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799ec0fde4
hdf5/release_docs/RELEASE.txt
Allen Byrne 799ec0fde4
Small fixes (#285) 
* OESS-98 convert plugin option to FetchContent, add tests

* Fixes for pkcfg files because of plugin option

* OESS-98 fix tools test for plugins

* Keep doxygen comments under 100 chars long - format hint

* Whitespace

* HDFFV-11144 - Reclassify CMake messages

* HDFFV-11099/11100 added help text

* Reworked switch statement to compare string instead

* Fix typo

* Update CDash mode

* Correct name of threadsafe

* Correct option name

* Undo accidental commit

* Small changes plus merge of tools arg parse from 1.12
2021-01-27 07:56:28 -06:00

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HDF5 version 1.13.0 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 The HDF5 web page:
https://portal.hdfgroup.org/display/HDF5/HDF5
The official HDF5 releases can be obtained from:
https://www.hdfgroup.org/downloads/hdf5/
Changes from Release to Release and New Features in the HDF5-1.13.x release series
can be found at:
https://portal.hdfgroup.org/display/HDF5/HDF5+Application+Developer%27s+Guide
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 HDF5-1.12.0
- Supported Platforms
- Tested Configuration Features Summary
- More Tested Platforms
- Known Problems
- CMake vs. Autotools installations
New Features
============
Configuration:
-------------
- CMake option to build the HDF filter plugins project as an external project
The HDF filter plugins project is a collection of registered compression
filters that can be dynamically loaded when needed to access data stored
in a hdf5 file. This CMake-only option allows the plugins to be built and
distributed with the hdf5 library and tools. Like the options for szip and
zlib, either a tgz file or a git repository can be specified for the source.
The option was refactored to use the CMake FetchContent process. This allows
more control over the filter targets, but required external project command
options to be moved to a CMake include file, HDF5PluginCache.cmake. Also
enabled the filter examples to be used as tests for operation of the
filter plugins.
(ADB - 2020/12/10, OESS-98)
- FreeBSD Autotools configuration now defaults to 'cc' and 'c++' compilers
On FreeBSD, the autotools defaulted to 'gcc' as the C compiler and did
not process C++ options. Since FreeBSD 10, the default compiler has
been clang (via 'cc').
The default compilers have been set to 'cc' for C and 'c++' for C++,
which will pick up clang and clang++ respectively on FreeBSD 10+.
Additionally, clang options are now set correctly for both C and C++
and g++ options will now be set if that compiler is being used (an
omission from the former functionality).
(DER - 2020/11/28, HDFFV-11193)
- Fixed POSIX problems when building w/ gcc on Solaris
When building on Solaris using gcc, the POSIX symbols were not
being set correctly, which could lead to issues like clock_gettime()
not being found.
The standard is now set to gnu99 when building with gcc on Solaris,
which allows POSIX things to be #defined and linked correctly. This
differs slightly from the gcc norm, where we set the standard to c99
and manually set POSIX #define symbols.
(DER - 2020/11/25, HDFFV-11191)
- Added a configure-time option to consider certain compiler warnings
as errors
A new configure-time option was added that converts some compiler warnings
to errors. This is mainly intended for library developers and currently
only works for gcc and clang. The warnings that are considered errors
will appear in the generated libhdf5.settings file. These warnings apply
to C and C++ code and will appear in "H5 C Flags" and H5 C++ Flags",
respectively. They will NOT be exported to h5cc, etc.
The default is OFF. Building with this option may fail when compiling
on operating systems and with compiler versions not commonly used by
the library developers. Compilation may also fail when headers not
under the control of the library developers (e.g., mpi.h, hdfs.h) raise
warnings.
Autotools: --enable-warnings-as-errors
CMake: HDF5_ENABLE_WARNINGS_AS_ERRORS
(DER - 2020/11/23, HDFFV-11189)
- Autotools and CMake target added to produce doxygen generated documentation
The default is OFF or disabled.
Autoconf option is '--enable-doxygen'
autotools make target is 'doxygen' and will build all doxygen targets
CMake configure option is 'HDF5_BUILD_DOC'.
CMake target is 'doxygen' for all available doxygen targets
CMake target is 'hdf5lib_doc' for the src subdirectory
(ADB - 2020/11/03)
- CMake option to use MSVC naming conventions with MinGW
HDF5_MSVC_NAMING_CONVENTION option enable to use MSVC naming conventions
