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Neil Fortner e0dbcebe0d Minor addendums to latest file image fix (#5489) (#5496) 
* Enable bitwise comparison of file image in file_image.c for all file
format versions. Add RELEASE.txt note for file image fix with latest
format (#1915).

* Fix error message in file image test.
2025-04-28 13:37:30 -05:00

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HDF5 version 2.0.0 currently under development
================================================================================
INTRODUCTION
============
This document describes the differences between this release and the previous
HDF5 release. It contains information on the platforms tested and known
problems in this release. For more details check the HISTORY*.txt files in the
HDF5 source.
Note that documentation in the links below will be updated at the time of each
final release.
Links to HDF5 documentation can be found on:
https://support.hdfgroup.org/releases/hdf5/latest-docs.html
The official HDF5 releases can be obtained from:
https://support.hdfgroup.org/downloads/index.html
Changes from Release to Release and New Features in the HDF5-2.x.y release series
can be found at:
https://support.hdfgroup.org/releases/hdf5/documentation/release_specific_info.md
If you have any questions or comments, please send them to the HDF Help Desk:
help@hdfgroup.org
CONTENTS
========
- New Features
- Support for new platforms and languages
- Bug Fixes since HDF5-2.0.0
- Platforms Tested
- Known Problems
- CMake vs. Autotools installations
New Features
============
Configuration:
-------------
- Added CMake configuration options to override compilers in h5cc:
HDF5_H5CC_C_COMPILER for the C compiler
HDF5_H5CC_CXX_COMPILER for the C++ compiler
HDF5_H5CC_Fortran_COMPILER for the Fortran compiler
These default to the currently used compiler, preserving the current
behavior. However, they can be overridden by users who need to use
a different compiler at runtime, for example when they build via ccache.
- Added CMAKE_INSTALL_PREFIX to the default plugin path
To help users find their plugins, the default plugin path has been
changed to include the CMAKE_INSTALL_PREFIX. Adding the install prefix
allows users to skip setting the HDF5_PLUGIN_PATH environment variable
when using plugins with the default lib/plugin location.
- Removed support for autotools build system.
- The documentation in the source folder, doc, has been converted to doxygen files.
- Added configuration option for API concurrency support:
CMake: HDF5_ENABLE_CONCURRENCY (ON/OFF) (Default: OFF)
Autotools: --enable-concurrency (yes/no) (Default: no)
This option enables support for concurrent multithreaded operation
of supported API routines. This option also provides threadsafe
execution of all other, non-concurrent operations. The 'concurrency'
option thus is a superset of the existing 'threadsafe' option. Both
options are currently available, although mutually exclusive. As the
'concurrency' code becomes more stable over time, the 'threadsafe' option
may be deprecated in favor of the new 'concurrency' option.
The following API routines support concurrent multithreaded operation:
<none yet>
- ************ Renamed the option: HDF5_ENABLE_Z_LIB_SUPPORT ************
The option has been renamed to HDF5_ENABLE_ZLIB_SUPPORT to be consistent
with the naming of other options.
*** Also, the option defaults to OFF. This requires the user to explicitly ***
*** enable zlib support when configuring the library. ***
- Added support for MinGW + MSYS2 when building with CMake
We previously added support for this to the Autotools and the appropriate
configure-time checks have been added to CMake.
CMake + MinGW + MSYS2 is now tested with the following environments:
* mingw32
* mingw64
* ucrt64
* clang64
- Added CMake build mode flags to the libhdf5.settings file
Flags from the CMake build mode (e.g., optimization) are not a part of
CMAKE_<language>_FLAGS and were not exported to the libhdf5.settings file. This
has been fixed and the C, Fortran, and C++ build mode flags are now exported to
the file.
This also affects the text output of H5check_version() and the libhdf5.settings
string stored in the library (for those who use strings(1), etc. to get
build info from the binary).
- CMake: Split compiler specific flags into separate files
The compiler specific flags have been split into separate files to make
it easier to maintain and add new compiler flags. The flags for NVHPC,
Intel, GNU and Clang compilers are now in separate files included from
the current compiler flags files; HDFCompiler<language>Flags.cmake.
- Added support for native zlib-ng compression.
Changed the zlib-ng CMake logic to prefer the native zlib-ng library. Added
#ifdef around the compression function calls. Added including the correct
header file with the same #ifdef.
- Renamed remaining HDF5 library CMake options except for CMake BUILD* variables
DEFAULT_API_VERSION to HDF5_DEFAULT_API_VERSION
DISABLE_PDB_FILES to HDF5_DISABLE_PDB_FILES
ONLY_SHARED_LIBS to HDF5_ONLY_SHARED_LIBS
ALLOW_UNSUPPORTED to HDF5_ALLOW_UNSUPPORTED
TEST_SHELL_SCRIPTS to HDF5_TEST_SHELL_SCRIPTS
All other HDF5 library CMake options are prefixed with HDF5_
- bin/cmakehdf5 has been removed
This was an unsupported build script that made building HDF5 via CMake
work like building HDF5 via the Autotools. It has been unmaintained
for a long time, has been marked deprecated, and is being removed.
