impls/hdf5/hdf5v.c

#include <petsc/private/viewerhdf5impl.h> /*I "petscviewerhdf5.h" I*/

static PetscErrorCode PetscViewerHDF5Traverse_Internal(PetscViewer, const char[], PetscBool, PetscBool *, H5O_type_t *);
static PetscErrorCode PetscViewerHDF5HasAttribute_Internal(PetscViewer, const char[], const char[], PetscBool *);

/*@C
  PetscViewerHDF5GetGroup - Get the current HDF5 group name (full path), set with `PetscViewerHDF5PushGroup()`/`PetscViewerHDF5PopGroup()`.

  Not collective

  Input Parameters:
+ viewer - the `PetscViewer` of type `PETSCVIEWERHDF5`
- path - (Optional) The path relative to the pushed group

  Output Parameter:
. abspath - The absolute HDF5 path (group)

  Level: intermediate

  Notes:
  If path starts with '/', it is taken as an absolute path overriding currently pushed group, else path is relative to the current pushed group.
  So NULL or empty path means the current pushed group.

  The output abspath is newly allocated so needs to be freed.

.seealso: `PETSCVIEWERHDF5`, `PetscViewerHDF5Open()`, `PetscViewerHDF5PushGroup()`, `PetscViewerHDF5PopGroup()`, `PetscViewerHDF5OpenGroup()`
@*/
PetscErrorCode PetscViewerHDF5GetGroup(PetscViewer viewer, const char path[], char *abspath[]) {
  size_t      len;
  PetscBool   relative = PETSC_FALSE;
  const char *group;
  char        buf[PETSC_MAX_PATH_LEN] = "";

  PetscFunctionBegin;
  PetscValidHeaderSpecific(viewer, PETSC_VIEWER_CLASSID, 1);
  if (path) PetscValidCharPointer(path, 2);
  PetscValidPointer(abspath, 3);
  PetscCall(PetscViewerHDF5GetGroup_Internal(viewer, &group));
  PetscCall(PetscStrlen(path, &len));
  relative = (PetscBool)(!len || path[0] != '/');
  if (relative) {
    PetscCall(PetscStrcpy(buf, group));
    if (!group || len) PetscCall(PetscStrcat(buf, "/"));
    PetscCall(PetscStrcat(buf, path));
    PetscCall(PetscStrallocpy(buf, abspath));
  } else {
    PetscCall(PetscStrallocpy(path, abspath));
  }
  PetscFunctionReturn(0);
}

static PetscErrorCode PetscViewerHDF5CheckNamedObject_Internal(PetscViewer viewer, PetscObject obj) {
  PetscBool has;

  PetscFunctionBegin;
  PetscCall(PetscViewerHDF5HasObject(viewer, obj, &has));
  if (!has) {
    char *group;
    PetscCall(PetscViewerHDF5GetGroup(viewer, NULL, &group));
    SETERRQ(PetscObjectComm((PetscObject)viewer), PETSC_ERR_FILE_UNEXPECTED, "Object (dataset) \"%s\" not stored in group %s", obj->name, group);
  }
  PetscFunctionReturn(0);
}

static PetscErrorCode PetscViewerSetFromOptions_HDF5(PetscViewer v, PetscOptionItems *PetscOptionsObject) {
  PetscBool         flg  = PETSC_FALSE, set;
  PetscViewer_HDF5 *hdf5 = (PetscViewer_HDF5 *)v->data;

  PetscFunctionBegin;
  PetscOptionsHeadBegin(PetscOptionsObject, "HDF5 PetscViewer Options");
  PetscCall(PetscOptionsBool("-viewer_hdf5_base_dimension2", "1d Vectors get 2 dimensions in HDF5", "PetscViewerHDF5SetBaseDimension2", hdf5->basedimension2, &hdf5->basedimension2, NULL));
  PetscCall(PetscOptionsBool("-viewer_hdf5_sp_output", "Force data to be written in single precision", "PetscViewerHDF5SetSPOutput", hdf5->spoutput, &hdf5->spoutput, NULL));
  PetscCall(PetscOptionsBool("-viewer_hdf5_collective", "Enable collective transfer mode", "PetscViewerHDF5SetCollective", flg, &flg, &set));
  if (set) PetscCall(PetscViewerHDF5SetCollective(v, flg));
  flg = PETSC_FALSE;
  PetscCall(PetscOptionsBool("-viewer_hdf5_default_timestepping", "Set default timestepping state", "PetscViewerHDF5SetDefaultTimestepping", flg, &flg, &set));
  if (set) PetscCall(PetscViewerHDF5SetDefaultTimestepping(v, flg));
  PetscOptionsHeadEnd();
  PetscFunctionReturn(0);
}

static PetscErrorCode PetscViewerView_HDF5(PetscViewer v, PetscViewer viewer) {
  PetscViewer_HDF5 *hdf5 = (PetscViewer_HDF5 *)v->data;
  PetscBool         flg;

  PetscFunctionBegin;
  if (hdf5->filename) PetscCall(PetscViewerASCIIPrintf(viewer, "Filename: %s\n", hdf5->filename));
  PetscCall(PetscViewerASCIIPrintf(viewer, "Vectors with blocksize 1 saved as 2D datasets: %s\n", PetscBools[hdf5->basedimension2]));
  PetscCall(PetscViewerASCIIPrintf(viewer, "Enforce single precision storage: %s\n", PetscBools[hdf5->spoutput]));
  PetscCall(PetscViewerHDF5GetCollective(v, &flg));
  PetscCall(PetscViewerASCIIPrintf(viewer, "MPI-IO transfer mode: %s\n", flg ? "collective" : "independent"));
  PetscCall(PetscViewerASCIIPrintf(viewer, "Default timestepping: %s\n", PetscBools[hdf5->defTimestepping]));
  PetscFunctionReturn(0);
}

static PetscErrorCode PetscViewerFileClose_HDF5(PetscViewer viewer) {
  PetscViewer_HDF5 *hdf5 = (PetscViewer_HDF5 *)viewer->data;

  PetscFunctionBegin;
  PetscCall(PetscFree(hdf5->filename));
  if (hdf5->file_id) PetscCallHDF5(H5Fclose, (hdf5->file_id));
  PetscFunctionReturn(0);
}

static PetscErrorCode PetscViewerFlush_HDF5(PetscViewer viewer) {
  PetscViewer_HDF5 *hdf5 = (PetscViewer_HDF5 *)viewer->data;

  PetscFunctionBegin;
  if (hdf5->file_id) PetscCallHDF5(H5Fflush, (hdf5->file_id, H5F_SCOPE_LOCAL));
  PetscFunctionReturn(0);
}

static PetscErrorCode PetscViewerDestroy_HDF5(PetscViewer viewer) {
  PetscViewer_HDF5 *hdf5 = (PetscViewer_HDF5 *)viewer->data;

  PetscFunctionBegin;
  PetscCallHDF5(H5Pclose, (hdf5->dxpl_id));
  PetscCall(PetscViewerFileClose_HDF5(viewer));
  while (hdf5->groups) {
    PetscViewerHDF5GroupList *tmp = hdf5->groups->next;

    PetscCall(PetscFree(hdf5->groups->name));
    PetscCall(PetscFree(hdf5->groups));
    hdf5->groups = tmp;
  }
  PetscCall(PetscFree(hdf5));
  PetscCall(PetscObjectComposeFunction((PetscObject)viewer, "PetscViewerFileSetName_C", NULL));
  PetscCall(PetscObjectComposeFunction((PetscObject)viewer, "PetscViewerFileGetName_C", NULL));
  PetscCall(PetscObjectComposeFunction((PetscObject)viewer, "PetscViewerFileSetMode_C", NULL));
  PetscCall(PetscObjectComposeFunction((PetscObject)viewer, "PetscViewerFileGetMode_C", NULL));
  PetscCall(PetscObjectComposeFunction((PetscObject)viewer, "PetscViewerHDF5SetBaseDimension2_C", NULL));
  PetscCall(PetscObjectComposeFunction((PetscObject)viewer, "PetscViewerHDF5SetSPOutput_C", NULL));
  PetscCall(PetscObjectComposeFunction((PetscObject)viewer, "PetscViewerHDF5SetCollective_C", NULL));
  PetscCall(PetscObjectComposeFunction((PetscObject)viewer, "PetscViewerHDF5GetCollective_C", NULL));
  PetscCall(PetscObjectComposeFunction((PetscObject)viewer, "PetscViewerHDF5GetDefaultTimestepping_C", NULL));
  PetscCall(PetscObjectComposeFunction((PetscObject)viewer, "PetscViewerHDF5SetDefaultTimestepping_C", NULL));
  PetscFunctionReturn(0);
}

static PetscErrorCode PetscViewerFileSetMode_HDF5(PetscViewer viewer, PetscFileMode type) {
  PetscViewer_HDF5 *hdf5 = (PetscViewer_HDF5 *)viewer->data;

  PetscFunctionBegin;
  hdf5->btype = type;
  PetscFunctionReturn(0);
}

static PetscErrorCode PetscViewerFileGetMode_HDF5(PetscViewer viewer, PetscFileMode *type) {
  PetscViewer_HDF5 *hdf5 = (PetscViewer_HDF5 *)viewer->data;

  PetscFunctionBegin;
  *type = hdf5->btype;
  PetscFunctionReturn(0);
}

static PetscErrorCode PetscViewerHDF5SetBaseDimension2_HDF5(PetscViewer viewer, PetscBool flg) {
  PetscViewer_HDF5 *hdf5 = (PetscViewer_HDF5 *)viewer->data;

  PetscFunctionBegin;
  hdf5->basedimension2 = flg;
  PetscFunctionReturn(0);
}

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

    Logically Collective on viewer

  Input Parameters:
+  viewer - the `PetscViewer`; if it is a `PETSCVIEWERHDF5` then this command is ignored
-  flg - if `PETSC_TRUE` the vector will always have at least a dimension of 2 even if that first dimension is of size 1

  Options Database Key:
.  -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

  Note:
  Setting this option allegedly makes code that reads the HDF5 in easier since they do not have a "special case" of a bs/dof
  of one when the dimension is lower. Others think the option is crazy.

