xref: /petsc/src/sys/classes/viewer/impls/hdf5/hdf5v.c (revision b723ab350d0baf03346dec3580dd2ced69abe84a)

#include <petsc/private/viewerimpl.h>    /*I   "petscsys.h"   I*/
#include <petscviewerhdf5.h>    /*I   "petscviewerhdf5.h"   I*/
#if (H5_VERS_MAJOR * 10000 + H5_VERS_MINOR * 100 + H5_VERS_RELEASE < 10800)
#error "PETSc needs HDF5 version >= 1.8.0"
#endif

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

typedef struct GroupList {
  const char       *name;
  struct GroupList *next;
} GroupList;

typedef struct {
  char          *filename;
  PetscFileMode btype;
  hid_t         file_id;
  PetscInt      timestep;
  GroupList     *groups;
  PetscBool     basedimension2;  /* save vectors and DMDA vectors with a dimension of at least 2 even if the bs/dof is 1 */
  PetscBool     spoutput;  /* write data in single precision even if PETSc is compiled with double precision PetscReal */
  char          *mataij_iname;
  char          *mataij_jname;
  char          *mataij_aname;
  char          *mataij_cname;
  PetscBool     mataij_names_set;
} PetscViewer_HDF5;

struct _n_HDF5ReadCtx {
  hid_t file, group, dataset, dataspace, plist;
  PetscInt timestep;
  PetscBool complexVal, dim2, horizontal;
};
typedef struct _n_HDF5ReadCtx* HDF5ReadCtx;

static PetscErrorCode PetscViewerHDF5GetAbsolutePath_Internal(PetscViewer viewer, const char objname[], char **fullpath)
{
  const char *group;
  char buf[PETSC_MAX_PATH_LEN]="";
  PetscErrorCode ierr;

  PetscFunctionBegin;
  ierr = PetscViewerHDF5GetGroup(viewer, &group);CHKERRQ(ierr);
  ierr = PetscStrcat(buf, group);CHKERRQ(ierr);
  ierr = PetscStrcat(buf, "/");CHKERRQ(ierr);
  ierr = PetscStrcat(buf, objname);CHKERRQ(ierr);
  ierr = PetscStrallocpy(buf, fullpath);CHKERRQ(ierr);
  PetscFunctionReturn(0);
}

static PetscErrorCode PetscViewerHDF5CheckNamedObject_Internal(PetscViewer viewer, PetscObject obj)
{
  PetscBool has;
  const char *group;
  PetscErrorCode ierr;

  PetscFunctionBegin;
  if (!obj->name) SETERRQ(PetscObjectComm((PetscObject)viewer), PETSC_ERR_ARG_WRONG, "Object must be named");
  ierr = PetscViewerHDF5HasObject(viewer, obj, &has);CHKERRQ(ierr);
  if (!has) {
    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);
  }
  PetscFunctionReturn(0);
}

static PetscErrorCode PetscViewerSetFromOptions_HDF5(PetscOptionItems *PetscOptionsObject,PetscViewer v)
{
  PetscErrorCode   ierr;
  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 = PetscOptionsTail();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);
}

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

  PetscFunctionBegin;
  ierr = PetscViewerFileClose_HDF5(viewer);CHKERRQ(ierr);
  while (hdf5->groups) {
    GroupList *tmp = hdf5->groups->next;

    ierr         = PetscFree(hdf5->groups->name);CHKERRQ(ierr);
    ierr         = PetscFree(hdf5->groups);CHKERRQ(ierr);
    hdf5->groups = tmp;
  }
  ierr = PetscFree(hdf5->mataij_iname);CHKERRQ(ierr);
  ierr = PetscFree(hdf5->mataij_jname);CHKERRQ(ierr);
  ierr = PetscFree(hdf5->mataij_aname);CHKERRQ(ierr);
  ierr = PetscFree(hdf5->mataij_cname);CHKERRQ(ierr);
  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);
  ierr = PetscObjectComposeFunction((PetscObject)viewer,"PetscViewerHDF5SetAIJNames_C",NULL);CHKERRQ(ierr);
  ierr = PetscObjectComposeFunction((PetscObject)viewer,"PetscViewerHDF5GetAIJNames_C",NULL);CHKERRQ(ierr);
  PetscFunctionReturn(0);
}

