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HDF5 2.0.0.50d6458
API Reference
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HDF5 2.0.0.50d6458
API Reference
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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:
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.
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.
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.
The interface compatibility report provides a full list of the changed symbols.
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.
The following are new C functions in this release:
| Function | Description |
|---|---|
| H5Pget_fapl_hdfs | Gets the information of the given Read-Only HDFS virtual file driver |
| H5Pget_fapl_ros3 | Gets the information of the given Read-Only S3 virtual file driver |
| H5Pset_fapl_hdfs | Sets up Read-Only HDFS virtual file driver |
| H5Pset_fapl_ros3 | Sets up Read-Only S3 virtual file driver |
The interface compatibility report provides a full list of the changed symbols.
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.
The interface compatibility report provides a full list of the changed symbols.
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.
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
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.
The following new C functions were added:
The following new C function was added:
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.
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
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.
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
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.
The following new C functions and environment variable enable setting a relative path for raw data files associated with datasets using external storage:
Functions:
Environment variable:
The following new functions have been added in the Packet Table (H5PT) high-level interface:
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:
An updated form of H5PTfree_vlen_readbuff reinstated as:
New member function added in DSetCreatPropList:
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.
The datamembers ArrayType::rank and ArrayType::dimensions have been removed. This is an implementation detail and should not affect applications.
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().Changed shared library interface version numbers (soname)
For HDF5 Release 1.8.17, the shared object version numbers have changed as follows.
| Library | Release 1.8.16 | Release 1.8.17 | Reason for Change |
|---|---|---|---|
| HDF5 C Library | 10.1.0 | 10.2.0 | Added APIs |
| HDF5 High-level C Library | 10.0.2 | 10.1.0 | Added APIs |
| C++ Library | 11.0.0 | 12.0.0 | Changes in existing APIs |
| High-level C++ Library | 11.0.0 | 11.1.0 | Added APIs |
| All others | 10.0.2 | 10.0.3 | Code changes that did not result in interface changes |
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
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 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:
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.
The following flag has been removed:
The following features have been added:
The following wrappers were added to the class H5::ObjCreatPropList for the respective C functions:
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:
–disable-hl to disable the high-level library. (Recommended) –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:
HDF5_BUILD_HL_LIB=OFF to disable the high-level library. (Recommended) 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.
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.
For HDF5 Release 1.8.16, the shared object version numbers have changed as follows.
| Library | Release 1.8.15 | Release 1.8.16 | Reason for Change |
|---|---|---|---|
| HDF5 Library | 10.0.1 | 10.1.0 | Added APIs |
| C++ Library | 10.0.1 | 11.0.0 | Changes in existing APIs |
| High-level C++ Library | 10.0.1 | 11.0.0 | Changes in existing APIs |
| All others | 10.0.1 | 10.0.2 | Code changes that did not result in interface changes |
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
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.
The following new C functions have been added: Memory allocation functions that use the library's allocator.
The following functions enable programmatic control of the loading of dynamic plugin filters in user applications:
For preliminary documentation, see New HDF5 APIs Provide Programmatic Control of Dynamic Plugins. Final documentation is anticipated in July 2015.
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.
The following Fortran 2003 API has been added:
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:
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().
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.
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.
The behavior of the following C function has been changed:
The following performance optimization has been implemented in the Parallel HDF5 library: The algorithm 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:
No new C++ methods have been added.
The following changes have been made in the C++ interface:
Changed defaults
In HDF5 Release 1.8.13 and earlier, the above were initialized to 0 (zero).
Changed file access flags
Changed Fortran INTEGER parameter types:
Types of the following Fortran parameter constants have been changed from INTEGER to INTEGER(HID_T):
Other internal int types have been changed to hid_t, but this change is expected to be transparent to the user.
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)
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.
The following new C functions have been added:
To free memory allocated by HDF5 function calls:
New configuration property for the CORE driver:
The following C functions have been modified:
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:
void DSetMemXferPropList(const char* expression) void setDataTransform(const char* 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::getVFDHandleAdditional 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)The following new Fortran subroutines have been added:
Fortran2003 subroutines:
The following Fortran subroutine has been changed:
Parallel I/O support:
Also see Build and Configuration below.
h5repack has been updated to correctly handle dynamically loaded filters.
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.
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:
Applications performing parallel I/O should use the MPI-IO driver, H5Pset_fapl_mpio.
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.
The following C functions have been modified:
const void * (previously: void *).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 - Retrieves the type of the object that an object reference points to.H5Location::attrExists - Determines whether an attribute with a given name exists.H5Location::setComment - Attaches a comment to an object.In the classes DataSet, DataType, and Group, the following constructors have changed as follows:
These constructors
DataSet(H5Object& obj, const void* ref, H5R_type_t ref_type = H5R_OBJECT); DataSet(H5File& h5file, const void* ref, H5R_type_t ref_type = H5R_OBJECT); DataSet(Attribute& attr, const void* ref, H5R_type_t ref_type = H5R_OBJECT); have changed to DataSet(const H5Location& loc, const void* ref, H5R_type_t ref_type = H5R_OBJECT); DataSet(const Attribute& attr, const void* ref, H5R_type_t ref_type = H5R_OBJECT);These constructors
DataType(H5Object& obj, const void* ref, H5R_type_t ref_type = H5R_OBJECT); DataType(H5File& h5file, const void* ref, H5R_type_t ref_type = H5R_OBJECT); DataType(Attribute& attr, const void* ref, H5R_type_t ref_type = H5R_OBJECT); have changed to DataType(const H5Location& loc, const void* ref, H5R_type_t ref_type = H5R_OBJECT); DataType(const Attribute& attr, const void* ref, H5R_type_t ref_type = H5R_OBJECT);These constructors
Group(H5Object& obj, const void* ref, H5R_type_t ref_type = H5R_OBJECT); Group(H5File& h5file, const void* ref, H5R_type_t ref_type = H5R_OBJECT); Group(Attribute& attr, const void* ref, H5R_type_t ref_type = H5R_OBJECT); have changed to Group(const H5Location& loc, const void* ref, H5R_type_t ref_type = H5R_OBJECT); Group(const Attribute& attr, const void* ref, H5R_type_t ref_type = H5R_OBJECT);h5dump has a new option for identifying objects by a full or partial path:
-NP –any-path=PThe 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.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 has three new options for setting print thresholds: For attributes:
-aN –attribute=NFor links in a group:
-lN –links=NFor dimension sizes:
-mN –dims=NA new configuration option can be used to change the default plugin path:
–with-default-plugindir=location CMake configuration
Autotools configure flag
Compile Scripts with Changed Behavior
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.