- Generated files in src are now checked into version control
These files are infrequently updated and generating them adds a
dependency on Perl. The listed files are now checked in and do
not need to be recreated when checking out development branches.
* H5Edefin.h
* H5Einit.h
* H5Emajdef.h
* H5Emindef.h
* H5Epubgen.h
* H5Eterm.h
* H5overflow.h
* H5version.h
- Dropped some old Solaris Studio work-arounds
Solaris Studio no longer seems to be maintained and the last version
(12.4, circa 2015) doesn't seem to fully support C11. We've removed
some hacks that work around things like __attribute__() support.
- Dropped support for the traditional MSVC preprocessor
Visual Studio has recently started using a standards-compliant
preprocessor (In VS2019+) and this is the default in C11.
https://learn.microsoft.com/en-us/cpp/preprocessor/preprocessor-experimental-overview?view=msvc-170
Because of this, we've dropped support for the traditional
MSVC preprocessor.
- The standard for building the library is now C11
We have updated the build files to set the C standard to C11, though
some platforms use gnu11 to get some GNU things to work.
Library:
--------
- The ROS3 VFD now includes the HTTP status code and a generic message
in the HDF5 error stack when a 400 or 500 error occurs
Previously, the ROS3 VFD would always include the simple message "curl
cannot perform request" in the HDF5 error stack when a 400 or 500 error
occurs. The only way of getting more information about what error
occurred was to change the value of the S3COMMS_CURL_VERBOSITY macro
when compiling HDF5. The ROS3 VFD has been updated to include the HTTP
status code, along with a generic message, in the HDF5 error stack.
- The H5Iregister_type() signature has changed
The hash_size parameter has not been used since early versions of HDF5
1.8, so it has been removed and the API call has been versioned.
The old signature has been renamed to H5Iregister_type1() and is considered
deprecated:
H5I_type_t H5Iregister_type1(size_t hash_size, unsigned reserved, H5I_free_t free_func);
The new signature is H5Iregister_type2(). New code should use this
version:
H5I_type_t H5Iregister_type2(unsigned reserved, H5I_free_t free_func);
H5Iregister_type() will map to the new signature unless the library is
explicitly configured to use an older version of the API.
- The H5Tdecode() signature has changed
When provided malformed or too-small buffers, H5Tdecode() would crash.
The new buffer size parameter allows this to be reliably avoided.
The old signature has been renamed to H5Tdecode1() and is considered
deprecated:
hid_t H5Tdecode1(const void *buf);
The new signature is H5Tdecode2(). New code should use this version:
hid_t H5Tdecode2(const void *buf, size_t buf_size);
H5Tdecode() will map to the new signature unless the library is
explicitly configured to use an older version of the API.
- H5F_LIBVER_LATEST is now an enum value
This was previously #defined to the latest H5F_libver_t API version, but
is now an enum value with an integer value equal to the latest H5F_libver_t
API version's value. e.g.:
<snip>
H5F_LIBVER_V200 = 5,
H5F_LIBVER_LATEST = 5,
</snip>
- Added support for complex number datatypes
Support for the C99 "float _Complex", "double _Complex" and "long double _Complex"
(with MSVC, "_Fcomplex", "_Dcomplex" and "_Lcomplex") types has been added for
platforms/compilers that support them. These types have been implemented with a
new datatype class, H5T_COMPLEX. Note that any datatypes of class H5T_COMPLEX
will not be readable with previous versions of HDF5. If a file is accessed with
a library version bounds "high" setting less than H5F_LIBVER_V200, an error will
occur if the application tries to create an object with a complex number datatype.
If compatibility with previous versions of HDF5 is desired, applications should
instead consider adopting one of the existing conventions at
https://nc-complex.readthedocs.io/en/latest/#conventions-used-in-applications.
The following new macros have been added:
- H5_HAVE_COMPLEX_NUMBERS
This macro is defined in H5pubconf.h and will have the value 1 if native
support for complex numbers is available. It will not be defined otherwise.
- H5_HAVE_C99_COMPLEX_NUMBERS
This macro is defined in H5pubconf.h and will have the value 1 if native
support for C99 complex numbers is available. It will not be defined otherwise.
If this macro is not defined but H5_HAVE_COMPLEX_NUMBERS is defined, the
complex number types supported are the MSVC types.
- H5_SIZEOF_FLOAT_COMPLEX
This macro is defined in H5pubconf.h and will have a value corresponding
to the size of the native float complex datatype, as computed by sizeof().
If C99 complex number support is available, this will be the size of the
"float _Complex" type. Otherwise, it will be the size of the "_Fcomplex"
type. It will have the value 0 if support for a native float complex datatype
is not available.
- H5_SIZEOF_DOUBLE_COMPLEX
This macro is defined in H5pubconf.h and will have a value corresponding
to the size of the native double complex datatype, as computed by sizeof().
If C99 complex number support is available, this will be the size of the
"double _Complex" type. Otherwise, it will be the size of the "_Dcomplex"
type. It will have the value 0 if support for a native double complex datatype
is not available.