  Level: intermediate

.seealso: `PETSCVIEWERHDF5`, PetscViewerFileSetMode()`, `PetscViewerCreate()`, `PetscViewerSetType()`, `PetscViewerBinaryOpen()`
@*/
PetscErrorCode PetscViewerHDF5SetBaseDimension2(PetscViewer viewer, PetscBool flg) {
  PetscFunctionBegin;
  PetscValidHeaderSpecific(viewer, PETSC_VIEWER_CLASSID, 1);
  PetscTryMethod(viewer, "PetscViewerHDF5SetBaseDimension2_C", (PetscViewer, PetscBool), (viewer, flg));
  PetscFunctionReturn(0);
}

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

    Logically Collective on viewer

  Input Parameter:
.  viewer - the `PetscViewer`, must be `PETSCVIEWERHDF5`

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

  Note:
  Setting this option allegedly makes code that reads the HDF5 in easier since they do not have a "special case" of a bs/dof
  of one when the dimension is lower. Others think the option is crazy.

  Level: intermediate

.seealso: `PETSCVIEWERHDF5`, `PetscViewerFileSetMode()`, `PetscViewerCreate()`, `PetscViewerSetType()`, `PetscViewerBinaryOpen()`
@*/
PetscErrorCode PetscViewerHDF5GetBaseDimension2(PetscViewer viewer, PetscBool *flg) {
  PetscViewer_HDF5 *hdf5 = (PetscViewer_HDF5 *)viewer->data;

  PetscFunctionBegin;
  PetscValidHeaderSpecific(viewer, PETSC_VIEWER_CLASSID, 1);
  *flg = hdf5->basedimension2;
  PetscFunctionReturn(0);
}

static PetscErrorCode PetscViewerHDF5SetSPOutput_HDF5(PetscViewer viewer, PetscBool flg) {
  PetscViewer_HDF5 *hdf5 = (PetscViewer_HDF5 *)viewer->data;

  PetscFunctionBegin;
  hdf5->spoutput = flg;
  PetscFunctionReturn(0);
}

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

    Logically Collective on viewer

  Input Parameters:
+  viewer - the PetscViewer; if it is a `PETSCVIEWERHDF5` then this command is ignored
-  flg - if `PETSC_TRUE` the data will be written to disk with single precision

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

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

  Level: intermediate

.seealso: `PETSCVIEWERHDF5`, `PetscViewerFileSetMode()`, `PetscViewerCreate()`, `PetscViewerSetType()`, `PetscViewerBinaryOpen()`,
          `PetscReal`, `PetscViewerHDF5GetSPOutput()`
@*/
PetscErrorCode PetscViewerHDF5SetSPOutput(PetscViewer viewer, PetscBool flg) {
  PetscFunctionBegin;
  PetscValidHeaderSpecific(viewer, PETSC_VIEWER_CLASSID, 1);
  PetscTryMethod(viewer, "PetscViewerHDF5SetSPOutput_C", (PetscViewer, PetscBool), (viewer, flg));
  PetscFunctionReturn(0);
}

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

    Logically Collective on viewer

  Input Parameter:
.  viewer - the PetscViewer, must be of type `PETSCVIEWERHDF5`

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

  Level: intermediate

.seealso: `PetscViewerFileSetMode()`, `PetscViewerCreate()`, `PetscViewerSetType()`, `PetscViewerBinaryOpen()`,
          `PetscReal`, `PetscViewerHDF5SetSPOutput()`
@*/
PetscErrorCode PetscViewerHDF5GetSPOutput(PetscViewer viewer, PetscBool *flg) {
  PetscViewer_HDF5 *hdf5 = (PetscViewer_HDF5 *)viewer->data;

  PetscFunctionBegin;
  PetscValidHeaderSpecific(viewer, PETSC_VIEWER_CLASSID, 1);
  *flg = hdf5->spoutput;
  PetscFunctionReturn(0);
}

static PetscErrorCode PetscViewerHDF5SetCollective_HDF5(PetscViewer viewer, PetscBool flg) {
  PetscFunctionBegin;
  /* H5FD_MPIO_COLLECTIVE is wrong in hdf5 1.10.2, and is the same as H5FD_MPIO_INDEPENDENT in earlier versions
     - see e.g. https://gitlab.cosma.dur.ac.uk/swift/swiftsim/issues/431 */
#if H5_VERSION_GE(1, 10, 3) && defined(H5_HAVE_PARALLEL)
  {
    PetscViewer_HDF5 *hdf5 = (PetscViewer_HDF5 *)viewer->data;
    PetscCallHDF5(H5Pset_dxpl_mpio, (hdf5->dxpl_id, flg ? H5FD_MPIO_COLLECTIVE : H5FD_MPIO_INDEPENDENT));
  }
#else
  if (flg) PetscCall(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"));
#endif
  PetscFunctionReturn(0);
}

/*@
  PetscViewerHDF5SetCollective - Use collective MPI-IO transfer mode for HDF5 reads and writes.

  Logically Collective; flg must contain common value

  Input Parameters:
+ viewer - the `PetscViewer`; if it is not `PETSCVIEWERHDF5` then this command is ignored
- flg - `PETSC_TRUE` for collective mode; `PETSC_FALSE` for independent mode (default)

  Options Database Key:
. -viewer_hdf5_collective - turns on (true) or off (false) collective transfers

  Note:
  Collective mode gives the MPI-IO layer underneath HDF5 a chance to do some additional collective optimizations and hence can perform better.
  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.

  Developer Note:
  In the HDF5 layer, `PETSC_TRUE` / `PETSC_FALSE` means `H5Pset_dxpl_mpio()` is called with `H5FD_MPIO_COLLECTIVE` / `H5FD_MPIO_INDEPENDENT`, respectively.
  This in turn means use of MPI_File_{read,write}_all /  MPI_File_{read,write} in the MPI-IO layer, respectively.
  See HDF5 documentation and MPI-IO documentation for details.

  Level: intermediate

.seealso: `PETSCVIEWERHDF5`, `PetscViewerHDF5GetCollective()`, `PetscViewerCreate()`, `PetscViewerSetType()`, `PetscViewerHDF5Open()`
@*/
PetscErrorCode PetscViewerHDF5SetCollective(PetscViewer viewer, PetscBool flg) {
  PetscFunctionBegin;
  PetscValidHeaderSpecific(viewer, PETSC_VIEWER_CLASSID, 1);
  PetscValidLogicalCollectiveBool(viewer, flg, 2);
  PetscTryMethod(viewer, "PetscViewerHDF5SetCollective_C", (PetscViewer, PetscBool), (viewer, flg));
  PetscFunctionReturn(0);
}

static PetscErrorCode PetscViewerHDF5GetCollective_HDF5(PetscViewer viewer, PetscBool *flg) {
#if defined(H5_HAVE_PARALLEL)
  PetscViewer_HDF5 *hdf5 = (PetscViewer_HDF5 *)viewer->data;
  H5FD_mpio_xfer_t  mode;
#endif

  PetscFunctionBegin;
#if !defined(H5_HAVE_PARALLEL)
  *flg = PETSC_FALSE;
#else
  PetscCallHDF5(H5Pget_dxpl_mpio, (hdf5->dxpl_id, &mode));
  *flg = (mode == H5FD_MPIO_COLLECTIVE) ? PETSC_TRUE : PETSC_FALSE;
#endif
  PetscFunctionReturn(0);
}

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

  Not Collective

  Input Parameters:
. viewer - the `PETSCVIEWERHDF5` `PetscViewer`

  Output Parameters:
. flg - the flag

  Level: intermediate

  Note:
  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.
  For more details, see `PetscViewerHDF5SetCollective()`.