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.
Fortran90 subroutines:
h5oclose_f was introduced in HDF5 Release 1.8.8 but remained undocumented until this release.
Fortran2003 subroutines:
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 Data Pipeline Dynamically Loaded Filters for further information.
h5dump has a new option to output the DDL structure of a file or object:
-O<filename> –ddl=<file_name> [-O above is dash-uppercase-o.]h5import can now take the output of h5dump -O<ddl_filename> -o<data_filename> directly as input files. See Export from h5dump and Import into HDF5.
The return value of the following high-level C function has changed:
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 - has been updated to display the compression ratio for user-defined filters. In h5dump output, UNKNOWN_FILTER has been changed to USER_DEFINED_FILTER.
The following C functions and the corresponding C++ wrappers have been removed:
H5Pset_dxpl_multi H5Pget_dxpl_multi H5::DSetMemXferPropList:setMulti H5::DSetMemXferPropList:getMultiThis 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.
The following new Fortran subroutine has been added:
The syntax of the following high-level C function has changed:
Changed Command-line Tool h5import has been updated to accept an input file created by h5dump.
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.
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:
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.
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 behavior:
New functions and callback function:
The following C functions and Fortran subroutines were added to provide a mechanism to ensure sequential consistency in parallel environments using MPI I/O:
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:
The following Fortran subroutines have been added in this release:
Where a subroutine is part of a new HDF5 feature, that feature is described above.
The content of the buffer returned by the following Fortran subroutine has changed as noted:
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. 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:
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.
Two new parallel I/O functions enable an application to query whether or how a collective I/O operation actually completed:
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:
Terminology:
–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 subroutines available only 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:
Subroutines with support for the derived type C_PTR and a changed signature in Fortran 2003 environments:
Subroutine with additional optional parameters in Fortran 2003 environments:
New Fortran 90 subroutines:
Updated Fortran 90 subroutines:
New Fortran utility functions:
New Fortran derived types in Fortran 2003 environments:
New Fortran subroutines in the HDF5 Dimension Scale high-level interface, H5DS:
These subtroutines are available in both Fortran 90 and Fortran 2003 environments.
Changed behavior:
New default driver:
–delta option reports two NaN values as equal regardless of the type of NaN (as described in the reference manual entry). 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-fortran2003Note 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.
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.
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.
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:
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:
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:
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:
Two new flags have been added:
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.
h5diff has a new verbose with levels option to display additional attribute information:
-vn, –verbose=nh5dump has one new option to enable reporting of the HDF5 Library's error stack:
–enable-error-stackh5ls has one changed option name:
–enable-error-stack replaces –error.. The –error option is deprecated but remains available.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:
H5T_REFERENCE {H5T_STD_REF_OBJ} - Object reference H5T_REFERENCE {H5T_STD_REF_DSETREG} - Dataset region referenceConfigure 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:
–disable-silent-rules flag at configure time to override the default and view actual compile and link lines during the build. 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.
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.
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.
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:
The function H5Tget_order returns this value when called on a compound datatype whose members are not all of the same endianness.
h5diff has one new option:
–exclude-pathh5ls and h5diff have two new options:
–follow-symlinks –no-dangling-links\ttemp in the file, h5ls will output that name as \ttemp rather than converting the leading \t to a tab. 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_linkThis 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.
The Parallel HDF5 build process has changed to use mpiexec instead of mpirun.
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.
The following function was added to the HDF5 Library at this release, but was not documented at that time:
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.
The following C++ member function is new in this release:
size_t DataSet::getInMemDataSize - To simplify getting a dataset's data size in memory.The overloaded forms of the following C++ member functions are new in this release:
CommonFG::getObjnameByIdx - Overloaded to take char* for name. CommonFG::getObjTypeByIdx - Overloaded to return type name as char*.h5diff has two new options:
–follow-links –no-dangling-linksThe link type parameter values associated with the following Fortran subroutines have changed in this release:
Valid values for the parameter link_type have changed to the following:
These values previously began with the string H5L_LINK_.
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 focused 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.
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.
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.
The following Fortran subroutine is new in this release:
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() constThe size in each case is in bytes.
The function has also been changed to suppress the warning message entirely if $HDF5_DISABLE_VERSION_CHECK is set to 2 or higher.
The following Fortran subroutines have changed syntax in this release:
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.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).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 specified when subsetting a dataset.
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.This section lists API-level changes and changes in behavior in the transition from HDF5 Release 1.8.2 to Release 1.8.3.
The following C functions are new for this release and are documented in the HDF5 Reference Manual.