- H5_SIZEOF_LONG_DOUBLE_COMPLEX
This macro is defined in H5pubconf.h and will have a value corresponding
to the size of the native long double complex datatype, as computed by sizeof().
If C99 complex number support is available, this will be the size of the
"long double _Complex" type. Otherwise, it will be the size of the "_Lcomplex"
type. It will have the value 0 if support for a native long double complex
datatype is not available.
- H5T_NATIVE_FLOAT_COMPLEX
This macro maps to the ID of an HDF5 datatype representing the native C
float complex datatype (either "float _Complex" or "_Fcomplex") for the
platform. If support for a native float complex datatype is not available
(H5_HAVE_COMPLEX_NUMBERS is not defined), the macro will map to
H5I_INVALID_HID and should not be used.
- H5T_NATIVE_DOUBLE_COMPLEX
This macro maps to the ID of an HDF5 datatype representing the native C
double complex datatype (either "double _Complex" or "_Dcomplex") for the
platform. If support for a native double complex datatype is not available
(H5_HAVE_COMPLEX_NUMBERS is not defined), the macro will map to
H5I_INVALID_HID and should not be used.
- H5T_NATIVE_LDOUBLE_COMPLEX
This macro maps to the ID of an HDF5 datatype representing the native C
long double complex datatype (either "long double _Complex" or "_Lcomplex")
for the platform. If support for a native long double complex datatype is
not available (H5_HAVE_COMPLEX_NUMBERS is not defined), the macro will map
to H5I_INVALID_HID and should not be used.
- H5T_COMPLEX_IEEE_F16LE / H5T_COMPLEX_IEEE_F16BE
These macros map to IDs of HDF5 datatypes representing a complex number of
two parts, each of which is an IEEE 754 16-bit floating-point datatype in
little- or big-endian order. These datatypes are available regardless of
whether complex number support is available or not.
- H5T_COMPLEX_IEEE_F32LE / H5T_COMPLEX_IEEE_F32BE
These macros map to IDs of HDF5 datatypes representing a complex number of
two parts, each of which is an IEEE 754 32-bit floating-point datatype in
little- or big-endian order. These datatypes are available regardless of
whether complex number support is available or not.
- H5T_COMPLEX_IEEE_F64LE / H5T_COMPLEX_IEEE_F64BE
These macros map to IDs of HDF5 datatypes representing a complex number of
two parts, each of which is an IEEE 754 64-bit floating-point datatype in
little- or big-endian order. These datatypes are available regardless of
whether complex number support is available or not.
The following new API function has been added:
hid_t H5Tcomplex_create(hid_t base_type_id);
Creates a new complex number datatype from the base datatype specified
by the given HDF5 ID `base_type_id`. The base datatype must be a
floating-point datatype.
The following new hard datatype conversion paths have been added, but
will only be used when complex number support is available:
H5T_NATIVE_SCHAR <-> H5T_NATIVE_FLOAT_COMPLEX | H5T_NATIVE_UCHAR <-> H5T_NATIVE_FLOAT_COMPLEX
H5T_NATIVE_SHORT <-> H5T_NATIVE_FLOAT_COMPLEX | H5T_NATIVE_USHORT <-> H5T_NATIVE_FLOAT_COMPLEX
H5T_NATIVE_INT <-> H5T_NATIVE_FLOAT_COMPLEX | H5T_NATIVE_UINT <-> H5T_NATIVE_FLOAT_COMPLEX
H5T_NATIVE_LONG <-> H5T_NATIVE_FLOAT_COMPLEX | H5T_NATIVE_ULONG <-> H5T_NATIVE_FLOAT_COMPLEX
H5T_NATIVE_LLONG <-> H5T_NATIVE_FLOAT_COMPLEX | H5T_NATIVE_ULLONG <-> H5T_NATIVE_FLOAT_COMPLEX
H5T_NATIVE_FLOAT16 <-> H5T_NATIVE_FLOAT_COMPLEX | H5T_NATIVE_FLOAT <-> H5T_NATIVE_FLOAT_COMPLEX
H5T_NATIVE_DOUBLE <-> H5T_NATIVE_FLOAT_COMPLEX | H5T_NATIVE_LDOUBLE <-> H5T_NATIVE_FLOAT_COMPLEX
H5T_NATIVE_SCHAR <-> H5T_NATIVE_DOUBLE_COMPLEX | H5T_NATIVE_UCHAR <-> H5T_NATIVE_DOUBLE_COMPLEX
H5T_NATIVE_SHORT <-> H5T_NATIVE_DOUBLE_COMPLEX | H5T_NATIVE_USHORT <-> H5T_NATIVE_DOUBLE_COMPLEX
H5T_NATIVE_INT <-> H5T_NATIVE_DOUBLE_COMPLEX | H5T_NATIVE_UINT <-> H5T_NATIVE_DOUBLE_COMPLEX
H5T_NATIVE_LONG <-> H5T_NATIVE_DOUBLE_COMPLEX | H5T_NATIVE_ULONG <-> H5T_NATIVE_DOUBLE_COMPLEX
H5T_NATIVE_LLONG <-> H5T_NATIVE_DOUBLE_COMPLEX | H5T_NATIVE_ULLONG <-> H5T_NATIVE_DOUBLE_COMPLEX
H5T_NATIVE_FLOAT16 <-> H5T_NATIVE_DOUBLE_COMPLEX | H5T_NATIVE_FLOAT <-> H5T_NATIVE_DOUBLE_COMPLEX
