Software Changes from Release to Release for HDF5-1.8

This document is designed to help developers maintain HDF5-based applications as they are used with successive releases of HDF5. To that end, this document lists the changes at each release that a maintenance developer needs to be aware of:

• New or changed features or tools
• Syntax and behavioral changes in the existing application programming interface (the API)
• Certain types of changes in configuration or build processes

Bugfixes and performance enhancements in the C library are automatically picked up by the C++ and Fortran libraries. The Java library will pick up the same bugfixes and enhancements at its next subsequent release as it is always built with the latest released version of the C library.

The release notes also list changes made to the library, but these notes tend to be more at a more detail oriented level. The release notes may include new features, bugs fixed, supported configuration features, platforms on which the library has been tested, and known problems. The release note files are listed below and can be found at the top level of the HDF5 source code tree in the release_docs directory of the distributed HDF5 source code.

Are you porting an existing application from HDF5 Release 1.6.x to HDF5 Release 1.8.x?
If you are porting an existing application from any HDF5 version in the Release 1.6.x series to any version in the Release 1.8.x series, refer to “What's New in HDF5 1.8.0”. This document, with the documents linked in its introduction, provides a guide to the changes introduced in the transition from the 1.6.x series to HDF5 Release 1.8.0 and discussions of various compatibility issues.

Release 1.8.23 of February 2023 versus Release 1.8.22

This section lists interface-level changes and other user-visible changes in behavior in the transition from HDF5 Release 1.8.22 to Release 1.8.23.

New and Changed Functions, Classes, Subroutines, Wrappers, and Macros

In the C Interface (main library)

None.

In the C High Level Interface

None.

In the C++ Wrapper

None.

Compatibility Notes and Report and Comments

The interface compatibility report provides a full list of the changed symbols.

Release 1.8.22 of February 2021 versus Release 1.8.21

This section lists interface-level changes and other user-visible changes in behavior in the transition from HDF5 Release 1.8.21 to Release 1.8.22.

New and Changed Functions, Classes, Subroutines, Wrappers, and Macros

In the C Interface (main library)

The following are new C functions in this release:

In the C High Level Interface

None.

In the C++ Wrapper

None.

Compatibility Notes and Report and Comments

The interface compatibility report provides a full list of the changed symbols.

Release 1.8.21 of May 2018 versus Release 1.8.20

This section lists interface-level changes and other user-visible changes in behavior in the transition from HDF5 Release 1.8.20 to Release 1.8.21.

New and Changed Functions, Classes, Subroutines, Wrappers, and Macros

In the C Interface (main library)

None.

In the C High Level Interface

None.

In the C++ Wrapper

Many changes were made to improve the C++ API model. Please review the RELEASE.txt file or the compatibility report below for complete information on the C++ changes in this release.

Compatibility Notes and Report and Comments

The interface compatibility report provides a full list of the changed symbols.

Release 1.8.20 of November 2017 versus Release 1.8.19

This section lists interface-level changes and other user-visible changes in behavior in the transition from HDF5 Release 1.8.19 to Release 1.8.20.

New and Changed Functions, Classes, Subroutines, Wrappers, and Macros

In the C Interface (main library)

None.

In the C High Level Interface

None.

In the C++ Wrapper

Many changes were made to improve the C++ API model. Please review the RELEASE.txt file or the compatibility report below for complete information on the C++ changes in this release.

Compatibility Notes and Report and Comments

Compatibility report for Release 1.8.20 versus Release 1.8.19

The following interface compatibility report provides a full list of the changed symbols:

API compatibility report for the HDF5 Library between 1.8.19 and 1.8.20 versions on x86_64

Release 1.8.19 of June 2017 versus Release 1.8.18

This section lists interface-level changes and other user-visible changes in behavior in the transition from HDF5 Release 1.8.18 to Release 1.8.19.

New and Changed Functions, Classes, Subroutines, Wrappers, and Macros

In the C Interface (main library)

The following new C functions were added:

In the C High Level Interface

The following new C function was added:

In the C++ Wrapper

Many changes were made to improve the C++ API model. Please review the RELEASE.txt file or Compatibility report below for complete information on the C++ changes in this release.

Compatibility Notes and Report and Comments

Compatibility report for Release 1.8.19 versus Release 1.8.18

The following interface compatibility report provides a full list of the changed symbols:

API compatibility report for the HDF5 Library between 1.8.18 and 1.8.19 versions on x86_64

Release 1.8.18 of November 2016 versus Release 1.8.17

This section lists interface-level changes and other user-visible changes in behavior in the transition from HDF5 Release 1.8.17 to Release 1.8.18.

New and Changed Functions, Classes, Subroutines, Wrappers, and Macros

In the C Interface (main library)

None.

In the C++ Interface (main library wrappers)

The macro H5_NO_NAMESPACE was deprecated.

New member functions added to provide const versions:

DSetCreatPropList::allFiltersAvail() const

DSetCreatPropList::getAllocTime () const

DSetCreatPropList::getFillTime () const

DSetCreatPropList::isFillValueDefined () const

DSetCreatPropList::setAllocTime (H5D_alloc_time_t alloc_time) const

DSetCreatPropList::setFillTime (H5D_fill_time_t fill_time) const

DSetMemXferPropList::getEDCCheck () const

DSetMemXferPropList::getHyperVectorSize () const

DSetMemXferPropList::getSmallDataBlockSize () const

DSetMemXferPropList::setEDCCheck (H5Z_EDC_t check) const

DSetMemXferPropList::setHyperVectorSize (size_t vector_size) const

DSetMemXferPropList::setSmallDataBlockSize (hsize_t size) const

FileAccPropList::getFcloseDegree () const

FileAccPropList::setFcloseDegree (H5F_close_degree_t degree) const

The following member functions were removed:

ArrayType::getArrayDims (hsize_t* dims)

ArrayType::getArrayNDims ()

DataType::commit (H5Location& loc, char const* name)

DataType::commit (H5Location& loc, std::string const& name)

DSetCreatPropList::allFiltersAvail ()

DSetCreatPropList::getAllocTime ()

DSetCreatPropList::getFillTime ()

DSetCreatPropList::isFillValueDefined ()

DSetCreatPropList::setAllocTime (H5D_alloc_time_t alloc_time)

DSetCreatPropList::setFillTime (H5D_fill_time_t fill_time)

DSetMemXferPropList::getEDCCheck ()

DSetMemXferPropList::getHyperVectorSize ()

DSetMemXferPropList::getSmallDataBlockSize ()

DSetMemXferPropList::setEDCCheck (H5Z_EDC_t check)

DSetMemXferPropList::setHyperVectorSize (size_t vector_size)

DSetMemXferPropList::setSmallDataBlockSize (hsize_t size)

FileAccPropList::getFcloseDegree ()

FileAccPropList::setFcloseDegree (H5F_close_degree_t degree)

H5Location::H5Location [in-charge] (hid_t const loc_id)

H5Location::H5Location [not-in-charge] (hid_t const loc_id)

H5Object::H5Object [in-charge] (hid_t const object_id)

H5Object::H5Object [not-in-charge] (hid_t const object_id)

CommonFG::mount (char const* name, H5File& child, PropList& plist) const

DataSet::getVlenBufSize (DataType& type, DataSpace& space) const

DataType::commit (H5Location& loc, char const* name)

DataType::commit (H5Location& loc, std::string const& name)

Compatibility Notes and Report and Comments

Compatibility report for Release 1.8.18 versus Release 1.8.17

The following interface compatibility report provides a full list of the changed symbols:

API compatibility report for the HDF5 Library between 1.8.17 and 1.8.18 versions on x86_64

Release 1.8.17 of May 2016 versus Release 1.8.16

This section lists interface-level changes and other user-visible changes in behavior in the transition from HDF5 Release 1.8.16 to Release 1.8.17.

New and Changed Functions, Classes, Subroutines, Wrappers, and Macros

In the C Interface (main library)

The following new C functions and environment variable enable setting a relative path for raw data files associated with datasets using external storage:

In the C High-Level Interface

The following new functions have been added in the Packet Table (H5PT) high-level interface:

H5PTcreate
H5PTget_dataset
H5PTget_type

H5PTcreate replaces H5PTcreate_fl, which is deprecated and may be removed in a future release.

