Date: 2021-03-03T22:25:33+00:00

Actual source code: hdf5v.c
petsc-3.14.5 2021-03-03
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      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:     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          = NULL;
    458:   hdf5->btype            = (PetscFileMode) -1;
    459:   hdf5->filename         = NULL;
    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:   Notes: If the datatype is PETSC_STRING one must PetscFree() the obtained value when it is no longer needed.

    919:   Level: advanced

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

    935:   PetscViewerHDF5GetAbsolutePath_Internal(viewer, dataset, &parent);
    936:   PetscViewerHDF5Traverse_Internal(viewer, parent, PETSC_FALSE, &has, NULL);
    937:   if (has) {PetscViewerHDF5HasAttribute_Internal(viewer, parent, name, &has);}
    938:   if (!has) SETERRQ2(PetscObjectComm((PetscObject)viewer), PETSC_ERR_FILE_UNEXPECTED, "Attribute %s/%s does not exist", parent, name);
    939:   PetscDataTypeToHDF5DataType(datatype, &dtype);
    940:   PetscViewerHDF5GetFileId(viewer, &h5);
    941:   PetscStackCallHDF5Return(obj,H5Oopen,(h5, parent, H5P_DEFAULT));
    942:   PetscStackCallHDF5Return(attribute,H5Aopen_name,(obj, name));
    943:   if (datatype == PETSC_STRING) {
    944:     size_t len;
    945:     PetscStackCallHDF5Return(atype,H5Aget_type,(attribute));
    946:     PetscStackCall("H5Tget_size",len = H5Tget_size(atype));
    947:     PetscMalloc((len+1) * sizeof(char), value);
    948:     PetscStackCallHDF5(H5Tset_size,(dtype, len+1));
    949:     PetscStackCallHDF5(H5Aread,(attribute, dtype, *(char**)value));
    950:   } else {
    951:     PetscStackCallHDF5(H5Aread,(attribute, dtype, value));
    952:   }
    953:   PetscStackCallHDF5(H5Aclose,(attribute));
    954:   /* H5Oclose can be used to close groups, datasets, or committed datatypes */
    955:   PetscStackCallHDF5(H5Oclose,(obj));
    956:   PetscFree(parent);
    957:   return(0);
    958: }

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

    963:   Input Parameters:
    964: + viewer   - The HDF5 viewer
    965: . obj      - The object whose name is used to lookup the parent dataset, relative to the current group.
    966: . name     - The attribute name
    967: - datatype - The attribute type

    969:   Output Parameter:
    970: . value    - The attribute value

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

    976:   Level: advanced

    978: .seealso: PetscViewerHDF5Open(), PetscViewerHDF5ReadAttribute() PetscViewerHDF5WriteObjectAttribute(), PetscViewerHDF5HasObjectAttribute(), PetscViewerHDF5PushGroup(),PetscViewerHDF5PopGroup(),PetscViewerHDF5GetGroup()
    979: @*/
    980: PetscErrorCode PetscViewerHDF5ReadObjectAttribute(PetscViewer viewer, PetscObject obj, const char name[], PetscDataType datatype, void *value)
    981: {

    989:   PetscViewerHDF5CheckNamedObject_Internal(viewer, obj);
    990:   PetscViewerHDF5ReadAttribute(viewer, obj->name, name, datatype, value);
    991:   return(0);
    992: }

    994: PETSC_STATIC_INLINE PetscErrorCode PetscViewerHDF5Traverse_Inner_Internal(hid_t h5, const char name[], PetscBool createGroup, PetscBool *exists_)
    995: {
    996:   htri_t exists;
    997:   hid_t group;

    1000:   PetscStackCallHDF5Return(exists,H5Lexists,(h5, name, H5P_DEFAULT));
    1001:   if (exists) PetscStackCallHDF5Return(exists,H5Oexists_by_name,(h5, name, H5P_DEFAULT));
    1002:   if (!exists && createGroup) {
    1003:     PetscStackCallHDF5Return(group,H5Gcreate2,(h5, name, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT));
    1004:     PetscStackCallHDF5(H5Gclose,(group));
    1005:     exists = PETSC_TRUE;
    1006:   }
    1007:   *exists_ = (PetscBool) exists;
    1008:   return(0);
    1009: }

    1011: static PetscErrorCode PetscViewerHDF5Traverse_Internal(PetscViewer viewer, const char name[], PetscBool createGroup, PetscBool *has, H5O_type_t *otype)
    1012: {
    1013:   const char     rootGroupName[] = "/";
    1014:   hid_t          h5;
    1015:   PetscBool      exists=PETSC_FALSE;
    1016:   PetscInt       i;
    1017:   int            n;
    1018:   char           **hierarchy;
    1019:   char           buf[PETSC_MAX_PATH_LEN]="";

