impls/hdf5/hdf5v.c

#include <petsc/private/viewerimpl.h>
#include <petsc/private/viewerhdf5impl.h>
#include <petscviewerhdf5.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*);

static PetscErrorCode PetscViewerHDF5GetAbsolutePath_Internal(PetscViewer viewer, const char path[], char *abspath[])
{
  PetscBool      relative = PETSC_FALSE;
  const char     *group;
  char           buf[PETSC_MAX_PATH_LEN] = "";
  PetscErrorCode ierr;

  PetscFunctionBegin;
  ierr = PetscViewerHDF5GetGroup(viewer, &group);CHKERRQ(ierr);
  ierr = PetscViewerHDF5PathIsRelative(path, PETSC_TRUE, &relative);CHKERRQ(ierr);
  if (relative) {
    ierr = PetscStrcpy(buf, group);CHKERRQ(ierr);
    ierr = PetscStrcat(buf, "/");CHKERRQ(ierr);
    ierr = PetscStrcat(buf, path);CHKERRQ(ierr);
    ierr = PetscStrallocpy(buf, abspath);CHKERRQ(ierr);
  } else {
    ierr = PetscStrallocpy(path, abspath);CHKERRQ(ierr);
  }
  PetscFunctionReturn(0);
}

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

  PetscFunctionBegin;
  ierr = PetscViewerHDF5HasObject(viewer, obj, &has);CHKERRQ(ierr);
  if (!has) {
    const char *group;
    ierr = PetscViewerHDF5GetGroup(viewer, &group);CHKERRQ(ierr);
    SETERRQ2(PetscObjectComm((PetscObject)viewer), PETSC_ERR_FILE_UNEXPECTED, "Object (dataset) \"%s\" not stored in group %s", obj->name, group ? group : "/");
  }
  PetscFunctionReturn(0);
}

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

  PetscFunctionBegin;
  ierr = PetscOptionsHead(PetscOptionsObject,"HDF5 PetscViewer Options");CHKERRQ(ierr);
  ierr = PetscOptionsBool("-viewer_hdf5_base_dimension2","1d Vectors get 2 dimensions in HDF5","PetscViewerHDF5SetBaseDimension2",hdf5->basedimension2,&hdf5->basedimension2,NULL);CHKERRQ(ierr);
  ierr = PetscOptionsBool("-viewer_hdf5_sp_output","Force data to be written in single precision","PetscViewerHDF5SetSPOutput",hdf5->spoutput,&hdf5->spoutput,NULL);CHKERRQ(ierr);
  ierr = PetscOptionsBool("-viewer_hdf5_collective","Enable collective transfer mode","PetscViewerHDF5SetCollective",flg,&flg,&set);CHKERRQ(ierr);
  if (set) {ierr = PetscViewerHDF5SetCollective(v,flg);CHKERRQ(ierr);}
  ierr = PetscOptionsTail();CHKERRQ(ierr);
  PetscFunctionReturn(0);
}

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

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

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

  PetscFunctionBegin;
  ierr = PetscFree(hdf5->filename);CHKERRQ(ierr);
  if (hdf5->file_id) PetscStackCallHDF5(H5Fclose,(hdf5->file_id));
  PetscFunctionReturn(0);
}

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

  PetscFunctionBegin;
  PetscStackCallHDF5(H5Pclose,(hdf5->dxpl_id));
  ierr = PetscViewerFileClose_HDF5(viewer);CHKERRQ(ierr);
  while (hdf5->groups) {
    PetscViewerHDF5GroupList *tmp = hdf5->groups->next;

    ierr         = PetscFree(hdf5->groups->name);CHKERRQ(ierr);
    ierr         = PetscFree(hdf5->groups);CHKERRQ(ierr);
    hdf5->groups = tmp;
  }
  ierr = PetscFree(hdf5);CHKERRQ(ierr);
  ierr = PetscObjectComposeFunction((PetscObject)viewer,"PetscViewerFileSetName_C",NULL);CHKERRQ(ierr);
  ierr = PetscObjectComposeFunction((PetscObject)viewer,"PetscViewerFileGetName_C",NULL);CHKERRQ(ierr);
  ierr = PetscObjectComposeFunction((PetscObject)viewer,"PetscViewerFileSetMode_C",NULL);CHKERRQ(ierr);
  ierr = PetscObjectComposeFunction((PetscObject)viewer,"PetscViewerHDF5SetBaseDimension2_C",NULL);CHKERRQ(ierr);
  ierr = PetscObjectComposeFunction((PetscObject)viewer,"PetscViewerHDF5SetSPOutput_C",NULL);CHKERRQ(ierr);
  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 PetscViewer