The following functions were previously removed from the library distribution but are once again publicly available.

Reinstated in its original form:

H5PTis_varlen

An updated form of H5PTfree_vlen_readbuff reinstated as:

H5PTfree_vlen_buff

In the C++ Interface (main library wrappers)

New member function added in DSetCreatPropList:

DSetCreatPropList::setNbit() was added to set up N-bit compression for a dataset.

New overloaded const member functions added in ArrayType:

The following functions were added to provide const versions; the non-const versions have been marked deprecated.

    ArrayType::getArrayNDims() const

    ArrayType::getArrayDims() const

The datamembers ArrayType::rank and ArrayType::dimensions have been removed. This is an implementation detail and should not affect applications.

In the C++ High-Level Interface

New constructor added in FL_PacketTable:

An overloaded constructor has been added to FL_PacketTable. The function now takes a property list identifier to provide flexibility on creation properties such as compression.

    FL_PacketTable(hid_t fileID, const char* name, hid_t dtypeID,

                   hsize_t chunkSize = 0, hid_t plistID = H5P_DEFAULT)

New member functions added in PacketTable:

Two accessor wrappers were added to class PacketTable.

PacketTable::GetDataset() returns the identifier of the dataset associated with the packet table.

PacketTable::GetDatatype() returns the identifier of the datatype that the packet table uses.

New member functions added with a char* argument:

Overloaded functions have been added to provide a const char* argument. The existing versions of these functions will be deprecated in future releases.

This also removes the following warning:

    deprecated conversion from string constant to "char*" [-Wwrite-strings]

Ifdef blocks removed:

The #ifdef VLPT_REMOVED blocks have been removed from the packet table library source code except for the following functions:

VL_PacketTable::IsVariableLength() was moved to PacketTable.

VL_PacketTable::FreeReadBuff() is now PacketTable::FreeBuff().

Compatibility Notes and Report

Changed shared library interface version numbers (soname)

For HDF5 Release 1.8.17, the shared object version numbers have changed as follows.

Compatibility report for Release 1.8.17 versus Release 1.8.16

The following interface compatibility report provides a full list of the changed symbols:

API compatibility report for the HDF5 Library between 1.8.16 and 1.8.17 versions on x86

Release 1.8.16 of November 2015 versus Release 1.8.15

This section lists interface-level changes and other user-visible changes in behavior in the transition from HDF5 Release 1.8.15 to Release 1.8.16.

New and Changed Functions, Classes, Subroutines, Wrappers, and Macros

In the C Interface (main library)

New HDF5 Plugin Interface (H5PL)

A new HDF5 Plugin Interface (H5PL), enabling programmatic control of dynamically loaded plugins, was introduced at HDF5 Release 1.8.15. This interface was only partially documented at that time, but more complete documentation is now available:

• “Dynamic Plugins in HDF5” in Advanced Topics in HDF5
• “H5PL: Plugin Interface” in the HDF5 Reference Manual
  • H5PLset_loading_state
  • H5PLget_loading_state

The following new C function has been added:

This function reports whether the linked version of the HDF5 Library was built with the thread-safety feature enabled.

• H5is_library_threadsafe

The following flag has been removed:

H5F_ACC_DEBUG flag for H5Fopen/create
 
The flag H5F_ACC_DEBUG was used to provide extra debugging information for HDF Library developers. This flag and the underlying functionality have been removed from the library due to disuse. The symbol remains defined since it was visible in H5Fpublic.h, but it has been set to zero (0) and has no effect anywhere in the library.

• H5Fopen

In the C++ Interface

The following features have been added:

• New class H5::ObjCreatPropList for the object creation property list class

The new class H5::ObjCreatPropList is derived from H5::PropList and is a baseclass of H5::DSetCreatPropList. Additional property list classes will be added to the library in future releases and some of those will be derived from H5::ObjCreatPropList.

• New wrappers for the C functions H5P[s/g]et_attr_phase_change and H5P[s/g]et_attr_creation_order

The following wrappers were added to the class H5::ObjCreatPropList for the respective C functions:

Library Configuration

Use of thread-safety with the HDF5 High-level Library has been declared unsupported in the build tools: Autotools and CMake.
 

The global lock used by the thread-safety mechanism is not raised to the high-level library level, making it possible that the library state could change if a context switch were to occur in a high-level library call. Because of this, the combination of thread-safety and the high-level library is officially unsupported by The HDF Group.

Though this combination has never been supported in HDF5, this was not enforced by the build systems. With this release, the combination has been explicitly flagged as unsupported in Autotools and CMake, the build systems used with HDF5.

The new unsupported declaration will cause an Autotools configure step to fail if --enable-threadsafe and --enable-hl are combined unless additional options are specified (see below). Since the high-level library is built by default, this means that these extra configuration options will need to be used any time --enable-threadsafe is selected.

To use Autotools to build an application with --enable-threadsafe, use one of the following approaches:

• Use --disable-hl to disable the high-level library. (Recommended)
• Use --enable-unsupported to build the high-level library with the thread-safety feature.

To use CMake to build an application with HDF5_ENABLE_THREADSAFE=ON, use one of the following approaches:

• Use HDF5_BUILD_HL_LIB=OFF to disable the high-level library. (Recommended)
• Use HDF5_ALLOW_UNSUPPORTED=ON to build the high-level library with the thread-safety feature.

Since this combination is unsupported, applications using it must be carefully tested for potential thread-safety failures.

Compatibility Notes and Report

Decoupled shared object version numbers (soname)

Shared object version numbers, soname, for HDF5 wrapper libraries, such as the C++ and Fortran libraries, have been decoupled from the shared object version number for the HDF5 library. In this and future releases, each library’s soname will be maintained on an individual basis according to the interface changes specific to each wrapper library.

Changed shared library interface version numbers (soname)

For HDF5 Release 1.8.16, the shared object version numbers have changed as follows.

Compatibility report for Release 1.8.16 versus Release 1.8.15

The following interface compatibility report provides a full list of the changed symbols:

API compatibility report for the HDF5 Library between 1.8.15 and 1.8.16 versions on x86

Release 1.8.15 of May 2015 versus Release 1.8.14

This section lists interface-level changes and other user-visible changes in behavior in the transition from HDF5 Release 1.8.14 to Release 1.8.15.

New and Changed Functions, Classes, Subroutines, Wrappers, and Macros

In the C Interface (main library)

The following new C functions have been added:

Memory allocation functions that use the library’s allocator.

• H5allocate_memory
• H5resize_memory

The following functions enable programmatic control of the loading of dynamic plugin filters in user applications:

• H5PLset_loading_state
• H5PLget_loading_state
  For preliminary documentation, see “New HDF5 APIs Provide Programmatic Control of Dynamic Plugins.”
  Final documentation is anticipated in July 2015.

In the C++ Interface

The following features have been added:

• New wrappers for the C functions H5Pset_libver_bounds and H5Pget_libver_bounds

The following wrappers have been added to class H5::FileAccPropList. The first sets the bounds on versions of the HDF5 Library format to be used when creating or writing objects; the second retrieves the current settings:

    void setLibverBounds(H5F_libver_t libver_low, H5F_libver_t libver_high) const;

    void getLibverBounds(H5F_libver_t& libver_low, H5F_libver_t& libver_high) const;

• New wrappers to retrieve the version of an object header

The following wrappers have been added to class H5::CommonFG to retrieve the object header version of an object in a file or group, given the object’s name.

    unsigned childObjVersion(const char* objname) const;

    unsigned childObjVersion(const H5std_string& objname) const;

• A new DataType constructor

A new DataType constructor takes a PredType object and invokes H5Tcopy to generate another datatype identifier from a predefined datatype.