H5T_NATIVE_DOUBLE <-> H5T_NATIVE_DOUBLE_COMPLEX | H5T_NATIVE_LDOUBLE <-> H5T_NATIVE_DOUBLE_COMPLEX
H5T_NATIVE_SCHAR <-> H5T_NATIVE_LDOUBLE_COMPLEX | H5T_NATIVE_UCHAR <-> H5T_NATIVE_LDOUBLE_COMPLEX
H5T_NATIVE_SHORT <-> H5T_NATIVE_LDOUBLE_COMPLEX | H5T_NATIVE_USHORT <-> H5T_NATIVE_LDOUBLE_COMPLEX
H5T_NATIVE_INT <-> H5T_NATIVE_LDOUBLE_COMPLEX | H5T_NATIVE_UINT <-> H5T_NATIVE_LDOUBLE_COMPLEX
H5T_NATIVE_LONG <-> H5T_NATIVE_LDOUBLE_COMPLEX | H5T_NATIVE_ULONG <-> H5T_NATIVE_LDOUBLE_COMPLEX
H5T_NATIVE_LLONG <-> H5T_NATIVE_LDOUBLE_COMPLEX | H5T_NATIVE_ULLONG <-> H5T_NATIVE_LDOUBLE_COMPLEX
H5T_NATIVE_FLOAT16 <-> H5T_NATIVE_LDOUBLE_COMPLEX | H5T_NATIVE_FLOAT <-> H5T_NATIVE_LDOUBLE_COMPLEX
H5T_NATIVE_DOUBLE <-> H5T_NATIVE_LDOUBLE_COMPLEX | H5T_NATIVE_LDOUBLE <-> H5T_NATIVE_LDOUBLE_COMPLEX
H5T_NATIVE_FLOAT_COMPLEX <-> H5T_NATIVE_DOUBLE_COMPLEX
H5T_NATIVE_FLOAT_COMPLEX <-> H5T_NATIVE_LDOUBLE_COMPLEX
H5T_NATIVE_DOUBLE_COMPLEX <-> H5T_NATIVE_LDOUBLE_COMPLEX
Alternative software implementation conversion paths have been added for all of
the above for use when native complex number support is not available. All of these
conversion paths follow the behavior outlined in the C standard for conversions of
complex number values.
Additionally, a special datatype conversion path has been added between complex number
datatypes and array or compound datatypes where the in-memory layout of data is the
same between the datatypes and data can be directly converted. This conversion path
is subject to the following rules:
- An array datatype must consist of exactly two elements where each element is of
the same floating-point datatype as the complex number datatype's base floating-point
datatype.
- A compound datatype must consist of exactly two fields where each field is of the
same floating-point datatype as the complex number datatype's base floating-point
datatype. The compound datatype must not have any leading or trailing structure
padding or any padding between its two fields. The fields must also have compatible
names, must have compatible offsets within the datatype and must be in the order
of "real" part -> "imaginary" part, such that the compound datatype matches the
following representation:
H5T_COMPOUND {
<float_type> "r(e)(a)(l)"; OFFSET 0
<float_type> "i(m)(a)(g)(i)(n)(a)(r)(y)"; OFFSET SIZEOF("r(e)(a)(l)")
}
where "r(e)(a)(l)" means the field may be named any substring of "real", such as
"r", or "re" and "i(m)(a)(g)(i)(n)(a)(r)(y)" means the field may be named any
substring of "imaginary", such as "im" or "imag".
Support for complex numbers has been added to the h5dump, h5ls and h5diff/ph5diff
tools. The h5dump command-line option '-m' can be used to change the floating-point
printing format for the float complex and double complex datatypes, as well as
the long double complex datatype if it has the same size as a double complex
datatype.
Support for the predefined complex number datatypes and the H5Tcomplex_create
function has been added to the Java wrappers. However, Java does not have
official types for complex numbers, so an application must be sure that
data is in an appropriate format in-memory when using these datatypes.
Support for the Fortran wrappers has not yet been added.
Support for the predefined complex number datatypes and the H5Tcomplex_create
function has been added to the high level library, allowing them to work
with the H5LTtext_to_dtype and H5LTdtype_to_text functions.
Simple example programs showing how to use complex number datatypes have
been added in the following files:
- HDF5Examples/C/H5T/200/h5ex_t_complex.c (Uses C99 complex number types)
- HDF5Examples/C/H5T/200/h5ex_t_complex_msvc.c (Uses MSVC complex number types)
- HDF5Examples/C/H5T/200/h5ex_t_complex_custom.c (Uses H5Tcomplex_create to create
a custom complex number type)
- FOR VOL DEVELOPERS: Renamed H5VLstart_lib_state and H5VLfinish_lib_state
The APIs H5VLstart_lib_state and H5VLfinish_lib_state have been renamed to
H5VLopen_lib_context and H5VLclose_lib_context, respectively, with the addition
of a "context" argument.