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

  PetscFunctionBegin;
  PetscValidHeaderSpecific(viewer, PETSC_VIEWER_CLASSID, 1);
  hdf5->btype = type;
  PetscFunctionReturn(0);
}

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);
}

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);
}

PetscErrorCode  PetscViewerFileSetName_HDF5(PetscViewer viewer, const char name[])
{
  PetscViewer_HDF5 *hdf5 = (PetscViewer_HDF5*) viewer->data;
#if defined(PETSC_HAVE_H5PSET_FAPL_MPIO)
  MPI_Info          info = MPI_INFO_NULL;
#endif
  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(PETSC_HAVE_H5PSET_FAPL_MPIO)
  PetscStackCallHDF5(H5Pset_fapl_mpio,(plist_id, PetscObjectComm((PetscObject)viewer), info));
#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:
    PetscStackCallHDF5Return(hdf5->file_id,H5Fopen,(name, H5F_ACC_RDWR, plist_id));
    break;
  case FILE_MODE_WRITE:
    PetscStackCallHDF5Return(hdf5->file_id,H5Fcreate,(name, H5F_ACC_TRUNC, H5P_DEFAULT, plist_id));
    break;
  default:
    SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ORDER, "Must call PetscViewerFileSetMode() before PetscViewerFileSetName()");
  }
  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);
}

PetscErrorCode  PetscViewerHDF5SetAIJNames_HDF5(PetscViewer viewer, const char iname[], const char jname[], const char aname[], const char cname[])
{
  PetscViewer_HDF5 *hdf5 = (PetscViewer_HDF5*) viewer->data;
  PetscErrorCode ierr;

  PetscFunctionBegin;
  ierr = PetscFree(hdf5->mataij_iname);CHKERRQ(ierr);
  ierr = PetscFree(hdf5->mataij_jname);CHKERRQ(ierr);
  ierr = PetscFree(hdf5->mataij_aname);CHKERRQ(ierr);
  ierr = PetscFree(hdf5->mataij_cname);CHKERRQ(ierr);
  ierr = PetscStrallocpy(iname,&hdf5->mataij_iname);CHKERRQ(ierr);
  ierr = PetscStrallocpy(jname,&hdf5->mataij_jname);CHKERRQ(ierr);
  ierr = PetscStrallocpy(aname,&hdf5->mataij_aname);CHKERRQ(ierr);
  ierr = PetscStrallocpy(cname,&hdf5->mataij_cname);CHKERRQ(ierr);
  hdf5->mataij_names_set = PETSC_TRUE;
  PetscFunctionReturn(0);
}

/*@C
  PetscViewerHDF5SetAIJNames - Set the names of the datasets representing the three AIJ (CRS) arrays and the name of the attribute storing the number of columns within the HDF5 file.

  Collective on PetscViewer

  Input Parameters:
+  viewer - the PetscViewer; either ASCII or binary
.  iname - name of dataset i representing row pointers; that is i[0] = 0, i[row] = i[row-1] + number of elements in that row of the matrix
.  jname - name of dataset j representing column indices
.  aname - name of dataset a representing matrix values
-  cname - name of attribute stoting column count

  Level: advanced

  Notes:
  Current defaults are (iname, jname, aname, cname) = ("jc", "ir", "data", "MATLAB_sparse") so that MAT files can be readily loaded.