The following features have been changed:

• Combined H5File::getObjCount overloaded methods

The following methods:

    ssize_t getObjCount(unsigned types) const;

    ssize_t getObjCount() const;

have been combined into the following:

    ssize_t getObjCount(unsigned types = H5F_OBJ_ALL) const;

• Deprecated constructors

The following two constructors of the classes AbstractDs, IdComponent, H5Location, and H5Object are no longer appropriate after the data member id was moved from IdComponent to the sub-classes in previous releases:

    <Classname>(const hid_t h5_id);

    <Classname>(const <Classname>& original);

The copy constructors have been no-ops and are removed in this HDF5 Release 1.8.15. The other constructors will be removed in HDF5 Release 1.10 and are expected to be removed from HDF5 Release 1.8.17 if their removal causes no problems.

In the Fortran Interface

The following Fortran 2003 API has been added:

h5tenum_insert_f

Operation of the new Fortran 2003 version of this API is more consistent with the operation of the C API than was the Fortran 90 version.

Users are strongly encouraged to use the Fortran 2003 API.

Several global variables have been added in the Fortran API. These global variables are equivalent in definition to the comparable C definitions:

H5G_UDLINK_F

H5G_SAME_LOC_F

H5O_TYPE_UNKNOWN_F

H5O_TYPE_GROUP_F

H5O_TYPE_DATASET_F

H5O_NAMED_DATATYPE_F

H5O_TYPE_NTYPES_F   

For parallel applications

A fix for issues encountered upon calling MPI_Finalize without having closed everything in an HDF5 file

An attribute destroy callback has been attached to MPI_COMM_SELF that shuts down the HDF5 Library when MPI_COMM_SELF is destroyed, that is, on MPI_Finalize. This should fix several issues that users see when they forget to close HDF5 objects before calling MPI_Finalize().

Compatibility Report and Comments

Compatibility report for Release 1.8.15 versus Release 1.8.14

API compatibility report for the HDF5 Library between 1.8.14 and 1.8.15 versions on x86

Changed shared library interface version number (soname)

In the C++ interface, two overloaded methods have been combined into a single method and one constructor has been deprecated.

Due to these changes, the shared library interface version number (soname) has been increased. For a full list of the changed symbols, see the interface compatibility report linked immediately above.

Release 1.8.14 of November 2014 versus Release 1.8.13

This section lists interface-level changes and other user-visible changes in behavior in the transition from HDF5 Release 1.8.13 to Release 1.8.14.

New and Changed Functions, Classes, Subroutines, Wrappers, and Macros

In the main library C Interface

No new C functions have been added.

The behavior of the following C function has been changed:

The function H5Pset_core_write_tracking has been modified to enforce the limitation that the value of the page_size parameter cannot equal 0 (zero):

• H5Pset_core_write_tracking

The following performance optimization has been implemented in the Parallel HDF5 library:

The algoritm for writing chunk fill values for new datasets has been optimized to write out all chunk fill values collectively in a single MPI-IO call. This was previously done independently by rank 0 (zero) one block at a time. This optimization should produce a significant performance improvement when creating chunked datasets in parallel, most notably when chunk dimensions are relatively small. This optimization will be evident in use of the following function:

• H5Dcreate

In the high-level library C Interface

High-level HDF5 interfaces now ensure that strings are null-terminated and will not overflow a buffer.

In several high-level functions, the type from the file was previously re-used as the memory type and no check is made to ensure that a string was actually null-terminated.

All high-level functions now check for NULL pointers; verify that a received a string is null-terminated; and verify that the string will not overflow the buffer. The minimum length of the buffers is now used in strncmp to avoid overflow.

In the main library C++ Interface

No new C++ methods have been added.

The following changes have been made in the C++ interface:

Changed defaults

• Default value of class member id:
  The data member id in several classes that represent HDF5 objects are now initialized to H5I_INVALID_ID.
• Default value of a PropList member id:
  The data member id in class PropList is now initialized to H5P_DEFAULT.
• In HDF5 Release 1.8.13 and earlier, the above were initialized to 0 (zero).

Changed file access flags

• The flag H5F_ACC_CREAT has been removed from the C++ interface.

In the main library Fortran Interface

No new Fortran subroutines have been added.

Changed Fortran INTEGER parameter types:

Types of the following Fortran parameter constants have been changed from INTEGER to INTEGER(HID_T):

    H5FD_CORE            H5FD_MULTI

    H5FD_FAMILY          H5FD_SEC2

    H5FD_LOG             H5FD_STDIO

    H5FD_MPIO       

Other internal int types have been changed to hid_t, but this change is expected to be transparent to the user.

Compatibility Report and Comments

Compatibility report for Release 1.8.14 versus Release 1.8.13

API compatibility report for the HDF5 Library between 1.8.13 and 1.8.14 versions on x86

Changed shared library interface version number (soname)

To increase the maintainability of HDF5, an architectural change has been made that required renaming several public symbols in H5Ppublic.h.

Due to these changes, the shared library interface version number (soname) has been increased. For a full list of the changed symbols, see the interface compatibility report linked immediately above.

Release 1.8.13 of May 2014 versus Release 1.8.12

This section lists interface-level changes and other user-visible changes in behavior in the transition from HDF5 Release 1.8.12 to Release 1.8.13.

New and Changed Functions, Classes, Subroutines, Wrappers, and Macros

In the C Interface (main library)

The following new C functions have been added:

To free memory allocated by HDF5 function calls:

• H5free_memory
  This function should be used to free memory that has been allocated by HDF5 API calls such as H5Tget_member_name and H5Pget_class_name.

The primary value for this call is on Windows systems, where it is common for application code and the HDF5 Library to be using different C run-time libraries (CRT). Using this new call ensures that the same CRT handles both the allocation and free.

This function can also be useful in any case where the library uses a different memory manager than the application, such as when a debug memory manager is in use or when the HDF5 Library is wrapped for use in a managed language like Python or Java.

New configuration property for the CORE driver:

• H5Pset_core_write_tracking
H5Pget_core_write_tracking
  With this property, the CORE driver, H5Pset_fapl_core, can be configured to track dirty regions in the file and write out only the changed regions on flush or close operations. Additionally, a page aggregation size can be set that will aggregate small writes into larger writes. For example, setting a 1 mebibyte (1 MiB) page aggregation size will logically partition the the in-memory file into 1 MiB pages that will be written out in their entirety if even a single byte is dirtied.

The following C functions have been modified:

• H5Rget_name
  If the name parameter is passed as NULL, then the size parameter is ignored and the function returns the size of the buffer required to read the name (not including the NULL terminator).
• H5Zfilter_avail
  This function has been updated to correctly identify dynamically loaded filters. If a filter is not found among registered filters, the function now checks for dynamically loaded filters.

In the C++ Interface

The following new features have been added:

Wrappers to the class H5Object to get an object’s name:

    ssize_t getObjName(char *obj_name, size_t buf_size = 0)

    ssize_t getObjName(H5std_string& obj_name, size_t len = 0)

    H5std_string getObjName()

Wrappers to the class H5CommonFG to get a child object’s type from a group or file:

    H5O_type_t childObjType(const H5std_string& objname)

    H5O_type_t childObjType(const char* objname)

    H5O_type_t childObjType(hsize_t index,

        H5_index_t index_type=H5_INDEX_NAME,

        H5_iter_order_t order=H5_ITER_INC, const char* objname=".")

Wrappers to the class DSetMemXferPropList for setting or getting a transform property list:

    DSetMemXferPropList(const char* expression);

    void setDataTransform(const char* expression)

    void setDataTransform(const H5std_string& expression)

    ssize_t getDataTransform(char* exp, size_t buf_size=0)

    H5std_string getDataTransform()

Wrapper to CompType for setting the size of a compound datatype:

    void setSize(size_t size)

Overloaded functions to provide prototypes that declare constant arguments const:

    DataSet::fillMemBuf

    DataSet::getVlenBufSize

    DataSpace::extentCopy

    DataType::commit

    FileAccPropList::setSplit

    H5File::getVFDHandle

Additional overload to the class H5Location to get a comment as a char*:

    ssize_t getComment(const char* name, size_t buf_size, char* comment) 

Additional overloads to the class Attribute to get an attribute’s name for convenience:

    ssize_t getName(char* attr_name, size_t buf_size=0)

    ssize_t getName(H5std_string& attr_name, size_t buf_size=0)

In the Fortran Interface

The following new Fortran subroutines have been added:

Fortran2003 subroutines:

The following Fortran subroutine has been changed:

• h5pset_chunk_cache_f
  The values of the constants H5D_CHUNK_CACHE_NSLOTS_DFLT_F and H5D_CHUNK_CACHE_NBYTES_DFLT_F have been changed to INTEGER(KIND=size_t).