- Removed H5FDperform_init API routine. Virtual File Driver (VFD)
developers who wish to provide an ID for their driver should create
a routine specific to their individual implementation.
- H5Pset_external() now uses HDoff_t, which is always a 64-bit type
The H5Pset_external() call took an off_t parameter in HDF5 1.14.x and
earlier. On POSIX systems, off_t is specified as a 64-bit type via
POSIX large-file support (LFS). On Windows, however, off_t is defined
as a 32-bit type, even on 64-bit Windows.
HDoff_t has been added to H5public.h and is defined to be int64_t on
Windows and the library has been updated to use HDoff_t in place of
off_t throughout. The H5Pset_external() offset parameter has also been
updated to be HDoff_t.
There is no API compatibility wrapper for this change.
Fixes GitHub issue #3506
- H5Pset* routines now fail when used on default property lists
Modifying default property lists was never fully supported and could produce
inconsistent and unexpected behavior.
- H5Pset_vol() now fails when used on a non-file-access property list
Similar to the above. Setting the connector on a non-FAPL had no effect on
library behavior, and the connector ID and information could not be read back
from that plist later.
Parallel Library:
-----------------
-
Fortran Library:
----------------
-
C++ Library:
------------
-
Java Library:
-------------
-
Tools:
------
- Added h5dump command option to set the floating point format for long double
The new option is --lformat, which allows the user to set the
floating point format for long double. The default format is %Lg.
There is already an option --format to set the floating point format
for double and float. The default format is %g.
- Remove the high-level GIF tools
The high-level GIF tools, h52gif and gif2h5, have unfixed CVE issues
(with no proof-of-concept files). They are not critical tools, are not
well maintained, and are an odd fit for building with the library.
Because of this, they have been removed. We may move them to a separate
repository in the future.
This also removes the following configure options:
Autotools: --(dis|en)able-hlgiftools
CMake: HDF5_BUILD_HL_GIF_TOOLS
High-Level APIs:
----------------
-
C Packet Table API:
-------------------
-
Internal header file:
---------------------
-
Documentation:
--------------
- The COPYING file has been renamed to LICENSE
This is where most people will expect to find license information. The
COPYING_LBNL_HDF5 file has also been renamed to LICENSE_LBNL_HDF5.
The licenses are unchanged.
Support for new platforms, languages and compilers
==================================================
-
Bug Fixes since HDF5-2.0.0 release
===================================
Library
-------
- Fixed an error with H5Fget_file_image() with the latest file format
When using H5Fget_file_image() on a file created with the latest file
format (or any format newer than the earliest), the library failed to
recalculate the superblock checksum after changing the access flags in the
superblock, causing any subsequent attempt to open the returned file image
to fail due to the checksum failing to verify. Fixed H5Fget_file_image()
to recalculate the checksum.
Fixes GitHub issue #1915
- Fixed an assertion failure in H5S__hyper_make_spans()
Calling H5Sselect_hyperslab() on dataspaces with invalid extents could
result in an assertion failure in debug builds of the library if the
dataspace has an extent with a rank value of 0. This has been fixed by
converting the assertion failure into a normal error check.
- Fixed an assertion failure in H5S__hyper_new_span_info()
Calling H5Scopy() on hyperslab selection dataspaces with invalid extents
could result in an assertion failure in debug builds of the library if
the dataspace has an extent with a rank value of 0. This has been fixed
by converting the assertion failure into a normal error check.
- Fixed a segfault in H5S__get_select_hyper_blocklist()
When attempting to retrieve the list of hyperslab blocks selected
within a dataspace, a segfault or bus error could occur when the
dataspace has an extent with a rank value of 0. This would cause
indexing into an array variable on the stack using a negative
value. An error check was added to return failure from the function
for such dataspaces.
- Fixed an error in H5Ddebug
H5Ddebug would fail for any chunked dataset with a chunk index, due to its
failure to tag the dataset before performing metadata operations. This
caused h5ls -va to silently fail to print chunk addresses. This has been
fixed.
- Fixed a bug in the H5Oexists and H5Oexists_by_name API routines that
would cause those routines to return FAIL instead of FALSE when checking
the existence of a non-existent object with a file ID instead of a
group ID.
- Fixed a segfault in h5dump when a B-tree node level is corrupted
h5dump produced a segfault on a mal-formed file because a B-tree node
level was corrupted.
An internal function was modified to help detecting when a decoded B-tree
node level has an unexpected value and an error will be produced.
Fixes GitHub issue #4432
- Fixed H5Ovisit2 to recursively visit all objects
H5Ovisit2 visited only the root group and not all the nested groups.
This behavior occurred when the fields are not H5O_INFO_BASIC or
H5O_INFO_ALL because an internal function did not obtain the basic
information needed by its caller. This problem is now fixed.
