impls/hdf5/hdf5v.c

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

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 */
} PetscViewer_HDF5;

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);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);
  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);
}

/*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->flush          = 0;
  hdf5->btype            = (PetscFileMode) -1;
  hdf5->filename         = 0;
  hdf5->timestep         = -1;
  hdf5->groups           = NULL;

  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);
  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()
@*/
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()
@*/
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 for output. 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()
@*/
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);
}

PetscErrorCode PetscViewerHDF5OpenGroup(PetscViewer viewer, hid_t *fileId, hid_t *groupId)
{
  hid_t          file_id, group;
  htri_t         found;
  const char     *groupName = NULL;
  PetscErrorCode ierr;

  PetscFunctionBegin;
  ierr = PetscViewerHDF5GetFileId(viewer, &file_id);CHKERRQ(ierr);
  ierr = PetscViewerHDF5GetGroup(viewer, &groupName);CHKERRQ(ierr);
  /* Open group */
  if (groupName) {
    PetscBool root;

    ierr = PetscStrcmp(groupName, "/", &root);CHKERRQ(ierr);
    PetscStackCall("H5Lexists",found = H5Lexists(file_id, groupName, H5P_DEFAULT));
    if (!root && (found <= 0)) {
#if (H5_VERS_MAJOR * 10000 + H5_VERS_MINOR * 100 + H5_VERS_RELEASE >= 10800)
      PetscStackCallHDF5Return(group,H5Gcreate2,(file_id, groupName, 0, H5P_DEFAULT, H5P_DEFAULT));
#else /* deprecated HDF5 1.6 API */
      PetscStackCallHDF5Return(group,H5Gcreate,(file_id, groupName, 0));
#endif
      PetscStackCallHDF5(H5Gclose,(group));
    }
#if (H5_VERS_MAJOR * 10000 + H5_VERS_MINOR * 100 + H5_VERS_RELEASE >= 10800)
    PetscStackCallHDF5Return(group,H5Gopen2,(file_id, groupName, H5P_DEFAULT));
#else
    PetscStackCallHDF5Return(group,H5Gopen,(file_id, groupName));
#endif
  } else group = file_id;

  *fileId  = file_id;
  *groupId = group;
  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_DOUBLE;
  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 a scalar attribute

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

  Level: advanced

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

  PetscFunctionBegin;
  PetscValidHeaderSpecific(viewer,PETSC_VIEWER_CLASSID,1);
  PetscValidPointer(parent, 2);
  PetscValidPointer(name, 3);
  PetscValidPointer(value, 4);
  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 (H5_VERS_MAJOR * 10000 + H5_VERS_MINOR * 100 + H5_VERS_RELEASE >= 10800)
  PetscStackCallHDF5Return(attribute,H5Acreate2,(obj, name, dtype, dataspace, H5P_DEFAULT, H5P_DEFAULT));
#else
  PetscStackCallHDF5Return(attribute,H5Acreate,(obj, name, dtype, dataspace, H5P_DEFAULT));
#endif
  PetscStackCallHDF5(H5Awrite,(attribute, dtype, value));
  if (datatype == PETSC_STRING) PetscStackCallHDF5(H5Tclose,(dtype));
  PetscStackCallHDF5(H5Aclose,(attribute));
  PetscStackCallHDF5(H5Oclose,(obj));
  PetscStackCallHDF5(H5Sclose,(dataspace));
  PetscFunctionReturn(0);
}

/*@C
 PetscViewerHDF5ReadAttribute - Read a scalar attribute

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

  Output Parameter:
. value    - The attribute value

  Level: advanced

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

  PetscFunctionBegin;
  PetscValidHeaderSpecific(viewer,PETSC_VIEWER_CLASSID,1);
  PetscValidPointer(parent, 2);
  PetscValidPointer(name, 3);
  PetscValidPointer(value, 4);
  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));
  PetscStackCallHDF5Return(atype,H5Aget_type,(attribute));
  if (datatype == PETSC_STRING) {
    size_t len;

    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));
  PetscStackCallHDF5(H5Dclose,(obj));
  PetscFunctionReturn(0);
}

static PetscErrorCode PetscViewerHDF5HasObject(PetscViewer viewer, const char name[], H5O_type_t otype, PetscBool *has)
{
  hid_t          h5;
  PetscErrorCode ierr;

  PetscFunctionBegin;
  PetscValidHeaderSpecific(viewer,PETSC_VIEWER_CLASSID,1);
  PetscValidPointer(name, 2);
  PetscValidPointer(has, 3);
  *has = PETSC_FALSE;
  ierr = PetscViewerHDF5GetFileId(viewer, &h5);CHKERRQ(ierr);
  if (H5Lexists(h5, name, H5P_DEFAULT)) {
    H5O_info_t info;
    hid_t      obj;

    PetscStackCallHDF5Return(obj,H5Oopen,(h5, name, H5P_DEFAULT));
    PetscStackCallHDF5(H5Oget_info,(obj, &info));
    if (otype == info.type) *has = PETSC_TRUE;
    PetscStackCallHDF5(H5Oclose,(obj));
  }
  PetscFunctionReturn(0);
}

/*@C
 PetscViewerHDF5HasAttribute - Check whether a scalar attribute exists

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

  Output Parameter:
. has    - Flag for attribute existence

  Level: advanced

.seealso: PetscViewerHDF5Open(), PetscViewerHDF5WriteAttribute(), PetscViewerHDF5ReadAttribute()
@*/
PetscErrorCode PetscViewerHDF5HasAttribute(PetscViewer viewer, const char parent[], const char name[], PetscBool *has)
{
  hid_t          h5, dataset;
  htri_t         hhas;
  PetscBool      exists;
  PetscErrorCode ierr;

  PetscFunctionBegin;
  PetscValidHeaderSpecific(viewer,PETSC_VIEWER_CLASSID,1);
  PetscValidPointer(parent, 2);
  PetscValidPointer(name, 3);
  PetscValidPointer(has, 4);
  *has = PETSC_FALSE;
  ierr = PetscViewerHDF5GetFileId(viewer, &h5);CHKERRQ(ierr);
  ierr = PetscViewerHDF5HasObject(viewer, parent, H5O_TYPE_DATASET, &exists);CHKERRQ(ierr);
  if (exists) {
#if (H5_VERS_MAJOR * 10000 + H5_VERS_MINOR * 100 + H5_VERS_RELEASE >= 10800)
    PetscStackCall("H5Dopen2",dataset = H5Dopen2(h5, parent, H5P_DEFAULT));
#else
    PetscStackCall("H5Dopen",dataset = H5Dopen(h5, parent));
#endif
    if (dataset < 0) PetscFunctionReturn(0);
    PetscStackCall("H5Aexists",hhas = H5Aexists(dataset, name));
    if (hhas < 0) {
      PetscStackCallHDF5(H5Dclose,(dataset));
      PetscFunctionReturn(0);
    }
    PetscStackCallHDF5(H5Dclose,(dataset));
    *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 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);
}