The following subroutines are new in this release:
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.
h5diff default behavior 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 now correctly specifies an XML DTD or a schema URL.
h5dump binary output now defaults to NATIVE.
-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.
This section lists API-level changes and changes in behavior in the transition from HDF5 Release 1.8.1 to Release 1.8.2.
The following C functions are new for this release and are documented in the HDF5 Reference Manual.
The following subroutine is new in this release:
A number of C++ wrappers were added/removed. See RELEASE.txt for details.
The following function syntaxes have changed; the affected return values and parameter are noted as underscored red text.
The optional parameter mounted has been added to the following subroutines:
Changed Data Structure
h5repack [OPTIONS] file1 file2h5diff [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:
-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.'-f' or '–filter' option, allowing the use of multiple I/O filters with an object. '-b' option, optionally accepting NATIVE, FILE, BE, and LE. '-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.
The following functions are deprecated as of this release:
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.
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.
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.
There are no new C functions for Release 1.8.1.
The following Fortran subroutines are new for Release 1.8.1 and are documented in the HDF5 Reference Manual. H5A
H5D
H5G
H5L
H5O
H5P
H5R
H5S
H5T
There are no new C++ wrappers for Release 1.8.1.
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:
In addition, data member IdComponent::id was moved into subclasses:
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:
h5repack [OPTIONS] in_file out_file h5repack -i in_file -o out_file [OPTIONS] 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 –indexed=min_indexed_links.In Release 1.8.1, the -i form has been changed to -d as follows:
-d min_indexed_links –indexed=min_indexed_linksThe 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 outputChanged library behavior:
C functions with changed behavior:
Tools with changed behavior and changed output:
h5dump -p option now prints the compression ratio if a compression filter is associated with a dataset. The following configuration flag is new with this release:
–disable-sharedlib-rpathThe 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.
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.
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 for a full description.
Macros are identified in reference manual function indexes by an italic typeface.
The new macros and the old and new 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.)
C functions The following C functions are new for Release 1.8.0 and, unless otherwise noted, are documented in the HDF5 Reference Manual.
Recursive iteration
herr_t H5Lvisit(hid_t group_id, H5_index_t index_type, H5_iter_order_t order, H5L_iterate_t op, void *op_data) herr_t H5Lvisit_by_name(hid_t loc_id, const char *group_name, H5_index_t index_type, H5_iter_order_t order, H5L_iterate_t op, void *op_data, hid_t lapl_id) herr_t H5Ovisit(hid_t group_id, H5_index_t index_type, H5_iter_order_t order, H5O_iterate_t op, void *op_data) herr_t H5Ovisit_by_name(hid_t loc_id, const char *object_name, H5_index_t index_type, H5_iter_order_t order, H5O_iterate_t op, void *op_data, hid_t lapl_id)"Format bounds" property Release-to-release format compatibility
herr_t H5Pset_libver_bounds(hid_t fapl_id, H5F_libver_t low, H5F_libver_t high) herr_t H5Pget_libver_bounds(hid_t fapl_id, H5F_libver_t *low, H5F_libver_t *high)Configurable compact-or-indexed groups (compact and large groups)
herr_t H5Pset_link_phase_change(hid_t gcpl_id, unsigned max_compact, unsigned min_dense) herr_t H5Pget_link_phase_change(hid_t gcpl_id, unsigned *max_compact, unsigned *min_dense) herr_t H5Pset_est_link_info(hid_t gcpl_id, unsigned est_num_entries, unsigned est_name_len) herr_t H5Pget_est_link_info(hid_t gcpl_id, unsigned *est_num_entries, unsigned *est_name_len) herr_t H5Pset_nlinks(hid_t lapl_id, size_t nlinks) herr_t H5Pget_nlinks(hid_t lapl_id, size_t *nlinks)User-defined links
herr_t H5Lcreate_ud(hid_t link_loc_id, const char *link_name, H5L_type_t link_type, const char *udata, size_t udata_size, hid_t lcpl_id, hid_t lapl_id) herr_t H5Lregister(const H5L_class_t *link_class) herr_t H5Lunregister(H5L_type_t link_cls_id) herr_t H5Oincr_refcount(hid_t object_id) herr_t H5Odecr_refcount(hid_t object_id)External links