Fixes GitHub issue #4941
- Only clear FE_INVALID when that symbol is present on the system
When we initialize the floating-point types at library startup, it's
possible to raise floating-point exceptions when we check which things
are supported. Normally, we clear these floating-point exceptions via
feclearexcept(FE_INVALID), but FE_INVALID may not be present on all
systems. Specifically, this was reported as being a problem when using
Emscripten 3.1.68 to compile HDF5 1.14.5 to WebAssembly.
We've added an #ifdef FE_INVALID block around the exception clearing
code to correct this.
Fixes GitHub issue #4952
Java Library
------------
- Renamed the Callbacks.java file to H5Callbacks.java
The Callbacks.java file was renamed to H5Callbacks.java to match the file
pattern used by doxygen. This change only affects the Java filenames and
does not change the classname or the package name.
Configuration
-------------
- The relative rpaths ($ORIGIN / @loader_path) are appended to the CMAKE_INSTALL_RPATH
The RPATH settings were removed by a pull-request #5271, but the settings are needed
under certain conditions. These settings have been restored by appending the necessary paths
and will not override/overwrite any existing settings.
- When using a system installed zlib library, the shared library is expected to
be found in the system library path.
Setting the HDF5_MODULE_MODE_ZLIB option to OFF will force find_package to
use config mode first. An installed zlib, or an alternate installed zlib
library, is expected to have a correct zlib-config.cmake file for config mode.
Current zlib installs usually do not have a zlib-config.cmake file, so the
option is set to ON by default.
- Use pre-installed libaec compression library
The CMake logic for finding the libaec compression library has been
modified for a system-installed version of the library. Two options
must be set;
HDF5_ALLOW_EXTERNAL_SUPPORT:STRING=NO
<LIB_PKG_NAME>_USE_EXTERNAL:BOOL=OFF
where <LIB_PKG_NAME> is one of ZLIB, ZLIBNG, SZIP, PLUGIN.
Note that HDF5_ALLOW_EXTERNAL_SUPPORT:STRING=NO disables building all plugins
and external libraries in-line with the HDF5 library.
In addition, the <LIB_PKG_NAME>_ROOT environment variables must be set,
where <LIB_PKG_NAME> is one of ZLIB, ZLIBNG, SZIP, libaec, PLUGIN.
Note that libaec is the expected name for using the libaec library in place of original szip.
See INSTALL_CMake.txt for more detailed information.
- Changed the zlib/szip compression find message to FATAL ERROR
The message was changed to indicate that zlib/szip compression was requested and
that it was not found. If an option is requested, not finding it should always
be an error.
- Removed the module search find_package for szip library
There is not a szip module file to use, so the find_package only uses
find_package in config mode. The choice then is to either build szip, with libaec,
inline or find a system installed szip library, built with CMake.
- Changed name of libhdf5hl_fortran installed by autotools to libhdf5_hl_fortran. The
new name is consistent with the name of the lib when installed by CMake and with the
other hl libs.
Fixes GitHub issue #4811
Tools
-----
-
Performance
-------------
-
Fortran API
-----------
-
High-Level Library
------------------
- Fixed an issue with H5TB functions
The H5TB functions were not correctly creating the FILL_INFO attribute
for tables. This has been fixed by using the field offsets array from
the call to H5TBAget_fill instead of using the compound type member
offsets from the H5Tget_member_offset call for each compound type.
Fortran High-Level APIs
-----------------------
-
Documentation
-------------
-
F90 APIs
--------
-
C++ APIs
--------
-
Testing
-------
- Fixed an allocation in the t_bigio parallel test on 32-bit systems
A test in t_bigio.c attempts to allocate more than 4 GiB of memory,
which will overflow (and wrap) the size_t type on 32-bit systems,
creating a very small allocation instead of a very large allocation.
The test then segfaults when it accesses memory outside of the small
buffer.
The test has been fixed by limiting the buffer to 2 GiB on 32-bit
systems.
Fixes GitHub #2510
- Added skipping of a few parallel tests for OpenMPI 5.0.5
An issue in OpenMPI 5.0.5 causes a few parallel HDF5 tests
(mpiodup, props, fapl_preserve) to fail. These tests are
now skipped for that release of OpenMPI. The issue has
been fixed in the 5.0.6 release of OpenMPI.
Platforms Tested
===================
- HDF5 is tested with the two latest macOS versions that are available
on github runners. As new major macOS versions become available, HDF5
will discontinue support for the older version and add the new latest
version to its list of compatible systems, along with the previous
version.
