HDF5 documents and links 
Introduction to HDF5 
HDF5 User's Guide 
HDF5 Reference Manual 
HDF5 Application Developer's Guide 


HDF5 Software Changes from Release to Release
for HDF5 Releases 1.4.0 through 1.6.10


This document covers HDF5 releases in the HDF5 Release 1.4.x and 1.6.x series. For each release, we list new features and changes in the existing HDF5 feature set, the HDF5 application programming interface (API), and the command-line tools distributed with the HDF5 Library. The intent is to note changes that application developers must be aware of when maintaining applications or libraries that must work with progressively newer versions of HDF5.

See “HDF5 Software Changes from Release to Release” for:

See “HDF5 Software Changes from Release to Release for HDF5 Releases 1.8.x” for:


Release 1.6.10 versus Release 1.6.9, November 2009

This section lists interface-level changes and other user-visible changes in behavior in the transition from HDF5 Release 1.6.9 to Release 1.6.10.

Embedded HDF5 Library Settings Information

Library settings are now embedded in an HDF5 executable so that an “orphaned” executable can be queried (via the Unix strings command, for example) to display the library settings used to build it. The embedded settings information is the same as that normally found in the libhdf5.settings file.

This capability may be disabled with the use of the --disable-embedded-libin flag during configure.

Function with Changed Interface or Behavior

H5check_version now displays embedded library information (see above) if a version mismatch is detected.

The function has also been changed to suppress the warning message entirely if $HDF5_DISABLE_VERSION_CHECK is set to 2 or higher.

New C++ Member Function

New C++ member functions are provided to determine a dataset’s or attribute’s data size in memory:

   size_t DataSet::getInMemDataSize() const
   size_t Attribute::getInMemDataSize() const

The size in each case is in bytes.

Tool with Changed Interface or Behavior

h5diff has one new option:

    --use-system-epsilon

With this option, h5diff returns a difference if and only if the difference between two data values exceeds the system value for epsilon (that is, if |a-b| > epsilon).

The tool’s default behavior has also changed; without this option, the tool now checks for strict equality.

This option has no short form.

Release 1.6.9 versus Release 1.6.8, May 2009

This section lists API-level changes and changes in behavior in the transition from HDF5 Release 1.6.8 to Release 1.6.9.

API Compatibility Macros

To facilitate writing applications that work with both the HDF5 Release 1.6 series and the 1.8 series, API compatibility macros analogous to those in 1.8 have been defined. These macros map directly to the relevant functions and typedefs. Note that only the 1.6-style macros are supported in this branch.

Any program that is written using these macros exculsively will work with both the 1.6 and 1.8 series HDF5 Libraries. The program will work without having to use any special flags or definitions, as long as the 1.8 library was compiled with support for deprecated symbols, which is the default.

Following is a list of macros and the symbols they alias:

Macro Symbol
H5Acreate1 H5Acreate
H5Aiterate1 H5Aiterate
H5A_operator1_t H5A_operator_t
H5Dcreate1 H5Dcreate
H5Dopen1 H5Dopen
H5Eclear1 H5Eclear
H5Eget_auto1 H5Eget_auto
H5Eprint1 H5Eprint
H5Epush1 H5Epush
H5Eset_auto1 H5Eset_auto
H5Ewalk1 H5Ewalk
H5E_walk1_t H5E_walk_t
H5E_error1_t H5E_error_t
H5Gcreate1 H5Gcreate
H5Gopen1 H5Gopen
H5Pget_filter1 H5Pget_filter
H5Pget_filter_by_id1 H5Pget_filter_by_id
H5Pinsert1 H5Pinsert
H5Pregister1 H5Pregister
H5Rget_obj_type1 H5Rget_obj_type
H5Tarray_create1 H5Tarray_create
H5Tcommit1 H5Tcommit
H5Tget_array_dims1 H5Tget_array_dims
H5Topen1 H5Topen
H5E_auto1_t H5E_auto_t
H5Z_class1_t H5Z_class_t

Note that for the 1.6 series, the numbered symbols are macros, while in the 1.8 series, the non-numbered symbols are macros. This was done because there is no need to switch between different API versions in the 1.6 series.

H5Z_class1_t was introduced in Release 1.6.9 while all the others were introduced in Release 1.6.8. For more information see API Compatibility Macros, an HDF5 Release 1.8-series document.

Tools with Changed Interface or Behavior

h5diff
The default behavior of h5diff is now to detect and compare NaNs. Use the -N or --nan option (below) to turn this behavior off and avoid the performance penalty that NaN detection and comparison entalis. (NaN detection and comparison became the default in in HDF5 Release 1.6.8.)

This tool has two new options:

     -c, --compare      Lists objects that are not comparable.

     -N, --nan          Avoids NaNs detection.

h5dump
h5dump now correctly specifies an XML DTD or a schema URL.

h5dump binary output now defaults to NATIVE.

The new -b, --binary option can be used to specify alternate binary formats.

h5repack
When a user does not specify a chunk size, h5repack now defines the default chunk size to be the same same as the size of the hyperslab used to read the chunks.

Release 1.6.8 versus Release 1.6.7, November 2008

This section lists API-level changes and changes in behavior in the transition from HDF5 Release 1.6.7 to Release 1.6.8.

Functions with Changed Syntax

The following function syntaxes have changed; the affected return values and parameter are noted as underscored red text.

C function:
H5Fget_obj_count
ssize_t H5Fget_obj_count( hid_t file_id, unsigned int types )

H5Fget_obj_ids
ssize_t H5Fget_obj_ids( hid_t file_id, unsigned int types,
        size_t max_objs, hid_t *obj_id_list )

Tools with Changed Interface or Behavior

h5repack and h5diff
The standard command-line syntax of both tools has been changed to parallel that of h5dump. The new syntax of each is as follows:

     h5repack [OPTIONS] file1 file2

     h5diff [OPTIONS] file1 file2 [object1 [object2]]

In each case, the old syntax remains available (though undocumented) to avoid breaking existing scripts.

h5diff
h5diff now returns 1 if the files differ in structure, i.e., if the file graphs differ by any object.