herr_t H5Lcreate_external(const char *file_name, const char *object_name, hid_t link_loc_id, const char *link_name, hid_t lcpl_id, hid_t lapl_id) herr_t H5Lunpack_elink_val(char *ext_linkval, size_t link_size, const char **filename, const char **obj_path) herr_t H5Pset_elink_prefix(hid_t lapl_id, const char *prefix) herr_t H5Pget_elink_prefix(hid_t lapl_id, const char **prefix)Link creation order tracking and indexing
herr_t H5Pset_link_creation_order(hid_t ocpl_id, unsigned crt_order_flags) herr_t H5Pget_link_creation_order(hid_t ocpl_id, unsigned *crt_order_flags) hid_t H5Gget_create_plist(hid_t group_id) herr_t H5Gget_info_by_idx(hid_t loc_id, const char *group_name, H5_index_t index_type, H5_iter_order_t order, hsize_t n, H5G_info_t *group_info, hid_t lapl_id) hid_t H5Tget_create_plist(hid_t dtype_id)Link API (H5L), an all-new interface (includes user-defined and external links)
herr_t H5Lcopy(hid_t src_loc_id, const char *src_name, hid_t dest_loc_id, const char *dest_name, hid_t lcpl_id, hid_t lapl_id) herr_t H5Lcreate_external(const char *file_name, const char *object_name, hid_t link_loc_id, const char *link_name, hid_t lcpl_id, hid_t lapl_id) herr_t H5Lcreate_hard(hid_t obj_loc_id, const char *obj_name, hid_t link_loc_id, const char *link_name, hid_t lcpl_id, hid_t lapl_id) herr_t H5Lcreate_soft(const char *target_path, hid_t link_loc_id, const char *link_name, hid_t lcpl_id, hid_t lapl_id) herr_t H5Lcreate_ud(hid_t link_loc_id, const char *link_name, H5L_type_t link_type, const char *udata, size_t udata_size, hid_t lcpl_id, hid_t lapl_id) herr_t H5Ldelete(hid_t loc_id, const char *name, hid_t lapl_id) herr_t H5Ldelete_by_idx(hid_t loc_id, const char *group_name, H5_index_t index_field, H5_iter_order_t order, hsize_t n, hid_t lapl_id) htri_t H5Lexists(hid_t loc_id, const char *name, hid_t lapl_id) herr_t H5Lget_info(hid_t link_loc_id, const char *link_name, H5L_info_t *link_buff, hid_t lapl_id) herr_t H5Lget_info_by_idx(hid_t loc_id, const char *group_name, H5_index_t index_field, H5_iter_order_t order, hsize_t n, H5L_info_t *link_val, hid_t lapl_id) ssize_t H5Lget_name_by_idx(hid_t loc_id, const char *group_name, H5_index_t index_field, H5_iter_order_t order, hsize_t n, char *name, size_t size, hid_t lapl_id) herr_t H5Lget_val(hid_t link_loc_id, const char *link_name, void *linkval_buff, size_t size, hid_t lapl_id) ssize_t H5Lget_val_by_idx(hid_t loc_id, const char *group_name, H5_index_t index_field, H5_iter_order_t order, hsize_t n, char *value_buf, size_t size, hid_t lapl_id) htri_t H5Lis_registered(H5L_type_t link_cls_id) herr_t H5Literate(hid_t loc_id, H5_index_t index_type, H5_iter_order_t order, hsize_t *idx, H5L_iterate_t op, void *op_data) herr_t H5Literate_by_name(hid_t loc_id, const char *group_name, H5_index_t index_type, H5_iter_order_t order, hsize_t *idx, H5L_iterate_t op, void *op_data, hid_t *lapl_id) herr_t H5Lmove(hid_t src_loc_id, const char *src_name, hid_t dest_loc_id, const char *dest_name, hid_t lcpl, hid_t lapl) herr_t H5Lregister(const H5L_class_t *link_class) herr_t H5Lunpack_elink_val(char *ext_linkval, size_t link_size, const char **filename, const char **obj_path) herr_t H5Lunregister(H5L_type_t link_cls_id) herr_t H5Lvisit(hid_t group_id, H5_index_t index_type, H5_iter_order_t order, H5L_iterate_t op, void *op_data) herr_t H5Lvisit_by_name(hid_t loc_id, const char *group_name, H5_index_t index_type, H5_iter_order_t order, H5L_iterate_t op, void *op_data, hid_t lapl_id)Enhanced attribute handling
hid_t H5Acreate2(hid_t loc_id, const char *attr_name, hid_t type_id, hid_t space_id, hid_t acpl_id, hid_t aapl_id, hid_t lapl_id) herr_t H5Adelete_by_idx(hid_t loc_id, const char *obj_name, H5_index_t idx_type, H5_iter_order_t order, hsize_t n, hid_t lapl_id) herr_t H5Adelete_by_name(hid_t loc_id, const char *obj_name, const char *attr_name, hid_t lapl_id) herr_t H5Aget_info(hid_t attr_id, H5A_info_t *ainfo) herr_t H5Aget_info_by_idx(hid_t loc_id, const char *obj_name, H5_index_t idx_type, H5_iter_order_t order, hsize_t n, H5A_info_t *ainfo, hid_t lapl_id) herr_t H5Aget_info_by_name(hid_t loc_id, const char *obj_name, const char *attr_name, H5A_info_t *ainfo, hid_t lapl_id) ssize_t H5Aget_name_by_idx(hid_t loc_id, const char *obj_name, H5_index_t idx_type, H5_iter_order_t order, hsize_t n, char *name, size_t size, hid_t lapl_id) hsize_t H5Aget_storage_size(hid_t attr_id) herr_t H5Aiterate2(hid_t obj_id, H5_index_t idx_type, H5_iter_order_t order, hsize_t *n, H5A_operator2_t op, void *op_data) herr_t H5Aiterate_by_name(hid_t loc_id, const char *obj_name, H5_index_t idx_type, H5_iter_order_t order, hsize_t *n, H5A_operator2_t op, void *op_data, hid_t lapd_id) hid_t H5Aopen(hid_t loc_id, const char *obj_name, const char *attr_name, hid_t aapl_id, hid_t lapl_id) hid_t H5Aopen_by_idx(hid_t loc_id, const char *obj_name, H5_index_t idx_type, H5_iter_order_t order, hsize_t n, hid_t aapl_id, hid_t lapl_id) herr_t H5Arename_by_name(hid_t loc_id, const char *obj_name, const char *old_attr_name, const char *new_attr_name, hid_t lapl_id)Managing large numbers of attributes