when using a MinGW toolchain
(xan - 2020/10/30)
- CMake option to statically link gcc libs with MinGW
HDF5_MINGW_STATIC_GCC_LIBS allows to statically link libg/libstdc++
with the MinGW toolchain
(xan - 2020/10/30)
- CMake option to build the HDF filter plugins project as an external project
The HDF filter plugins project is a collection of registered compression
filters that can be dynamically loaded when needed to access data stored
in a hdf5 file. This CMake-only option allows the plugins to be built and
distributed with the hdf5 library and tools. Like the options for szip and
zlib, either a tgz file or a git repository can be specified for the source.
The necessary options are (see the INSTALL_CMake.txt file):
HDF5_ENABLE_PLUGIN_SUPPORT
PLUGIN_TGZ_NAME or PLUGIN_GIT_URL
There are more options necessary for various filters and the plugin project
documents should be referenced.
(ADB - 2020/09/27, OESS-98)
- Added CMake option to format source files
HDF5_ENABLE_FORMATTERS option will enable creation of targets using the
pattern - HDF5_*_SRC_FORMAT - where * corresponds to the source folder
or tool folder. All sources can be formatted by executing the format target;
make format
(ADB - 2020/08/24)
- Add file locking configure and CMake options
HDF5 1.10.0 introduced a file locking scheme, primarily to help
enforce SWMR setup. Formerly, the only user-level control of the scheme
was via the HDF5_USE_FILE_LOCKING environment variable.
This change introduces configure-time options that control whether
or not file locking will be used and whether or not the library
ignores errors when locking has been disabled on the file system
(useful on some HPC Lustre installations).
In both the Autotools and CMake, the settings have the effect of changing
the default property list settings (see the H5Pset/get_file_locking()
entry, below).
The yes/no/best-effort file locking configure setting has also been
added to the libhdf5.settings file.
Autotools:
An --enable-file-locking=(yes|no|best-effort) option has been added.
yes: Use file locking.
no: Do not use file locking.
best-effort: Use file locking and ignore "disabled" errors.
CMake:
Two self-explanatory options have been added:
HDF5_USE_FILE_LOCKING
HDF5_IGNORE_DISABLED_FILE_LOCKS
Setting both of these to ON is the equivalent to the Autotools'
best-effort setting.
NOTE:
The precedence order of the various file locking control mechanisms is:
1) HDF5_USE_FILE_LOCKING environment variable (highest)
2) H5Pset_file_locking()
3) configure/CMake options (which set the property list defaults)
4) library defaults (currently best-effort)
(DER - 2020/07/30, HDFFV-11092)
- CMake option to link the generated Fortran MOD files into the include
directory.
The Fortran generation of MOD files by a Fortran compile can produce
different binary files between SHARED and STATIC compiles with different
compilers and/or different platforms. Note that it has been found that
different versions of Fortran compilers will produce incompatible MOD
files. Currently, CMake will locate these MOD files in subfolders of
the include directory and add that path to the Fortran library target
in the CMake config file, which can be used by the CMake find library
process. For other build systems using the binary from a CMake install,
a new CMake configuration can be used to copy the pre-chosen version
of the Fortran MOD files into the install include directory.
The default will depend on the configuration of
BUILD_STATIC_LIBS and BUILD_SHARED_LIBS:
YES YES Default to SHARED
YES NO Default to STATIC
NO YES Default to SHARED
NO NO Default to SHARED
The defaults can be overriden by setting the config option
HDF5_INSTALL_MOD_FORTRAN to one of NO, SHARED, or STATIC
(ADB - 2020/07/09, HDFFV-11116)
- CMake option to use AEC (open source SZip) library instead of SZip
The open source AEC library is a replacement library for SZip. In
order to use it for hdf5 the libaec CMake source was changed to add
"-fPIC" and exclude test files. Autotools does not build the
compression libraries within hdf5 builds. New option USE_LIBAEC is
required to compensate for the different files produced by AEC build.
(ADB - 2020/04/22, OESS-65)
- CMake ConfigureChecks.cmake file now uses CHECK_STRUCT_HAS_MEMBER
Some handcrafted tests in HDFTests.c has been removed and the CMake
CHECK_STRUCT_HAS_MEMBER module has been used.
(ADB - 2020/03/24, TRILAB-24)
- Both build systems use same set of warnings flags
GNU C, C++ and gfortran warnings flags were moved to files in a config
sub-folder named gnu-warnings. Flags that only are available for a specific
version of the compiler are in files named with that version.