The tool’s error return code has been changed to 2.

h5repack
The following new options control the addition of user block data to an existing HDF5 file:
-u U
--ublock=U
     Specifies the name of the file containing the user block data to be added.

-b B
--block=B
    
Specifies the size of the block to be added.

The following new options set parameters governing the tool’s use of H5Pset_alignment:
-t T
--threshold=T
     Specifies the threshold value for H5Pset_alignment.

-a A
--alignment=A
    
Specifies the alignment value for H5Pset_alignment.

h5repack now supports multiple instances of the '-f' or '--filter' option, allowing the use of multiple I/O filters with an object.

With no change in the command-line syntax, h5repack now retains an existing userblock when repacking an HDF5 file.

h5import
The floating point format flag TEXTFPE, for scientific notation, has been deprecated. The flag TEXTFP, which accepts scientific notation, should be used instead.

h5import now imports string data with the STR keyword in the INPUT-CLASS configuration field.

h5dump
The new '-m T' or '--format T' option enables a user-defined formatting string for printing floating-point numbers.

With no change in the command-line syntax, h5dump now prints a compression ratio when compression filters are in use.

Deprecated Functions

The following functions are deprecated as of this release:
        H5Pset_preserve
        H5Pget_preserve 

The original role of these functions is now part of the core HDF5 Library functionality.

Changed File Installation

The file libhdf5_fortran.settings is no longer installed with the HDF5 Library; the original content of that file is now included in libhdf5.settings.

Release 1.6.7 versus Release 1.6.6

This section lists the API-level changes that have been made in the transition from the HDF5 Release 1.6.6 to Release 1.6.7. As this is primarily a bug-fix release, the only interface changes are one changed function signature and the changes related to the removal of the stream I/O driver, as outlined below.

Function with Changed Syntax

The following function syntax has changed; the affected parameter is noted in red.

C function:
H5Sselect_elements
herr_t H5Sselect_elements( hid_t space_id, H5S_seloper_t op,
        size_t num_elements, const hsize_t *coord )

(This syntax change was listed on 10 September 2008, several months after Release 1.6.7.)

Stream I/O Driver Removed

The stream I/O driver, H5FD_STREAM, has been removd from and is no longer distributed with the HDF5 Library. The following APIs have therefore been removed from this release.
    H5Pset_fapl_stream
    H5Pget_fapl_stream
The stream driver ENUM value H5FD_STREAM has also been removed.

While the stream driver is no longer distributed by The HDF Group, it will be made available as a source code distribution from http://hdf5-addons.origo.ethz.ch/. An integration mechanism will be developed and instructions for using the driver with HDF5 will be posted on that site.

Release 1.6.6 versus Release 1.6.5

This section lists the API-level changes that have been made in the transition from the HDF5 Release 1.6.5 to Release 1.6.6.

Release 1.6.6 is primarily a bug-fix release and includes no changes in the syntax or intended behavior of the library’s public interfaces. There are, however, two changes in tool interfaces.

Tools with Changed Options and/or Behavior

The following tools have changed in this release; these changes are documented on the Tools page of the HDF5 Reference Manual.
 
h5repack:
A new -n option allows the user to specify that a new file created by h5repack will use native datatypes. The default behavior is to use the original file datatypes.
     -n   Use native HDF5 datatypes when repacking.
(Default behavior is to use the original file datatypes.)
Note that the default behavior of this tool has changed; prior to Release 1.6.6, h5repack generated files only with native datatypes.

h5dump:
This tool includes a new -b option for binary output.
     -b B   or
--binary=B   
Output dataset to a binary file using the datatype specified by B.
B must have one of the following values:
     LE        Little-endian
     BE        Big-endian
     MEMORY    Memory datatype
     FILE      File datatype
Recommended usage is with the -d and -o options.

 

Release 1.6.5 versus Release 1.6.4

This section lists the API-level changes that have been made in the transition from the HDF5 Release 1.6.4 to Release 1.6.5.

New Functions and Tools

C functions and
Fortran subroutines:
HDF5 Release 1.6.5 is primarily a maintenance release, focusing on bugfixes, optimization and portability; there are no new C APIs or Fortran subroutines.
 
High Level C APIs:
The High Level C APIs (HL), including the HDF5 Image, HDF5 Table, and HDF5 Lite interfaces (H5IM, H5TB, and H5LT, respectively), have been distributed with the main HDF5 source code distribution since Release 1.6.4 and are documented in HDF5: High Level APIs. (Note: In release 1.8 and later, the HL APIs are documented in the HDF5 Reference Manual.)
 
C++ wrappers:
void PropList::copyProp(PropList& dest, const char* name) const
void PropList::copyProp(PropList& dest, const string& name) const
string CommonFG::getComment(const string& name) const
void CommonFG::removeComment(const char* name) const
void CommonFG::removeComment(const string& name) const
hsize_t Attribute::getStorageSize() const
void Attribute::close()
void DataSet::close()
void DataSpace::close()
void DataType::close()
void H5File::close()
void Group::close()
void PropList::close()
H5T_order_t AtomType::getOrder() const
void H5Object::renameAttr(const char* oldname, const char* newname) const
void H5Object::renameAttr(const string& oldname, const string& newname) const
string CommonFG::getObjnameByIdx(hsize_t idx) const
ArrayType AbstractDs::getArrayType() const
VarLenType AbstractDs::getVarLenType() const
ArrayType CommonFG::openArrayType(const char* name) const
ArrayType CommonFG::openArrayType(const string& name) const
VarLenType CommonFG::openVarLenType(const char* name) const
VarLenType CommonFG::openVarLenType(const string& name) const
ArrayType CompType::getMemberArrayType(unsigned member_num) const
VarLenType CompType::getMemberVarLenType(unsigned member_num) const
 

Functions with New or Changed Symbols or Fixed Values

Symbols and preset values associated with the following functions have changed as noted.

C functions:
H5Fget_obj_count
H5F_OBJ_LOCAL has been added as a qualifier on the types of objects to be counted. H5F_OBJ_LOCAL restricts the search to objects opened through current file identifier.
H5Tset_tag
The H5T_OPAQUE_TAG_MAX macro constant, specifying the maximum size of an opaque datatype tag, was added in H5Tpublic.h.