herr_t H5Pset_attr_phase_change(hid_t ocpl_id, unsigned max_compact, unsigned min_dense) herr_t H5Pget_attr_phase_change(hid_t ocpl_id, unsigned *max_compact, unsigned *min_dense)Attribute creation order tracking and indexing
herr_t H5Pset_attr_creation_order(hid_t ocpl_id, unsigned crt_order_flags) herr_t H5Pget_attr_creation_order(hid_t ocpl_id, unsigned *crt_order_flags) hid_t H5Aget_create_plist(hid_t attr_id)Shared object header messages (SOHM)
herr_t H5Pset_shared_mesg_index(hid_t fcpl_id, unsigned index_num, unsigned mesg_type_flags, unsigned min_mesg_size) herr_t H5Pset_shared_mesg_nindexes(hid_t plist_id, unsigned nindexes) herr_t H5Pset_shared_mesg_phase_change(hid_t fcpl_id, unsigned max_list, unsigned min_btree) herr_t H5Pget_shared_mesg_index(hid_t fcpl_id, unsigned index_num, unsigned *mesg_type_flags, unsigned *min_mesg_size) herr_t H5Pget_shared_mesg_nindexes(hid_t fcpl_id, unsigned *nindexes) herr_t H5Pget_shared_mesg_phase_change(hid_t fcpl_id, unsigned *max_list, unsigned *min_btree)Enhanced local heap size management (group meta data)
herr_t H5Pset_local_heap_size_hint(hid_t gcpl_id, size_t size_hint) herr_t H5Pget_local_heap_size_hint(hid_t gcpl_id, size_t size_hint)UNICODE support
herr_t H5Pset_char_encoding(hid_t plist_id, H5T_cset_t encoding) herr_t H5Pget_char_encoding(hid_t plist_id, H5T_cset_t encoding)Object API (H5O), all new
herr_t H5Oclose(hid_t object_id) herr_t H5Ocopy(hid_t src_loc_id, const char *src_name, hid_t dst_loc_id, const char *dst_name, hid_t ocp_plist_id, hid_t lcpl_id) herr_t H5Odecr_refcount(hid_t object_id) ssize_t H5Oget_comment(hid_t object_id, char *comment, size_t bufsize) ssize_t H5Oget_comment_by_name(hid_t loc_id, const char *name, char *comment, size_t bufsize, hid_t lapl_id) herr_t H5Oget_info(hid_t object_id, H5O_info_t *obj_info) herr_t H5Oget_info_by_idx(hid_t loc_id, const char *group_name, H5_index_t index_field, H5_iter_order_t order, hsize_t n, H5O_info_t *obj_info, hid_t lapl_id) herr_t H5Oget_info_by_name(hid_t loc_id, const char *object_name, H5O_info_t *object_info, hid_t lapl_id) herr_t H5Oincr_refcount(hid_t object_id) herr_t H5Olink(hid_t obj_id, hid_t new_loc_id, const char *new_link_name, hid_t lcpl, hid_t lapl) hid_t H5Oopen(hid_t loc_id, const char *name, hid_t lapl_id) hid_t H5Oopen_by_addr(hid_t loc_id, haddr_t addr) hid_t H5Oopen_by_idx(hid_t loc_id, const char *group_name, H5_index_t index_field, H5_iter_order_t order, hsize_t n, hid_t lapl_id) herr_t H5Oset_comment(hid_t object_id, const char *comment) herr_t H5Oset_comment_by_name(hid_t loc_id, const char *name, const char *comment, hid_t lapl_id) herr_t H5Ovisit(hid_t group_id, H5_index_t index_type, H5_iter_order_t order, H5O_iterate_t op, void *op_data) herr_t H5Ovisit_by_name(hid_t loc_id, const char *object_name, H5_index_t index_type, H5_iter_order_t order, H5O_iterate_t op, void *op_data, hid_t lapl_id)Object creation or copying with "create intermediate groups" property
herr_t H5Pset_create_intermediate_group(hid_t gcpl_id, unsigned crt_intermed_group) herr_t H5Pget_create_intermediate_group(hid_t gcpl_id, unsigned *crt_intermed_group)Object copy properties
herr_t H5Ocopy(hid_t src_loc_id, const char *src_name, hid_t dst_loc_id, const char *dst_name, hid_t ocp_plist_id, hid_t lcpl_id) herr_t H5Pset_copy_object(hid_t cplist_id, unsigned copy_options) herr_t H5Pget_copy_object(hid_t cplist_id, unsigned *copy_options)Improved object and file information retrieval
herr_t H5Aget_info(hid_t attr_id, H5A_info_t *ainfo) herr_t H5Aget_info_by_name(hid_t loc_id, const char *obj_name, const char *attr_name, H5A_info_t *ainfo, hid_t lapl_id) herr_t H5Aget_info_by_idx(hid_t loc_id, const char *obj_name, H5_index_t idx_type, H5_iter_order_t order, hsize_t n, H5A_info_t *ainfo, hid_t lapl_id) herr_t H5Fget_info(hid_t obj_id, H5F_info_t *bh_info) herr_t H5Gget_info(hid_t group_id, H5G_info_t group_info) herr_t H5Gget_info_by_name(hid_t loc_id, const char *group_name, H5G_info_t group_info, hid_t lapl_id) herr_t H5Gget_info_by_idx(hid_t loc_id, const char *group_name, H5_index_t index_type, H5_iter_order_t order, hsize_t n, H5G_info_t group_info, hid_t lapl_id) herr_t H5Lget_info(hid_t link_loc_id, const char *link_name, H5L_info_t *link_buff, hid_t lapl_id) herr_t H5Lget_info_by_idx(hid_t loc_id, const char *group_name, H5_index_t index_field, H5_iter_order_t order, hsize_t n, H5L_info_t *link_val, hid_t lapl_id) herr_t H5Oget_info(hid_t object_id, H5O_info_t *obj_info) herr_t H5Oget_info_by_name(hid_t loc_id, const char *object_name, H5O_info_t *object_info, hid_t lapl_id) herr_t H5Oget_info_by_idx(hid_t loc_id, const char *group_name, H5_index_t index_field, H5_iter_order_t order, hsize_t n, H5O_info_t *obj_info, hid_t lapl_id)Name of referenced object