.seealso: MatLoad(), PetscViewerCreate(), PetscViewerSetType(), PETSCVIEWERHDF5, PetscViewerHDF5GetAIJNames()
@*/
PetscErrorCode  PetscViewerHDF5SetAIJNames(PetscViewer viewer, const char iname[], const char jname[], const char aname[], const char cname[])
{
  PetscErrorCode ierr;

  PetscFunctionBegin;
  PetscValidHeaderSpecific(viewer,PETSC_VIEWER_CLASSID,1);
  PetscValidCharPointer(iname,2);
  PetscValidCharPointer(jname,3);
  PetscValidCharPointer(aname,4);
  PetscValidCharPointer(cname,5);
  ierr = PetscTryMethod(viewer,"PetscViewerHDF5SetAIJNames_C",(PetscViewer,const char[],const char[],const char[],const char[]),(viewer,iname,jname,aname,cname));CHKERRQ(ierr);
  PetscFunctionReturn(0);
}

PetscErrorCode  PetscViewerHDF5GetAIJNames_HDF5(PetscViewer viewer, const char *iname[], const char *jname[], const char *aname[], const char *cname[])
{
  PetscViewer_HDF5 *hdf5 = (PetscViewer_HDF5*) viewer->data;

  PetscFunctionBegin;
  *iname = hdf5->mataij_iname;
  *jname = hdf5->mataij_jname;
  *aname = hdf5->mataij_aname;
  *cname = hdf5->mataij_cname;
  PetscFunctionReturn(0);
}

/*@C
  PetscViewerHDF5GetAIJNames - Get the names of the datasets representing the three AIJ (CRS) arrays and the name of the attribute storing the number of columns within the HDF5 file.

  Collective on PetscViewer

  Input Parameters:
.  viewer - the PetscViewer; either ASCII or binary

  Output Parameters:
+  iname - name of dataset i representing row pointers; that is i[0] = 0, i[row] = i[row-1] + number of elements in that row of the matrix
.  jname - name of dataset j representing column indices
.  aname - name of dataset a representing matrix values
-  cname - name of attribute stoting column count

  Level: advanced

  Notes:
  Current defaults are (iname, jname, aname, cname) = ("jc", "ir", "data", "MATLAB_sparse") so that MAT files can be readily loaded.

.seealso: MatLoad(), PetscViewerCreate(), PetscViewerSetType(), PETSCVIEWERHDF5, PetscViewerHDF5SetAIJNames()
@*/
PetscErrorCode  PetscViewerHDF5GetAIJNames(PetscViewer viewer, const char *iname[], const char *jname[], const char *aname[], const char *cname[])
{
  PetscErrorCode ierr;

  PetscFunctionBegin;
  PetscValidHeaderSpecific(viewer,PETSC_VIEWER_CLASSID,1);
  PetscValidPointer(iname,2);
  PetscValidPointer(jname,3);
  PetscValidPointer(aname,4);
  PetscValidPointer(cname,5);
  ierr = PetscUseMethod(viewer,"PetscViewerHDF5GetAIJNames_C",(PetscViewer,const char*[],const char*[],const char*[],const char*[]),(viewer,iname,jname,aname,cname));CHKERRQ(ierr);
  PetscFunctionReturn(0);
}

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

  PetscFunctionBegin;
  if (!hdf5->mataij_names_set) {
    ierr = PetscViewerHDF5SetAIJNames_HDF5(viewer,"jc","ir","data","MATLAB_sparse");CHKERRQ(ierr);
  }
  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->flush          = 0;
  hdf5->btype            = (PetscFileMode) -1;
  hdf5->filename         = 0;
  hdf5->timestep         = -1;
  hdf5->groups           = NULL;

  hdf5->mataij_iname     = NULL;
  hdf5->mataij_jname     = NULL;
  hdf5->mataij_aname     = NULL;
  hdf5->mataij_cname     = NULL;
  hdf5->mataij_names_set = PETSC_FALSE;

  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,"PetscViewerHDF5SetBaseDimension2_C",PetscViewerHDF5SetBaseDimension2_HDF5);CHKERRQ(ierr);
  ierr = PetscObjectComposeFunction((PetscObject)v,"PetscViewerHDF5SetSPOutput_C",PetscViewerHDF5SetSPOutput_HDF5);CHKERRQ(ierr);
  ierr = PetscObjectComposeFunction((PetscObject)v,"PetscViewerHDF5SetAIJNames_C",PetscViewerHDF5SetAIJNames_HDF5);CHKERRQ(ierr);
  ierr = PetscObjectComposeFunction((PetscObject)v,"PetscViewerHDF5GetAIJNames_C",PetscViewerHDF5GetAIJNames_HDF5);CHKERRQ(ierr);
  PetscFunctionReturn(0);
}