Other New Features

Parallel I/O support:

Parallel I/O support has been enhanced to allow collective I/O on point selections.

Thread safety (Windows only)

The thread-safe HDF5 library no longer leaks thread-local storage resources on Windows with Win32 threads. This cleanup can only be performed when the library is built as a shared library, so a thread-safe HDF5 static library with Win32 threads is no longer supported.

This change affects only Windows environments.

Also see “Build and Configuration” below.

Command-line Tools with Changed Behavior

h5repack

h5repack has been updated to correctly handle dynamically loaded filters.

Build and Configuration

Thread safety

When configuring a thread-safe HDF5 Library with --enable-threadsafe, it is no longer necessary to specify --with-pthreads if the Pthreads library is in a standard location.

Removed Functions and Wrappers

The MPI-POSIX driver has been removed. The following C functions and the corresponding Fortran subroutines and C++ wrappers therefore are no longer included in the HDF5 distribution:

• H5Pset_fapl_mpiposix
• H5Pget_fapl_mpiposix

Applications performing parallel I/O should use the MPI-IO driver, H5Pset_fapl_mpio.

Release 1.8.12 of November 2013 versus Release 1.8.11

This section lists interface-level changes and other user-visible changes in behavior in the transition from HDF5 Release 1.8.11 to Release 1.8.12.

New and Changed Functions, Classes, Subroutines, Wrappers, and Macros

In the C Interface (main library)

The following C functions have been modified:

• H5Zunregister now checks for open objects using a filter before allowing the filter to be unregistered.
• H5Dscatter and H5Dgather signatures have changed slightly.
  The src_buff parameter type is now 'const void *'  (previously: 'void *').

In the C++ Interface

The following new C++ class has been added:

H5::H5Location

The class H5::H5Location has been added as a base class of H5File and H5Object. It represents the location concept in the C library, where an identifier of an HDF5 object or an HDF5 file being passed in as a loc_id parameter.

The following member functions and their overloaded versions have been moved from various subclasses into the base class H5Location:

The following wrappers for C functions have been added:

H5Location::getRefObjType

Corresponding C function: H5Rget_obj_type2

Retrieves the type of the object that an object reference points to.

H5Location::attrExists

Corresponding C function: H5Aexist

Determines whether a given attribute exists.

H5Location::setComment

Two overloaded versions of H5Location::setComment have been added to take "." in lieue of the name of the object.

In the classes DataSet, DataType, and Group, the following constructors have changed as follows:

New Command-line Tool Options and Option Parameters

h5dump

h5dump has a new option for identifying objects by a full or partial path:
   -NP
   --any-path=P
 

The h5dump attributes-only option, -A or --only-attr, now accepts an optional parameter value of 0 (zero):
   -A 0
   --only-attr=0
Specifying this value has the effect of reversing the role of the option to display everything except attributes.
 

h5repack

The h5repack option -f, --filter has a new parameter, UD, to enable the use of user-defined filters:
   -f UD=<filter_parameters>
   --filter=UD=<filter_parameters>
 

h5stat

h5stat has three new options for setting print thresholds:
   For attributes:
      -aN
      --attribute=N
 
   For links in a group:
      -lN
      --links=N
 
   For dimension sizes:
      -mN
      --dims=N

Build and Configuration

CMake and Autotools configuration

A new configuration option can be used to change the default plugin path:

CMake configuration

CMake builds of HDF5 now create *.so.{lt_version} files with the same version as configure.

Autotools configure flag

The configure flag FFLAGS has been renamed to FCFLAGS.

Compile Scripts with Changed Behavior

h5cc and h5pcc

h5c++

h5fc and h5pfc

These compile scripts have been modified to change the default behavior to link to shared libraries in environments where HDF5 has been configured with --disable-static.

Command-line Tools with Changed Behavior

h5dump

h5dump output now displays
    USER_DEFINED_FILTER
where it previously displayed UNKNOWN_FILTER.
 

h5dump now correctly exports subsetted data to a file using the -o, --output option.

Release 1.8.11 of May 2013 versus Release 1.8.10

This section lists interface-level changes and other user-visible changes in behavior in the transition from HDF5 Release 1.8.10 to Release 1.8.11.

New and Changed Functions and Subroutines

The following new high-level C function has been added:

• H5DOwrite_chunk

This function writes a data chunk directly into a file, bypassing hyperslab selection, data conversion, and the filter pipeline. The user must be careful with the function and clearly understand the I/O process of the library. See “Direct Chunk Write” for additional information.

H5DOwrite_chunk is the first function in HDF5’s new high-level “HDF5 Optimized Functions” library.

The following new C functions have been added:

• H5Dscatter
• H5Dgather

These functions scatter data to and gather data from a selection within a memory buffer.

The following new Fortran subroutines have been added:

Fortran90 subroutines:

Fortran2003 subroutines:

New Feature: Dynamically Loaded Filters

HDF5 now detects and dynamically loads external filters, reducing the need for an application to register custom filters or for a developer building on HDF5 to compile a custom filter into a customized HDF5 distribution.

See “HDF5 Dynamically Loaded Filters” (PDF only) for further information.

New Command-line Tool Option

h5dump and h5import

h5dump has a new option to output the DDL structure of a file or object:
   -O<file_name>
   --ddl=<file_name>
[‘-O’ above is ‘dash-uppercase-o’.]

h5import can now take the output of
   h5dump -O<ddl_file_name> -o<data_file_name>
directly as input files.
See “Using h5dump to create input for h5import” in the h5import reference manual entry.

New Configuration and Build Tool

cmakehdf5

This new build command script is similar to buildhdf5 and is available in the bin/ directory of the distributed source code.

For HDF5, the CMake minimum is now 2.8.10.

Function, Subroutines, and Feature with Changed Syntax or Behavior

The return value of the following high-level C function has changed:

• H5DSget_scale_name

This function has been changed to not include the NULL terminator in the returned size of of the dimension scale name (bug fix).

In the Fortran subroutines

• h5pset_external_f and
• h5pget_external_f

the type of the offset parameter has changed to INTEGER(KIND=OFF_T) to support 8-byte integers, matching the C type definition of off_t.

The HDF5 Library now supports data conversion from enumeration to integer and floating-point numeric datatypes.

Command-line Tools with Changed Behavior

h5diff

When comparing two files or objects, h5diff now recognizes a unique extra attribute attached to an object as a difference and returns with an exit code of 1.

Previously, h5diff did not recognize the extra attribute as a difference.

h5ls

The content of the h5ls --help output has been revised.

h5dump

h5dump has been updated to display the compression ratio for user-defined filters.

In h5dump output, UNKNOWN_FILTER has been changed to USER_DEFINED_FILTER.

Removed Functions and Wrappers

The following C functions and the corresponding C++ wrappers have been removed:

• H5Pset_dxpl_multi
• H5Pget_dxpl_multi
   
• H5::DSetMemXferPropList:setMulti
• H5::DSetMemXferPropList:getMulti

Release 1.8.10 of November 2012 versus Release 1.8.9

This section lists interface-level changes and other user-visible changes in behavior in the transition from HDF5 Release 1.8.9 to Release 1.8.10.

New and Changed Functions and Subroutines

The following new C function has been added:

• H5Pget_mpio_no_collective_cause

The following new Fortran subroutine has been added:

• h5pget_mpio_actual_io_mode_f

The syntax of the following high-level C function has changed:

• H5TBAget_fill
  This function’s return type has been changed to h5tri_t. A return value of 1 indicates that a fill value is present, 0 indicates that no fill value is present, and a negative value indicates an error. (The former return type was herr_t.)

Note that H5TBAget_fill and a companion function H5TBAget_title, both in the HDF5 Table (H5TB) high-level API, are undocumented. These functions will be added to the HDF5 Reference Manual shortly after HDF5 Release 1.8.10.

Changed Command-line Tool

h5import has been updated to accept an input file created by h5dump.