  Input Parameters:
+  viewer - the PetscViewer; if it is not hdf5 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:
.  -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


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

  Level: intermediate

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

@*/
PetscErrorCode PetscViewerHDF5SetBaseDimension2(PetscViewer viewer,PetscBool flg)
{
  PetscErrorCode ierr;

  PetscFunctionBegin;
  PetscValidHeaderSpecific(viewer,PETSC_VIEWER_CLASSID,1);
  ierr = PetscTryMethod(viewer,"PetscViewerHDF5SetBaseDimension2_C",(PetscViewer,PetscBool),(viewer,flg));CHKERRQ(ierr);
  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 PetscViewer

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

  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

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

  Level: intermediate

.seealso: 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 PetscViewer

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

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


  Notes:
    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: PetscViewerFileSetMode(), PetscViewerCreate(), PetscViewerSetType(), PetscViewerBinaryOpen(),
          PetscReal

@*/
PetscErrorCode PetscViewerHDF5SetSPOutput(PetscViewer viewer,PetscBool flg)
{
  PetscErrorCode ierr;

  PetscFunctionBegin;
  PetscValidHeaderSpecific(viewer,PETSC_VIEWER_CLASSID,1);
  ierr = PetscTryMethod(viewer,"PetscViewerHDF5SetSPOutput_C",(PetscViewer,PetscBool),(viewer,flg));CHKERRQ(ierr);
  PetscFunctionReturn(0);
}

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

    Logically Collective on PetscViewer

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

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

  Notes:
    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: PetscViewerFileSetMode(), PetscViewerCreate(), PetscViewerSetType(), PetscViewerBinaryOpen(),
          PetscReal

@*/
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;
    PetscStackCallHDF5(H5Pset_dxpl_mpio,(hdf5->dxpl_id, flg ? H5FD_MPIO_COLLECTIVE : H5FD_MPIO_INDEPENDENT));
  }
#else
  if (flg) {
    PetscErrorCode ierr;
    ierr = 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");CHKERRQ(ierr);
  }
#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 hdf5 then this command is ignored
- flg - PETSC_TRUE for collective mode; PETSC_FALSE for independent mode (default)

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

  Notes:
  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 notes:
  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: PetscViewerHDF5GetCollective(), PetscViewerCreate(), PetscViewerSetType(), PetscViewerHDF5Open()

@*/
PetscErrorCode PetscViewerHDF5SetCollective(PetscViewer viewer,PetscBool flg)
{
  PetscErrorCode ierr;

  PetscFunctionBegin;
  PetscValidHeaderSpecific(viewer,PETSC_VIEWER_CLASSID,1);
  PetscValidLogicalCollectiveBool(viewer,flg,2);
  ierr = PetscTryMethod(viewer,"PetscViewerHDF5SetCollective_C",(PetscViewer,PetscBool),(viewer,flg));CHKERRQ(ierr);
  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
  PetscStackCallHDF5(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 HDF5 PetscViewer

  Output Parameters:
. flg - the flag

  Level: intermediate

  Notes:
  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: PetscViewerHDF5SetCollective(), PetscViewerCreate(), PetscViewerSetType(), PetscViewerHDF5Open()

@*/
PetscErrorCode PetscViewerHDF5GetCollective(PetscViewer viewer,PetscBool *flg)
{
  PetscErrorCode ierr;

  PetscFunctionBegin;
  PetscValidHeaderSpecific(viewer,PETSC_VIEWER_CLASSID,1);
  PetscValidBoolPointer(flg,2);