ssize_t H5Rget_name(hid_t loc_id, H5R_type_t ref_type, void *ref, char *name, size_t size)Anonymous object creation
hid_t H5Dcreate_anon(hid_t loc_id, hid_t type_id, hid_t space_id, hid_t dcpl_id, hid_t dapl_id) hid_t H5Gcreate_anon(hid_t loc_id, const char *name, hid_t gcpl_id, hid_t gapl_id) herr_t H5Tcommit_anon(hid_t loc_id, hid_t type_id, hid_t tcpl_id, hid_t tapl_id) herr_t H5Lcreate_hard(hid_t obj_loc_id, const char *obj_name, hid_t link_loc_id, const char *link_name, hid_t lcpl, hid_t lapl)New-style object creation and open functions (includes anonymous object creation)
hid_t H5Dcreate_anon(hid_t loc_id, hid_t type_id, hid_t space_id, hid_t dcpl_id, hid_t dapl_id) hid_t H5Dcreate2(hid_t loc_id, const char *name, hid_t type_id, hid_t space_id, hid_t lcpl_id, hid_t dcpl_id, hid_t dapl_id) hid_t H5Dopen2(hid_t loc_id, const char *name, hid_t dapl_id) hid_t H5Gcreate_anon(hid_t loc_id, const char *name, hid_t gcpl_id, hid_t gapl_id) hid_t H5Gcreate2(hid_t loc_id, const char *name, hid_t lcpl_id, hid_t gcpl_id, hid_t gapl_id) hid_t H5Gopen2(hid_t loc_id, const char *name, hid_t gapl_id) herr_t H5Tcommit_anon(hid_t loc_id, hid_t type_id, hid_t tcpl_id, hid_t tapl_id) herr_t H5Tcommit2(hid_t loc_id, const char *name, hid_t type_id, hid_t lcpl_id, hid_t tcpl_id, hid_t tapl_id) hid_t H5Topen2(hid_t loc_id, const char *name, hid_t tapl_id)User-defined identifiers
hid_t H5Iregister(H5I_type_t type, void *object) H5I_type_t H5Iregister_type(size_t hash_size, unsigned reserved, H5I_free_t free_func) herr_t H5Idestroy_type(H5I_type_t type) int H5Iinc_type_ref(H5I_type_t type) int H5Idec_type_ref(H5I_type_t type) int H5Iget_type_ref(H5I_type_t type)Other identifier API (H5I) enhancements
herr_t H5Iclear_type(H5I_type_t type, hbool_t force) int H5Inmembers(H5I_type_t type, hsize_t *num_members) void * H5Iobject_verify(hid_t id, H5I_type_t id_type) void * H5Iremove_verify(hid_t id, H5I_type_t id_type) void * H5Isearch(H5I_type_t type, H5I_search_func_t func, void *key) htri_t H5Itype_exists(H5I_type_t type)Compression filters: N-bit and scale-offset
herr_t H5Pset_nbit(hid_t plist_id) herr_t H5Pset_scaleoffset(hid_t plist_id, H5Z_SO_scale_type_t scale_type, int scale_factor)User-defined datatype conversion callback functions
herr_t H5Pget_type_conv_cb(hid_t plist, H5T_conv_except_func_t *func, void **op_data) herr_t H5Pset_type_conv_cb(hid_t plist, H5T_conv_except_func_t func, void *op_data)Datatype compiler conversion check
Dataset array size reduction
herr_t H5Dset_extent(hid_t dset_id, const hsize_t *size)Dataspace equivalence
Direct I/O, bypassing system cache
herr_t H5Pset_fapl_direct(hid_t fapl_id, size_t alignment, size_t block_size, size_t cbuf_size) herr_t H5Pget_fapl_direct(hid_t fapl_id, size_t *alignment, size_t *block_size, size_t *cbuf_size)Parallel I/O optimization (collective chunk I/O)
herr_t H5Pset_dxpl_mpio_chunk_opt(hid_t dxpl_id, H5FD_mpio_chunk_opt_t opt_mode) herr_t H5Pset_dxpl_mpio_chunk_opt_num(hid_t dxpl_id, unsigned num_chunk_per_proc) herr_t H5Pset_dxpl_mpio_chunk_opt_ratio(hid_t dxpl_id, unsigned percent_num_proc_per_chunk) Enhanced error handling (H5E)
herr_t H5Eauto_is_v2( hid_t estack_id, unsigned *is_stack ) herr_t H5Eclear2( hid_t estack_id ) herr_t H5Eclose_msg( hid_t mesg_id ) herr_t H5Eclose_stack( hid_t estack_id ) hid_t H5Ecreate_msg( hid_t class, H5E_type_t msg_type, const char* mesg ) herr_t H5Eget_auto2( hid_t estack_id, H5E_auto2_t *func, void **client_data ) ssize_t H5Eget_class_name( hid_t class_id, char* name, size_t size ) hid_t H5Eget_current_stack( void ) ssize_t H5Eget_msg( hid_t mesg_id, H5E_type_t mesg_type, char mesg, size_t size ) ssize_t H5Eget_num( hid_t estack_id ) herr_t H5Epop( hid_t estack_id, size_t count ) herr_t H5Eprint2( hid_t estack_id, FILE * stream ) herr_t H5Epush2( hid_t estack_id, const char *file, const char *func, unsigned line, hid_t class_id, hid_t major_id, hid_t minor_id, const char *msg, ...) hid_t H5Eregister_class( const char* cls_name, const char* lib_name, const char* version ) herr_t H5Eset_auto2( hid_t estack_id, H5E_auto2_t func, void *client_data ) herr_t H5Eset_current_stack( hid_t estack_id ) herr_t H5Eunregister_class( hid_t class_id ) herr_t H5Ewalk2( hid_t estack_id, H5E_direction_t direction, H5E_walk2_t func, void * client_data )Meta data cache management