.seealso: `PETSCVIEWERHDF5`, `PetscViewerHDF5SetCollective()`, `PetscViewerCreate()`, `PetscViewerSetType()`, `PetscViewerHDF5Open()`
@*/
PetscErrorCode PetscViewerHDF5GetCollective(PetscViewer viewer, PetscBool *flg) {
  PetscFunctionBegin;
  PetscValidHeaderSpecific(viewer, PETSC_VIEWER_CLASSID, 1);
  PetscValidBoolPointer(flg, 2);

  PetscUseMethod(viewer, "PetscViewerHDF5GetCollective_C", (PetscViewer, PetscBool *), (viewer, flg));
  PetscFunctionReturn(0);
}

static PetscErrorCode PetscViewerFileSetName_HDF5(PetscViewer viewer, const char name[]) {
  PetscViewer_HDF5 *hdf5 = (PetscViewer_HDF5 *)viewer->data;
  hid_t             plist_id;

  PetscFunctionBegin;
  if (hdf5->file_id) PetscCallHDF5(H5Fclose, (hdf5->file_id));
  if (hdf5->filename) PetscCall(PetscFree(hdf5->filename));
  PetscCall(PetscStrallocpy(name, &hdf5->filename));
  /* Set up file access property list with parallel I/O access */
  PetscCallHDF5Return(plist_id, H5Pcreate, (H5P_FILE_ACCESS));
#if defined(H5_HAVE_PARALLEL)
  PetscCallHDF5(H5Pset_fapl_mpio, (plist_id, PetscObjectComm((PetscObject)viewer), MPI_INFO_NULL));
#endif
  /* Create or open the file collectively */
  switch (hdf5->btype) {
  case FILE_MODE_READ:
    if (PetscDefined(USE_DEBUG)) {
      PetscMPIInt rank;
      PetscBool   flg;

      PetscCallMPI(MPI_Comm_rank(PetscObjectComm((PetscObject)viewer), &rank));
      if (rank == 0) {
        PetscCall(PetscTestFile(hdf5->filename, 'r', &flg));
        PetscCheck(flg, PETSC_COMM_SELF, PETSC_ERR_FILE_OPEN, "File %s requested for reading does not exist", hdf5->filename);
      }
      PetscCallMPI(MPI_Barrier(PetscObjectComm((PetscObject)viewer)));
    }
    PetscCallHDF5Return(hdf5->file_id, H5Fopen, (name, H5F_ACC_RDONLY, plist_id));
    break;
  case FILE_MODE_APPEND:
  case FILE_MODE_UPDATE: {
    PetscBool flg;
    PetscCall(PetscTestFile(hdf5->filename, 'r', &flg));
    if (flg) PetscCallHDF5Return(hdf5->file_id, H5Fopen, (name, H5F_ACC_RDWR, plist_id));
    else PetscCallHDF5Return(hdf5->file_id, H5Fcreate, (name, H5F_ACC_EXCL, H5P_DEFAULT, plist_id));
    break;
  }
  case FILE_MODE_WRITE: PetscCallHDF5Return(hdf5->file_id, H5Fcreate, (name, H5F_ACC_TRUNC, H5P_DEFAULT, plist_id)); break;
  case FILE_MODE_UNDEFINED: SETERRQ(PetscObjectComm((PetscObject)viewer), PETSC_ERR_ORDER, "Must call PetscViewerFileSetMode() before PetscViewerFileSetName()");
  default: SETERRQ(PetscObjectComm((PetscObject)viewer), PETSC_ERR_SUP, "Unsupported file mode %s", PetscFileModes[hdf5->btype]);
  }
  PetscCheck(hdf5->file_id >= 0, PETSC_COMM_SELF, PETSC_ERR_LIB, "H5Fcreate failed for %s", name);
  PetscCallHDF5(H5Pclose, (plist_id));
  PetscFunctionReturn(0);
}

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

  PetscFunctionBegin;
  *name = vhdf5->filename;
  PetscFunctionReturn(0);
}

static PetscErrorCode PetscViewerSetUp_HDF5(PetscViewer viewer) {
  /*
  PetscViewer_HDF5 *hdf5 = (PetscViewer_HDF5*) viewer->data;
  */

  PetscFunctionBegin;
  PetscFunctionReturn(0);
}

static PetscErrorCode PetscViewerHDF5SetDefaultTimestepping_HDF5(PetscViewer viewer, PetscBool flg) {
  PetscViewer_HDF5 *hdf5 = (PetscViewer_HDF5 *)viewer->data;

  PetscFunctionBegin;
  hdf5->defTimestepping = flg;
  PetscFunctionReturn(0);
}

static PetscErrorCode PetscViewerHDF5GetDefaultTimestepping_HDF5(PetscViewer viewer, PetscBool *flg) {
  PetscViewer_HDF5 *hdf5 = (PetscViewer_HDF5 *)viewer->data;

  PetscFunctionBegin;
  *flg = hdf5->defTimestepping;
  PetscFunctionReturn(0);
}

/*@
  PetscViewerHDF5SetDefaultTimestepping - Set the flag for default timestepping

  Logically Collective on viewer

  Input Parameters:
+ viewer - the `PetscViewer`; if it is not `PETSCVIEWERHDF5` then this command is ignored
- flg    - if `PETSC_TRUE` we will assume that timestepping is on

  Options Database Key:
. -viewer_hdf5_default_timestepping - turns on (true) or off (false) default timestepping

  Note:
  If the timestepping attribute is not found for an object, then the default timestepping is used

  Level: intermediate

.seealso: `PETSCVIEWERHDF5`, `PetscViewerHDF5GetDefaultTimestepping()`, `PetscViewerHDF5PushTimestepping()`, `PetscViewerHDF5GetTimestep()`
@*/
PetscErrorCode PetscViewerHDF5SetDefaultTimestepping(PetscViewer viewer, PetscBool flg) {
  PetscFunctionBegin;
  PetscValidHeaderSpecific(viewer, PETSC_VIEWER_CLASSID, 1);
  PetscTryMethod(viewer, "PetscViewerHDF5SetDefaultTimestepping_C", (PetscViewer, PetscBool), (viewer, flg));
  PetscFunctionReturn(0);
}

/*@
  PetscViewerHDF5GetDefaultTimestepping - Get the flag for default timestepping

  Not collective

  Input Parameter:
. viewer - the `PetscViewer` of type `PETSCVIEWERHDF5`

  Output Parameter:
. flg    - if `PETSC_TRUE` we will assume that timestepping is on

  Level: intermediate

.seealso: `PETSCVIEWERHDF5`, `PetscViewerHDF5SetDefaultTimestepping()`, `PetscViewerHDF5PushTimestepping()`, `PetscViewerHDF5GetTimestep()`
@*/
PetscErrorCode PetscViewerHDF5GetDefaultTimestepping(PetscViewer viewer, PetscBool *flg) {
  PetscFunctionBegin;
  PetscValidHeaderSpecific(viewer, PETSC_VIEWER_CLASSID, 1);
  PetscUseMethod(viewer, "PetscViewerHDF5GetDefaultTimestepping_C", (PetscViewer, PetscBool *), (viewer, flg));
  PetscFunctionReturn(0);
}

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

  Level: beginner

.seealso: `PetscViewerHDF5Open()`, `PetscViewerStringSPrintf()`, `PetscViewerSocketOpen()`, `PetscViewerDrawOpen()`, `PETSCVIEWERSOCKET`,
          `PetscViewerCreate()`, `PetscViewerASCIIOpen()`, `PetscViewerBinaryOpen()`, `PETSCVIEWERBINARY`, `PETSCVIEWERDRAW`, `PETSCVIEWERSTRING`,
          `PetscViewerMatlabOpen()`, `VecView()`, `DMView()`, `PetscViewerMatlabPutArray()`, `PETSCVIEWERASCII`, `PETSCVIEWERMATLAB`,
          `PetscViewerFileSetName()`, `PetscViewerFileSetMode()`, `PetscViewerFormat`, `PetscViewerType`, `PetscViewerSetType()`
M*/

PETSC_EXTERN PetscErrorCode PetscViewerCreate_HDF5(PetscViewer v) {
  PetscViewer_HDF5 *hdf5;

  PetscFunctionBegin;
#if !defined(H5_HAVE_PARALLEL)
  {
    PetscMPIInt size;
    PetscCallMPI(MPI_Comm_size(PetscObjectComm((PetscObject)v), &size));
    PetscCheck(size <= 1, PetscObjectComm((PetscObject)v), PETSC_ERR_SUP, "Cannot use parallel HDF5 viewer since the given HDF5 does not support parallel I/O (H5_HAVE_PARALLEL is unset)");
  }
#endif

  PetscCall(PetscNewLog(v, &hdf5));

  v->data                = (void *)hdf5;
  v->ops->destroy        = PetscViewerDestroy_HDF5;
  v->ops->setfromoptions = PetscViewerSetFromOptions_HDF5;
  v->ops->setup          = PetscViewerSetUp_HDF5;
  v->ops->view           = PetscViewerView_HDF5;
  v->ops->flush          = PetscViewerFlush_HDF5;
  hdf5->btype            = FILE_MODE_UNDEFINED;
  hdf5->filename         = NULL;
  hdf5->timestep         = -1;
  hdf5->groups           = NULL;

  PetscCallHDF5Return(hdf5->dxpl_id, H5Pcreate, (H5P_DATASET_XFER));

  PetscCall(PetscObjectComposeFunction((PetscObject)v, "PetscViewerFileSetName_C", PetscViewerFileSetName_HDF5));
  PetscCall(PetscObjectComposeFunction((PetscObject)v, "PetscViewerFileGetName_C", PetscViewerFileGetName_HDF5));
  PetscCall(PetscObjectComposeFunction((PetscObject)v, "PetscViewerFileSetMode_C", PetscViewerFileSetMode_HDF5));
  PetscCall(PetscObjectComposeFunction((PetscObject)v, "PetscViewerFileGetMode_C", PetscViewerFileGetMode_HDF5));
  PetscCall(PetscObjectComposeFunction((PetscObject)v, "PetscViewerHDF5SetBaseDimension2_C", PetscViewerHDF5SetBaseDimension2_HDF5));
  PetscCall(PetscObjectComposeFunction((PetscObject)v, "PetscViewerHDF5SetSPOutput_C", PetscViewerHDF5SetSPOutput_HDF5));
  PetscCall(PetscObjectComposeFunction((PetscObject)v, "PetscViewerHDF5SetCollective_C", PetscViewerHDF5SetCollective_HDF5));
  PetscCall(PetscObjectComposeFunction((PetscObject)v, "PetscViewerHDF5GetCollective_C", PetscViewerHDF5GetCollective_HDF5));
  PetscCall(PetscObjectComposeFunction((PetscObject)v, "PetscViewerHDF5GetDefaultTimestepping_C", PetscViewerHDF5GetDefaultTimestepping_HDF5));
  PetscCall(PetscObjectComposeFunction((PetscObject)v, "PetscViewerHDF5SetDefaultTimestepping_C", PetscViewerHDF5SetDefaultTimestepping_HDF5));
  PetscFunctionReturn(0);
}

/*@C
   PetscViewerHDF5Open - Opens a file for HDF5 input/output as a `PETSCVIEWERHDF5` `PetscViewer`

   Collective

   Input Parameters:
+  comm - MPI communicator
.  name - name of file
-  type - type of file

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

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

   Level: beginner

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

   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.