    1025:   else name = rootGroupName;
    1026:   if (has) {
    1028:     *has = PETSC_FALSE;
    1029:   }
    1030:   if (otype) {
    1032:     *otype = H5O_TYPE_UNKNOWN;
    1033:   }
    1034:   PetscViewerHDF5GetFileId(viewer, &h5);

    1036:   /*
    1037:      Unfortunately, H5Oexists_by_name() fails if any object in hierarchy is missing.
    1038:      Hence, each of them needs to be tested separately:
    1039:      1) whether it's a valid link
    1040:      2) whether this link resolves to an object
    1041:      See H5Oexists_by_name() documentation.
    1042:   */
    1043:   PetscStrToArray(name,'/',&n,&hierarchy);
    1044:   if (!n) {
    1045:     /*  Assume group "/" always exists in accordance with HDF5 >= 1.10.0. See H5Lexists() documentation. */
    1046:     if (has)   *has   = PETSC_TRUE;
    1047:     if (otype) *otype = H5O_TYPE_GROUP;
    1048:     PetscStrToArrayDestroy(n,hierarchy);
    1049:     return(0);
    1050:   }
    1051:   for (i=0; i<n; i++) {
    1052:     PetscStrcat(buf,"/");
    1053:     PetscStrcat(buf,hierarchy[i]);
    1054:     PetscViewerHDF5Traverse_Inner_Internal(h5, buf, createGroup, &exists);
    1055:     if (!exists) break;
    1056:   }
    1057:   PetscStrToArrayDestroy(n,hierarchy);

    1059:   /* If the object exists, get its type */
    1060:   if (exists && otype) {
    1061:     H5O_info_t info;

    1063:     /* We could use H5Iget_type() here but that would require opening the object. This way we only need its name. */
    1064:     PetscStackCallHDF5(H5Oget_info_by_name,(h5, name, &info, H5P_DEFAULT));
    1065:     *otype = info.type;
    1066:   }
    1067:   if (has) *has = exists;
    1068:   return(0);
    1069: }

    1071: /*@
    1072:  PetscViewerHDF5HasGroup - Check whether the current (pushed) group exists in the HDF5 file

    1074:   Input Parameters:
    1075: . viewer - The HDF5 viewer

    1077:   Output Parameter:
    1078: . has    - Flag for group existence

    1080:   Notes:
    1081:   If the path exists but is not a group, this returns PETSC_FALSE as well.

    1083:   Level: advanced

    1085: .seealso: PetscViewerHDF5Open(), PetscViewerHDF5PushGroup(), PetscViewerHDF5PopGroup(), PetscViewerHDF5OpenGroup()
    1086: @*/
    1087: PetscErrorCode PetscViewerHDF5HasGroup(PetscViewer viewer, PetscBool *has)
    1088: {
    1089:   H5O_type_t type;
    1090:   const char *name;

    1096:   PetscViewerHDF5GetGroup(viewer, &name);
    1097:   PetscViewerHDF5Traverse_Internal(viewer, name, PETSC_FALSE, has, &type);
    1098:   *has = (type == H5O_TYPE_GROUP) ? PETSC_TRUE : PETSC_FALSE;
    1099:   return(0);
    1100: }

    1102: /*@
    1103:  PetscViewerHDF5HasObject - Check whether a dataset with the same name as given object exists in the HDF5 file under current group

    1105:   Input Parameters:
    1106: + viewer - The HDF5 viewer
    1107: - obj    - The named object

    1109:   Output Parameter:
    1110: . has    - Flag for dataset existence; PETSC_FALSE for unnamed object

    1112:   Notes:
    1113:   If the path exists but is not a dataset, this returns PETSC_FALSE as well.

    1115:   Level: advanced

    1117: .seealso: PetscViewerHDF5Open(), PetscViewerHDF5HasAttribute(), PetscViewerHDF5PushGroup(),PetscViewerHDF5PopGroup(),PetscViewerHDF5GetGroup()
    1118: @*/
    1119: PetscErrorCode PetscViewerHDF5HasObject(PetscViewer viewer, PetscObject obj, PetscBool *has)
    1120: {
    1121:   H5O_type_t type;
    1122:   char *path;