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

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

  PetscFunctionBegin;
  if (hdf5->file_id) PetscStackCallHDF5(H5Fclose,(hdf5->file_id));
  if (hdf5->filename) {ierr = PetscFree(hdf5->filename);CHKERRQ(ierr);}
  ierr = PetscStrallocpy(name, &hdf5->filename);CHKERRQ(ierr);
  /* Set up file access property list with parallel I/O access */
  PetscStackCallHDF5Return(plist_id,H5Pcreate,(H5P_FILE_ACCESS));
#if defined(H5_HAVE_PARALLEL)
  PetscStackCallHDF5(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:
    PetscStackCallHDF5Return(hdf5->file_id,H5Fopen,(name, H5F_ACC_RDONLY, plist_id));
    break;
  case FILE_MODE_APPEND:
  case FILE_MODE_UPDATE:
  {
    PetscBool flg;
    ierr = PetscTestFile(hdf5->filename, 'r', &flg);CHKERRQ(ierr);
    if (flg) PetscStackCallHDF5Return(hdf5->file_id,H5Fopen,(name, H5F_ACC_RDWR, plist_id));
    else     PetscStackCallHDF5Return(hdf5->file_id,H5Fcreate,(name, H5F_ACC_EXCL, H5P_DEFAULT, plist_id));
    break;
  }
  case FILE_MODE_WRITE:
    PetscStackCallHDF5Return(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:
    SETERRQ1(PetscObjectComm((PetscObject)viewer),PETSC_ERR_SUP, "Unsupported file mode %s",PetscFileModes[hdf5->btype]);
  }
  if (hdf5->file_id < 0) SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_LIB, "H5Fcreate failed for %s", name);
  PetscStackCallHDF5(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;
  PetscErrorCode   ierr;
  */

  PetscFunctionBegin;
  PetscFunctionReturn(0);
}

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


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

  Level: beginner
M*/

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

  PetscFunctionBegin;
  ierr = PetscNewLog(v,&hdf5);CHKERRQ(ierr);

  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          = NULL;
  hdf5->btype            = FILE_MODE_UNDEFINED;
  hdf5->filename         = NULL;
  hdf5->timestep         = -1;
  hdf5->groups           = NULL;

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

  ierr = PetscObjectComposeFunction((PetscObject)v,"PetscViewerFileSetName_C",PetscViewerFileSetName_HDF5);CHKERRQ(ierr);
  ierr = PetscObjectComposeFunction((PetscObject)v,"PetscViewerFileGetName_C",PetscViewerFileGetName_HDF5);CHKERRQ(ierr);
  ierr = PetscObjectComposeFunction((PetscObject)v,"PetscViewerFileSetMode_C",PetscViewerFileSetMode_HDF5);CHKERRQ(ierr);
  ierr = PetscObjectComposeFunction((PetscObject)v,"PetscViewerFileGetMode_C",PetscViewerFileGetMode_HDF5);CHKERRQ(ierr);
  ierr = PetscObjectComposeFunction((PetscObject)v,"PetscViewerHDF5SetBaseDimension2_C",PetscViewerHDF5SetBaseDimension2_HDF5);CHKERRQ(ierr);
  ierr = PetscObjectComposeFunction((PetscObject)v,"PetscViewerHDF5SetSPOutput_C",PetscViewerHDF5SetSPOutput_HDF5);CHKERRQ(ierr);
  ierr = PetscObjectComposeFunction((PetscObject)v,"PetscViewerHDF5SetCollective_C",PetscViewerHDF5SetCollective_HDF5);CHKERRQ(ierr);
  ierr = PetscObjectComposeFunction((PetscObject)v,"PetscViewerHDF5GetCollective_C",PetscViewerHDF5GetCollective_HDF5);CHKERRQ(ierr);
  PetscFunctionReturn(0);
}

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

   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:
+  -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
+  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

   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: 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)
{
  PetscErrorCode ierr;

  PetscFunctionBegin;
  ierr = PetscViewerCreate(comm, hdf5v);CHKERRQ(ierr);
  ierr = PetscViewerSetType(*hdf5v, PETSCVIEWERHDF5);CHKERRQ(ierr);
  ierr = PetscViewerFileSetMode(*hdf5v, type);CHKERRQ(ierr);
  ierr = PetscViewerFileSetName(*hdf5v, name);CHKERRQ(ierr);
  ierr = PetscViewerSetFromOptions(*hdf5v);CHKERRQ(ierr);
  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: 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
- name - The group name

  Level: intermediate

  Notes:
  This is designed to mnemonically resemble the Unix cd command.
  + 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.

