer, &name);
1110:   PetscViewerHDF5Traverse_Internal(viewer, name, PETSC_FALSE, has, &type);
1111:   *has = (type == H5O_TYPE_GROUP) ? PETSC_TRUE : PETSC_FALSE;
1112:   return(0);
1113: }

1115: /*@
1116:  PetscViewerHDF5HasObject - Check whether a dataset with the same name as given object exists in the HDF5 file under current group

1118:   Input Parameters:
1119: + viewer - The HDF5 viewer
1120: - obj    - The named object

1122:   Output Parameter:
1123: . has    - Flag for dataset existence; PETSC_FALSE for unnamed object

1125:   Notes:
1126:   If the path exists but is not a dataset, this returns PETSC_FALSE as well.

1128:   Level: advanced

1130: .seealso: PetscViewerHDF5Open(), PetscViewerHDF5HasAttribute(), PetscViewerHDF5PushGroup(),PetscViewerHDF5PopGroup(),PetscViewerHDF5GetGroup()
1131: @*/
1132: PetscErrorCode PetscViewerHDF5HasObject(PetscViewer viewer, PetscObject obj, PetscBool *has)
1133: {
1134:   H5O_type_t type;
1135:   char *path;

1142:   *has = PETSC_FALSE;
1143:   if (!obj->name) return(0);
1144:   PetscViewerHDF5GetAbsolutePath_Internal(viewer, obj->name, &path);
1145:   PetscViewerHDF5Traverse_Internal(viewer, path, PETSC_FALSE, has, &type);
1146:   *has = (type == H5O_TYPE_DATASET) ? PETSC_TRUE : PETSC_FALSE;
1147:   PetscFree(path);
1148:   return(0);
1149: }

1151: /*@C
1152:  PetscViewerHDF5HasAttribute - Check whether an attribute exists

1154:   Input Parameters:
1155: + viewer - The HDF5 viewer
1156: . dataset - The parent dataset name, relative to the current group. NULL means a group-wise attribute.
1157: - name   - The attribute name

1159:   Output Parameter:
1160: . has    - Flag for attribute existence

1162:   Level: advanced

1164: .seealso: PetscViewerHDF5Open(), PetscViewerHDF5HasObjectAttribute(), PetscViewerHDF5WriteAttribute(), PetscViewerHDF5ReadAttribute(), PetscViewerHDF5PushGroup(),PetscViewerHDF5PopGroup(),PetscViewerHDF5GetGroup()
1165: @*/
1166: PetscErrorCode PetscViewerHDF5HasAttribute(PetscViewer viewer, const char dataset[], const char name[], PetscBool *has)
1167: {
1168:   char           *parent;

1176:   PetscViewerHDF5GetAbsolutePath_Internal(viewer, dataset, &parent);
1177:   PetscViewerHDF5Traverse_Internal(viewer, parent, PETSC_FALSE, has, NULL);
1178:   if (*has) {PetscViewerHDF5HasAttribute_Internal(viewer, parent, name, has);}
1179:   PetscFree(parent);
1180:   return(0);
1181: }

1183: /*@C
1184:  PetscViewerHDF5HasObjectAttribute - Check whether an attribute is attached to the dataset matching the given PetscObject by name

1186:   Input Parameters:
1187: + viewer - The HDF5 viewer
1188: . obj    - The object whose name is used to lookup the parent dataset, relative to the current group.
1189: - name   - The attribute name

1191:   Output Parameter:
1192: . has    - Flag for attribute existence

1194:   Notes:
1195:   This fails if current_group/object_name doesn't resolve to a dataset (the path doesn't exist or is not a dataset).
1196:   You might want to check first if it does using PetscViewerHDF5HasObject().

1198:   Level: advanced

1200: .seealso: PetscViewerHDF5Open(), PetscViewerHDF5HasAttribute(), PetscViewerHDF5WriteObjectAttribute(), PetscViewerHDF5ReadObjectAttribute(), PetscViewerHDF5HasObject(), PetscViewerHDF5PushGroup(),PetscViewerHDF5PopGroup(),PetscViewerHDF5GetGroup()
1201: @*/
1202: PetscErrorCode PetscViewerHDF5HasObjectAttribute(PetscViewer viewer, PetscObject obj, const char name[], PetscBool *has)
1203: {

1211:   PetscViewerHDF5CheckNamedObject_Internal(viewer, obj);
1212:   PetscViewerHDF5HasAttribute(viewer, obj->name, name, has);
1213:   return(0);
1214: }

1216: static PetscErrorCode PetscViewerHDF5HasAttribute_Internal(PetscViewer viewer, const char parent[], const char name[], PetscBool *has)
1217: {
1218:   hid_t          h5;
1219:   htri_t         hhas;

1223:   PetscViewerHDF5GetFileId(viewer, &h5);
1224:   PetscStackCallHDF5Return(hhas,H5Aexists_by_name,(h5, parent, name, H5P_DEFAULT));
1225:   *has = hhas ? PETSC_TRUE : PETSC_FALSE;
1226:   return(0);
1227: }

1229: /*
1230:   The variable Petsc_Viewer_HDF5_keyval is used to indicate an MPI attribute that
1231:   is attached to a communicator, in this case the attribute is a PetscViewer.
1232: */
1233: PetscMPIInt Petsc_Viewer_HDF5_keyval = MPI_KEYVAL_INVALID;

1235: /*@C
1236:   PETSC_VIEWER_HDF5_ - Creates an HDF5 PetscViewer shared by all processors in a communicator.