Linux 6.8.0-1010-aws GNU gcc, gfortran, g++
#10-Ubuntu SMP 2024 x86_64 (Ubuntu 13.2.0-23ubuntu4) 13.2.0
GNU/Linux Ubuntu 24.04 Ubuntu clang version 18.1.3 (1ubuntu1)
Intel(R) oneAPI DPC++/C++ Compiler 2024.2.0
ifx (IFX) 2024.2.0 20240602
(cmake and autotools)
Linux 6.5.0-1018-aws GNU gcc, gfortran, g++
#18-Ubuntu SMP x86_64 GNU/Linux (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
Ubuntu 22.04 Ubuntu clang version 14.0.0-1ubuntu1
Intel(R) oneAPI DPC++/C++ Compiler 2024.0.2
ifx (IFX) 2024.0.2 20231213
(cmake and autotools)
Linux 5.14.21-cray_shasta_c cray-mpich/8.1.28
#1 SMP x86_64 GNU/Linux cce/15.0.0
(frontier) gcc/13.2
(cmake)
Linux 5.14.0-427.24.1.el9_4 GNU gcc, gfortran, g++ (Red Hat 11.4.1-3)
#1 SMP x86_64 GNU/Linux clang version 17.0.6
Rocky 9 Intel(R) oneAPI DPC++/C++ Compiler 2024.2.0
ifx (IFX) 2024.2.0
(cmake and autotools)
Linux-4.18.0-553.16.1.1toss.t4 openmpi/4.1.2
#1 SMP x86_64 GNU/Linux clang 14.0.6
(corona, dane) GCC 12.1.1
Intel(R) oneAPI DPC++/C++ Compiler 2023.2.1
ifx (IFX) 2023.2.1
Linux-4.18.0-553.5.1.1toss.t4 openmpi/4.1/4.1.6
#1 SMP x86_64 GNU/Linux clang 16.0.6
(eclipse) GCC 12.3.0
Intel(R) oneAPI DPC++/C++ Compiler 2024.0.2
ifx (IFX) 2024.0.2
(cmake)
Linux 4.14.0-115.35.1.3chaos spectrum-mpi/rolling-release
#1 SMP ppc64le GNU/Linux clang 17.0.6
(vortex) GCC 12.2.1
nvhpc 24.1
XL 2023.06.28
(cmake)
Linux-4.14.0-115.35.1 spectrum-mpi/rolling-release
#1 SMP ppc64le GNU/Linux clang 14.0.5, 15.0.6
(lassen) GCC 8.3.1
XL 2021.09.22, 2022.08.05
(cmake)
Linux 3.10.0-1160.36.2.el7.ppc64 gcc (GCC) 4.8.5 20150623 (Red Hat 4.8.5-39)
#1 SMP ppc64be GNU/Linux g++ (GCC) 4.8.5 20150623 (Red Hat 4.8.5-39)
Power8 (echidna) GNU Fortran (GCC) 4.8.5 20150623 (Red Hat 4.8.5-39)
Linux 3.10.0-1160.80.1.el7 GNU C (gcc), Fortran (gfortran), C++ (g++)
#1 SMP x86_64 GNU/Linux compilers:
Centos7 Version 4.8.5 20150623 (Red Hat 4.8.5-4)
(jelly/kituo/moohan) Version 4.9.3, Version 7.2.0, Version 8.3.0,
Version 9.1.0, Version 10.2.0
Intel(R) C (icc), C++ (icpc), Fortran (icc)
compilers:
Version 17.0.0.098 Build 20160721
GNU C (gcc) and C++ (g++) 4.8.5 compilers
with NAG Fortran Compiler Release 7.1(Hanzomon)
Intel(R) C (icc) and C++ (icpc) 17.0.0.098 compilers
with NAG Fortran Compiler Release 7.1(Hanzomon)
MPICH 3.1.4 compiled with GCC 4.9.3
MPICH 3.3 compiled with GCC 7.2.0
OpenMPI 3.1.3 compiled with GCC 7.2.0 and 4.1.2
compiled with GCC 9.1.0
PGI C, Fortran, C++ for 64-bit target on
x86_64;
Versions 18.4.0 and 19.10-0
NVIDIA nvc, nvfortran and nvc++ version 22.5-0
(autotools and cmake)
Linux-3.10.0-1160.119.1.1chaos openmpi/4.1.4
#1 SMP x86_64 GNU/Linux clang 16.0.6
(skybridge) Intel(R) oneAPI DPC++/C++ Compiler 2023.2.0
ifx (IFX) 2023.2.0
(cmake)
Linux-3.10.0-1160.90.1.1chaos openmpi/4.1
#1 SMP x86_64 GNU/Linux clang 16.0.6
(attaway) GCC 12.1.0
Intel(R) oneAPI DPC++/C++ Compiler 2024.0.2
ifx (IFX) 2024.0.2
(cmake)
Linux 2.6.32-573.22.1.el6 GNU C (gcc), Fortran (gfortran), C++ (g++)
#1 SMP x86_64 GNU/Linux compilers:
Centos6 Version 4.4.7 20120313
(platypus) Version 4.9.3, 5.3.0, 6.2.0
MPICH 3.1.4 compiled with GCC 4.9.3
PGI C, Fortran, C++ for 64-bit target on
x86_64;
Version 19.10-0
Windows 10 x64 Visual Studio 2019 w/ clang 12.0.0
with MSVC-like command-line (C/C++ only - cmake)
Visual Studio 2019 w/ Intel (C/C++ only - cmake)
Visual Studio 2022 w/ clang 17.0.3
with MSVC-like command-line (C/C++ only - cmake)
Visual Studio 2022 w/ Intel C/C++ oneAPI 2023 (cmake)
Visual Studio 2019 w/ MSMPI 10.1 (C only - cmake)
Known Problems
==============
- When building with the NAG Fortran compiler using the Autotools and libtool
2.4.2 or earlier, the -shared flag will be missing '-Wl,', which will cause
compilation to fail. This is due to a bug in libtool that was fixed in 2012
and released in 2.4.4 in 2014.