Functions with Changed Syntax

The following functions have changed as noted. Changed items are indicated in red.

C++ wrappers:
In all cases below, a parameter datatype has changed from int to unsigned.
string CompType::getMemberName( unsigned member_num ) const
size_t CompType::getMemberOffset( unsigned member_num ) const
int CompType::getMemberDims( unsigned member_num, size_t* dims, int* perm ) const
H5T_class_t CompType::getMemberClass( unsigned member_num ) const
hid_t CompType::p_get_member_type( unsigned member_num) const
DataType CompType::getMemberDataType( unsigned member_num ) const
ArrayType CompType::getMemberArrayType( unsigned member_num ) const
CompType CompType::getMemberCompType( unsigned member_num ) const
EnumType CompType::getMemberEnumType( unsigned member_num ) const
IntType CompType::getMemberIntType( unsigned member_num ) const
FloatType CompType::getMemberFloatType( unsigned member_num ) const
StrType CompType::getMemberStrType( unsigned member_num ) const
VarLenType CompType::getMemberVarLenType( unsigned member_num ) const

Changed Library Configuration

 

Release 1.6.4 versus Release 1.6.3

This section lists the API-level changes that have been made in the transition from the HDF5 Release 1.6.3 to Release 1.6.4.

New Functions and Tools

C functions and
Fortran subroutines:
HDF5 Release 1.6.4 "Bugfix Release"; there are no new C APIs or Fortran subroutines.
 
High Level C APIs:
The High Level C APIs (HL), including the HDF5 Image, HDF5 Table, and HDF5 Lite interfaces (H5IM, H5TB, and H5LT, respectively) , have been brought into the main HDF5 source code distribution. A link to the HL documentation appears on the opening page of the HDF5 document set or can be accessed directly at /HDF5/hdf5_hl/doc/RM_hdf5hl.html

The HL library, libhdf5_hl.a(so), is built and installed by default but can be disabled with the --disable-hl configure flag.
 
Tools:
A new pair of tools, h5jam and h5unjam, is available to manage user blocks in HDF5 files. See their entry in the HDF5 Reference Manual.

Deleted Functions

The following functions have been removed in this release.
 
C++ wrappers:
The C++ wrappers now rely on the C library's reference counting in place of the class RefCounter, which existed before the C mechanism was available. RefCounter has therefore been removed.

Functions with Changed Syntax

The following functions have changed as noted. In general, one or more parameters or the return value has changed from a signed to an unsigned datatype. Changed items are indicated in red.

C functions:
H5Pget_version
herr_t H5Pget_version(hid_t plist_id, unsigned *boot/*out*/,
unsigned *freelist/*out*/, unsigned *stab/*out*/, unsigned *shhdr/*out*/)
H5Pset_sym_k
H5Pset_sym_k(hid_t plist_id, unsigned ik, unsigned lk)
H5Pget_sym_k
H5Pget_sym_k(hid_t plist_id, unsigned *ik/*out*/, unsigned *lk/*out*/)
H5Pset_istore_k
herr_t H5Pset_istore_k(hid_t plist_id, unsigned ik)
H5Pget_istore_k
herr_t H5Pget_istore_k(hid_t plist_id, unsigned *ik/*out*/)
H5Pget_external
herr_t H5Pget_external(hid_t plist_id, unsigned idx, size_t name_size,
char *name/*out*/, off_t *offset/*out*/, hsize_t *size/*out*/)
H5Pget_filter
H5Z_filter_t H5Pget_filter(hid_t plist_id, unsigned filter,
unsigned int *flags/*out*/, size_t *cd_nelmts/*out*/,
unsigned cd_values[]/*out*/, unsigned int *flags/*out*/,
size_t namelen, char name[])
H5Sselect_hyperslab
herr_t H5Sselect_hyperslab(hid_t space_id, H5S_seloper_t op,
const hsize_t start[], const hsize_t _stride[], const hsize_t count[],
const hsize_t _block[])
H5Sselect_elements
herr_t H5Sselect_elements(hid_t space_id, H5S_seloper_t op,
size_t num_elemn, const hsize_t **coord)
H5Tget_member_name
char *H5Tget_member_name(hid_t type_id, unsigned membno)
H5Tget_member_offset
size_t H5Tget_member_offset(hid_t type_id, unsigned membno)
H5Tget_member_class
H5T_class_t H5Tget_member_class(hid_t type_id, unsigned membno)
H5Tget_member_type
hid_t H5Tget_member_type(hid_t type_id, unsigned membno)
H5Tget_member_value
herr_t H5Tget_member_value(hid_t type_id, unsigned membno,
void *value/*out*/)

H5Diterate is affected by a similar change in the syntax of H5D_operator_t.
herr_t (*H5D_operator_t)(void *elem, hid_t type_id, unsigned ndim,
const hsize_t *point, void *operator_data)

Fortran subroutines:
h5sselect_hyperslab_f
SUBROUTINE h5sselect_hyperslab_f(space_id, operator, start, count, &
hdferr, stride, block)
h5sselect_elements_f
SUBROUTINE h5sselect_elements_f(space_id, operator, rank, &
num_elements, coord, hdferr)