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

   Collective on MPI_Comm

   Input Parameters:
+  comm - MPI communicator
.  name - name of file
-  type - type of file
$    FILE_MODE_WRITE - create new file for binary output
$    FILE_MODE_READ - open existing file for binary input
$    FILE_MODE_APPEND - open existing file for binary output

   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

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

   Concepts: HDF5 files
   Concepts: PetscViewerHDF5^creating

.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);
  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

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

  PetscFunctionBegin;
  PetscValidHeaderSpecific(viewer,PETSC_VIEWER_CLASSID,1);
  PetscValidCharPointer(name,2);
  ierr = PetscNew(&groupNode);CHKERRQ(ierr);
  ierr = PetscStrallocpy(name, (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;
  GroupList        *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

  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;
  PetscErrorCode ierr;

  PetscFunctionBegin;
  ierr = PetscViewerHDF5GetFileId(viewer, &file_id);CHKERRQ(ierr);
  ierr = PetscViewerHDF5GetGroup(viewer, &groupName);CHKERRQ(ierr);
  ierr = PetscViewerHDF5Traverse_Internal(viewer, groupName, PETSC_TRUE, 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_DOUBLE;
  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
. dataset - The parent dataset name, relative to the current group. NULL means a group-wise attribute.
. name   - The attribute name
. datatype - The attribute type
- value    - The attribute value

  Level: advanced

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

  PetscFunctionBegin;
  PetscValidHeaderSpecific(viewer,PETSC_VIEWER_CLASSID,1);
  if (dataset) PetscValidCharPointer(dataset, 2);
  PetscValidCharPointer(name, 3);
  PetscValidPointer(value, 5);
  ierr = PetscViewerHDF5GetAbsolutePath_Internal(viewer, dataset, &parent);CHKERRQ(ierr);
  ierr = PetscViewerHDF5Traverse_Internal(viewer, parent, PETSC_TRUE, NULL, NULL);CHKERRQ(ierr);
  ierr = PetscViewerHDF5HasAttribute_Internal(viewer, parent, 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, parent, 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(parent);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 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(), 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
. dataset - The parent dataset name, relative to the current group. NULL means a group-wise attribute.
. name   - The attribute name
- datatype - The attribute type

  Output Parameter:
. value    - The attribute value

  Level: advanced

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

  PetscFunctionBegin;
  PetscValidHeaderSpecific(viewer,PETSC_VIEWER_CLASSID,1);
  if (dataset) PetscValidCharPointer(dataset, 2);
  PetscValidCharPointer(name, 3);
  PetscValidPointer(value, 5);
  ierr = PetscViewerHDF5GetAbsolutePath_Internal(viewer, dataset, &parent);CHKERRQ(ierr);
  ierr = PetscViewerHDF5Traverse_Internal(viewer, parent, PETSC_FALSE, &has, NULL);CHKERRQ(ierr);
  if (has) {ierr = PetscViewerHDF5HasAttribute_Internal(viewer, parent, name, &has);CHKERRQ(ierr);}
  if (!has) SETERRQ2(PetscObjectComm((PetscObject)viewer), PETSC_ERR_FILE_UNEXPECTED, "Attribute %s/%s does not exist", parent, name);
  ierr = PetscDataTypeToHDF5DataType(datatype, &dtype);CHKERRQ(ierr);
  ierr = PetscViewerHDF5GetFileId(viewer, &h5);CHKERRQ(ierr);
  PetscStackCallHDF5Return(obj,H5Oopen,(h5, parent, H5P_DEFAULT));
  PetscStackCallHDF5Return(attribute,H5Aopen_name,(obj, name));
  if (datatype == PETSC_STRING) {
    size_t len;
    PetscStackCallHDF5Return(atype,H5Aget_type,(attribute));
    PetscStackCallHDF5Return(len,H5Tget_size,(atype));
    PetscStackCallHDF5(H5Tclose,(atype));
    ierr = PetscMalloc((len+1) * sizeof(char *), &value);CHKERRQ(ierr);
  }
  PetscStackCallHDF5(H5Aread,(attribute, dtype, value));
  PetscStackCallHDF5(H5Aclose,(attribute));
  /* H5Oclose can be used to close groups, datasets, or committed datatypes */
  PetscStackCallHDF5(H5Oclose,(obj));
  ierr = PetscFree(parent);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,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);
}