Release 1.8.9 of May 2012 versus Release 1.8.8

This section lists interface-level changes and other user-visible changes in behavior in the transition from HDF5 Release 1.8.8 to Release 1.8.9.

New and Changed Functions

A new high level C function and Fortran subroutine were added to HDF5 Lite (H5LT) to determine whether an HDF5 path is correct and resolves to a valid HDF5 object:

• H5LTpath_valid
• h5ltpath_valid_f

The new file image operations feature consists of the following functions and their associated callbacks, struct, and ENUM. This feature enables an application to load a file into memory (as a file image) and to operate on that file image without the overhead of disk I/O. This feature provides the following functions:

For the callbacks, struct, and ENUM, see H5Pset_file_image_callbacks.

Use of this feature is described in “HDF5 File Image Operations” (PDF).
 

The following functions were modified or added to the HDF5 Library to allow an application to control the operation of copying committed datatypes with H5Ocopy:

Function with changed interface:

• H5Pset_copy_object

New flag for use with H5Pset_copy_object:

• H5O_COPY_MERGE_COMMITTED_DTYPE_FLAG

Function with changed behavior:

• H5Ocopy
  This function’s behavior is changed, but only with the use of the new flag, H5O_COPY_MERGE_COMMITTED_DTYPE_FLAG.

New functions and callback function:

Use of this capability is described in “Copying Committed Datatypes with H5Ocopy” (PDF).
 

The following C functions and Fortran subroutines were added to provide a mechanism to ensure sequential consistency in parallel environments using MPI I/O:

Use of this capability is described in “Enabling a Strict Consistency Semantics Model in Parallel HDF5” (PDF).
 

The following function was added at Release 1.8.5 but was not documented at that time. It is mentioned here for those who may have missed its introduction:

• H5Oexists_by_name

New Fortran Subroutines

The following Fortran subroutines have been added in this release:

• h5ltpath_valid_f
• h5ocopy_f
• h5fset_mpi_atomicity_f
• h5fget_mpi_atomicity_f

Where a subroutine is part of a new HDF5 feature, that feature is described above.

Fortran Subroutine with Changed Behavior

The content of the buffer returned by the following Fortran subroutine has changed as noted:

• h5ltget_attribute_string_f
  If the returned buffer requires padding, h5ltget_attribute_string_f now employs space padding; this buffer was previously returned with a C NULL terminator.

Command-line Utilities with New Options and/or Changed Behavior

h5repack has one new option and improved performance under certain circumstances:

• ‐Mn, ‐‐metadata_block_size=n
  Sets the metadata block size in the output file.
   
• Performance is improved when repacking large chunked datasets (for example, when dataset size exceeds 128 MB).

h5stat has one new option:

• ‐S, ‐‐summary
  Displays a summary of file space usage for a file.

h5dump has one new option, a new capability, and updated output:

• ‐‐no-compact-subset
  Disables compact subsetting to allow the left-hand square bracket character ( [ ) in a dataset name.
   
• The files parameter now accommodates wildcards. With this change, h5dump command-line options can be applied across multiple files without listing the files individually.
   
• h5dump output has been updated for this release to improve compliance with the HDF5 DDL specification and to improve readablilty. This output is now fully compliant with the HDF5 DDL specification, but these changes may affect some user scripts:
  • Whitespace has been modified.
  • Display errors, such as misplaced brackets, have been fixed.
  • When printing superblock content, user block content is now properly displayed within the superblock.

Release 1.8.8 of November 2011 versus Release 1.8.7

This section lists interface-level changes and other user-visible changes in behavior in the transition from HDF5 Release 1.8.7 to Release 1.8.8.

New C Functions

Two new parallel I/O functions enable an application to query whether or how a collective I/O operation actually completed:

• H5Pget_mpio_actual_chunk_opt_mode
• H5Pget_mpio_actual_io_mode

Updated Fortran Interface, including Fortran 2003 Features

The HDF5 Fortran interface has been extended and upgraded to Fortran 2003 for this release.

See “Configure and Build Changes” below for the configure options to use when building HDF5 with Fortran 2003 enabled.

Features enabled in this upgrade are described in New Features in the HDF5 Fortran Library: Adding Support for the Fortran 2003 Standard (PDF only). In general, the links below are to technical descriptions (reference manual entries, for example) of specific interfaces.

Terminology: If the Fortran compiler in use is Fortran 2003 compliant and the installed HDF5 Library was configured using both the --enable-fortran and --enable-fortran2003 flags, the resulting HDF5 Fortran Library is referred to below as a Fortran 2003 environment. Without either of the Fortran 2003 compliant compiler or the --enable-fortran2003 flag, the resulting HDF5 Fortran Library is referred to below as a Fortran 90 environment.

New Fortran 2003-only subroutines
New subroutines available only in Fortran 2003 environments:

• h5dvlen_reclaim_f
• h5eset_auto_f
• h5literate_by_name_f
• h5literate_f
• h5ovisit_f
• h5oget_info_by_name_f
• h5tconvert_f

Subroutines with Fortran 90 versions and extended features in Fortran 2003 environments
Subroutines in this section have extended support in Fortran 2003 environments, but are new or unchanged in Fortran 90 environments.

All existing Fortran 90 subroutines, including those not mentioned below, are available in both Fortran 90 and Fortran 2003 environments.

Subroutines with support for the derived type C_PTR in Fortran 2003 environments:

• h5pget_f
• h5pget_fill_value_f
• h5pinsert_f
• h5pregister_f
• h5pset_f
• h5pset_fill_value_f
• h5rcreate_f
• h5rdereference_f
• h5rget_name_f
• h5rget_object_type_f

Subroutines with support for the derived type C_PTR and a changed signature in Fortran 2003 environments:

• h5aread_f
• h5awrite_f
• h5dread_f
• h5dwrite_f

Subroutine with additional optional parameters in Fortran 2003 environments:

• h5pcreate_class_f

New and updated Fortran 90 subroutines
New Fortran 90 subroutines:

• h5pset_nbit_f
• h5pset_scaleoffset_f

Updated Fortran 90 subroutines:

• h5open_f
• h5close_f *
• h5check_version_f
• h5get_libversion_f
• h5garbage_collect_f
• h5dont_atexit_f

* h5close_f has been modified in this release to close only the HDF5 Fortran Library interface; it no longer closes the underlying HDF5 Library.

New Fortran utility functions and derived types
New Fortran utility functions:

• h5offsetof         Available only in Fortran 2003 environments.
• h5kind_to_type     Available in either Fortran environment.

New Fortran derived types in Fortran 2003 environments:

• hvl_t              Described in New Features.
• h5o_info_t         See h5ovisit_f.

New high level Fortran interface
New Fortran subroutines in the HDF5 Dimension Scale high-level interface, H5DS:

• h5dsset_scale_f
• h5dsattach_scale_f
• h5dsdetach_scale_f
• h5dsis_attached_f
• h5dsis_scale_f
• h5dsset_label_f
• h5dsget_label_f
• h5dsget_scale_name_f
• h5dsget_num_scales_f

These subtroutines are available in both Fortran 90 and Fortran 2003 environments.

C Functions with Changed Capability

H5Tcreate now supports fixed-length and variable-length string types.

Driver Changes on Windows Systems

Changed behavior:

HDF5’s Windows driver has been modified in this release to be a wrapper of the POSIX-compliant SEC2 driver. This change should be transparent to all user applications.

New default driver:

As of this release, the default driver on Windows systems is changed to SEC2; it had previously been the Windows driver.

If you wish to use the Windows driver in an application, it remains fully available. In such cases, the driver must be set explicitly with a H5Pset_fapl_windows call.

Command-line Utilities with Changed Behavior

h5jam now checks the file that is to be inserted into the user block and does not allow the insertion if it is an HDF5 file. This is necessary because an HDF5 file in the user block will make the original HDF5 portion of the file inaccessable.

h5diff with the --delta option reports two NaN values as equal regardless of the type of NaN (as described in the reference manual entry).

h5diff, when comparing a file to itself, now reports no differences.

Configure and Build Changes

configure now uses the same flags and symbols in its tests as are used to build the library.