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

.seealso: 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;
  PetscErrorCode            ierr;

  PetscFunctionBegin;
  PetscValidHeaderSpecific(viewer,PETSC_VIEWER_CLASSID,1);
  if (name) PetscValidCharPointer(name,2);
  ierr = PetscStrlen(name, &len);CHKERRQ(ierr);
  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 : "";
      ierr = PetscSNPrintf(buf, sizeof(buf), "%s/%s", parent, name);CHKERRQ(ierr);
      gname = buf;
    }
  }
  ierr = PetscNew(&groupNode);CHKERRQ(ierr);
  ierr = PetscStrallocpy(gname, (char**) &groupNode->name);CHKERRQ(ierr);
  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

  Level: intermediate

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

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

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

  Not collective

  Input Parameter:
. viewer - the PetscViewer

  Output Parameter:
. name - The group name

  Level: intermediate

.seealso: PetscViewerHDF5Open(),PetscViewerHDF5PushGroup(),PetscViewerHDF5PopGroup(),PetscViewerHDF5OpenGroup()
@*/
PetscErrorCode  PetscViewerHDF5GetGroup(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

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

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

  Level: intermediate

.seealso: 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;
  PetscBool      create;
  PetscErrorCode ierr;

  PetscFunctionBegin;
  ierr = PetscViewerWritable(viewer, &create);CHKERRQ(ierr);
  ierr = PetscViewerHDF5GetFileId(viewer, &file_id);CHKERRQ(ierr);
  ierr = PetscViewerHDF5GetGroup(viewer, &groupName);CHKERRQ(ierr);
  ierr = PetscViewerHDF5Traverse_Internal(viewer, groupName, create, NULL, &type);CHKERRQ(ierr);
  if (type != H5O_TYPE_GROUP) SETERRQ1(PetscObjectComm((PetscObject)viewer), PETSC_ERR_FILE_UNEXPECTED, "Path %s resolves to something which is not a group", groupName);
  PetscStackCallHDF5Return(*groupId,H5Gopen2,(file_id, groupName ? groupName : "/", H5P_DEFAULT));
  *fileId  = file_id;
  PetscFunctionReturn(0);
}

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

  Not collective

  Input Parameter:
. viewer - the PetscViewer

  Level: intermediate

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

  PetscFunctionBegin;
  PetscValidHeaderSpecific(viewer,PETSC_VIEWER_CLASSID,1);
  ++hdf5->timestep;
  PetscFunctionReturn(0);
}

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

  Not collective

  Input Parameters:
+ viewer - the PetscViewer
- timestep - The timestep number

  Level: intermediate

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

  PetscFunctionBegin;
  PetscValidHeaderSpecific(viewer,PETSC_VIEWER_CLASSID,1);
  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

  Output Parameter:
. timestep - The timestep number

  Level: intermediate

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

  PetscFunctionBegin;
  PetscValidHeaderSpecific(viewer,PETSC_VIEWER_CLASSID,1);
  PetscValidPointer(timestep,2);
  *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 MPI datatype (for example MPI_DOUBLE, ...)

  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

  Input Parameters:
+ viewer - The HDF5 viewer
. parent - The parent dataset/group name
. name   - The attribute name
. datatype - The attribute type
- value    - The attribute value

  Level: advanced

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

.seealso: 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;
  PetscErrorCode ierr;

  PetscFunctionBegin;
  PetscValidHeaderSpecific(viewer,PETSC_VIEWER_CLASSID,1);
  if (parent) PetscValidCharPointer(parent, 2);
  PetscValidCharPointer(name, 3);
  PetscValidLogicalCollectiveEnum(viewer,datatype,4);
  PetscValidPointer(value, 5);
  ierr = PetscViewerHDF5GetAbsolutePath_Internal(viewer, parent, &parentAbsPath);CHKERRQ(ierr);
  ierr = PetscViewerHDF5Traverse_Internal(viewer, parentAbsPath, PETSC_TRUE, NULL, NULL);CHKERRQ(ierr);
  ierr = PetscViewerHDF5HasAttribute_Internal(viewer, parentAbsPath, name, &has);CHKERRQ(ierr);
  ierr = PetscDataTypeToHDF5DataType(datatype, &dtype);CHKERRQ(ierr);
  if (datatype == PETSC_STRING) {
    size_t len;
    ierr = PetscStrlen((const char *) value, &len);CHKERRQ(ierr);
    PetscStackCallHDF5(H5Tset_size,(dtype, len+1));
  }
  ierr = PetscViewerHDF5GetFileId(viewer, &h5);CHKERRQ(ierr);
  PetscStackCallHDF5Return(dataspace,H5Screate,(H5S_SCALAR));
  PetscStackCallHDF5Return(obj,H5Oopen,(h5, parentAbsPath, H5P_DEFAULT));
  if (has) {
    PetscStackCallHDF5Return(attribute,H5Aopen_name,(obj, name));
  } else {
    PetscStackCallHDF5Return(attribute,H5Acreate2,(obj, name, dtype, dataspace, H5P_DEFAULT, H5P_DEFAULT));
  }
  PetscStackCallHDF5(H5Awrite,(attribute, dtype, value));
  if (datatype == PETSC_STRING) PetscStackCallHDF5(H5Tclose,(dtype));
  PetscStackCallHDF5(H5Aclose,(attribute));
  PetscStackCallHDF5(H5Oclose,(obj));
  PetscStackCallHDF5(H5Sclose,(dataspace));
  ierr = PetscFree(parentAbsPath);CHKERRQ(ierr);
  PetscFunctionReturn(0);
}