C++ wrappers:
FileCreatPropList::getVersion
void FileCreatPropList::getVersion( unsigned& super, unsigned& freelist,
unsigned& stab, unsigned& shhdr) const
FileCreatPropList::setSymk
void FileCreatPropList::setSymk( unsigned ik, unsigned lk ) const
FileCreatPropList::getSymk
void FileCreatPropList::getSymk( unsigned& ik, unsigned& lk ) const
FileCreatPropList::setIstorek
void FileCreatPropList::setIstorek( unsigned ik ) const
FileCreatPropList::getIstorek
unsigned FileCreatPropList::getIstorek() const
DSetCreatPropList::getExternal
void DSetCreatPropList::getExternal( unsigned idx, size_t name_size,
char* name, off_t& offset, hsize_t& size ) const
DSetCreatPropList::getFilter
H5Z_filter_t DSetCreatPropList::getFilter( ine filter_number,
unsigned int &flags, size_t &cd_nelmts, unsigned int* cd_values,
size_t namelen, char name[] ) const
DataSpace::selectHyperslab
void DataSpace::selectHyperslab( H5S_seloper_t op, const hsize_t *count,
const hsize_t *start, const hsize_t *stride, const hsize_t *block ) const
DataSpace::selectElements
void DataSpace::selectElements( H5S_seloper_t op,
const size_t num_elements, const hsize_t *coord[ ] ) const
CompType::getMemberName
string CompType::getMemberName( unsigned member_num ) const
CompType::getMemberOffset
size_t CompType::getMemberOffset( unsigned member_num ) const
CompType::getMemberClass
H5T_class_t CompType::getMemberClass( unsigned member_num ) const
EnumType::getMemberValue
void EnumType::getMemberValue( unsigned member_no, void *value ) const

(These lists of syntax changes were added on 31 March and 5 April 2005, shortly after Release 1.6.4.)

Deleted Constants

The following constants have been removed from the HDF5 Library: (This list of deleted constants was added on 21 March 2005, shortly after Release 1.6.4.)

Changed Library Configuration

HDF5 Library configuration has been upgraded from GNU autoconf 2.53 to autoconf 2.59.

 

Release 1.6.3 versus Release 1.6.2

This section lists the API-level changes that have been made in the transition from the HDF5 Release 1.6.2 to Release 1.6.3.

New Functions and Tools

C functions:
The following C functions are new for Release 1.6.3 and are documented in the HDF5 Reference Manual.
H5Fget_name      ssize_t H5Fget_name (hid_t obj_id, char *name, size_t size)
See entry.
H5Fget_filesize      herr_t H5Fget_filesize (hid_t file_id, hsize_t * size)
See entry.
H5Iget_file_id      hid_t H5Iget_file_id (hid_t obj_id)
See entry.
H5Premove_filter      herr_t H5Premove_filter (hid_t obj_id, H5Z_filter_t filter)
See entry.
H5Zget_filter_info      herr_t H5Zget_filter_info (H5Z_filter_t filter, unsigned int * flags)
See entry.
 
Fortran subroutines:
The following Fortran90 subroutines are new for Release 1.6.3 and are documented in the HDF5 Reference Manual.
New Fortran90 subroutines corresponding to the new C functions listed above:
    h5fget_name_f
    h5fget_filesize_f
    h5iget_file_id_f
    h5premove_filter_f
    h5zget_filter_info_f
New Fortran90 subroutines corresponding to C functions from prior releases:
    None
    
 
C++ wrappers:
C++ wrappers have been brought in sync with the C library, rendering the C++ API significantly more complete. Most of the new wrappers are for H5P and H5T APIs.

All available C++ elements are now documented in the HDF5 C++ API Reference Manual. (The HDF5 C++ API Reference Manual is also a new addition in this release.)

 
Tools:
The following tools are new for Release 1.6.3 and are documented on the Tools page of the HDF5 Reference Manual.
h5new_tool is designed to do whatever this sentence says. (Clearly, this is a placeholder entry that should be removed before release.)
 
The following tool was in Release 1.6.2 but was not included in formal documentation. A full description is now included on the Tools page of the HDF5 Reference Manual.
h5repack is designed to copy an HDF5 file to a new file with or without compression and/or chunking.

Deleted Functions

The following function has been removed in this release.
 
C++ wrapper:
CompType::getMemberDims

Functions with Changed Syntax

The following functions have changed as noted.

C functions:
H5Pset_fapl_multi
The prototype for this function was changed from:
  • herr_t H5Pset_fapl_multi (hid_t fapl_id, const H5FD_mem_t * memb_map, const hid_t * memb_fapl, const char ** memb_name, const haddr_t * memb_addr, hbool_t relax)
to:
  • herr_t H5Pset_fapl_multi (hid_t fapl_id, const H5FD_mem_t * memb_map, const hid_t * memb_fapl, const char * const * memb_name, const haddr_t * memb_addr, hbool_t relax)

This change should not appreciably affect application programs.

H5Tconvert
The prototype for this function was changed from:
  • herr_t H5Tconvert (hid_t src_id, hid_t dst_id, hsize_t nelmts, void * buf, void * background, hid_t plist_id)
to:
  • herr_t H5Tconvert (hid_t src_id, hid_t dst_id, size_t nelmts, void * buf, void * background, hid_t plist_id)

This was changed to prevent overflows when hsize_t and size_t types are different sizes. Application code may need to be modified to take this into account. Application code using this function may also be affected by the changes to H5Tregister and H5Tunregister described below.

H5Tregister and H5Tunregister
These two routines are affected by the change to the H5T_conv_t typedef (described below) and may require application registered datatype conversion routines to be modified to conform to the changed typedef.
 
C++ wrappers:
H5::Exception and its subclasses
Constructors used by H5::Exception and its subclasses that were previously overloaded to take char pointers have been removed. Constructors that passed in a reference of string have been changed to pass by value. In addition, the default value of the detailed message has been changed from 0/NULL to DEFAULT_MSG (meaning "No detailed information provided").
 
DSetCreatPropList::setLayout
The prototype for DSetCreatPropList::setLayout has been changed: the first parameter has been removed.

Constants with Changed Values

The following library structures have changed as noted.

C API:
H5T_conv_t
This function pointer typedef's definition has been changed from:
  • typedef herr_t (*H5T_conv_t) (hid_t src_id, hid_t dst_id, H5T_cdata_t * cdata, hsize_t nelmts, size_t buf_stride, size_t bkg_stride, void * buf, void * bkg, hid_t plist_id)
to:
  • typedef herr_t (*H5T_conv_t) (hid_t src_id, hid_t dst_id, H5T_cdata_t * cdata, size_t nelmts, size_t buf_stride, size_t bkg_stride, void * buf, void * bkg, hid_t plist_id)

This was changed to prevent overflows when hsize_t and size_t types are different sizes. Application code may need to be modified to take this into account.