Clang C warnings flags were moved to files in a config sub-folder
named clang-warnings.
Intel C, Fortran warnings flags were moved to files in a config sub-folder
named intel-warnings.
There are flags in named "error-xxx" files with warnings that may
be promoted to errors. Some source files may still need fixes.
There are also pairs of files named "developer-xxx" and "no-developer-xxx"
that are chosen by the CMake option:HDF5_ENABLE_DEV_WARNINGS or the
configure option:--enable-developer-warnings.
In addition, CMake no longer applies these warnings for examples.
(ADB - 2020/03/24, TRILAB-192)
- Added test script for file size compare
If CMake minimum version is at least 3.14, the fileCompareTest.cmake
script will compare file sizes.
(ADB - 2020/02/24, HDFFV-11036)
- Update CMake minimum version to 3.12
Updated CMake minimum version to 3.12 and added version checks
for Windows features.
(ADB - 2020/02/05, TRILABS-142)
- Fixed CMake include properties for Fortran libraries
Corrected the library properties for Fortran to use the
correct path for the Fortran module files.
(ADB - 2020/02/04, HDFFV-11012)
- Added common warnings files for gnu and intel
Added warnings files to use one common set of flags
during configure for both autotools and CMake build
systems. The initial implementation only affects a
general set of flags for gnu and intel compilers.
(ADB - 2020/01/17)
- Added new options to CMake for control of testing
Added CMake options (default ON);
HDF5_TEST_SERIAL AND/OR HDF5_TEST_PARALLEL
combined with:
HDF5_TEST_TOOLS
HDF5_TEST_EXAMPLES
HDF5_TEST_SWMR
HDF5_TEST_FORTRAN
HDF5_TEST_CPP
HDF5_TEST_JAVA
(ADB - 2020/01/15, HDFFV-11001)
- Added Clang sanitizers to CMake for analyzer support if compiler is clang.
Added CMake code and files to execute the Clang sanitizers if
HDF5_ENABLE_SANITIZERS is enabled and the USE_SANITIZER option
is set to one of the following:
Address
Memory
MemoryWithOrigins
Undefined
Thread
Leak
'Address;Undefined'
(ADB - 2019/12/12, TRILAB-135)
- Update CMake for VS2019 support
CMake added support for VS2019 in version 3.15. Changes to the CMake
generator setting required changes to scripts. Also updated version
references in CMake files as necessary.
(ADB - 2019/11/18, HDFFV-10962)
- Update CMake options to match new autotools options
Add configure options (autotools - CMake):
enable-asserts HDF5_ENABLE_ASSERTS
enable-symbols HDF5_ENABLE_SYMBOLS
enable-profiling HDF5_ENABLE_PROFILING
enable-optimization HDF5_ENABLE_OPTIMIZATION
In addition NDEBUG is no longer forced defined and relies on the CMake
process.
(ADB - 2019/10/07, HDFFV-100901, HDFFV-10637, TRILAB-97)
Library:
--------
- Improved performance of H5Sget_select_elem_pointlist
Modified library to cache the point after the last block of points
retrieved by H5Sget_select_elem_pointlist, so a subsequent call to the
same function to retrieve the next block of points from the list can
proceed immediately without needing to iterate over the point list.
(NAF - 2021/01/19)
- Replaced H5E_ATOM with H5E_ID in H5Epubgen.h
The term "atom" is archaic and not in line with current HDF5 library
terminology, which uses "ID" instead. "Atom" has mostly been purged
from the library internals and this change removes H5E_ATOM from
the H5Epubgen.h (exposed via H5Epublic.h) and replaces it with
H5E_ID.
(DER - 2020/11/24, HDFFV-11190)
- Add new public function H5Ssel_iter_reset
This function resets a dataspace selection iterator back to an
initial state so that it may be used for iteration once more.
This can be useful when needing to iterate over a selection
multiple times without having to repeatedly create/destroy
a selection iterator for that dataspace selection.
(JTH - 2020/09/18)
- Remove HDFS VFD stubs
The original implementation of the HDFS VFD included non-functional
versions of the following public API calls when the HDFS VFD is
not built as a part of the HDF5 library:
* H5FD_hdfs_init()
* H5Pget_fapl_hdfs()
* H5Pset_fapl_hdfs()
They will remain present in HDF5 1.10 and HDF5 1.12 releases
for binary compatibility purposes but have been removed as of 1.14.0.
Note that this has nothing to do with the real HDFS VFD API calls
that are fully functional when the HDFS VFD is configured and built.
We simply changed:
#ifdef LIBHDFS
<real API call>
#else
<useless stub>
#endif
to:
#ifdef LIBHDFS
<real API call>
#endif
Which is how the other optional VFDs are handled.
(DER - 2020/08/27)
- Add Mirror VFD
Use TCP/IP sockets to perform write-only (W/O) file I/O on a remote
machine. Must be used in conjunction with the Splitter VFD.
(JOS - 2020/03/13, TBD)
- Add Splitter VFD