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

  Input Parameters:
. viewer - The HDF5 viewer

  Output Parameter:
. has    - Flag for group existence

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

  Level: advanced

.seealso: PetscViewerHDF5Open(), PetscViewerHDF5PushGroup(), PetscViewerHDF5PopGroup(), PetscViewerHDF5OpenGroup()
@*/
PetscErrorCode PetscViewerHDF5HasGroup(PetscViewer viewer, PetscBool *has)
{
  H5O_type_t type;
  const char *name;
  PetscErrorCode ierr;

  PetscFunctionBegin;
  PetscValidHeaderSpecific(viewer,PETSC_VIEWER_CLASSID,1);
  PetscValidIntPointer(has,2);
  ierr = PetscViewerHDF5GetGroup(viewer, &name);CHKERRQ(ierr);
  ierr = PetscViewerHDF5Traverse_Internal(viewer, name, PETSC_FALSE, has, &type);CHKERRQ(ierr);
  *has = (type == H5O_TYPE_GROUP) ? PETSC_TRUE : PETSC_FALSE;
  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; PETSC_FALSE for unnamed object

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

  Level: advanced

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

  PetscFunctionBegin;
  PetscValidHeaderSpecific(viewer,PETSC_VIEWER_CLASSID,1);
  PetscValidHeader(obj,2);
  PetscValidIntPointer(has,3);
  *has = PETSC_FALSE;
  if (!obj->name) PetscFunctionReturn(0);
  ierr = PetscViewerHDF5GetAbsolutePath_Internal(viewer, obj->name, &path);CHKERRQ(ierr);
  ierr = PetscViewerHDF5Traverse_Internal(viewer, path, PETSC_FALSE, has, &type);CHKERRQ(ierr);
  *has = (type == H5O_TYPE_DATASET) ? PETSC_TRUE : PETSC_FALSE;
  ierr = PetscFree(path);CHKERRQ(ierr);
  PetscFunctionReturn(0);
}

/*@C
 PetscViewerHDF5HasAttribute - Check whether an attribute exists

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

  Output Parameter:
. has    - Flag for attribute existence

  Level: advanced

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

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

static PetscErrorCode PetscViewerHDF5ReadInitialize_Private(PetscViewer viewer, const char name[], HDF5ReadCtx *ctx)
{
  HDF5ReadCtx    h=NULL;
  PetscErrorCode ierr;

  PetscFunctionBegin;
  ierr = PetscNew(&h);CHKERRQ(ierr);
  ierr = PetscViewerHDF5OpenGroup(viewer, &h->file, &h->group);CHKERRQ(ierr);
  PetscStackCallHDF5Return(h->dataset,H5Dopen2,(h->group, name, H5P_DEFAULT));
  PetscStackCallHDF5Return(h->dataspace,H5Dget_space,(h->dataset));
  ierr = PetscViewerHDF5GetTimestep(viewer, &h->timestep);CHKERRQ(ierr);
  ierr = PetscViewerHDF5HasAttribute(viewer,name,"complex",&h->complexVal);CHKERRQ(ierr);
  if (h->complexVal) {ierr = PetscViewerHDF5ReadAttribute(viewer,name,"complex",PETSC_BOOL,&h->complexVal);CHKERRQ(ierr);}
  /* MATLAB stores column vectors horizontally */
  ierr = PetscViewerHDF5HasAttribute(viewer,name,"MATLAB_class",&h->horizontal);CHKERRQ(ierr);
  /* Create property list for collective dataset read */
  PetscStackCallHDF5Return(h->plist,H5Pcreate,(H5P_DATASET_XFER));
#if defined(PETSC_HAVE_H5PSET_FAPL_MPIO)
  PetscStackCallHDF5(H5Pset_dxpl_mpio,(h->plist, H5FD_MPIO_COLLECTIVE));
#endif
  /* To write dataset independently use H5Pset_dxpl_mpio(plist_id, H5FD_MPIO_INDEPENDENT) */
  *ctx = h;
  PetscFunctionReturn(0);
}

static PetscErrorCode PetscViewerHDF5ReadFinalize_Private(PetscViewer viewer, HDF5ReadCtx *ctx)
{
  HDF5ReadCtx    h;
  PetscErrorCode ierr;