 

Release 1.6.2 versus Release 1.6.1

This section lists the API-level changes that have been made in the transition from the HDF5 Release 1.6.1 to Release 1.6.2.

New Functions and Tools

C functions:
The following C functions are new for Release 1.6.2 and are documented in the HDF5 Reference Manual.
H5Iget_ref      int H5Iget_ref (hid_t obj_id)
See entry.
H5Iinc_ref      int H5Iinc_ref (hid_t obj_id)
See entry.
H5Idec_ref      int H5Idec_ref (hid_t obj_id)
See entry.
 
Fortran subroutines:
The following Fortran90 subroutines are new for Release 1.6.2 and are documented in the HDF5 Reference Manual.
Corresponding to the new C functions listed above:
    h5iget_ref_f
    h5iinc_ref_f
    h5idec_ref_f
    
 
Tools:
The following tools are new for Release 1.6.2 and are documented on the Tools page of the HDF5 Reference Manual.
h5pcc is designed to aid in the compilation of C applications that employ the HDF5 Library.
h5pfc is designed to aid in the compilation of Fortran90 applications that employ the HDF5 Library.

Deleted Functions

None.

Functions with Changed Syntax

None.

Constants with Changed Values

None.

 

Release 1.6.1 versus Release 1.6.0

This section lists the API-level changes that have been made in the transition from the HDF5 Release 1.6.0 to Release 1.6.1.

New Functions and Tools

C functions:
The following C function is new for Release 1.6.1 and is documented in the HDF5 Reference Manual.
H5Fget_freespace      hssize_t H5Fget_freespace (hid_t file_id)
See entry.
 
Fortran subroutines
The following Fortran90 subroutines were new for Release 1.6.0 but were not documented. They are now included in the HDF5 Reference Manual.
h5get_fapl_mpiposix_f      h5pget_fapl_mpiposix_f(prp_id, comm, use_gpfs, hdferr)
See entry.
h5set_fapl_mpiposix_f      h5pset_fapl_mpiposix_f(prp_id, comm, use_gpfs, hdferr)
See entry.
 
Tools:
Release 1.6.1 contains no new tools.

Deleted Functions

None.

Functions with Changed Syntax

The following functions have changed as noted.
C functions:
H5Gget_obj_info
The H5G_stat_t struct contains two new fields.
This change will be transparent to existing applications, though those calling H5Gget_obj_info will have to be recompiled before linking with the updated library.
 
Fortran90 subroutines:
h5pset_cache_f
The rdcc_nbytes parameter has changed from INTEGER to INTEGER(SIZE_T) to better match the C API and the h5pget_cache_f subroutine.

Constants with Changed Values

None.

 

Release 1.6.0 versus Release 1.4.5

This section lists the API-level changes that have been made in the transition from the HDF5 Release 1.4.x series to Release 1.6.0.

New Functions and Tools

The following functions are new for Release 1.6.0 and are included in the HDF5 Reference Manual.
H5set_free_list_limits herr_t H5set_free_list_limits (int reg_global_lim, int reg_list_lim, int arr_global_lim, int arr_list_lim, int blk_global_lim, int blk_list_lim)
H5Dget_offset hsize_t H5Dget_offset (hid_t dset_id)
H5Dget_space_status hid_t H5Dget_space_status (hid_t dset_id, H5D_space_status_t *status)
H5Fget_obj_ids int H5Fget_obj_ids (hid_t file_id, unsigned int types, int max_objs, hid_t *obj_id_list)
H5Fget_vfd_handle herr_t H5Fget_vfd_handle (hid_t file_id, hid_t fapl_id, void *file_handle)
H5Gget_num_objs herr_t H5Gget_num_objs (hid_t loc_id, hsize_t* num_obj)
H5Gget_objname_by_idx ssize_t H5Gget_objname_by_idx (hid_t group_id, hsize_t idx, char *name, size_t* size)
H5Gget_objtype_by_idx int H5Gget_objtype_by_idx (hid_t group_id, hsize_t idx)
H5Iget_name ssize_t H5Iget_name (hid_t obj_id, char *name, size_t size)
H5Pall_filters_avail htri_t H5Pall_filters_avail (hid_t dcpl_id)
H5Pfill_value_defined herr_t H5Pfill_value_defined (hid_t plist_id, H5D_fill_value_t *status)
H5Pget_alloc_time herr_t H5Pget_alloc_time (hid_t plist_id, H5D_alloc_time_t *alloc_time)
H5Pget_edc_check H5Z_EDC_t H5Pget_edc_check (hid_t plist)
H5Pget_family_offset herr_t H5Pget_family_offset (hid_t fapl_id, hsize_t *offset)
H5Pget_fapl_mpiposix herr_t H5Pget_fapl_mpiposix (hid_t fapl_id, MPI_Comm *comm)
H5Pget_fclose_degree herr_t H5Pget_fclose_degree(hid_t fapl_id, H5F_close_degree_t *fc_degree)
(This item corrected 14 September 2004.)
H5Pget_fill_time herr_t H5Pget_fill_time (hid_t plist_id, H5D_fill_time_t *fill_time)
H5Pget_filter_by_id herr_t H5Pget_filter_by_id (hid_t plist_id, H5Z_filter_t filter, unsigned int *flags, size_t *cd_nelmts, unsigned int cd_values[], size_t namelen, char *name[])
H5Pget_hyper_vector_size herr_t H5Pget_hyper_vector_size (hid_t dxpl_id, size_t *vector_size)
H5Pget_multi_type herr_t H5Pget_multi_type (hid_t fapl_id, H5FD_mem_t *type)
H5Pmodify_filter herr_t H5Pmodify_filter (hid_t plist, H5Z_filter_t filter, unsigned int flags, size_t cd_nelmts, const unsigned int cd_values[])
H5Pset_alloc_time herr_t H5Pset_alloc_time (hid_t plist_id, H5D_alloc_time_t alloc_time)
H5Pset_edc_check herr_t H5Pset_edc_check (hid_t plist, H5Z_EDC_t check)
H5Pset_family_offset herr_t H5Pset_family_offset (hid_t fapl_id, hsize_t offset)
H5Pset_fapl_mpiposix herr_t H5Pset_fapl_mpiposix (hid_t fapl_id, MPI_Comm comm)
H5Pset_fclose_degree herr_t H5Pset_fclose_degree(hid_t fapl_id, H5F_close_degree_t fc_degree)
(This item corrected 14 September 2004.)
H5Pset_fill_time herr_t H5Pset_fill_time (hid_t plist_id, H5D_fill_time_t fill_time)
H5Pset_filter herr_t H5Pset_filter (hid_t plist, H5Z_filter_t filter, unsigned int flags, size_t cd_nelmts, const unsigned int cd_values[])
H5Pset_filter_callback herr_t H5Pset_filter_callback (hid_t plist, H5Z_filter_func_t func, void *op_data)
H5Pset_fletcher32 herr_t H5Pset_fletcher32 (hid_t plist)
H5Pset_hyper_vector_size  herr_t H5Pset_hyper_vector_size (hid_t dxpl_id, size_t vector_size)
H5Pset_multi_type herr_t H5Pset_multi_type (hid_t fapl_id, H5FD_mem_t type)
H5Pset_shuffle herr_t H5Pset_shuffle (hid_t plist_id)
H5Pset_szip herr_t H5Pset_szip (hid_t plist, unsigned int options_mask, unsigned int pixels_per_block)
H5Rget_object_type int H5Rget_object_type (hid_t id, void *ref)
H5Sget_select_type H5S_sel_type H5Sget_select_type (hid_t space_id)
H5Tdetect_class htri_t H5Tdetect_class (hid_t dtype_id, H5T_class_t dtype_class)
H5Tget_native_type hid_t H5Tget_native_type (hid_t type_id, H5T_direction_t direction)
H5Tis_variable_str htri_t H5Tis_variable_str (hid_t dtype_id)
H5Zfilter_avail herr_t H5Zfilter_avail (H5Z_filter_t filter)
H5Zunregister herr_t H5Zunregister (H5Z_filter_t filter)
 