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

  Input Parameters:
+ viewer   - The HDF5 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

  Notes:
  This fails if currentGroup/objectName 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: PetscViewerHDF5Open(), PetscViewerHDF5WriteAttribute(), PetscViewerHDF5ReadObjectAttribute(), PetscViewerHDF5HasObjectAttribute(), PetscViewerHDF5HasObject(), PetscViewerHDF5PushGroup(),PetscViewerHDF5PopGroup(),PetscViewerHDF5GetGroup()
@*/
PetscErrorCode PetscViewerHDF5WriteObjectAttribute(PetscViewer viewer, PetscObject obj, const char name[], PetscDataType datatype, const void *value)
{
  PetscErrorCode ierr;

  PetscFunctionBegin;
  PetscValidHeaderSpecific(viewer,PETSC_VIEWER_CLASSID,1);
  PetscValidHeader(obj,2);
  PetscValidCharPointer(name,3);
  PetscValidPointer(value,5);
  ierr = PetscViewerHDF5CheckNamedObject_Internal(viewer, obj);CHKERRQ(ierr);
  ierr = PetscViewerHDF5WriteAttribute(viewer, obj->name, name, datatype, value);CHKERRQ(ierr);
  PetscFunctionReturn(0);
}

/*@C
 PetscViewerHDF5ReadAttribute - Read an attribute

  Input Parameters:
+ viewer - The HDF5 viewer
. parent - The parent dataset/group name
. name   - The attribute name
- datatype - The attribute type

  Output Parameter:
. value    - The attribute value

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

  Level: advanced

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

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

  PetscFunctionBegin;
  PetscValidHeaderSpecific(viewer,PETSC_VIEWER_CLASSID,1);
  if (parent) PetscValidCharPointer(parent, 2);
  PetscValidCharPointer(name, 3);
  PetscValidPointer(value, 5);
  ierr = PetscViewerHDF5GetAbsolutePath_Internal(viewer, parent, &parentAbsPath);CHKERRQ(ierr);
  ierr = PetscViewerHDF5Traverse_Internal(viewer, parentAbsPath, PETSC_FALSE, &has, NULL);CHKERRQ(ierr);
  if (has) {ierr = PetscViewerHDF5HasAttribute_Internal(viewer, parentAbsPath, name, &has);CHKERRQ(ierr);}
  if (!has) SETERRQ2(PetscObjectComm((PetscObject)viewer), PETSC_ERR_FILE_UNEXPECTED, "Attribute %s/%s does not exist", parentAbsPath, name);
  ierr = PetscDataTypeToHDF5DataType(datatype, &dtype);CHKERRQ(ierr);
  ierr = PetscViewerHDF5GetFileId(viewer, &h5);CHKERRQ(ierr);
  PetscStackCallHDF5Return(obj,H5Oopen,(h5, parentAbsPath, H5P_DEFAULT));
  PetscStackCallHDF5Return(attribute,H5Aopen_name,(obj, name));
  if (datatype == PETSC_STRING) {
    size_t len;
    PetscStackCallHDF5Return(atype,H5Aget_type,(attribute));
    PetscStackCall("H5Tget_size",len = H5Tget_size(atype));
    ierr = PetscMalloc((len+1) * sizeof(char), value);CHKERRQ(ierr);
    PetscStackCallHDF5(H5Tset_size,(dtype, len+1));
    PetscStackCallHDF5(H5Aread,(attribute, dtype, *(char**)value));
  } else {
    PetscStackCallHDF5(H5Aread,(attribute, dtype, value));
  }
  PetscStackCallHDF5(H5Aclose,(attribute));
  /* H5Oclose can be used to close groups, datasets, or committed datatypes */
  PetscStackCallHDF5(H5Oclose,(obj));
  ierr = PetscFree(parentAbsPath);CHKERRQ(ierr);
  PetscFunctionReturn(0);
}