  PetscFunctionBegin;
  h = *ctx;
  PetscStackCallHDF5(H5Pclose,(h->plist));
  PetscStackCallHDF5(H5Gclose,(h->group));
  PetscStackCallHDF5(H5Sclose,(h->dataspace));
  PetscStackCallHDF5(H5Dclose,(h->dataset));
  ierr = PetscFree(*ctx);CHKERRQ(ierr);
  PetscFunctionReturn(0);
}

static PetscErrorCode PetscViewerHDF5ReadSizes_Private(PetscViewer viewer, HDF5ReadCtx ctx, PetscLayout *map_)
{
  int            rdim, dim;
  hsize_t        dims[4];
  PetscInt       bsInd, lenInd, bs, len, N;
  PetscLayout    map;
  PetscErrorCode ierr;

  PetscFunctionBegin;
  if (!(*map_)) {
    ierr = PetscLayoutCreate(PetscObjectComm((PetscObject)viewer),map_);CHKERRQ(ierr);
  }
  map = *map_;
  /* calculate expected number of dimensions */
  dim = 0;
  if (ctx->timestep >= 0) ++dim;
  ++dim; /* length in blocks */
  if (ctx->complexVal) ++dim;
  /* get actual number of dimensions in dataset */
  PetscStackCallHDF5Return(rdim,H5Sget_simple_extent_dims,(ctx->dataspace, dims, NULL));
  /* calculate expected dimension indices */
  lenInd = 0;
  if (ctx->timestep >= 0) ++lenInd;
  bsInd = lenInd + 1;
  ctx->dim2 = PETSC_FALSE;
  if (rdim == dim) {
    bs = 1; /* support vectors stored as 1D array */
  } else if (rdim == dim+1) {
    bs = (PetscInt) dims[bsInd];
    if (bs == 1) ctx->dim2 = PETSC_TRUE; /* vector with blocksize of 1, still stored as 2D array */
  } else {
    SETERRQ2(PetscObjectComm((PetscObject)viewer), PETSC_ERR_FILE_UNEXPECTED, "Number of dimensions %d not %d as expected", rdim, dim);
  }
  len = dims[lenInd];
  if (ctx->horizontal) {
    if (len != 1) SETERRQ(PetscObjectComm((PetscObject)viewer), PETSC_ERR_SUP, "Cannot have horizontal array with number of rows > 1. In case of MATLAB MAT-file, vectors must be saved as column vectors.");
    len = bs;
    bs = 1;
  }
  N = (PetscInt) len*bs;

  /* Set Vec sizes,blocksize,and type if not already set */
  if (map->bs < 0) {
    ierr = PetscLayoutSetBlockSize(map, bs);CHKERRQ(ierr);
  } else if (map->bs != bs) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_FILE_UNEXPECTED, "Block size of array in file is %D, not %D as expected",bs,map->bs);
  if (map->N < 0) {
    ierr = PetscLayoutSetSize(map, N);CHKERRQ(ierr);
  } else if (map->N != N) SETERRQ2(PetscObjectComm((PetscObject)viewer),PETSC_ERR_FILE_UNEXPECTED, "Global size of array in file is %D, not %D as expected",N,map->N);
  PetscFunctionReturn(0);
}

static PetscErrorCode PetscViewerHDF5ReadSelectHyperslab_Private(PetscViewer viewer, HDF5ReadCtx ctx, PetscLayout map, hid_t *memspace)
{
  hsize_t        count[4], offset[4];
  int            dim;
  PetscInt       bs, n, low;
  PetscErrorCode ierr;