- When the library detects and builds in support for the _Float16 datatype, an
issue has been observed on at least one MacOS 14 system where the library
fails to initialize due to not being able to detect the byte order of the
_Float16 type (https://github.com/HDFGroup/hdf5/issues/4310):
#5: H5Tinit_float.c line 308 in H5T__fix_order(): failed to detect byte order
major: Datatype
minor: Unable to initialize object
If this issue is encountered, support for the _Float16 type can be disabled
with a configuration option:
CMake: HDF5_ENABLE_NONSTANDARD_FEATURE_FLOAT16=OFF
Autotools: --disable-nonstandard-feature-float16
- When HDF5 is compiled with NVHPC versions 23.5 - 23.9 (additional versions may
also be applicable) and with -O2 (or higher) and -DNDEBUG, test failures occur
in the following tests:
H5PLUGIN-filter_plugin
H5TEST-flush2
H5TEST-testhdf5-base
MPI_TEST_t_filters_parallel
Sporadic failures (even with lower -O levels):
Java JUnit-TestH5Pfapl
Java JUnit-TestH5D
Also, NVHPC will fail to compile the test/tselect.c test file with a compiler
error of 'use of undefined value' when the optimization level is -O2 or higher.
This is confirmed to be a bug in the nvc compiler that has been fixed as of
23.11. If you are using an affected version of the NVidia compiler, the
work-around is to set the optimization level to -O1.
https://forums.developer.nvidia.com/t/hdf5-no-longer-compiles-with-nv-23-9/269045
- CMake files do not behave correctly with paths containing spaces.
Do not use spaces in paths because the required escaping for handling spaces
results in very complex and fragile build files.
- At present, metadata cache images may not be generated by parallel
applications. Parallel applications can read files with metadata cache
images, but since this is a collective operation, a deadlock is possible
if one or more processes do not participate.
- The subsetting option in ph5diff currently will fail and should be avoided.
The subsetting option works correctly in serial h5diff.
- Flang Fortran compilation will fail (last check version 17) due to not yet
implemented: (1) derived type argument passed by value (H5VLff.F90),
and (2) support for REAL with KIND = 2 in intrinsic SPACING used in testing.
- Fortran tests HDF5_1_8.F90 and HDF5_F03.F90 will fail with Cray compilers
greater than version 16.0 due to a compiler bug. The latest version verified
as failing was version 17.0.
- Several tests currently fail on certain platforms:
MPI_TEST-t_bigio fails with spectrum-mpi on ppc64le platforms.
MPI_TEST-t_subfiling_vfd and MPI_TEST_EXAMPLES-ph5_subfiling fail with
cray-mpich on theta and with XL compilers on ppc64le platforms.
MPI_TEST_testphdf5_tldsc fails with cray-mpich 7.7 on cori and theta.
- File space may not be released when overwriting or deleting certain nested
variable length or reference types.
- Known problems in previous releases can be found in the HISTORY*.txt files
in the HDF5 source. Please report any new problems found to
help@hdfgroup.org.
CMake vs. Autotools installations
=================================
While both build systems produce similar results, there are differences.
Each system produces the same set of folders on Linux (only CMake works
on standard Windows); bin, include, lib and share. Autotools places the
LICENSE and RELEASE.txt file in the root folder, CMake places them in
the share folder.
The bin folder contains the tools and the build scripts. Additionally, CMake
creates dynamic versions of the tools with the suffix "-shared". Autotools
installs one set of tools depending on the "--enable-shared" configuration
option.
build scripts
-------------
Autotools: h5c++, h5cc, h5fc
CMake: h5c++, h5cc, h5hlc++, h5hlcc
The include folder holds the header files and the fortran mod files. CMake
places the fortran mod files into separate shared and static subfolders,
while Autotools places one set of mod files into the include folder. Because
CMake produces a tools library, the header files for tools will appear in
the include folder.
The lib folder contains the library files, and CMake adds the pkgconfig
subfolder with the hdf5*.pc files used by the bin/build scripts created by
the CMake build. CMake separates the C interface code from the fortran code by
creating C-stub libraries for each Fortran library. In addition, only CMake
installs the tools library. The names of the szip libraries are different
between the build systems.
The share folder will have the most differences because CMake builds include
a number of CMake specific files for support of CMake's find_package and support
for the HDF5 Examples CMake project.
The issues with the gif tool are:
HDFFV-10592 CVE-2018-17433
HDFFV-10593 CVE-2018-17436
HDFFV-11048 CVE-2020-10809
These CVE issues have not yet been addressed and are avoided by not building
the gif tool by default. Enable building the High-Level tools with these options:
autotools: --enable-hlgiftools
cmake: HDF5_BUILD_HL_GIF_TOOLS=ON
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