    1129:   *has = PETSC_FALSE;
    1130:   if (!obj->name) return(0);
    1131:   PetscViewerHDF5GetAbsolutePath_Internal(viewer, obj->name, &path);
    1132:   PetscViewerHDF5Traverse_Internal(viewer, path, PETSC_FALSE, has, &type);
    1133:   *has = (type == H5O_TYPE_DATASET) ? PETSC_TRUE : PETSC_FALSE;
    1134:   PetscFree(path);
    1135:   return(0);
    1136: }

    1138: /*@C
    1139:  PetscViewerHDF5HasAttribute - Check whether an attribute exists

    1141:   Input Parameters:
    1142: + viewer - The HDF5 viewer
    1143: . dataset - The parent dataset name, relative to the current group. NULL means a group-wise attribute.
    1144: - name   - The attribute name

    1146:   Output Parameter:
    1147: . has    - Flag for attribute existence

    1149:   Level: advanced

    1151: .seealso: PetscViewerHDF5Open(), PetscViewerHDF5HasObjectAttribute(), PetscViewerHDF5WriteAttribute(), PetscViewerHDF5ReadAttribute(), PetscViewerHDF5PushGroup(),PetscViewerHDF5PopGroup(),PetscViewerHDF5GetGroup()
    1152: @*/
    1153: PetscErrorCode PetscViewerHDF5HasAttribute(PetscViewer viewer, const char dataset[], const char name[], PetscBool *has)
    1154: {
    1155:   char           *parent;

    1163:   PetscViewerHDF5GetAbsolutePath_Internal(viewer, dataset, &parent);
    1164:   PetscViewerHDF5Traverse_Internal(viewer, parent, PETSC_FALSE, has, NULL);
    1165:   if (*has) {PetscViewerHDF5HasAttribute_Internal(viewer, parent, name, has);}
    1166:   PetscFree(parent);
    1167:   return(0);
    1168: }

    1170: /*@C
    1171:  PetscViewerHDF5HasObjectAttribute - Check whether an attribute is attached to the dataset matching the given PetscObject by name

    1173:   Input Parameters:
    1174: + viewer - The HDF5 viewer
    1175: . obj    - The object whose name is used to lookup the parent dataset, relative to the current group.
    1176: - name   - The attribute name

    1178:   Output Parameter:
    1179: . has    - Flag for attribute existence

    1181:   Notes:
    1182:   This fails if current_group/object_name doesn't resolve to a dataset (the path doesn't exist or is not a dataset).
    1183:   You might want to check first if it does using PetscViewerHDF5HasObject().

    1185:   Level: advanced

    1187: .seealso: PetscViewerHDF5Open(), PetscViewerHDF5HasAttribute(), PetscViewerHDF5WriteObjectAttribute(), PetscViewerHDF5ReadObjectAttribute(), PetscViewerHDF5HasObject(), PetscViewerHDF5PushGroup(),PetscViewerHDF5PopGroup(),PetscViewerHDF5GetGroup()
    1188: @*/
    1189: PetscErrorCode PetscViewerHDF5HasObjectAttribute(PetscViewer viewer, PetscObject obj, const char name[], PetscBool *has)
    1190: {

    1198:   PetscViewerHDF5CheckNamedObject_Internal(viewer, obj);
    1199:   PetscViewerHDF5HasAttribute(viewer, obj->name, name, has);
    1200:   return(0);
    1201: }

    1203: static PetscErrorCode PetscViewerHDF5HasAttribute_Internal(PetscViewer viewer, const char parent[], const char name[], PetscBool *has)
    1204: {
    1205:   hid_t          h5;
    1206:   htri_t         hhas;

    1210:   PetscViewerHDF5GetFileId(viewer, &h5);
    1211:   PetscStackCallHDF5Return(hhas,H5Aexists_by_name,(h5, parent, name, H5P_DEFAULT));
    1212:   *has = hhas ? PETSC_TRUE : PETSC_FALSE;
    1213:   return(0);
    1214: }

    1216: /*
    1217:   The variable Petsc_Viewer_HDF5_keyval is used to indicate an MPI attribute that
    1218:   is attached to a communicator, in this case the attribute is a PetscViewer.
    1219: */
    1220: PetscMPIInt Petsc_Viewer_HDF5_keyval = MPI_KEYVAL_INVALID;

    1222: /*@C
    1223:   PETSC_VIEWER_HDF5_ - Creates an HDF5 PetscViewer shared by all processors in a communicator.