   This PetscViewer should be destroyed with PetscViewerDestroy().

.seealso: `PETSCVIEWERHDF5`, `PetscViewerASCIIOpen()`, `PetscViewerPushFormat()`, `PetscViewerDestroy()`, `PetscViewerHDF5SetBaseDimension2()`,
          `PetscViewerHDF5SetSPOutput()`, `PetscViewerHDF5GetBaseDimension2()`, `VecView()`, `MatView()`, `VecLoad()`,
          `MatLoad()`, `PetscFileMode`, `PetscViewer`, `PetscViewerSetType()`, `PetscViewerFileSetMode()`, `PetscViewerFileSetName()`
@*/
PetscErrorCode PetscViewerHDF5Open(MPI_Comm comm, const char name[], PetscFileMode type, PetscViewer *hdf5v) {
  PetscFunctionBegin;
  PetscCall(PetscViewerCreate(comm, hdf5v));
  PetscCall(PetscViewerSetType(*hdf5v, PETSCVIEWERHDF5));
  PetscCall(PetscViewerFileSetMode(*hdf5v, type));
  PetscCall(PetscViewerFileSetName(*hdf5v, name));
  PetscCall(PetscViewerSetFromOptions(*hdf5v));
  PetscFunctionReturn(0);
}

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

  Not collective

  Input Parameter:
. viewer - the `PetscViewer`

  Output Parameter:
. file_id - The file id

  Level: intermediate

.seealso: `PETSCVIEWERHDF5`, `PetscViewerHDF5Open()`
@*/
PetscErrorCode PetscViewerHDF5GetFileId(PetscViewer viewer, hid_t *file_id) {
  PetscViewer_HDF5 *hdf5 = (PetscViewer_HDF5 *)viewer->data;

  PetscFunctionBegin;
  PetscValidHeaderSpecific(viewer, PETSC_VIEWER_CLASSID, 1);
  if (file_id) *file_id = hdf5->file_id;
  PetscFunctionReturn(0);
}

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

  Not collective

  Input Parameters:
+ viewer - the `PetscViewer` of type `PETSCVIEWERHDF5`
- name - The group name

  Level: intermediate

  Notes:
  This is designed to mnemonically resemble the Unix cd command.
.vb
  If name begins with '/', it is interpreted as an absolute path fully replacing current group, otherwise it is taken as relative to the current group.
  NULL, empty string, or any sequence of all slashes (e.g. "///") is interpreted as the root group "/".
  "." means the current group is pushed again.
.ve

  Example:
  Suppose the current group is "/a".
  + If name is NULL, empty string, or a sequence of all slashes (e.g. "///"), then the new group will be "/".
  . If name is ".", then the new group will be "/a".
  . If name is "b", then the new group will be "/a/b".
  - If name is "/b", then the new group will be "/b".

  Developer Note:
  The root group "/" is internally stored as NULL.

.seealso: `PETSCVIEWERHDF5`, `PetscViewerHDF5Open()`, `PetscViewerHDF5PopGroup()`, `PetscViewerHDF5GetGroup()`, `PetscViewerHDF5OpenGroup()`
@*/
PetscErrorCode PetscViewerHDF5PushGroup(PetscViewer viewer, const char name[]) {
  PetscViewer_HDF5         *hdf5 = (PetscViewer_HDF5 *)viewer->data;
  PetscViewerHDF5GroupList *groupNode;
  size_t                    i, len;
  char                      buf[PETSC_MAX_PATH_LEN];
  const char               *gname;

  PetscFunctionBegin;
  PetscValidHeaderSpecific(viewer, PETSC_VIEWER_CLASSID, 1);
  if (name) PetscValidCharPointer(name, 2);
  PetscCall(PetscStrlen(name, &len));
  gname = NULL;
  if (len) {
    if (len == 1 && name[0] == '.') {
      /* use current name */
      gname = (hdf5->groups && hdf5->groups->name) ? hdf5->groups->name : NULL;
    } else if (name[0] == '/') {
      /* absolute */
      for (i = 1; i < len; i++) {
        if (name[i] != '/') {
          gname = name;
          break;
        }
      }
    } else {
      /* relative */
      const char *parent = (hdf5->groups && hdf5->groups->name) ? hdf5->groups->name : "";
      PetscCall(PetscSNPrintf(buf, sizeof(buf), "%s/%s", parent, name));
      gname = buf;
    }
  }
  PetscCall(PetscNew(&groupNode));
  PetscCall(PetscStrallocpy(gname, (char **)&groupNode->name));
  groupNode->next = hdf5->groups;
  hdf5->groups    = groupNode;
  PetscFunctionReturn(0);
}

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

  Not collective

  Input Parameter:
. viewer - the `PetscViewer` of type `PETSCVIEWERHDF5`

  Level: intermediate

.seealso: `PETSCVIEWERHDF5`, `PetscViewerHDF5Open()`, `PetscViewerHDF5PushGroup()`, `PetscViewerHDF5GetGroup()`, `PetscViewerHDF5OpenGroup()`
@*/
PetscErrorCode PetscViewerHDF5PopGroup(PetscViewer viewer) {
  PetscViewer_HDF5         *hdf5 = (PetscViewer_HDF5 *)viewer->data;
  PetscViewerHDF5GroupList *groupNode;

  PetscFunctionBegin;
  PetscValidHeaderSpecific(viewer, PETSC_VIEWER_CLASSID, 1);
  PetscCheck(hdf5->groups, PetscObjectComm((PetscObject)viewer), PETSC_ERR_ARG_WRONGSTATE, "HDF5 group stack is empty, cannot pop");
  groupNode    = hdf5->groups;
  hdf5->groups = hdf5->groups->next;
  PetscCall(PetscFree(groupNode->name));
  PetscCall(PetscFree(groupNode));
  PetscFunctionReturn(0);
}

PetscErrorCode PetscViewerHDF5GetGroup_Internal(PetscViewer viewer, const char *name[]) {
  PetscViewer_HDF5 *hdf5 = (PetscViewer_HDF5 *)viewer->data;

  PetscFunctionBegin;
  PetscValidHeaderSpecific(viewer, PETSC_VIEWER_CLASSID, 1);
  PetscValidPointer(name, 2);
  if (hdf5->groups) *name = hdf5->groups->name;
  else *name = NULL;
  PetscFunctionReturn(0);
}

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

  Not collective

  Input Parameter:
. viewer - the `PetscViewer` of type `PETSCVIEWERHDF5`

  Output Parameters:
+ fileId - The HDF5 file ID
- groupId - The HDF5 group ID

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

  Level: intermediate

.seealso: `PETSCVIEWERHDF5`, `PetscViewerHDF5Open()`, `PetscViewerHDF5PushGroup()`, `PetscViewerHDF5PopGroup()`, `PetscViewerHDF5GetGroup()`
@*/
PetscErrorCode PetscViewerHDF5OpenGroup(PetscViewer viewer, hid_t *fileId, hid_t *groupId) {
  hid_t       file_id;
  H5O_type_t  type;
  const char *groupName = NULL, *fileName = NULL;
  PetscBool   writable, has;

  PetscFunctionBegin;
  PetscCall(PetscViewerWritable(viewer, &writable));
  PetscCall(PetscViewerHDF5GetFileId(viewer, &file_id));
  PetscCall(PetscViewerFileGetName(viewer, &fileName));
  PetscCall(PetscViewerHDF5GetGroup_Internal(viewer, &groupName));
  PetscCall(PetscViewerHDF5Traverse_Internal(viewer, groupName, writable, &has, &type));
  if (!has) {
    PetscCheck(writable, PetscObjectComm((PetscObject)viewer), PETSC_ERR_FILE_UNEXPECTED, "Group %s does not exist and file %s is not open for writing", groupName, fileName);
    SETERRQ(PetscObjectComm((PetscObject)viewer), PETSC_ERR_LIB, "HDF5 failed to create group %s although file %s is open for writing", groupName, fileName);
  }
  PetscCheck(type == H5O_TYPE_GROUP, PetscObjectComm((PetscObject)viewer), PETSC_ERR_FILE_UNEXPECTED, "Path %s in file %s resolves to something which is not a group", groupName, fileName);
  PetscCallHDF5Return(*groupId, H5Gopen2, (file_id, groupName ? groupName : "/", H5P_DEFAULT));
  *fileId = file_id;
  PetscFunctionReturn(0);
}

/*@
  PetscViewerHDF5PushTimestepping - Activate timestepping mode for subsequent HDF5 reading and writing.