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

  Input Parameters:
+ viewer   - The HDF5 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

  Notes:
  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: PetscViewerHDF5Open(), PetscViewerHDF5ReadAttribute() PetscViewerHDF5WriteObjectAttribute(), PetscViewerHDF5HasObjectAttribute(), PetscViewerHDF5PushGroup(),PetscViewerHDF5PopGroup(),PetscViewerHDF5GetGroup()
@*/
PetscErrorCode PetscViewerHDF5ReadObjectAttribute(PetscViewer viewer, PetscObject obj, const char name[], PetscDataType datatype, void *value)
{
  PetscErrorCode ierr;

  PetscFunctionBegin;
  PetscValidHeaderSpecific(viewer,PETSC_VIEWER_CLASSID,1);
  PetscValidHeader(obj,2);
  PetscValidCharPointer(name,3);
  PetscValidPointer(value, 5);
  ierr = PetscViewerHDF5CheckNamedObject_Internal(viewer, obj);CHKERRQ(ierr);
  ierr = PetscViewerHDF5ReadAttribute(viewer, obj->name, name, datatype, value);CHKERRQ(ierr);
  PetscFunctionReturn(0);
}

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

  PetscFunctionBegin;
  PetscStackCallHDF5Return(exists,H5Lexists,(h5, name, H5P_DEFAULT));
  if (exists) PetscStackCallHDF5Return(exists,H5Oexists_by_name,(h5, name, H5P_DEFAULT));
  if (!exists && createGroup) {
    PetscStackCallHDF5Return(group,H5Gcreate2,(h5, name, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT));
    PetscStackCallHDF5(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]="";
  PetscErrorCode ierr;

  PetscFunctionBegin;
  PetscValidHeaderSpecific(viewer,PETSC_VIEWER_CLASSID,1);
  if (name) PetscValidCharPointer(name, 2);
  else name = rootGroupName;
  if (has) {
    PetscValidIntPointer(has, 3);
    *has = PETSC_FALSE;
  }
  if (otype) {
    PetscValidIntPointer(otype, 4);
    *otype = H5O_TYPE_UNKNOWN;
  }
  ierr = PetscViewerHDF5GetFileId(viewer, &h5);CHKERRQ(ierr);

  /*
     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.
  */
  ierr = PetscStrToArray(name,'/',&n,&hierarchy);CHKERRQ(ierr);
  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;
    ierr = PetscStrToArrayDestroy(n,hierarchy);CHKERRQ(ierr);
    PetscFunctionReturn(0);
  }
  for (i=0; i<n; i++) {
    ierr = PetscStrcat(buf,"/");CHKERRQ(ierr);
    ierr = PetscStrcat(buf,hierarchy[i]);CHKERRQ(ierr);
    ierr = PetscViewerHDF5Traverse_Inner_Internal(h5, buf, createGroup, &exists);CHKERRQ(ierr);
    if (!exists) break;
  }
  ierr = PetscStrToArrayDestroy(n,hierarchy);CHKERRQ(ierr);

  /* 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. */
    PetscStackCallHDF5(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

  Input Parameters:
+ viewer - The HDF5 viewer
- path - The group path

  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 the dataset/group is relative to the current pushed group. NULL means the current pushed group.
  If the path exists but is not a group, PETSC_FALSE is returned.

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

  PetscFunctionBegin;
  PetscValidHeaderSpecific(viewer,PETSC_VIEWER_CLASSID,1);
  if (path) PetscValidCharPointer(path,2);
  PetscValidBoolPointer(has,3);
  ierr = PetscViewerHDF5GetAbsolutePath_Internal(viewer, path, &abspath);CHKERRQ(ierr);
  ierr = PetscViewerHDF5Traverse_Internal(viewer, abspath, PETSC_FALSE, NULL, &type);CHKERRQ(ierr);
  *has = (PetscBool)(type == H5O_TYPE_GROUP);
  ierr = PetscFree(abspath);CHKERRQ(ierr);
  PetscFunctionReturn(0);
}

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

  Input Parameters:
+ viewer - The HDF5 viewer
- path - The dataset path

  Output Parameter:
. has - Flag whether dataset exists

  Level: advanced

  Notes:
  If parent starts with '/', it is taken as an absolute path overriding currently pushed group, else the dataset/group is relative to the current pushed group.
  If path is NULL or empty, has is set to PETSC_FALSE.
  If the path exists but is not a dataset, has is set to PETSC_FALSE as well.