1238:   Collective

1240:   Input Parameter:
1241: . comm - the MPI communicator to share the HDF5 PetscViewer

1243:   Level: intermediate

1245:   Options Database Keys:
1246: . -viewer_hdf5_filename <name>

1248:   Environmental variables:
1249: . PETSC_VIEWER_HDF5_FILENAME

1251:   Notes:
1252:   Unlike almost all other PETSc routines, PETSC_VIEWER_HDF5_ does not return
1253:   an error code.  The HDF5 PetscViewer is usually used in the form
1254: $       XXXView(XXX object, PETSC_VIEWER_HDF5_(comm));

1256: .seealso: PetscViewerHDF5Open(), PetscViewerCreate(), PetscViewerDestroy()
1257: @*/
1258: PetscViewer PETSC_VIEWER_HDF5_(MPI_Comm comm)
1259: {
1261:   PetscBool      flg;
1262:   PetscViewer    viewer;
1263:   char           fname[PETSC_MAX_PATH_LEN];
1264:   MPI_Comm       ncomm;

1267:   PetscCommDuplicate(comm,&ncomm,NULL);if (ierr) {PetscError(PETSC_COMM_SELF,__LINE__,"PETSC_VIEWER_HDF5_",__FILE__,PETSC_ERR_PLIB,PETSC_ERROR_INITIAL," ");PetscFunctionReturn(NULL);}
1268:   if (Petsc_Viewer_HDF5_keyval == MPI_KEYVAL_INVALID) {
1269:     MPI_Comm_create_keyval(MPI_COMM_NULL_COPY_FN,MPI_COMM_NULL_DELETE_FN,&Petsc_Viewer_HDF5_keyval,NULL);
1270:     if (ierr) {PetscError(PETSC_COMM_SELF,__LINE__,"PETSC_VIEWER_HDF5_",__FILE__,PETSC_ERR_PLIB,PETSC_ERROR_INITIAL," ");PetscFunctionReturn(NULL);}
1271:   }
1272:   MPI_Comm_get_attr(ncomm,Petsc_Viewer_HDF5_keyval,(void**)&viewer,(int*)&flg);
1273:   if (ierr) {PetscError(PETSC_COMM_SELF,__LINE__,"PETSC_VIEWER_HDF5_",__FILE__,PETSC_ERR_PLIB,PETSC_ERROR_INITIAL," ");PetscFunctionReturn(NULL);}
1274:   if (!flg) { /* PetscViewer not yet created */
1275:     PetscOptionsGetenv(ncomm,"PETSC_VIEWER_HDF5_FILENAME",fname,PETSC_MAX_PATH_LEN,&flg);
1276:     if (ierr) {PetscError(PETSC_COMM_SELF,__LINE__,"PETSC_VIEWER_HDF5_",__FILE__,PETSC_ERR_PLIB,PETSC_ERROR_REPEAT," ");PetscFunctionReturn(NULL);}
1277:     if (!flg) {
1278:       PetscStrcpy(fname,"output.h5");
1279:       if (ierr) {PetscError(PETSC_COMM_SELF,__LINE__,"PETSC_VIEWER_HDF5_",__FILE__,PETSC_ERR_PLIB,PETSC_ERROR_REPEAT," ");PetscFunctionReturn(NULL);}
1280:     }
1281:     PetscViewerHDF5Open(ncomm,fname,FILE_MODE_WRITE,&viewer);
1282:     if (ierr) {PetscError(PETSC_COMM_SELF,__LINE__,"PETSC_VIEWER_HDF5_",__FILE__,PETSC_ERR_PLIB,PETSC_ERROR_REPEAT," ");PetscFunctionReturn(NULL);}
1283:     PetscObjectRegisterDestroy((PetscObject)viewer);
1284:     if (ierr) {PetscError(PETSC_COMM_SELF,__LINE__,"PETSC_VIEWER_HDF5_",__FILE__,PETSC_ERR_PLIB,PETSC_ERROR_REPEAT," ");PetscFunctionReturn(NULL);}
1285:     MPI_Comm_set_attr(ncomm,Petsc_Viewer_HDF5_keyval,(void*)viewer);
1286:     if (ierr) {PetscError(PETSC_COMM_SELF,__LINE__,"PETSC_VIEWER_HDF5_",__FILE__,PETSC_ERR_PLIB,PETSC_ERROR_INITIAL," ");PetscFunctionReturn(NULL);}
1287:   }
1288:   PetscCommDestroy(&ncomm);
1289:   if (ierr) {PetscError(PETSC_COMM_SELF,__LINE__,"PETSC_VIEWER_HDF5_",__FILE__,PETSC_ERR_PLIB,PETSC_ERROR_REPEAT," ");PetscFunctionReturn(NULL);}
1290:   PetscFunctionReturn(viewer);
1291: }