To build HDF5 with the Fortran 2003 interfaces requires the use of two configure options:
    --enable-fortran  
    --enable-fortran2003  
Note that building the Fortran 2003 interfaces requires a Fortran 2003-capable compiler and that --enable-fortran2003 cannot be used alone.

The --enable-h5dump-packed-bits configure option has been removed. The code that this option enabled is now always compiled into h5dump.

When building on Linux systems, the HDF5 Library now links with the bsd_compat library.

Parallel Library and Configuration Changes

The parallel HDF5 library now always compiles code to take advantage of MPI functionalities that allow for the use of complex derived datatypes during IO and that allow for collective IO when one or more processes do not contribute to the operation.

This was previously conditionally compiled into the library and controlled by configure via the hdf5_cv_mpi_special_collective_io_works and hdf5_cv_mpi_complex_derived_datatype_works cache values. These values were preset in the config/* files based on the compiler and/or system or could be set on the configure line. Support for these cache values has been removed and they no longer have an effect on the compilation of the use of these MPI functionalities.

Release 1.8.7 of May 2011 versus Release 1.8.6

This section lists interface-level changes and other user-visible changes in behavior in the transition from HDF5 Release 1.8.6 to Release 1.8.7.

New C Functions and Macros

Three new functions enable the caching of files opened through external links. This cache can improve the performance of external links in heavy use cases:

• H5Pset_elink_file_cache_size
• H5Pget_elink_file_cache_size
• H5Fclear_elink_file_cache

 
Two new macros enable compile-time inclusion or exclusion of code depending on the version of the HDF5 Library against which an application is to be linked:

• H5_VERSION_GE
• H5_VERSION_LE

C Functions with Changed Capability

HDF5 now allows the size of any dataspace dimension to be 0 (zero). This was previously allowed only if the maximum size of the dimension was unlimited. Though their signatures have not changed, the range of valid parameter values is affected for the following functions:

• H5Screate_simple
• H5Sset_extent_simple
• H5Pset_external

Note that no data can be written to a dataset in which the size of any dimension is set to zero.
 
In the logging file driver, implementation of the following flags has been completed: H5FD_LOG_TIME_OPEN, H5FD_LOG_TIME_READ, H5FD_LOG_TIME_WRITE, and H5FD_LOG_TIME_SEEK
Two new flags have been added: H5FD_LOG_NUM_TRUNCATE and H5FD_LOG_TIME_STAT.

• H5Pset_fapl_log

 
HDF5 now blocks committing a datatype that cannot hold any data. This currently includes compound datatypes with no fields and enumerated datatypes with no members.

• H5Tcommit1
• H5Tcommit2
• H5Tcommit_anon

HDF5 has long blocked creating a dataset or attribute with such a datatype.

Fortran Subroutines with Changed Capability

Several h5ltmake_dataset*_f and h5ltread_dataset*_f subroutines have been modified to allow them to create or read arrays of up to seven dimensions. They had previously been limited to three dimensions.

 
h5tbget_field_info_f has a new maxlen_out parameter. This parameter is optional.

Command-line Utilities with New Options

h5diff has a new verbose with levels option to display additional attribute information:

• -vn, --verbose=n

 
h5dump has one new option to enable reporting of the HDF5 Library’s error stack:

• --enable-error-stack

Command-line Utility with Changed Option Name

h5ls has one changed option name:

• --enable-error-stack replaces --error.

The --error option is deprecated but remains available.

Command-line Utilities with Changed Behavior

Attribute comparison with h5diff has been corrected to compare all attributes with common names when comparing objects. Previously, h5diff compared attributes correctly only when two objects had the same number of attributes and all attribute names were identical; if there was either a value or name difference between two attributes, subsequent attributes were not compared.

h5diff --use-system-epsilon now employs the formula '|a - b|' instead of '|a - b| / b'.

h5copy now accepts the same file as the source and target file; this enables object copying within a file.

h5dump now displays reference types as described in DDL in BNF for HDF5:

Configure and Build Changes

Configure now generates Makefiles that build in silent make mode by default. In this mode, compile and link lines are significantly simplified for clarity. You can opt out of this default with either of the following approaches:

• Use the --disable-silent-rules flag at configure time to override the default and view actual compile and link lines during the build.
• Use the make command with the V=1 option to run a verbose make.

The new configure option --enable-unsupported can be used to stop configure from preventing the use of unsupported configure option combinations. For example, use of this option enables building HDF5 with the unsupported and untested configurations of C++ in a parallel environment or Fortran with a threadsafe library.

• WARNING:
  Use   --enable-unsupported   at your own risk!
  This option may result in a library that does not compile or does not run as expected.

Parallel HDF5

mpicc and mpif90 are now the default C and Fortran compilers on Linux systems when --enable-parallel is specified but no $CC or $FC is defined.

Release 1.8.6 versus Release 1.8.5, February 2011

This section lists interface-level changes and other user-visible changes in behavior in the transition from HDF5 Release 1.8.5 to Release 1.8.6.

C Functions with Additional Capability

H5Tset_order and H5Tget_order can now be used with all datatypes. See the related note regarding H5T_ORDER_MIXED immediately below.

ENUM with New Member

H5T_order_t, an ENUM used to set or indicate datatype endianness, includes a new member:

     H5T_ORDER_MIXED

The function H5Tget_order returns this value when called on a compound datatype whose members are not all of the same endianness.

Command-line Utilities with New Options

h5diff has one new option:

• --exclude-path

h5ls and h5diff have two new options:

• --follow-symlinks
• --no-dangling-links

Command-line Utilities with Changed Behavior

h5diff now compares member objects and groups recursively when two files or groups are specified to be compared.

h5ls now displays object and attribute names exactly as stored in the file rather than interpreting them for output. For example, if an attribute is named \ttemp in the file, h5ls will output that name as \ttemp rather than converting the leading \t to a tab.

h5repack can now convert a dataset to compact layout.

Compiler Script Arguments and Environment Variables

h5cc, h5fc, h5c++, h5pcc, and h5pfc arguments have been expanded to enable the user to add compiler and linker flags that will take precedence over the flags from the HDF5 build.

The arguments CPPFLAGS, CFLAGS, LDFLAGS, and LIBS have been duplicated with the prefix H5BLD_ to put the flags and paths from the HDF5 build in the correct places and to allow the script user to add entries in CPPFLAGS, CFLAGS, LDFLAGS, and LIBS that will take precedence over those from the HDF5 build. Changes to these entries can be made persistent by editing CFLAGSBASE, CPPFLAGSBASE, LDFLAGSBASE, and LIBSBASE near the top of the script. If the change is to be temporary, the user can set HDF5_CFLAGS, HDF5_CPPFLAGS, HDF5_LDFLAGS, or HDF5_LIBS in the environment.

The new order of arguments for these scripts is as follows:

        $CLINKER 

        $H5BLD_CPPFLAGS 

        $CPPFLAGS 

        $H5BLD_CFLAGS 

        $CFLAGS 

        $LDFLAGS 

        $clibpath 

        $link_objs 

        $LIBS 

        $link_args 

        $shared_link

Thread Safety on Windows

This release adds support for thread safety on Windows using the Windows threads library. See the file RELEASE.txt in the distributed HDF5 source code (hdf5/release_docs/RELEASE.txt) for details.

Parallel HDF5

The Parallel HDF5 build process has changed to use mpiexec instead of mpirun.

Release 1.8.5 versus Release 1.8.4, June 2010

This section lists interface-level changes and other user-visible changes in behavior in the transition from HDF5 Release 1.8.4 to Release 1.8.5.

New C Function

The following function was added to the HDF5 Library at this release, but was not documented at that time:

• H5Oexists_by_name

(This note added in November 2011, shortly following Release 1.8.8.)

C Functions with Additional Capability

The following functions have been modified to accommodate filters set on a group creation property list:

Related to H5Zregister, the calling protocol for the can_apply and set_local callback functions has been extended to accommodate the use of filters on group creation property lists.