herr_t H5Fget_mdc_config(hid_t file_id, H5AC_cache_config_t *config_ptr) herr_t H5Fget_mdc_hit_rate(hid_t file_id, double *hit_rate_ptr) herr_t H5Fget_mdc_size(hid_t file_id, size_t *max_size_ptr, size_t *min_clean_size_ptr, size_t *cur_size_ptr, int *cur_num_entries_ptr) herr_t H5Freset_mdc_hit_rate_stats(hid_t file_id) herr_t H5Fset_mdc_config(hid_t file_id, H5AC_cache_config_t *config_ptr) herr_t H5Pget_mdc_config(hid_t plist_id, H5AC_cache_config_t *config_ptr) herr_t H5Pset_mdc_config(hid_t plist_id, H5AC_cache_config_t *config_ptr)File read/write status
Arithmetic data transform on I/O
herr_t H5Pget_data_transform( hid_t plist_id, char* expression, size_t size) herr_t H5Pset_data_transform( hid_t plist, const char* expression )Dataspace and datatype serial conversion
hid_t H5Sdecode( const void *buf ) herr_t H5Sencode( hid_t obj_id, void *buf, size_t *nalloc ) hid_t H5Tdecode( const void *buf ) herr_t H5Tencode( hid_t obj_id, void *buf, size_t *nalloc )Enhanced filter management
herr_t H5Pget_filter2( hid_t plist_id, unsigned idx, unsigned int *flags, size_t *cd_nelmts, unsigned cd_values[], size_t namelen, char name[], unsigned *filter_config) hid_t H5Pget_filter_by_id2( hid_t plist_id, H5Z_filter_t filter_id, unsigned int *flags, size_t *cd_nelmts, unsigned int cd_values[], size_t namelen, char name[], unsigned int *filter_config)Comparison of properties
herr_t H5Pinsert2( hid_t plid, const char *name, size_t size, void *value, H5P_prp_set_func_t set, H5P_prp_get_func_t get, H5P_prp_delete_func_t delete, H5P_prp_copy_func_t copy, H5P_prp_compare_func_t compare, H5P_prp_close_func_t close) herr_t H5Pregister2( hid_t class, const char * name, size_t size, void * default, H5P_prp_create_func_t create, H5P_prp_set_func_t set, H5P_prp_get_func_t get, H5P_prp_delete_func_t delete, H5P_prp_copy_func_t copy, H5P_prp_compare_func_t compare, H5P_prp_close_func_t close)Two-way conversion between datatype and text description of datatype
hid_t H5LTtext_to_datatype( const char *text, H5LT_lang_t lang_type) herr_t H5LTdtype_to_text( hid_t datatype, char *str, H5LT_lang_t lang_type, size_t *len)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:
hid_t H5LTtext_to_datatype( const char *text, H5LT_lang_t lang_type) herr_t H5LTdtype_to_text( hid_t datatype, char *str, H5LT_lang_t lang_type, size_t *len) herr_t H5LTset_attribute_long_long( hid_t loc_id, const char *obj_name, const char *attr_name, const long_long *data, size_t *size) herr_t H5LTget_attribute_long_long( hid_t loc_id, const char *obj_name, const char *attr_name, long_long *data)Two high-level C APIs are distributed for the first time with this release:
The new functions included in the packet table (H5PT) high-level APIs are as follows:
hid_t H5PTcreate_fl( hid_t loc_id, const char * dset_name, hid_t dtype_id, hsize_t chunk_size ) hid_t H5PTcreate_vl( hid_t loc_id, const char *dset_name, hsize_t chunk_size ) hid_t H5PTopen( hid_t loc_id, const char *dset_name ) herr_t H5PTclose( hid_t table_id ) herr_t H5PTappend( hid_t table_id, hsize_t nrecords, const void *data) herr_t H5PTcreate_index( hid_t table_id) herr_t H5PTset_index( hid_t table_id, hsize_t pt_index) herr_t H5PTread_packets( hid_t table_id, hsize_t start, hsize_t nrecords, void *data) herr_t H5PTget_next( hid_t table_id, hsize_t nrecords, void *data) herr_t H5PTget_num_packets( hid_t table_id, hsize_t * nrecords) herr_t H5PTis_valid( hid_t table_id) herr_t H5PTis_varlen( hid_t table_id) herr_t H5PTfree_vlen_readbuff( hid_t table_id, hsize_t bufflen, void * buff)The new functions included in the dimension scale (H5DS) high-level APIs are as follows:
herr_t H5DSset_scale(hid_t did, const char *dimname, hid_t dimscale_id) herr_t H5DSattach_scale(hid_t did, hid_t dsid, unsigned int idx) herr_t H5DSdetach_scale(hid_t did, hid_t dsid, unsigned int idx) htri_t H5DSis_attached(hid_t did, hid_t dsid, unsigned int idx) htri_t H5DSis_scale(hid_t did) herr_t H5DSiterate_scales(hid_t did, unsigned dim, int *idx, H5DS_iterate_t visitor, void *visitor_data) herr_t H5DSset_label(hid_t did, unsigned int idx, const char *label) ssize_t H5DSget_label(hid_t did, unsigned int idx, char *label, size_t size) hssize_t H5DSget_scale_name(hid_t did, char name, size_t *size) int H5DSget_num_scales(hid_t did, unsigned int idx)High Level Fortan90 APIs:
Fortran90 subroutines are now available for the following high-level APIs:
Tools:
The following functions, subroutines and wrappers have been removed in this release:
C functions: HDF5 no longer provides GASS support.