The following tools are new for Release 1.6.0 and are included in the HDF5 Reference Manual.
h5diff
h5import
h5fc
h5c++
h5perf
h5redeploy

Deleted Functions

The following functions are deprecated in HDF5 Release 1.6.0. A backward compatibility mode is provided in this release, enabling these functions and other Release 1.4.x compatibility features, but is available only when the HDF5 Library is configured with the flag H5_WANT_H5_V1_4_COMPAT. The backward compatibility mode is not enabled in the binaries distributed by NCSA.
       
H5Pset_hyper_cache
H5Pget_hyper_cache
      
H5Rget_object_type
      
 

The above functions will eventually be removed from the HDF5 distribution and from the HDF5 Reference Manual.

Functions with Changed Syntax

The following functions have changed as noted.
C functions:
H5FDflush and VFL "flush" callbacks
An extra parameter closing has been added to these functions, to allow the library to indicate that the file will be closed following the call to "flush". Actions in the "flush" call that are duplicated in the VFL "close" call may be omitted by the VFL driver.
* H5Gget_objtype_by_idx
The function return type has changed from int to the enumerated type H5G_obj_t.
* H5Pset(get)_buffer
The size parameter for H5Pset_buffer has changed from type hsize_t to size_t.
The H5Pget_buffer return type has similarly changed from hsize_t to size_t.
* H5Pset(get)_cache
The rdcc_nbytes parameter has changed from type int to size_t.
(This item corrected 3 March 2004.)
* H5Pset_fapl_log
The verbosity parameter has been removed.
Two new parameters have been added: flags of type unsigned and buf_size of type size_t.
* H5Pset(get)_fapl_mpiposix
A use_gpfs parameter of type hbool_t has been added.
* H5Pset(get)_sieve_buf_size
The size parameter has changed from type hsize_t to size_t.
* H5Pset(get)_sym_k
The lk parameter has changed from type int to unsigned.
* H5Sget_select_bounds
The start and end parameters have changed from type hsize_t * to hssize_t * to better match the rest of the dataspace API.
* H5Zregister
This function is substantially revised in Release 1.6.0 with a new H5Z_class_t struct and new set local and can apply callback functions.
 
Fortran90 functions:
h5pset(get)_fapl_core_f
The backing_store parameter has changed from INTEGER to LOGICAL to better match the C API.
h5pset(get)_preserve_f
The flag parameter has changed from INTEGER to LOGICAL to better match the C API.

Backward compatibility with the Release 1.4.x syntax is available for the functions indicated above with a leading asterisk (*). The backward compatibility features are available only when the HDF5 Library is configured with the flag H5_WANT_H5_V1_4_COMPAT, is not enabled in the binaries distributed by NCSA, and will eventually be removed from the HDF5 distribution.

Constants with Changed Values

 

Release 1.4.5 versus Release 1.4.4

C Library

Added functions:
herr_t H5Pset_fapl_mpiposix(hid_t fapl_id, MPI_Comm comm);
herr_t H5Pget_fapl_mpiposix(hid_t fapl_id, MPI_Comm *comm/*out*/);
Changed functions: The following functions have changed behavior.

H5Pset_fapl_mpio  
H5Pget_fapl_mpio
H5Fcreate
H5Fopen
H5Fclose
Previously, the Communicator and Info object arguments supplied to H5Pset_fapl_mpio were stored in the property with its handle values. This meant changes to the communicator or the Info object after calling H5Pset_fapl_mpio would affect the how the property list functioned. This was also the case when H5Fopen/create operated. They just stored the handle value. This is not according to the MPI-2 defined behavior of how Info objects should be handled. (MPI-2 defines Info objects must be parsed when called.)
H5Pset_fapl_mpio now stores a duplicate of each of the communicator and Info object.
H5Pget_fapl_mpio now returns a duplicate of its stored communicator and Info object. It is now the responsibility of the applications to free those objects when done.

H5Fcreate and H5Fopen also store a duplicate of the communicator and Info object supplied by the file access property List. H5Fclose frees the duplicates.