New C++ Member Function and Overloaded Member Functions

The following C++ member function is new in this release:

The overloaded forms of the following C++ member functions are new in this release:

Command-line Utility with New Options

h5diff has two new options:

• --follow-links
• --no-dangling-links

Fortran Subroutines with Changed Interface

The link type parameter values associated with the following Fortran subroutines have changed in this release:

• h5lget_info_f
• h5lget_info_by_idx_f

Valid values for the parameter link_type have changed to the following:
     H5L_TYPE_HARD_F
     H5L_TYPE_SOFT_F
     H5L_TYPE_EXTERNAL_F
     H5L_TYPE_ERROR_F
These values previously began with the string 'H5L_LINK_'.

CMake

This release includes an adaptation enabling HDF5 builds with CMake. This early-stage adaptation is distributed to provide an opportunity for early access and experimentation; the CMake-related files should not be viewed as final and may change before the next release.

While the initial development effort has been focussed on Microsoft Windows platforms, the HDF5 Library has been successfully built with CMake on Linux and Mac OS X.

See the file CMake.txt in the distributed HDF5 source code (hdf5/release_docs/CMake.txt) for details.

Release 1.8.4 versus Release 1.8.3, November 2009

This section lists interface-level changes and other user-visible changes in behavior in the transition from HDF5 Release 1.8.3 to Release 1.8.4.

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-libinfo flag during configure.

New Fortran Subroutine and Constant

The following Fortran subroutine is new in this release:

h5oopen_by_addr_f

The following Fortran constant, corresponding to the C constant H5T_ORDER_NONE, has been added in this release:

H5T_ORDER_NONE_F

New C++ Member Functions

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.

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.

Fortran Subroutines with Changed Syntax

The following Fortran subroutines have changed syntax in this release:

• h5lget_info_f

The type of the parameter address has changed from INTEGER to INTEGER(HADDR_T).
(This note added on 13 January 2010.)

• h5lget_info_by_idx_f

h5lget_info_by_idx_f (loc_id, group_name, index_field, order, n, &
     link_type, f_corder_valid, corder, cset, address, val_size, &
     hdferr, lapl_id)

The parameters link_type, address, and val_size have been added; the parameter data_size has been removed.

Tools 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. Prior default behavior was to use an epsilon internally defined in HDF5.

This option has no short form.

h5dump has one new option and the behavior of another set of options has changed:

-R or --region

With this option, h5dump prints the data pointed to by a region reference. Without this option, h5dump prints only the reference.

Usage of the subsetting parameters has changed. All of START, STRIDE, COUNT, and BLOCK now have default values. If those defaults are satisfactory, h5dump no longer requires that all four be specifiespecified when subsetting a dataset.

Changed Library Configuration

The following configuration flag is new with this release:

--disable-embedded-libinfo

This flag disables the embedding of HDF5 Library settings in an HDF5 executable.

Release 1.8.3 versus Release 1.8.2, May 2009

This section lists API-level changes and changes in behavior in the transition from HDF5 Release 1.8.2 to Release 1.8.3.

New Functions

C functions:

The following C functions are new for this release and are documented in the HDF5 Reference Manual.

Fortran Subroutines:

The following subroutines are new in this release:

h5dget_access_plist_f  
h5iis_valid_f  
h5pset_chunk_cache  
h5pget_chunk_cache  

Function with Changed Behavior

H5set_free_list_limits

The HDF5 Library now dynamically creates separate factory free lists to manage blocks of a fixed size; these blocks were previously managed within the blockfree lists. Factory free lists use the same settings as specified in H5set_free_list_limits for block free lists.

While the API has not changed, users may see both a performance boost and increased memory usage.

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 1.8.2 versus Release 1.8.1, November 2008

This section lists API-level changes and changes in behavior in the transition from HDF5 Release 1.8.1 to Release 1.8.2.

New Functions

C functions:

The following C functions are new for this release and are documented in the HDF5 Reference Manual.

Fortran Subroutine:

The following subroutine is new in this release:
     H5Tget_native_type_f

New C++ Wrappers

The following functions were added as wrappers for the C function H5Rdereference to replace the incorrect IdComponent::dereference():

        void H5Object::dereference(H5Object& obj, void* ref, 

                                   H5R_type_t ref_type=H5R_OBJECT)

        void H5Object::dereference(H5File& h5file, void* ref, 

                                   H5R_type_t ref_type=H5R_OBJECT)

        void H5Object::dereference(Attribute& obj, void* ref, 

                                   H5R_type_t ref_type=H5R_OBJECT)

The following constructors were added to create the associated objects by way of dereference:

        DataSet(H5Object& obj, void* ref, H5R_type_t ref_type=H5R_OBJECT)

        DataSet(H5File& file, void* ref, H5R_type_t ref_type=H5R_OBJECT)

        DataSet(Attribute& attr, void* ref, H5R_type_t ref_type=H5R_OBJECT)

        Group(H5Object& obj, void* ref, H5R_type_t ref_type=H5R_OBJECT)

        Group(H5File& obj, void* ref, H5R_type_t ref_type=H5R_OBJECT)

        Group(Attribute& attr, void* ref, H5R_type_t ref_type=H5R_OBJECT)

        DataType(H5Object& obj, void* ref, H5R_type_t ref_type=H5R_OBJECT)

        DataType(H5File& file, void* ref, H5R_type_t ref_type=H5R_OBJECT)

        DataType(Attribute& attr, void* ref, H5R_type_t ref_type=H5R_OBJECT)

Functions with Changed Syntax

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

C functions:

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 )

Changed Fortran Subroutines

The optional parameter mounted has been added to the following subroutines:

h5gget_info_f

h5gget_info_by_idx_f

h5gget_info_by_name_f     

Changed Data Structure

H5G_info_t

A mounted filed has been added to the H5G_info_t struct.

Tools with Changed Interface or Behavior

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 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.

h5repack

The following new options control the addition of user block data to an existing HDF5 file:

The following new options set parameters governing the tool’s use of 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 and h5ls

These tools now traverse external links when performing recursive traversals.

h5dump

Binary output now defaults to NATIVE with the '-b' option, optionally accepting NATIVE, FILE, BE, and LE.

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.

Changed Library Configuration

It is no longer necessary to manually set an SZIP library path in LD_LIBRARY_PATH when building HDF5 with shared SZIP libraries; configure will determine the correct path from the --with-szlib flag, prepending it to and exporting LD_LIBRARY_PATH.

Note that if an SZIP library path is set in a user-supplied LD_LIBRARY_PATH, in an existing script, for example, that does not necessarily need to be changed; configure will prepend the SZIP library path extracted from --with-szlib to the user-supplied LD_LIBRARY_PATH.

Release 1.8.1 versus Release 1.8.0

HDF5 Release 1.8.1 is a minor release with several bugfixes and optimizations and limited new features.

The most significant new feature is an expanded set of Fortran90 APIs, enabling essentially all new C library features of Release 1.8.0.

New Functions and Tools

C functions:

There are no new C functions for Release 1.8.1.

Fortran subroutines:

The following Fortran subroutines are new for Release 1.8.1 and are documented in the HDF5 Reference Manual.