  Not collective

  Input Parameter:
. viewer - the `PetscViewer` of type `PETSCVIEWERHDF5`

  Level: intermediate

  Notes:
  On first `PetscViewerHDF5PushTimestepping()`, the initial time step is set to 0.
  Next timesteps can then be set using `PetscViewerHDF5IncrementTimestep()` or `PetscViewerHDF5SetTimestep()`.
  Current timestep value determines which timestep is read from or written to any dataset on the next HDF5 I/O operation [e.g. `VecView()`].
  Use `PetscViewerHDF5PopTimestepping()` to deactivate timestepping mode; calling it by the end of the program is NOT mandatory.
  Current timestep is remembered between `PetscViewerHDF5PopTimestepping()` and the next `PetscViewerHDF5PushTimestepping()`.

  If a dataset was stored with timestepping, it can be loaded only in the timestepping mode again.
  Loading a timestepped dataset with timestepping disabled, or vice-versa results in an error.

  Developer note:
  Timestepped HDF5 dataset has an extra dimension and attribute "timestepping" set to true.

.seealso: `PETSCVIEWERHDF5`, `PetscViewerHDF5Open()`, `PetscViewerHDF5PopTimestepping()`, `PetscViewerHDF5IsTimestepping()`, `PetscViewerHDF5SetTimestep()`, `PetscViewerHDF5IncrementTimestep()`, `PetscViewerHDF5GetTimestep()`
@*/
PetscErrorCode PetscViewerHDF5PushTimestepping(PetscViewer viewer) {
  PetscViewer_HDF5 *hdf5 = (PetscViewer_HDF5 *)viewer->data;

  PetscFunctionBegin;
  PetscValidHeaderSpecific(viewer, PETSC_VIEWER_CLASSID, 1);
  PetscCheck(!hdf5->timestepping, PetscObjectComm((PetscObject)viewer), PETSC_ERR_ARG_WRONGSTATE, "Timestepping is already pushed");
  hdf5->timestepping = PETSC_TRUE;
  if (hdf5->timestep < 0) hdf5->timestep = 0;
  PetscFunctionReturn(0);
}

/*@
  PetscViewerHDF5PopTimestepping - Deactivate timestepping mode for subsequent HDF5 reading and writing.

  Not collective

  Input Parameter:
. viewer - the `PetscViewer` of type `PETSCVIEWERHDF5`

  Level: intermediate

  Note:
  See `PetscViewerHDF5PushTimestepping()` for details.

.seealso: `PETSCVIEWERHDF5`, `PetscViewerHDF5Open()`, `PetscViewerHDF5PushTimestepping()`, `PetscViewerHDF5IsTimestepping()`, `PetscViewerHDF5SetTimestep()`, `PetscViewerHDF5IncrementTimestep()`, `PetscViewerHDF5GetTimestep()`
@*/
PetscErrorCode PetscViewerHDF5PopTimestepping(PetscViewer viewer) {
  PetscViewer_HDF5 *hdf5 = (PetscViewer_HDF5 *)viewer->data;

  PetscFunctionBegin;
  PetscValidHeaderSpecific(viewer, PETSC_VIEWER_CLASSID, 1);
  PetscCheck(hdf5->timestepping, PetscObjectComm((PetscObject)viewer), PETSC_ERR_ARG_WRONGSTATE, "Timestepping has not been pushed yet. Call PetscViewerHDF5PushTimestepping() first");
  hdf5->timestepping = PETSC_FALSE;
  PetscFunctionReturn(0);
}

/*@
  PetscViewerHDF5IsTimestepping - Ask the viewer whether it is in timestepping mode currently.

  Not collective

  Input Parameter:
. viewer - the `PetscViewer` of type `PETSCVIEWERHDF5`

  Output Parameter:
. flg - is timestepping active?

  Level: intermediate

  Note:
  See `PetscViewerHDF5PushTimestepping()` for details.

.seealso: `PETSCVIEWERHDF5`, `PetscViewerHDF5Open()`, `PetscViewerHDF5PushTimestepping()`, `PetscViewerHDF5PopTimestepping()`, `PetscViewerHDF5SetTimestep()`, `PetscViewerHDF5IncrementTimestep()`, `PetscViewerHDF5GetTimestep()`
@*/
PetscErrorCode PetscViewerHDF5IsTimestepping(PetscViewer viewer, PetscBool *flg) {
  PetscViewer_HDF5 *hdf5 = (PetscViewer_HDF5 *)viewer->data;

  PetscFunctionBegin;
  PetscValidHeaderSpecific(viewer, PETSC_VIEWER_CLASSID, 1);
  *flg = hdf5->timestepping;
  PetscFunctionReturn(0);
}

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

  Not collective

  Input Parameter:
. viewer - the `PetscViewer` of type `PETSCVIEWERHDF5`

  Level: intermediate

  Note:
  This can be called only if the viewer is in timestepping mode. See `PetscViewerHDF5PushTimestepping()` for details.

.seealso: `PETSCVIEWERHDF5`, `PetscViewerHDF5Open()`, `PetscViewerHDF5PushTimestepping()`, `PetscViewerHDF5SetTimestep()`, `PetscViewerHDF5GetTimestep()`
@*/
PetscErrorCode PetscViewerHDF5IncrementTimestep(PetscViewer viewer) {
  PetscViewer_HDF5 *hdf5 = (PetscViewer_HDF5 *)viewer->data;

  PetscFunctionBegin;
  PetscValidHeaderSpecific(viewer, PETSC_VIEWER_CLASSID, 1);
  PetscCheck(hdf5->timestepping, PetscObjectComm((PetscObject)viewer), PETSC_ERR_ARG_WRONGSTATE, "Timestepping has not been pushed yet. Call PetscViewerHDF5PushTimestepping() first");
  ++hdf5->timestep;
  PetscFunctionReturn(0);
}

/*@
  PetscViewerHDF5SetTimestep - Set the current timestep for the HDF5 output. Fields are stacked in time.

  Logically collective

  Input Parameters:
+ viewer - the `PetscViewer` of type `PETSCVIEWERHDF5`
- timestep - The timestep

  Level: intermediate

  Note:
  This can be called only if the viewer is in timestepping mode. See `PetscViewerHDF5PushTimestepping()` for details.

.seealso: `PETSCVIEWERHDF5`, `PetscViewerHDF5Open()`, `PetscViewerHDF5PushTimestepping()`, `PetscViewerHDF5IncrementTimestep()`, `PetscViewerHDF5GetTimestep()`
@*/
PetscErrorCode PetscViewerHDF5SetTimestep(PetscViewer viewer, PetscInt timestep) {
  PetscViewer_HDF5 *hdf5 = (PetscViewer_HDF5 *)viewer->data;

  PetscFunctionBegin;
  PetscValidHeaderSpecific(viewer, PETSC_VIEWER_CLASSID, 1);
  PetscValidLogicalCollectiveInt(viewer, timestep, 2);
  PetscCheck(timestep >= 0, PetscObjectComm((PetscObject)viewer), PETSC_ERR_ARG_WRONGSTATE, "Timestep %" PetscInt_FMT " is negative", timestep);
  PetscCheck(hdf5->timestepping, PetscObjectComm((PetscObject)viewer), PETSC_ERR_ARG_WRONGSTATE, "Timestepping has not been pushed yet. Call PetscViewerHDF5PushTimestepping() first");
  hdf5->timestep = timestep;
  PetscFunctionReturn(0);
}

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

  Not collective

  Input Parameter:
. viewer - the `PetscViewer` of type `PETSCVIEWERHDF5`

  Output Parameter:
. timestep - The timestep

  Level: intermediate

  Note:
  This can be called only if the viewer is in the timestepping mode. See `PetscViewerHDF5PushTimestepping()` for details.

.seealso: `PETSCVIEWERHDF5`, `PetscViewerHDF5Open()`, `PetscViewerHDF5PushTimestepping()`, `PetscViewerHDF5IncrementTimestep()`, `PetscViewerHDF5SetTimestep()`
@*/
PetscErrorCode PetscViewerHDF5GetTimestep(PetscViewer viewer, PetscInt *timestep) {
  PetscViewer_HDF5 *hdf5 = (PetscViewer_HDF5 *)viewer->data;

  PetscFunctionBegin;
  PetscValidHeaderSpecific(viewer, PETSC_VIEWER_CLASSID, 1);
  PetscValidIntPointer(timestep, 2);
  PetscCheck(hdf5->timestepping, PetscObjectComm((PetscObject)viewer), PETSC_ERR_ARG_WRONGSTATE, "Timestepping has not been pushed yet. Call PetscViewerHDF5PushTimestepping() first");
  *timestep = hdf5->timestep;
  PetscFunctionReturn(0);
}

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

  Not collective

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

  Output Parameter:
. mtype - the HDF5  datatype

  Level: advanced

.seealso: `PetscDataType`, `PetscHDF5DataTypeToPetscDataType()`
@*/
PetscErrorCode PetscDataTypeToHDF5DataType(PetscDataType ptype, hid_t *htype) {
  PetscFunctionBegin;
  if (ptype == PETSC_INT)
#if defined(PETSC_USE_64BIT_INDICES)
    *htype = H5T_NATIVE_LLONG;
#else
    *htype = H5T_NATIVE_INT;
#endif
  else if (ptype == PETSC_DOUBLE) *htype = H5T_NATIVE_DOUBLE;
  else if (ptype == PETSC_LONG) *htype = H5T_NATIVE_LONG;
  else if (ptype == PETSC_SHORT) *htype = H5T_NATIVE_SHORT;
  else if (ptype == PETSC_ENUM) *htype = H5T_NATIVE_INT;
  else if (ptype == PETSC_BOOL) *htype = H5T_NATIVE_INT;
  else if (ptype == PETSC_FLOAT) *htype = H5T_NATIVE_FLOAT;
  else if (ptype == PETSC_CHAR) *htype = H5T_NATIVE_CHAR;
  else if (ptype == PETSC_BIT_LOGICAL) *htype = H5T_NATIVE_UCHAR;
  else if (ptype == PETSC_STRING) *htype = H5Tcopy(H5T_C_S1);
  else SETERRQ(PETSC_COMM_SELF, PETSC_ERR_ARG_OUTOFRANGE, "Unsupported PETSc datatype");
  PetscFunctionReturn(0);
}