Advice to users: User applications should release the communicator and Info object returned by H5Pget_fapl_mpio when they are no longer needed.

Removed functions:
None       
          
There were no other public API changes in the C library for this release.

Fortran90 Library

The following missing Fortran functions were added:

h5get_libversion_f, h5check_version_f, h5garbage_collect_f, h5dont_atexit_f
h5tget_member_index_f, h5tvlen_create_f
h5dget_storage_size_f, h5dvlen_get_max_len_f , h5dwrite_vl_f, h5dread_vl_f

Only integer, real and character types are supported for VL datatypes.

Release 1.4.4 versus Release 1.4.3

C Library

Added functions:
H5Pget_small_data_block_size
H5Pset_small_data_block_size
H5Tget_member_index
      
          
Changed functions:
None       
          
Removed functions:
None       
          
There were no other public API changes in the C library for this release.

Fortran90 Library

h5dwrite_f, h5dread_f, h5awrite_f, h5aread_f were overloaded with dims argument to be assumed size array of type INTEGER(HSIZE_T). We recommend to use the subroutines with the new type. Module subroutines that accept dims as INTEGER array of size 7 will be deprecated in the 1.6.0 release.

Release 1.4.3 versus Release 1.4.2

C Library

Removed function:
H5Pset_fapl_dpss 
      
          
      
          
There were no other public API changes in the C library for this release.

Fortran90 Library

There were no changes to the public Fortran90 APIs for this release.

Release 1.4.2 versus Release 1.4.1

C Library

The HDF5 Release 1.4.2 C library is a "Bugfix Release"; there are no API changes in the underlying HDF5 Library.

Fortran90 Library

The following functions in the HDF5 Release 1.4.2 Fortran90 library have an additional parameter, dims, that was not present in Release 1.4.1:
h5aread_f(attr_id, memtype_id,  buf, dims, hdferr)
h5awrite_f(attr_id, memtype_id,  buf, dims, hdferr)
h5dread_f(dset_id, mem_type_id, buf, dims, hdferr, mem_space_id, &
           file_space_id, xfer_prp)
h5dwrite_f(dset_id, mem_type_id, buf, dims, hdferr, mem_space_id, &
           file_space_id, xfer_prp)
The dims parameter enables library portability between the UNIX and Microsoft Windows platforms.

Release 1.4.1 versus Release 1.4.0

Release 1.4.1 is a "Tools Release"; there are no API changes in the underlying HDF5 Library.

Release 1.4.0 versus Release 1.2.2

Several functions were added to or removed from the HDF5 Library in the development of Release 1.4.0. A few functions have been modified in minor ways.

New Functions

The following functions are new for Release 1.4.0 and are included in the HDF5 Reference Manual.
herr_t H5Dvlen_get_buf_size (hid_t dataset_id, hid_t type_id, 
           hid_t space_id, hsize_t *size);
herr_t H5Epush (const char *file, const char *func,
           unsigned line, H5E_major_t maj, H5E_minor_t min, 
           const char *str);
hid_t H5Pget_driver (hid_t plist_id);
void *H5Pget_driver_info (hid_t plist_id);
herr_t H5Pget_dxpl_mpio (hid_t dxpl_id, 
           H5FD_mpio_xfer_t *xfer_mode/*out*/);
herr_t H5Pget_dxpl_multi (hid_t dxpl_id, 
           hid_t *memb_dxpl/*out*/);
herr_t H5Pget_fapl_core (hid_t fapl_id, size_t *increment/*out*/,
           hbool_t *backing_store/*out*/) 
herr_t H5Pget_fapl_family (hid_t fapl_id, 
           hsize_t *memb_size/*out*/, hid_t *memb_fapl_id/*out*/);
herr_t H5Pget_fapl_mpio (hid_t fapl_id, MPI_Comm *comm/*out*/,
           MPI_Info *info/*out*/);
herr_t H5Pget_fapl_multi (hid_t fapl_id, 
           H5FD_mem_t *memb_map/*out*/, hid_t *memb_fapl/*out*/, 
           char **memb_name/*out*/, haddr_t *memb_addr/*out*/, 
           hbool_t *relax/*out*/);
herr_t H5Pget_fapl_stream (hid_t fapl_id,
           H5FD_stream_fapl_t *fapl /*out*/ );
herr_t H5Pget_meta_block_size (hid_t fapl_id, 
           hsize_t *size/*out*/);
herr_t H5Pget_sieve_buf_size (hid_t fapl_id, 
           hsize_t *size/*out*/);
herr_t H5Pset_driver (hid_t plist_id, hid_t driver_id,
           const void *driver_info);
herr_t H5Pset_dxpl_mpio (hid_t dxpl_id, 
           H5FD_mpio_xfer_t xfer_mode);
herr_t H5Pset_dxpl_multi (hid_t dxpl_id, 
           const hid_t *memb_dxpl);
herr_t H5Pset_fapl_core (hid_t fapl_id, size_t increment, 
           hbool_t backing_store)
herr_t H5Pset_fapl_family (hid_t fapl_id, hsize_t memb_size,
           hid_t memb_fapl_id);
herr_t H5Pset_fapl_log (hid_t fapl_id, char *logfile, 
           int verbosity);
herr_t H5Pset_fapl_mpio (hid_t fapl_id, MPI_Comm comm, 
           MPI_Info info);
herr_t H5Pset_fapl_multi (hid_t fapl_id, 
           const H5FD_mem_t *memb_map, const hid_t *memb_fapl, 
           const char **memb_name, const haddr_t *memb_addr, 
           hbool_t relax);
herr_t H5Pset_fapl_sec2 (hid_t fapl_id);
herr_t H5Pset_fapl_split (hid_t fapl, const char *meta_ext,
           hid_t meta_plist_id, const char *raw_ext,
           hid_t raw_plist_id);
herr_t H5Pset_fapl_stdio (hid_t fapl_id);
herr_t H5Pset_fapl_stream (hid_t fapl_id,
           H5FD_stream_fapl_t *fapl);
herr_t H5Pset_meta_block_size(hid_t fapl_id, hsize_t size);
herr_t H5Pset_sieve_buf_size(hid_t fapl_id, hsize_t size);
hid_t H5Tarray_create (hid_t base, int rank, const hsize_t dims[], 
           const int perm[])
int H5Tget_array_dims (hid_t adtype_id, hsize_t *dims[], int *perm[])
int H5Tget_array_ndims (hid_t adtype_id)