h5acreate_f

h5acreate_by_name_f

h5adelete_by_idx_f

h5adelete_by_name_f

h5aexists_f

h5aexists_by_name_f

h5aget_create_plist_f

h5aget_info_f

h5aget_info_by_idx_f

h5aget_info_by_name_f

h5aget_name_by_idx_f

h5aget_storage_size_f

h5aopen_f

h5aopen_by_idx_f

h5aopen_by_name_f

h5arename_f

h5arename_by_name_f

h5dcreate_anon_f

h5dcreate_f

h5dopen_f

h5dset_extent_f

h5gcreate_anon_f

h5gcreate_f

h5gget_create_plist_f

h5gget_info_f

h5gget_info_by_idx_f

h5gget_info_by_name_f

h5gopen_f

h5lcopy_f

h5lcreate_external_f

h5lcreate_hard_f

h5lcreate_soft_f

h5ldelete_f

h5ldelete_by_idx_f

h5lexists_f

h5lget_info_f

h5lget_info_by_idx_f

h5lget_name_by_idx_f

h5lmove_f

h5olink_f

h5oopen_f

h5pget_attr_creation_order_f

h5pget_attr_phase_change_f

h5pget_char_encoding_f

h5pget_copy_object_f

h5pget_create_inter_group_f

h5pget_data_transform_f

h5pget_elink_prefix_f

h5pget_est_link_info_f

h5pget_fapl_direct_f

h5pget_link_creation_order_f

h5pget_link_phase_change_f

h5pget_local_heap_size_hint_f

h5pget_nlinks_f

h5pget_obj_track_times_f

h5pget_shared_mesg_index_f

h5pget_shared_mesg_nindexes_f

h5pset_attr_creation_order_f

h5pset_attr_phase_change_f

h5pset_char_encoding_f

h5pset_copy_object_f

h5pset_create_inter_group_f

h5pset_data_transform_f

h5pset_elink_prefix_f

h5pset_est_link_info_f

h5pset_fapl_direct_f

h5pset_libver_bounds_f

h5pset_link_creation_order_f

h5pset_link_phase_change_f

h5pset_local_heap_size_hint_f

h5pset_obj_track_times_f

h5pset_nbit_f

h5pset_nlinks_f

h5pset_scaleoffset_f

h5rget_name_f

h5sdecode_f

h5sencode_f

h5sextent_equal_f

h5tcommit_anon_f

h5tcommit_f

h5tcommitted_f

h5tcompiler_conv_f

h5tdecode_f

h5tencode_f

h5tget_create_plist_f

h5topen_f

C++ wrappers:

There are no new C++ wrappers for Release 1.8.1.

Functions and Tools with Changed Syntax

C functions with changed syntax:

There are no C functions with changed syntax in Release 1.8.1.

Fortran subroutines with changed syntax:

In the following Fortran subroutines, spos is a new parameter indicating the position of the sign bit:
     h5tset_fields_f(type_id, spos, epos, esize, mpos, msize, hdferr)
     h5tget_fields_f(type_id, spos, epos, esize, mpos, msize, hdferr)

Changed C++ wrappers:

• The class AbstractDS was moved out of H5Object.

The class Attribute now multiply inherits from IdComponent and AbstractDs; the class DataSet now multiply inherits from H5Object and AbstractDs.

In addition, data member IdComponent::id was moved into subclasses: Attribute, DataSet, DataSpace, DataType, H5File, Group, and PropList.

• IdComponent::dereference was incorrect; it was changed from:
       void IdComponent::dereference(IdComponent& obj, void* ref)
  to:
       void H5Object::dereference(H5File& h5file, void* ref)
     void H5Object::dereference(H5Object& obj, void* ref)

Tools with changed syntax:

• The command-line syntax of h5repack was changed in Release 1.8.0 to the following:
       h5repack [OPTIONS] in_file out_file

Since this would be imcompatible with existing user scripts, the original syntax has be re-enabled in this release:
     h5repack -i in_file -o out_file [OPTIONS]

h5repack now understands either syntax.

• An h5repack option to set the minimum number of links in indexed format was introduced in Release 1.8.0 as '-d min_indexed_links' or '--indexed=min_indexed_links'. In Release 1.8.1, the '-i' form has been changed to '-d' as follows:
       -d min_indexed_links
  or
       --indexed=min_indexed_links
• The command-line syntax of h5diff was changed in Release 1.8.0 to the following:
       h5diff [OPTIONS] file1 file2 [object1 [object2 ] ]

Tools with new options:

• h5dump

-m T  or  --format T   Sets format of floating point output

Changed Behavior or Output

Changed library behavior:

A 4GB limit on the size of dataset chunks is now properly enforced when a dataset is created.

The HDF5 Library now works more effectively with external links. Some valid external links that previously failed will now be properly recognized. See H5Lcreate_external.

C functions with changed behavior:

The behavior of H5Lcreate_external has changed as described immediately above.

Tools with changed behavior and changed output:

The h5dump -p option now prints the compression ratio if a compression filter is associated with a dataset.

h5dump now supports external links, displaying the target objects (datasets, groups, and named datatypes).

Tools with changed output:

Changed Library Configuration

The following configuration flag is new with this release:

--disable-sharedlib-rpath

Removed Patch Requirement

The patch that was required for Cygwin with HDF5 Release 1.8.0 has been rolled into this release and no longer needs to be applied by the user.

Release 1.8.0 versus Release 1.6.x

HDF5 Release 1.8.0 is a major release with several new features and a variety of bugfixes, optimizations, and portability enhancements.

See the document “What’s New in HDF5 1.8.0” for a high-level overview of the new functionality in this release. The following pages assume a familiarity with that overview.

This section provides details of the API-level changes that have been made in the transition to HDF5 Release 1.8.0 from the Release 1.6.x series.

API Compatibility Macros with Associated Renamed and New Functions

Release 1.8.0 introduces API compatibility macros designed to facilitate application migration. These macros are intended to facilitate developer management of a clean, step-by-step migration from an older HDF5 Library to the new release; they can also be used to enable older applications to use the new library without requiring that the application be rewritten. See API Compatibility Macros in HDF5 for a full description.

Macros are identified in reference manual function indexes by an italic typeface.

The new macros and the new and old functions to which they may be mapped are as follows:

(H5Dcreate and H5Dopen added to the above list in November 2010, prior to Release 1.8.6.)

New Functions and Tools

C functions:

The following C functions are new for Release 1.8.0 and, unless otherwise noted, are documented in the HDF5 Reference Manual.

Fortran subroutines:

New Fortran subroutines in the main library are not yet included for Release 1.8.0-beta.

See below for Fortran routines for High-Level HDF5 APIs.

C++ wrappers:

There no new C++ wrappers for Release 1.8.0-beta.

High Level C APIs:

H5LT: The following functions have been added to the HDF5 Lite (H5LT) API:

Two high-level C APIs are distributed for the first time with this release:
 

• H5PT, the HDF5 Packet Table interface
• H5DS, the HDF5 Dimension Scale interface

Full documentation for these interfaces can be accessed directly from the High Level APIs overview page.

The new functions included in the packet table (H5PT) high-level APIs are as follows:

The new functions included in the dimension scale (H5DS) high-level APIs are as follows:

High Level Fortan90 APIs:

Fortran90 subroutines are now available for the following high-level APIs:
     H5LT: HDF5 Lite
     H5IM: HDF5 Image
     H5TB: HDF5 Table

Tools:

h5stat

Deprecated and Deleted Functions

The following functions, subroutines and wrappers have been removed in this release:

C functions:

Several functions, subroutines, and wrappers are deprecated in this HDF5 release and may eventually be removed from the HDF5 distribution and from the HDF5 Reference Manual. A Release 1.6.x compatibility mode is provided enabling these and other Release 1.6.x compatibility features, but is available only if the HDF5 Library is configured with the default settings or with the flag --with-default-api-version=v16. Release 1.8.0 also provides macros that can be mapped selectively to 1.6.x and 1.8.0 function versions according to the needs of a user application. The backward compatibility mode is enabled in the Release 1.8.0 binaries distributed by NCSA. See API Compatibility Macros in HDF5 for full details.

 
Deprecated functions are marked in the function index at the beginning of each API section in the HDF5 Reference Manual.

Virtual File Driver Removed

The stream virtual file driver (H5FD_STREAM) have been removed in this release. This affects the functions H5Pset_fapl_stream and H5Pget_fapl_stream and the constant H5FD_STREAM.

This virtual file driver will remain available at http://hdf5-addons.origo.ethz.ch/. Note that as of this writing, this transition is still in progress; the necessary integration tools may not be available when HDF5 Release 1.8.0 first comes out.

Functions with New or Changed Symbols or Fixed Values

Symbols and preset values associated with the following functions, subroutines or wrappers have changed as noted.

C functions:

H5Tregister

Null is no longer a valid value for the parameter func.
 

H5Pget_filter_by_id

H5Pmodify_filter

H5Premove_filter

H5Pset_filter

H5Zfilter_avail

H5Zget_filter_info

Two new filter identifiers are available for the filter parameter:
    H5Z_FILTER_NBIT
    H5Z_FILTER_SCALEOFFSET
 

H5Pget_filter

Two new filter identifiers are available as the return value:
    H5Z_FILTER_NBIT
    H5Z_FILTER_SCALEOFFSET