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

  Not collective

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

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

  Level: advanced

.seealso: `PetscDataType`, `PetscHDF5DataTypeToPetscDataType()`
@*/
PetscErrorCode PetscHDF5DataTypeToPetscDataType(hid_t htype, PetscDataType *ptype) {
  PetscFunctionBegin;
#if defined(PETSC_USE_64BIT_INDICES)
  if (htype == H5T_NATIVE_INT) *ptype = PETSC_LONG;
  else if (htype == H5T_NATIVE_LLONG) *ptype = PETSC_INT;
#else
  if (htype == H5T_NATIVE_INT) *ptype = PETSC_INT;
#endif
  else if (htype == H5T_NATIVE_DOUBLE) *ptype = PETSC_DOUBLE;
  else if (htype == H5T_NATIVE_LONG) *ptype = PETSC_LONG;
  else if (htype == H5T_NATIVE_SHORT) *ptype = PETSC_SHORT;
  else if (htype == H5T_NATIVE_FLOAT) *ptype = PETSC_FLOAT;
  else if (htype == H5T_NATIVE_CHAR) *ptype = PETSC_CHAR;
  else if (htype == H5T_NATIVE_UCHAR) *ptype = PETSC_CHAR;
  else if (htype == H5T_C_S1) *ptype = PETSC_STRING;
  else SETERRQ(PETSC_COMM_SELF, PETSC_ERR_ARG_OUTOFRANGE, "Unsupported HDF5 datatype");
  PetscFunctionReturn(0);
}

/*@C
 PetscViewerHDF5WriteAttribute - Write an attribute

  Collective

  Input Parameters:
+ viewer - The `PETSCVIEWERHDF5` viewer
. parent - The parent dataset/group name
. name   - The attribute name
. datatype - The attribute type
- value    - The attribute value

  Level: advanced

  Note:
  If parent starts with '/', it is taken as an absolute path overriding currently pushed group, else parent is relative to the current pushed group. NULL means the current pushed group.

.seealso: `PETSCVIEWERHDF5`, `PetscViewerHDF5Open()`, `PetscViewerHDF5WriteObjectAttribute()`, `PetscViewerHDF5ReadAttribute()`, `PetscViewerHDF5HasAttribute()`,
          `PetscViewerHDF5PushGroup()`, `PetscViewerHDF5PopGroup()`, `PetscViewerHDF5GetGroup()`
@*/
PetscErrorCode PetscViewerHDF5WriteAttribute(PetscViewer viewer, const char parent[], const char name[], PetscDataType datatype, const void *value) {
  char     *parentAbsPath;
  hid_t     h5, dataspace, obj, attribute, dtype;
  PetscBool has;

  PetscFunctionBegin;
  PetscValidHeaderSpecific(viewer, PETSC_VIEWER_CLASSID, 1);
  if (parent) PetscValidCharPointer(parent, 2);
  PetscValidCharPointer(name, 3);
  PetscValidLogicalCollectiveEnum(viewer, datatype, 4);
  PetscValidPointer(value, 5);
  PetscCall(PetscViewerHDF5GetGroup(viewer, parent, &parentAbsPath));
  PetscCall(PetscViewerHDF5Traverse_Internal(viewer, parentAbsPath, PETSC_TRUE, NULL, NULL));
  PetscCall(PetscViewerHDF5HasAttribute_Internal(viewer, parentAbsPath, name, &has));
  PetscCall(PetscDataTypeToHDF5DataType(datatype, &dtype));
  if (datatype == PETSC_STRING) {
    size_t len;
    PetscCall(PetscStrlen((const char *)value, &len));
    PetscCallHDF5(H5Tset_size, (dtype, len + 1));
  }
  PetscCall(PetscViewerHDF5GetFileId(viewer, &h5));
  PetscCallHDF5Return(dataspace, H5Screate, (H5S_SCALAR));
  PetscCallHDF5Return(obj, H5Oopen, (h5, parentAbsPath, H5P_DEFAULT));
  if (has) {
    PetscCallHDF5Return(attribute, H5Aopen_name, (obj, name));
  } else {
    PetscCallHDF5Return(attribute, H5Acreate2, (obj, name, dtype, dataspace, H5P_DEFAULT, H5P_DEFAULT));
  }
  PetscCallHDF5(H5Awrite, (attribute, dtype, value));
  if (datatype == PETSC_STRING) PetscCallHDF5(H5Tclose, (dtype));
  PetscCallHDF5(H5Aclose, (attribute));
  PetscCallHDF5(H5Oclose, (obj));
  PetscCallHDF5(H5Sclose, (dataspace));
  PetscCall(PetscFree(parentAbsPath));
  PetscFunctionReturn(0);
}

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

  Collective

  Input Parameters:
+ viewer   - The `PETSCVIEWERHDF5` viewer
. obj      - The object whose name is used to lookup the parent dataset, relative to the current group.
. name     - The attribute name
. datatype - The attribute type
- value    - The attribute value

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

  Level: advanced

.seealso: `PETSCVIEWERHDF5`, `PetscViewerHDF5Open()`, `PetscViewerHDF5WriteAttribute()`, `PetscViewerHDF5ReadObjectAttribute()`, `PetscViewerHDF5HasObjectAttribute()`,
          `PetscViewerHDF5HasObject()`, `PetscViewerHDF5PushGroup()`, `PetscViewerHDF5PopGroup()`, `PetscViewerHDF5GetGroup()`
@*/
PetscErrorCode PetscViewerHDF5WriteObjectAttribute(PetscViewer viewer, PetscObject obj, const char name[], PetscDataType datatype, const void *value) {
  PetscFunctionBegin;
  PetscValidHeaderSpecific(viewer, PETSC_VIEWER_CLASSID, 1);
  PetscValidHeader(obj, 2);
  PetscValidCharPointer(name, 3);
  PetscValidPointer(value, 5);
  PetscCall(PetscViewerHDF5CheckNamedObject_Internal(viewer, obj));
  PetscCall(PetscViewerHDF5WriteAttribute(viewer, obj->name, name, datatype, value));
  PetscFunctionReturn(0);
}

/*@C
 PetscViewerHDF5ReadAttribute - Read an attribute

  Collective

  Input Parameters:
+ viewer - The `PETSCVIEWERHDF5` viewer
. parent - The parent dataset/group name
. name   - The attribute name
. datatype - The attribute type
- defaultValue - The pointer to the default value

  Output Parameter:
. value    - The pointer to the read HDF5 attribute value

  Notes:
  If defaultValue is NULL and the attribute is not found, an error occurs.
  If defaultValue is not NULL and the attribute is not found, defaultValue is copied to value.
  The pointers defaultValue and value can be the same; for instance
$  flg = `PETSC_FALSE`;
$  PetscCall(`PetscViewerHDF5ReadAttribute`(viewer,name,"attr",PETSC_BOOL,&flg,&flg));
  is valid, but make sure the default value is initialized.

  If the datatype is `PETSC_STRING`, the output string is newly allocated so one must `PetscFree()` it when no longer needed.

  If parent starts with '/', it is taken as an absolute path overriding currently pushed group, else parent is relative to the current pushed group. NULL means the current pushed group.

  Level: advanced

.seealso: `PETSCVIEWERHDF5`, `PetscViewerHDF5Open()`, `PetscViewerHDF5ReadObjectAttribute()`, `PetscViewerHDF5WriteAttribute()`, `PetscViewerHDF5HasAttribute()`, `PetscViewerHDF5HasObject()`, `PetscViewerHDF5PushGroup()`, `PetscViewerHDF5PopGroup()`, `PetscViewerHDF5GetGroup()`
@*/
PetscErrorCode PetscViewerHDF5ReadAttribute(PetscViewer viewer, const char parent[], const char name[], PetscDataType datatype, const void *defaultValue, void *value) {
  char     *parentAbsPath;
  hid_t     h5, obj, attribute, dtype;
  PetscBool has;