    1225:   Collective

    1227:   Input Parameter:
    1228: . comm - the MPI communicator to share the HDF5 PetscViewer

    1230:   Level: intermediate

    1232:   Options Database Keys:
    1233: . -viewer_hdf5_filename <name>

    1235:   Environmental variables:
    1236: . PETSC_VIEWER_HDF5_FILENAME

    1238:   Notes:
    1239:   Unlike almost all other PETSc routines, PETSC_VIEWER_HDF5_ does not return
    1240:   an error code.  The HDF5 PetscViewer is usually used in the form
    1241: $       XXXView(XXX object, PETSC_VIEWER_HDF5_(comm));

    1243: .seealso: PetscViewerHDF5Open(), PetscViewerCreate(), PetscViewerDestroy()
    1244: @*/
    1245: PetscViewer PETSC_VIEWER_HDF5_(MPI_Comm comm)
    1246: {
    1248:   PetscBool      flg;
    1249:   PetscViewer    viewer;
    1250:   char           fname[PETSC_MAX_PATH_LEN];
    1251:   MPI_Comm       ncomm;

    1254:   PetscCommDuplicate(comm,&ncomm,NULL);if (ierr) {PetscError(PETSC_COMM_SELF,__LINE__,"PETSC_VIEWER_HDF5_",__FILE__,PETSC_ERR_PLIB,PETSC_ERROR_INITIAL," ");PetscFunctionReturn(NULL);}
    1255:   if (Petsc_Viewer_HDF5_keyval == MPI_KEYVAL_INVALID) {
    1256:     MPI_Comm_create_keyval(MPI_COMM_NULL_COPY_FN,MPI_COMM_NULL_DELETE_FN,&Petsc_Viewer_HDF5_keyval,NULL);
    1257:     if (ierr) {PetscError(PETSC_COMM_SELF,__LINE__,"PETSC_VIEWER_HDF5_",__FILE__,PETSC_ERR_PLIB,PETSC_ERROR_INITIAL," ");PetscFunctionReturn(NULL);}
    1258:   }
    1259:   MPI_Comm_get_attr(ncomm,Petsc_Viewer_HDF5_keyval,(void**)&viewer,(int*)&flg);
    1260:   if (ierr) {PetscError(PETSC_COMM_SELF,__LINE__,"PETSC_VIEWER_HDF5_",__FILE__,PETSC_ERR_PLIB,PETSC_ERROR_INITIAL," ");PetscFunctionReturn(NULL);}
    1261:   if (!flg) { /* PetscViewer not yet created */
    1262:     PetscOptionsGetenv(ncomm,"PETSC_VIEWER_HDF5_FILENAME",fname,PETSC_MAX_PATH_LEN,&flg);
    1263:     if (ierr) {PetscError(PETSC_COMM_SELF,__LINE__,"PETSC_VIEWER_HDF5_",__FILE__,PETSC_ERR_PLIB,PETSC_ERROR_INITIAL," ");PetscFunctionReturn(NULL);}
    1264:     if (!flg) {
    1265:       PetscStrcpy(fname,"output.h5");
    1266:       if (ierr) {PetscError(PETSC_COMM_SELF,__LINE__,"PETSC_VIEWER_HDF5_",__FILE__,PETSC_ERR_PLIB,PETSC_ERROR_INITIAL," ");PetscFunctionReturn(NULL);}
    1267:     }
    1268:     PetscViewerHDF5Open(ncomm,fname,FILE_MODE_WRITE,&viewer);
    1269:     if (ierr) {PetscError(PETSC_COMM_SELF,__LINE__,"PETSC_VIEWER_HDF5_",__FILE__,PETSC_ERR_PLIB,PETSC_ERROR_INITIAL," ");PetscFunctionReturn(NULL);}
    1270:     PetscObjectRegisterDestroy((PetscObject)viewer);
    1271:     if (ierr) {PetscError(PETSC_COMM_SELF,__LINE__,"PETSC_VIEWER_HDF5_",__FILE__,PETSC_ERR_PLIB,PETSC_ERROR_INITIAL," ");PetscFunctionReturn(NULL);}
    1272:     MPI_Comm_set_attr(ncomm,Petsc_Viewer_HDF5_keyval,(void*)viewer);
    1273:     if (ierr) {PetscError(PETSC_COMM_SELF,__LINE__,"PETSC_VIEWER_HDF5_",__FILE__,PETSC_ERR_PLIB,PETSC_ERROR_INITIAL," ");PetscFunctionReturn(NULL);}
    1274:   }
    1275:   PetscCommDestroy(&ncomm);
    1276:   if (ierr) {PetscError(PETSC_COMM_SELF,__LINE__,"PETSC_VIEWER_HDF5_",__FILE__,PETSC_ERR_PLIB,PETSC_ERROR_INITIAL," ");PetscFunctionReturn(NULL);}
    1277:   PetscFunctionReturn(viewer);
    1278: }