  PetscFunctionBegin;
  /* Compute local size and ownership range */
  ierr = PetscLayoutSetUp(map);CHKERRQ(ierr);
  ierr = PetscLayoutGetBlockSize(map, &bs);CHKERRQ(ierr);
  ierr = PetscLayoutGetLocalSize(map, &n);CHKERRQ(ierr);
  ierr = PetscLayoutGetRange(map, &low, NULL);CHKERRQ(ierr);

  /* Each process defines a dataset and reads it from the hyperslab in the file */
  dim  = 0;
  if (ctx->timestep >= 0) {
    count[dim]  = 1;
    offset[dim] = ctx->timestep;
    ++dim;
  }
  if (ctx->horizontal) {
    count[dim]  = 1;
    offset[dim] = 0;
    ++dim;
  }
  {
    ierr = PetscHDF5IntCast(n/bs, &count[dim]);CHKERRQ(ierr);
    ierr = PetscHDF5IntCast(low/bs, &offset[dim]);CHKERRQ(ierr);
    ++dim;
  }
  if (bs > 1 || ctx->dim2) {
    if (PetscUnlikely(ctx->horizontal)) SETERRQ(PETSC_COMM_SELF, PETSC_ERR_SUP, "cannot have horizontal array with blocksize > 1");
    count[dim]  = bs;
    offset[dim] = 0;
    ++dim;
  }
  if (ctx->complexVal) {
    count[dim]  = 2;
    offset[dim] = 0;
    ++dim;
  }
  PetscStackCallHDF5Return(*memspace,H5Screate_simple,(dim, count, NULL));
  PetscStackCallHDF5(H5Sselect_hyperslab,(ctx->dataspace, H5S_SELECT_SET, offset, NULL, count, NULL));
  PetscFunctionReturn(0);
}

static PetscErrorCode PetscViewerHDF5ReadArray_Private(PetscViewer viewer, HDF5ReadCtx h, hid_t datatype, hid_t memspace, void *arr)
{
  PetscFunctionBegin;
  PetscStackCallHDF5(H5Dread,(h->dataset, datatype, memspace, h->dataspace, h->plist, arr));
  PetscFunctionReturn(0);
}

PetscErrorCode PetscViewerHDF5Load(PetscViewer viewer, const char *name, PetscLayout map, hid_t datatype, void **newarr)
{
  HDF5ReadCtx     h=NULL;
  hid_t           memspace=0;
  size_t          unitsize;
  void            *arr;
  PetscErrorCode  ierr;

  PetscFunctionBegin;
  ierr = PetscViewerHDF5ReadInitialize_Private(viewer, name, &h);CHKERRQ(ierr);
#if defined(PETSC_USE_COMPLEX)
  if (!h->complexVal) {
    H5T_class_t clazz = H5Tget_class(datatype);
    if (clazz == H5T_FLOAT) SETERRQ(PetscObjectComm((PetscObject)viewer),PETSC_ERR_SUP,"File contains real numbers but PETSc is configured for complex. The conversion is not yet implemented. Configure with --with-scalar-type=real.");
  }
#else
  if (h->complexVal) SETERRQ(PetscObjectComm((PetscObject)viewer),PETSC_ERR_SUP,"File contains complex numbers but PETSc not configured for them. Configure with --with-scalar-type=complex.");
#endif

  ierr = PetscViewerHDF5ReadSizes_Private(viewer, h, &map);CHKERRQ(ierr);
  ierr = PetscLayoutSetUp(map);CHKERRQ(ierr);
  ierr = PetscViewerHDF5ReadSelectHyperslab_Private(viewer, h, map, &memspace);CHKERRQ(ierr);

  unitsize = H5Tget_size(datatype);
  if (h->complexVal) unitsize *= 2;
  if (unitsize <= 0 || unitsize > PetscMax(sizeof(PetscInt),sizeof(PetscScalar))) SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_LIB,"Sanity check failed: HDF5 function H5Tget_size(datatype) returned suspicious value %D",unitsize);
  ierr = PetscMalloc(map->n*unitsize, &arr);CHKERRQ(ierr);

  ierr = PetscViewerHDF5ReadArray_Private(viewer, h, datatype, memspace, arr);CHKERRQ(ierr);
  PetscStackCallHDF5(H5Sclose,(memspace));
  ierr = PetscViewerHDF5ReadFinalize_Private(viewer, &h);CHKERRQ(ierr);
  *newarr = arr;
  PetscFunctionReturn(0);
}

/*@C
 PetscViewerHDF5ReadSizes - Read block size and global size of a vector (Vec or IS) stored in an HDF5 file.