  PetscFunctionBegin;
  PetscValidHeaderSpecific(viewer, PETSC_VIEWER_CLASSID, 1);
  if (parent) PetscValidCharPointer(parent, 2);
  PetscValidCharPointer(name, 3);
  if (defaultValue) PetscValidPointer(defaultValue, 5);
  PetscValidPointer(value, 6);
  PetscCall(PetscDataTypeToHDF5DataType(datatype, &dtype));
  PetscCall(PetscViewerHDF5GetGroup(viewer, parent, &parentAbsPath));
  PetscCall(PetscViewerHDF5Traverse_Internal(viewer, parentAbsPath, PETSC_FALSE, &has, NULL));
  if (has) PetscCall(PetscViewerHDF5HasAttribute_Internal(viewer, parentAbsPath, name, &has));
  if (!has) {
    if (defaultValue) {
      if (defaultValue != value) {
        if (datatype == PETSC_STRING) {
          PetscCall(PetscStrallocpy(*(char **)defaultValue, (char **)value));
        } else {
          size_t len;
          PetscCallHDF5ReturnNoCheck(len, H5Tget_size, (dtype));
          PetscCall(PetscMemcpy(value, defaultValue, len));
        }
      }
      PetscCall(PetscFree(parentAbsPath));
      PetscFunctionReturn(0);
    } else SETERRQ(PetscObjectComm((PetscObject)viewer), PETSC_ERR_FILE_UNEXPECTED, "Attribute %s/%s does not exist and default value not provided", parentAbsPath, name);
  }
  PetscCall(PetscViewerHDF5GetFileId(viewer, &h5));
  PetscCallHDF5Return(obj, H5Oopen, (h5, parentAbsPath, H5P_DEFAULT));
  PetscCallHDF5Return(attribute, H5Aopen_name, (obj, name));
  if (datatype == PETSC_STRING) {
    size_t len;
    hid_t  atype;
    PetscCallHDF5Return(atype, H5Aget_type, (attribute));
    PetscCallHDF5ReturnNoCheck(len, H5Tget_size, (atype));
    PetscCall(PetscMalloc((len + 1) * sizeof(char), value));
    PetscCallHDF5(H5Tset_size, (dtype, len + 1));
    PetscCallHDF5(H5Aread, (attribute, dtype, *(char **)value));
  } else {
    PetscCallHDF5(H5Aread, (attribute, dtype, value));
  }
  PetscCallHDF5(H5Aclose, (attribute));
  /* H5Oclose can be used to close groups, datasets, or committed datatypes */
  PetscCallHDF5(H5Oclose, (obj));
  PetscCall(PetscFree(parentAbsPath));
  PetscFunctionReturn(0);
}

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

  Collective

  Input Parameters:
+ viewer   - The `PETSCVIEWERHDF5` viewer
. obj      - The object whose name is used to lookup the parent dataset, relative to the current group.
. name     - The attribute name
- datatype - The attribute type

  Output Parameter:
. value    - The attribute value

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

  Level: advanced

.seealso: `PETSCVIEWERHDF5`, `PetscViewerHDF5Open()`, `PetscViewerHDF5ReadAttribute()` `PetscViewerHDF5WriteObjectAttribute()`, `PetscViewerHDF5HasObjectAttribute()`, `PetscViewerHDF5PushGroup()`, `PetscViewerHDF5PopGroup()`, `PetscViewerHDF5GetGroup()`
@*/
PetscErrorCode PetscViewerHDF5ReadObjectAttribute(PetscViewer viewer, PetscObject obj, const char name[], PetscDataType datatype, void *defaultValue, void *value) {
  PetscFunctionBegin;
  PetscValidHeaderSpecific(viewer, PETSC_VIEWER_CLASSID, 1);
  PetscValidHeader(obj, 2);
  PetscValidCharPointer(name, 3);
  PetscValidPointer(value, 6);
  PetscCall(PetscViewerHDF5CheckNamedObject_Internal(viewer, obj));
  PetscCall(PetscViewerHDF5ReadAttribute(viewer, obj->name, name, datatype, defaultValue, value));
  PetscFunctionReturn(0);
}

static inline PetscErrorCode PetscViewerHDF5Traverse_Inner_Internal(hid_t h5, const char name[], PetscBool createGroup, PetscBool *exists_) {
  htri_t exists;
  hid_t  group;

  PetscFunctionBegin;
  PetscCallHDF5Return(exists, H5Lexists, (h5, name, H5P_DEFAULT));
  if (exists) PetscCallHDF5Return(exists, H5Oexists_by_name, (h5, name, H5P_DEFAULT));
  if (!exists && createGroup) {
    PetscCallHDF5Return(group, H5Gcreate2, (h5, name, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT));
    PetscCallHDF5(H5Gclose, (group));
    exists = PETSC_TRUE;
  }
  *exists_ = (PetscBool)exists;
  PetscFunctionReturn(0);
}

static PetscErrorCode PetscViewerHDF5Traverse_Internal(PetscViewer viewer, const char name[], PetscBool createGroup, PetscBool *has, H5O_type_t *otype) {
  const char rootGroupName[] = "/";
  hid_t      h5;
  PetscBool  exists = PETSC_FALSE;
  PetscInt   i;
  int        n;
  char     **hierarchy;
  char       buf[PETSC_MAX_PATH_LEN] = "";

  PetscFunctionBegin;
  PetscValidHeaderSpecific(viewer, PETSC_VIEWER_CLASSID, 1);
  if (name) PetscValidCharPointer(name, 2);
  else name = rootGroupName;
  if (has) {
    PetscValidBoolPointer(has, 4);
    *has = PETSC_FALSE;
  }
  if (otype) {
    PetscValidIntPointer(otype, 5);
    *otype = H5O_TYPE_UNKNOWN;
  }
  PetscCall(PetscViewerHDF5GetFileId(viewer, &h5));

  /*
     Unfortunately, H5Oexists_by_name() fails if any object in hierarchy is missing.
     Hence, each of them needs to be tested separately:
     1) whether it's a valid link
     2) whether this link resolves to an object
     See H5Oexists_by_name() documentation.
  */
  PetscCall(PetscStrToArray(name, '/', &n, &hierarchy));
  if (!n) {
    /*  Assume group "/" always exists in accordance with HDF5 >= 1.10.0. See H5Lexists() documentation. */
    if (has) *has = PETSC_TRUE;
    if (otype) *otype = H5O_TYPE_GROUP;
    PetscCall(PetscStrToArrayDestroy(n, hierarchy));
    PetscFunctionReturn(0);
  }
  for (i = 0; i < n; i++) {
    PetscCall(PetscStrcat(buf, "/"));
    PetscCall(PetscStrcat(buf, hierarchy[i]));
    PetscCall(PetscViewerHDF5Traverse_Inner_Internal(h5, buf, createGroup, &exists));
    if (!exists) break;
  }
  PetscCall(PetscStrToArrayDestroy(n, hierarchy));

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

    /* We could use H5Iget_type() here but that would require opening the object. This way we only need its name. */
    PetscCallHDF5(H5Oget_info_by_name, (h5, name, &info, H5P_DEFAULT));
    *otype = info.type;
  }
  if (has) *has = exists;
  PetscFunctionReturn(0);
}

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

  Collective

  Input Parameters:
+ viewer - The `PETSCVIEWERHDF5` viewer
- path - The path relative to the pushed group, or NULL

  Output Parameter:
. has - Flag for group existence

  Level: advanced

  Notes:
  If path starts with '/', it is taken as an absolute path overriding currently pushed group, else path is relative to the current pushed group.
  So NULL or empty path means the current pushed group.

  If path exists but is not a group, `PETSC_FALSE` is returned.

.seealso: `PETSCVIEWERHDF5`, `PetscViewerHDF5HasAttribute()`, `PetscViewerHDF5HasDataset()`, `PetscViewerHDF5PushGroup()`, `PetscViewerHDF5PopGroup()`, `PetscViewerHDF5GetGroup()`, `PetscViewerHDF5OpenGroup()`
@*/
PetscErrorCode PetscViewerHDF5HasGroup(PetscViewer viewer, const char path[], PetscBool *has) {
  H5O_type_t type;
  char      *abspath;

  PetscFunctionBegin;
  PetscValidHeaderSpecific(viewer, PETSC_VIEWER_CLASSID, 1);
  if (path) PetscValidCharPointer(path, 2);
  PetscValidBoolPointer(has, 3);
  PetscCall(PetscViewerHDF5GetGroup(viewer, path, &abspath));
  PetscCall(PetscViewerHDF5Traverse_Internal(viewer, abspath, PETSC_FALSE, NULL, &type));
  *has = (PetscBool)(type == H5O_TYPE_GROUP);
  PetscCall(PetscFree(abspath));
  PetscFunctionReturn(0);
}

/*@C
 PetscViewerHDF5HasDataset - Check whether a given dataset exists in the HDF5 file

  Collective

  Input Parameters:
+ viewer - The `PETSCVIEWERHDF5` viewer
- path - The dataset path

  Output Parameter:
. has - Flag whether dataset exists

  Level: advanced

  Notes:
  If path starts with '/', it is taken as an absolute path overriding currently pushed group, else path is relative to the current pushed group.

  If path is NULL or empty, has is set to `PETSC_FALSE`.

  If path exists but is not a dataset, has is set to `PETSC_FALSE` as well.

.seealso: `PETSCVIEWERHDF5`, `PetscViewerHDF5HasObject()`, `PetscViewerHDF5HasAttribute()`, `PetscViewerHDF5HasGroup()`, `PetscViewerHDF5PushGroup()`, `PetscViewerHDF5PopGroup()`, `PetscViewerHDF5GetGroup()`
@*/
PetscErrorCode PetscViewerHDF5HasDataset(PetscViewer viewer, const char path[], PetscBool *has) {
  H5O_type_t type;
  char      *abspath;

  PetscFunctionBegin;
  PetscValidHeaderSpecific(viewer, PETSC_VIEWER_CLASSID, 1);
  if (path) PetscValidCharPointer(path, 2);
  PetscValidBoolPointer(has, 3);
  PetscCall(PetscViewerHDF5GetGroup(viewer, path, &abspath));
  PetscCall(PetscViewerHDF5Traverse_Internal(viewer, abspath, PETSC_FALSE, NULL, &type));
  *has = (PetscBool)(type == H5O_TYPE_DATASET);
  PetscCall(PetscFree(abspath));
  PetscFunctionReturn(0);
}

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

  Collective

  Input Parameters:
+ viewer - The `PETSCVIEWERHDF5` viewer
- obj    - The named object

  Output Parameter:
. has    - Flag for dataset existence

  Notes:
  If the object is unnamed, an error occurs.