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

  PetscFunctionBegin;
  PetscValidHeaderSpecific(viewer,PETSC_VIEWER_CLASSID,1);
  if (path) PetscValidCharPointer(path,2);
  PetscValidBoolPointer(has,3);
  ierr = PetscViewerHDF5GetAbsolutePath_Internal(viewer, path, &abspath);CHKERRQ(ierr);
  ierr = PetscViewerHDF5Traverse_Internal(viewer, abspath, PETSC_FALSE, NULL, &type);CHKERRQ(ierr);
  *has = (PetscBool)(type == H5O_TYPE_DATASET);
  ierr = PetscFree(abspath);CHKERRQ(ierr);
  PetscFunctionReturn(0);
}

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

  Input Parameters:
+ viewer - The HDF5 viewer
- obj    - The named object

  Output Parameter:
. has    - Flag for dataset existence

  Notes:
  If the object is unnamed, an error occurs.
  If the path currentGroup/objectName exists but is not a dataset, has is set to PETSC_FALSE as well.

  Level: advanced

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

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

/*@C
 PetscViewerHDF5HasAttribute - Check whether an attribute exists

  Input Parameters:
+ viewer - The HDF5 viewer
. parent - The parent dataset/group name
- name   - The attribute name

  Output Parameter:
. has    - Flag for attribute existence

  Level: advanced

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

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

  PetscFunctionBegin;
  PetscValidHeaderSpecific(viewer,PETSC_VIEWER_CLASSID,1);
  if (parent) PetscValidCharPointer(parent,2);
  PetscValidCharPointer(name,3);
  PetscValidBoolPointer(has,4);
  ierr = PetscViewerHDF5GetAbsolutePath_Internal(viewer, parent, &parentAbsPath);CHKERRQ(ierr);
  ierr = PetscViewerHDF5Traverse_Internal(viewer, parentAbsPath, PETSC_FALSE, has, NULL);CHKERRQ(ierr);
  if (*has) {ierr = PetscViewerHDF5HasAttribute_Internal(viewer, parentAbsPath, name, has);CHKERRQ(ierr);}
  ierr = PetscFree(parentAbsPath);CHKERRQ(ierr);
  PetscFunctionReturn(0);
}

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

  Input Parameters:
+ viewer - The HDF5 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

  Notes:
  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: PetscViewerHDF5Open(), PetscViewerHDF5HasAttribute(), PetscViewerHDF5WriteObjectAttribute(), PetscViewerHDF5ReadObjectAttribute(), PetscViewerHDF5HasObject(), PetscViewerHDF5PushGroup(),PetscViewerHDF5PopGroup(),PetscViewerHDF5GetGroup()
@*/
PetscErrorCode PetscViewerHDF5HasObjectAttribute(PetscViewer viewer, PetscObject obj, const char name[], PetscBool *has)
{
  PetscErrorCode ierr;

  PetscFunctionBegin;
  PetscValidHeaderSpecific(viewer,PETSC_VIEWER_CLASSID,1);
  PetscValidHeader(obj,2);
  PetscValidCharPointer(name,3);
  PetscValidBoolPointer(has,4);
  ierr = PetscViewerHDF5CheckNamedObject_Internal(viewer, obj);CHKERRQ(ierr);
  ierr = PetscViewerHDF5HasAttribute(viewer, obj->name, name, has);CHKERRQ(ierr);
  PetscFunctionReturn(0);
}

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

  PetscFunctionBegin;
  ierr = PetscViewerHDF5GetFileId(viewer, &h5);CHKERRQ(ierr);
  PetscStackCallHDF5Return(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 HDF5 PetscViewer shared by all processors in a communicator.

  Collective

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

  Level: intermediate

  Options Database Keys:
. -viewer_hdf5_filename <name>

  Environmental variables:
. PETSC_VIEWER_HDF5_FILENAME

  Notes:
  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: 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);
}