HDF5 no longer provides SRB support. SRB functionality is now supported through the mechanism described in SRB - The DICE Storage Resource Broker.
The stream virtual file driver (H5FD_STREAM) has been removed from the HDF5 distribution. The functionality was last available from http://hdf5-addons.origo.ethz.ch/.
These two functions are replaced by H5Pget_type_conv_cb and H5Pset_type_conv_cb.
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 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.
Symbols and preset values associated with the following functions, subroutines or wrappers have changed as noted.
C functions:
Fortran90 subroutines:
Functions with Changed Syntax Function syntax changes in this release are handled through the mechanism described in API Compatibility Macros.
Exceptions: The function H5Eget_minor is not governed by the above-mentioned macros and its return type has changed:
char *H5Eget_minor (H5E_minor_t n)An application calling H5Eget_minor from an HDF5 Library of Release 1.8.0 or later will have to free the memory associated with the return value to prevent a memory leak. (This note added at Release 1.8.4, November 2009.)
In the function H5Dextend, the size parameter signature was changed.
herr_t H5Dextend( hid_t dataset_id, const hsize_t size[] )The new function signature is generally considered equivalent to the old signature, but some compilers require an exact match. (This note added in February 2010, following Release 1.8.4.)
Renamed Functions The following C functions have been renamed. The original function names remain available under certain circumstances; see API Compatibility Macros for full details.
| Original Function | New Function |
|---|---|
| H5Acreate | H5Acreate1 |
| H5Aiterate | H5Aiterate1 |
| H5Dcreate | H5Dcreate1 |
| H5Dopen | H5Dopen1 |
| H5Eclear | H5Eclear1 |
| H5Eget_auto | H5Eget_auto1 |
| H5Eprint | H5Eprint1 |
| H5Epush | H5Epush1 |
| H5Eset_auto | H5Eset_auto1 |
| H5Ewalk | H5Ewalk1 |
| H5Gcreate | H5Gcreate1 |
| H5Gopen | H5Gopen1 |
| H5Pget_filter | H5Pget_filter1 |
| H5Pget_filter_by_id | H5Pget_filter_by_id1 |
| H5Pinsert | H5Pinsert1 |
| H5Pregister | H5Pregister1 |
| H5Rget_obj_type | H5Rget_obj_type1 |
| H5Tarray_create | H5Tarray_create1 |
| H5Tcommit | H5Tcommit1 |
| H5Tget_array_dims | H5Tget_array_dims1 |
| H5Topen | H5Topen1 |
Changed Library Structures The following library structures have changed as follows: C API:
typedef struct H5Z_class_t { int version; H5Z_filter_t filter_id; unsigned encoder_present unsigned decoder_present const char *comment; H5Z_can_apply_func_t can_apply_func; H5Z_set_local_func_t set_local_func; H5Z_func_t filter_func;
} H5Z_class_t; Changed ENUMs The following enumerated datatypes used by the library are discontinued in this release:
HDF5 error codes have changed from the ENUM format used in earlier releases to an identifier format. As ENUMs, error codes were constants defined at compile time; as identifiers, error codes are defined at runtime, in the same manner as HDF5 object identifiers (file, dataset, group, etc.).
Under normal circumstances, this change should be transparent to user applications.
The following enumerated datatypes used by the library have changed in the C and Fortran APIs as follows:
H5G_obj_t - Object types This ENUM has reordered as follows:
H5I_type_t - Identifier types The following symbols have been added to this ENUM:
Another new symbol
While visible in the public API, H5I_NTYPES functions as a limit value for the HDF5 Library and is not generally used at the application level. The same was true of H5I_NGROUPS.
H5S_class_t - Dataspace type identifiers The following symbol has been added:
H5T_cset_t - Character set encoding identifiers The following symbol has been added:
H5Z_filter_t - Filters identifiers The following symbols have been added:
The following OpenVMS-specific floating point datatypes are new with this release:
The following property lists are new with this release:
The following configuration features have changed as follows.
New with this release:
–disable-dependency-tracking –enable-hdf5v1_6 –enable-dconv-exception –disable-dconv-exception –enable-dconv-accuracy –disable-dconv-accuracy –program-prefix=PREFIX –program-prefix=SUFFIX –program-transform-name=PROGRAM –enable-maintainer-mode –disable-dependency-tracking –enable-dependency-tracking –enable-codestack –enable-direct-vfd –with-tags[=TAGS]New with this release, but expected to be useful only to those working inside the HDF5 Library or working very closely with HDF5 developers:
–enable-build-all –enable-metadata-trace-fileNew with this release, but not actively supported:
–enable-fphdf5Changed in this release:
–enable-shared[=PKGS] –enable-static[=PKGS] –enable-fast-install[=PKGS]Removed in this release:
–enable-hdf5v1_4 –enable-funcstack –with-ssl=LIB –with-gass=DIR –with-srb=DIRThe environment variables, which are deprecated in this release.
Additional new "influential environment variables" in this release include the following:
1.9.7