  If the path current_group/object_name exists but is not a dataset, has is set to `PETSC_FALSE` as well.

  Level: advanced

.seealso: `PETSCVIEWERHDF5`, `PetscViewerHDF5Open()`, `PetscViewerHDF5HasDataset()`, `PetscViewerHDF5HasAttribute()`, `PetscViewerHDF5PushGroup()`, `PetscViewerHDF5PopGroup()`, `PetscViewerHDF5GetGroup()`
@*/
PetscErrorCode PetscViewerHDF5HasObject(PetscViewer viewer, PetscObject obj, PetscBool *has) {
  size_t len;

  PetscFunctionBegin;
  PetscValidHeaderSpecific(viewer, PETSC_VIEWER_CLASSID, 1);
  PetscValidHeader(obj, 2);
  PetscValidBoolPointer(has, 3);
  PetscCall(PetscStrlen(obj->name, &len));
  PetscCheck(len, PetscObjectComm((PetscObject)viewer), PETSC_ERR_ARG_WRONG, "Object must be named");
  PetscCall(PetscViewerHDF5HasDataset(viewer, obj->name, has));
  PetscFunctionReturn(0);
}

/*@C
 PetscViewerHDF5HasAttribute - Check whether an attribute exists

  Collective

  Input Parameters:
+ viewer - The `PETSCVIEWERHDF5` viewer
. parent - The parent dataset/group name
- name   - The attribute name

  Output Parameter:
. has    - Flag for attribute existence

  Level: advanced

  Note:
  If parent starts with '/', it is taken as an absolute path overriding currently pushed group, else parent is relative to the current pushed group. NULL means the current pushed group.

.seealso: `PETSCVIEWERHDF5`, `PetscViewerHDF5Open()`, `PetscViewerHDF5HasObjectAttribute()`, `PetscViewerHDF5WriteAttribute()`, `PetscViewerHDF5ReadAttribute()`, `PetscViewerHDF5PushGroup()`, `PetscViewerHDF5PopGroup()`, `PetscViewerHDF5GetGroup()`
@*/
PetscErrorCode PetscViewerHDF5HasAttribute(PetscViewer viewer, const char parent[], const char name[], PetscBool *has) {
  char *parentAbsPath;

  PetscFunctionBegin;
  PetscValidHeaderSpecific(viewer, PETSC_VIEWER_CLASSID, 1);
  if (parent) PetscValidCharPointer(parent, 2);
  PetscValidCharPointer(name, 3);
  PetscValidBoolPointer(has, 4);
  PetscCall(PetscViewerHDF5GetGroup(viewer, parent, &parentAbsPath));
  PetscCall(PetscViewerHDF5Traverse_Internal(viewer, parentAbsPath, PETSC_FALSE, has, NULL));
  if (*has) PetscCall(PetscViewerHDF5HasAttribute_Internal(viewer, parentAbsPath, name, has));
  PetscCall(PetscFree(parentAbsPath));
  PetscFunctionReturn(0);
}

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

  Collective

  Input Parameters:
+ viewer - The `PETSCVIEWERHDF5` viewer
. obj    - The object whose name is used to lookup the parent dataset, relative to the current group.
- name   - The attribute name

  Output Parameter:
. has    - Flag for attribute existence

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

  Level: advanced

.seealso: `PETSCVIEWERHDF5`, `PetscViewerHDF5Open()`, `PetscViewerHDF5HasAttribute()`, `PetscViewerHDF5WriteObjectAttribute()`, `PetscViewerHDF5ReadObjectAttribute()`, `PetscViewerHDF5HasObject()`, `PetscViewerHDF5PushGroup()`, `PetscViewerHDF5PopGroup()`, `PetscViewerHDF5GetGroup()`
@*/
PetscErrorCode PetscViewerHDF5HasObjectAttribute(PetscViewer viewer, PetscObject obj, const char name[], PetscBool *has) {
  PetscFunctionBegin;
  PetscValidHeaderSpecific(viewer, PETSC_VIEWER_CLASSID, 1);
  PetscValidHeader(obj, 2);
  PetscValidCharPointer(name, 3);
  PetscValidBoolPointer(has, 4);
  PetscCall(PetscViewerHDF5CheckNamedObject_Internal(viewer, obj));
  PetscCall(PetscViewerHDF5HasAttribute(viewer, obj->name, name, has));
  PetscFunctionReturn(0);
}

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

  PetscFunctionBegin;
  PetscCall(PetscViewerHDF5GetFileId(viewer, &h5));
  PetscCallHDF5Return(hhas, H5Aexists_by_name, (h5, parent, name, H5P_DEFAULT));
  *has = hhas ? PETSC_TRUE : PETSC_FALSE;
  PetscFunctionReturn(0);
}

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

/*@C
  PETSC_VIEWER_HDF5_ - Creates an `PETSCVIEWERHDF5` `PetscViewer` shared by all processors in a communicator.

  Collective

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

  Level: intermediate

  Options Database Key:
. -viewer_hdf5_filename <name> - name of the HDF5 file

  Environmental variable:
. `PETSC_VIEWER_HDF5_FILENAME` - name of the HDF5 file

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

.seealso: `PETSCVIEWERHDF5`, `PetscViewerHDF5Open()`, `PetscViewerCreate()`, `PetscViewerDestroy()`
@*/
PetscViewer PETSC_VIEWER_HDF5_(MPI_Comm comm) {
  PetscErrorCode ierr;
  PetscBool      flg;
  PetscViewer    viewer;
  char           fname[PETSC_MAX_PATH_LEN];
  MPI_Comm       ncomm;

  PetscFunctionBegin;
  ierr = PetscCommDuplicate(comm, &ncomm, NULL);
  if (ierr) {
    PetscError(PETSC_COMM_SELF, __LINE__, "PETSC_VIEWER_HDF5_", __FILE__, PETSC_ERR_PLIB, PETSC_ERROR_INITIAL, " ");
    PetscFunctionReturn(NULL);
  }
  if (Petsc_Viewer_HDF5_keyval == MPI_KEYVAL_INVALID) {
    ierr = MPI_Comm_create_keyval(MPI_COMM_NULL_COPY_FN, MPI_COMM_NULL_DELETE_FN, &Petsc_Viewer_HDF5_keyval, NULL);
    if (ierr) {
      PetscError(PETSC_COMM_SELF, __LINE__, "PETSC_VIEWER_HDF5_", __FILE__, PETSC_ERR_PLIB, PETSC_ERROR_INITIAL, " ");
      PetscFunctionReturn(NULL);
    }
  }
  ierr = MPI_Comm_get_attr(ncomm, Petsc_Viewer_HDF5_keyval, (void **)&viewer, (int *)&flg);
  if (ierr) {
    PetscError(PETSC_COMM_SELF, __LINE__, "PETSC_VIEWER_HDF5_", __FILE__, PETSC_ERR_PLIB, PETSC_ERROR_INITIAL, " ");
    PetscFunctionReturn(NULL);
  }
  if (!flg) { /* PetscViewer not yet created */
    ierr = PetscOptionsGetenv(ncomm, "PETSC_VIEWER_HDF5_FILENAME", fname, PETSC_MAX_PATH_LEN, &flg);
    if (ierr) {
      PetscError(PETSC_COMM_SELF, __LINE__, "PETSC_VIEWER_HDF5_", __FILE__, PETSC_ERR_PLIB, PETSC_ERROR_REPEAT, " ");
      PetscFunctionReturn(NULL);
    }
    if (!flg) {
      ierr = PetscStrcpy(fname, "output.h5");
      if (ierr) {
        PetscError(PETSC_COMM_SELF, __LINE__, "PETSC_VIEWER_HDF5_", __FILE__, PETSC_ERR_PLIB, PETSC_ERROR_REPEAT, " ");
        PetscFunctionReturn(NULL);
      }
    }
    ierr = PetscViewerHDF5Open(ncomm, fname, FILE_MODE_WRITE, &viewer);
    if (ierr) {
      PetscError(PETSC_COMM_SELF, __LINE__, "PETSC_VIEWER_HDF5_", __FILE__, PETSC_ERR_PLIB, PETSC_ERROR_REPEAT, " ");
      PetscFunctionReturn(NULL);
    }
    ierr = PetscObjectRegisterDestroy((PetscObject)viewer);
    if (ierr) {
      PetscError(PETSC_COMM_SELF, __LINE__, "PETSC_VIEWER_HDF5_", __FILE__, PETSC_ERR_PLIB, PETSC_ERROR_REPEAT, " ");
      PetscFunctionReturn(NULL);
    }
    ierr = MPI_Comm_set_attr(ncomm, Petsc_Viewer_HDF5_keyval, (void *)viewer);
    if (ierr) {
      PetscError(PETSC_COMM_SELF, __LINE__, "PETSC_VIEWER_HDF5_", __FILE__, PETSC_ERR_PLIB, PETSC_ERROR_INITIAL, " ");
      PetscFunctionReturn(NULL);
    }
  }
  ierr = PetscCommDestroy(&ncomm);
  if (ierr) {
    PetscError(PETSC_COMM_SELF, __LINE__, "PETSC_VIEWER_HDF5_", __FILE__, PETSC_ERR_PLIB, PETSC_ERROR_REPEAT, " ");
    PetscFunctionReturn(NULL);
  }
  PetscFunctionReturn(viewer);
}