The following functions are new for Release 1.4.0, but are intended only for use in specialized environments. These are also included in the HDF5 Reference Manual.

herr_t H5Pget_fapl_dpss (hid_t fapl_id);
herr_t H5Pget_fapl_gass (hid_t fapl_id, GASS_Info *info/*out*/);
herr_t H5Pget_fapl_srb (hid_t fapl_id, SRB_Info *info);
herr_t H5Pset_fapl_dpss (hid_t fapl_id);
herr_t H5Pset_fapl_gass (hid_t fapl_id, GASS_Info info);
herr_t H5Pset_fapl_srb (hid_t fapl_id, SRB_Info info);

The following functions are new for Release 1.4.0 but are intended only for driver development work, not for general use. They are listed in the List of VFL Functions document in the HDF5 Technical Notes. They are described in detail only in the source code and do not appear in the HDF5 Reference Manual.

haddr_t H5FDalloc (H5FD_t *file, H5FD_mem_t type, 
          hsize_t size);
herr_t H5FDclose (H5FD_t *file);
int H5FDcmp (const H5FD_t *f1, const H5FD_t *f2);
herr_t H5FDflush (H5FD_t *file);
herr_t H5FDfree (H5FD_t *file, H5FD_mem_t type, 
          haddr_t addr, hsize_t size);
haddr_t H5FDget_eoa (H5FD_t *file);
haddr_t H5FDget_eof (H5FD_t *file);
H5FD_t *H5FDopen (const char *name, unsigned flags, 
          hid_t fapl_id, haddr_t maxaddr);
int H5FDquery (const H5FD_t *f, unsigned long *flags);
herr_t H5FDread (H5FD_t *file, hid_t dxpl_id, haddr_t addr, 
          hsize_t size, void *buf/*out*/);
haddr_t H5FDrealloc (H5FD_t *file, H5FD_mem_t type, 
          haddr_t addr, hsize_t old_size, hsize_t new_size);
hid_t H5FDregister (const H5FD_class_t *cls);
herr_t H5FDset_eoa (H5FD_t *file, haddr_t eof);
herr_t H5FDunregister (hid_t driver_id);
herr_t H5FDwrite (H5FD_t *file, H5FD_mem_t type, 
          hid_t dxpl_id, haddr_t addr, hsize_t size, 
          const void *buf);

Deleted Functions

The following functions have been removed from the HDF5 Library and from the HDF5 Reference Manual.
H5Pget_core
H5Pget_driver
H5Pget_family
H5Pget_mpi
H5Pget_sec2
H5Pget_split
H5Pget_stdio
H5Pget_xfer
      
H5Pset_core
H5Pset_family
H5Pset_mpi
H5Pset_sec2
H5Pset_split
H5Pset_stdio
H5Pset_xfer
      
H5RAclose
H5RAcreate
H5RAopen
H5RAread
H5RAwrite
H5Tget_member_dims
H5Tinsert_array
Note that the entire H5RA interface, an experimental interface for ragged arrays, has been removed from the library.

Functions with Changed Syntax

The following functions have changed slightly.
H5Pget_buffer
Return type has changed to hsize_t.
H5Pset_buffer
The type of the size parameter has changed to hsize_t.
H5Tconvert
The type of the nelmts parameter has changed to hsize_t.

Constants with Changed Values

The values of the constants H5P_DEFAULT and H5S_ALL have been changed from -2 to 0. These default values had to be special-cased in situations where they could be returned to distinguish them from error values.

 

Migration from Release 1.2.2 to Release 1.4.x

H5Tinsert_array

The functionality of H5Tinsert_array has been replaced by H5Tarray_create. Here is an example of changing code from H5Tinsert_array to H5Tarray_create.
V1.2.2
{
    struct tmp_struct {
        int a;
        float f[3];
        double d[2][4];
    };
    size_t f_dims[1]={3};
    size_t d_dims[2]={2,4};
    hid_t compound_type;

    compound_type=H5Tcreate(H5T_COMPOUND,sizeof(struct tmp_struct));
    H5Tinsert(compound_type,"a",HOFFSET(struct tmp_struct,a),H5T_NATIVE_INT);
    H5Tinsert_array(compound_type,"f",HOFFSET(struct tmp_struct,f),1,f_dims,NULL,H5T_NATIVE_FLOAT);
    H5Tinsert_array(compound_type,"d",HOFFSET(struct tmp_struct,d),2,d_dims,NULL,H5T_NATIVE_DOUBLE);
}

V1.4.0
{
    struct tmp_struct {
        int a;
        float f[3];
        double d[2][4];
    };
    hsize_t f_dims[1]={3};
    hsize_t d_dims[2]={2,4};
    hid_t compound_type;
    hid_t array_type;

    compound_type=H5Tcreate(H5T_COMPOUND,sizeof(struct tmp_struct));
    H5Tinsert(compound_type,"a",HOFFSET(struct tmp_struct,a),H5T_NATIVE_INT);
    array_type=H5Tarray_create(H5T_NATIVE_FLOAT,1,f_dims,NULL);
    H5Tinsert(compound_type,"f",HOFFSET(struct tmp_struct,f),array_type);
    H5Tclose(array_type);
    array_type=H5Tarray_create(H5T_NATIVE_DOUBLE,2,d_dims,NULL);
    H5Tinsert(compound_type,"d",HOFFSET(struct tmp_struct,d),array_type);
    H5Tclose(array_type);
}



HDF5 documents and links 
Introduction to HDF5 
HDF5 User's Guide 
HDF5 Reference Manual 
HDF5 Application Developer's Guide 

The HDF Group Help Desk:
Describes HDF5 Release 1.10.0
  Copyright by The HDF Group
and the Board of Trustees of the University of Illinois

Last modified: 26 September 2014