  Input Parameters:
+ viewer - The HDF5 viewer
- name   - The vector name

  Output Parameter:
+ bs     - block size
- N      - global size

  Note:
  A vector is stored as an HDF5 dataspace with 1-4 dimensions in this order:
  1) # timesteps (optional), 2) # blocks, 3) # elements per block (optional), 4) real and imaginary part (only for complex).

  A vectors can be stored as a 2D dataspace even if its blocksize is 1; see PetscViewerHDF5SetBaseDimension2().

  Level: advanced

.seealso: PetscViewerHDF5Open(), VecLoad(), ISLoad(), VecGetSize(), ISGetSize(), PetscViewerHDF5SetBaseDimension2()
@*/
PetscErrorCode PetscViewerHDF5ReadSizes(PetscViewer viewer, const char name[], PetscInt *bs, PetscInt *N)
{
  HDF5ReadCtx    h=NULL;
  PetscLayout    map=NULL;
  PetscErrorCode ierr;

  PetscFunctionBegin;
  PetscValidHeaderSpecific(viewer,PETSC_VIEWER_CLASSID,1);
  ierr = PetscViewerHDF5ReadInitialize_Private(viewer, name, &h);CHKERRQ(ierr);
  ierr = PetscViewerHDF5ReadSizes_Private(viewer, h, &map);CHKERRQ(ierr);
  ierr = PetscViewerHDF5ReadFinalize_Private(viewer, &h);CHKERRQ(ierr);
  if (bs) *bs = map->bs;
  if (N) *N = map->N;
  ierr = PetscLayoutDestroy(&map);CHKERRQ(ierr);
  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 on MPI_Comm

  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(0);}
  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,0);
    if (ierr) {PetscError(PETSC_COMM_SELF,__LINE__,"PETSC_VIEWER_HDF5_",__FILE__,PETSC_ERR_PLIB,PETSC_ERROR_INITIAL," ");PetscFunctionReturn(0);}
  }
  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(0);}
  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_INITIAL," ");PetscFunctionReturn(0);}
    if (!flg) {
      ierr = PetscStrcpy(fname,"output.h5");
      if (ierr) {PetscError(PETSC_COMM_SELF,__LINE__,"PETSC_VIEWER_HDF5_",__FILE__,PETSC_ERR_PLIB,PETSC_ERROR_INITIAL," ");PetscFunctionReturn(0);}
    }
    ierr = PetscViewerHDF5Open(ncomm,fname,FILE_MODE_WRITE,&viewer);
    if (ierr) {PetscError(PETSC_COMM_SELF,__LINE__,"PETSC_VIEWER_HDF5_",__FILE__,PETSC_ERR_PLIB,PETSC_ERROR_INITIAL," ");PetscFunctionReturn(0);}
    ierr = PetscObjectRegisterDestroy((PetscObject)viewer);
    if (ierr) {PetscError(PETSC_COMM_SELF,__LINE__,"PETSC_VIEWER_HDF5_",__FILE__,PETSC_ERR_PLIB,PETSC_ERROR_INITIAL," ");PetscFunctionReturn(0);}
    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(0);}
  }
  ierr = PetscCommDestroy(&ncomm);
  if (ierr) {PetscError(PETSC_COMM_SELF,__LINE__,"PETSC_VIEWER_HDF5_",__FILE__,PETSC_ERR_PLIB,PETSC_ERROR_INITIAL," ");PetscFunctionReturn(0);}
  PetscFunctionReturn(viewer);
}