Maintain separate R/W and W/O channels for "concurrent" file writes
to two files using a single HDF5 file handle.
(JOS - 2020/03/13, TBD)
- Refactored public exposure of haddr_t type in favor of "object tokens"
To better accommodate HDF5 VOL connectors where "object addresses in a file"
may not make much sense, the following changes were made to the library:
* Introduced new H5O_token_t "object token" type, which represents a
unique and permanent identifier for referencing an HDF5 object within
a container; these "object tokens" are meant to replace object addresses.
Along with the new type, a new H5Oopen_by_token API call was introduced
to open an object by a token, similar to how object addresses were
previously used with H5Oopen_by_addr.
* Introduced new H5Lget_info2, H5Lget_info_by_idx2, H5Literate2, H5Literate_by_name2,
H5Lvisit2 and H5Lvisit_by_name2 API calls, along with their associated H5L_info2_t
struct and H5L_iterate2_t callback function, which work with the newly-introduced
object tokens, instead of object addresses. The original functions have been
renamed to version 1 functions and are deprecated in favor of the new version 2
functions. The H5L_info_t and H5L_iterate_t types have been renamed to version 1
types and are now deprecated in favor of their version 2 counterparts. For each of
the functions and types, compatibility macros take place of the original symbols.
* Introduced new H5Oget_info3, H5Oget_info_by_name3, H5Oget_info_by_idx3,
H5Ovisit3 and H5Ovisit_by_name3 API calls, along with their associated H5O_info2_t
struct and H5O_iterate2_t callback function, which work with the newly-introduced
object tokens, instead of object addresses. The version 2 functions are now
deprecated in favor of the version 3 functions. The H5O_info_t and H5O_iterate_t
types have been renamed to version 1 types and are now deprecated in favor of their
version 2 counterparts. For each, compatibility macros take place of the original
symbols.
* Introduced new H5Oget_native_info, H5Oget_native_info_by_name and
H5Oget_native_info_by_idx API calls, along with their associated H5O_native_info_t
struct, which are used to retrieve the native HDF5 file format-specific information
about an object. This information (such as object header info and B-tree/heap info)
has been removed from the new H5O_info2_t struct so that the more generic
H5Oget_info(_by_name/_by_idx)3 routines will not try to retrieve it for non-native
VOL connectors.
* Added new H5Otoken_cmp, H5Otoken_to_str and H5Otoken_from_str routines to compare
two object tokens, convert an object token into a nicely-readable string format and
to convert an object token string back into a real object token, respectively.
(DER, QAK, JTH - 2020/01/16)
- Add new public function H5Sselect_adjust.
This function shifts a dataspace selection by a specified logical offset
within the dataspace extent. This can be useful for VOL developers to
implement chunked datasets.
(NAF - 2019/11/18)
- Add new public function H5Sselect_project_intersection.
This function computes the intersection between two dataspace selections
and projects that intersection into a third selection. This can be useful
for VOL developers to implement chunked or virtual datasets.
(NAF - 2019/11/13, ID-148)
- Add new public function H5VLget_file_type.
This function returns a datatype equivalent to the supplied datatype but
with the location set to be in the file. This datatype can then be used
with H5Tconvert to convert data between file and in-memory representation.
This funcition is intended for use only by VOL connector developers.
(NAF - 2019/11/08, ID-127)
Parallel Library:
-----------------
-
Fortran Library:
----------------
- Add wrappers for H5Pset/get_file_locking() API calls
h5pget_file_locking_f()
h5pset_file_locking_f()
See the configure option discussion for HDFFV-11092 (above) for more
information on the file locking feature and how it's controlled.
(DER - 2020/07/30, HDFFV-11092)
C++ Library:
------------
- Add wrappers for H5Pset/get_file_locking() API calls
FileAccPropList::setFileLocking()
FileAccPropList::getFileLocking()
See the configure option discussion for HDFFV-11092 (above) for more
information on the file locking feature and how it's controlled.
(DER - 2020/07/30, HDFFV-11092)
Java Library:
----------------
- Replaced HDF5AtomException with HDF5IdException
Since H5E_ATOM changed to H5E_ID in the C library, the Java exception
that wraps the error category was also renamed. Its functionality
remains unchanged aside from the name.
(See also the HDFFV-11190 note in the C library section)
(DER - 2020/11/24, HDFFV-11190)
- Added new H5S functions.
H5Sselect_copy, H5Sselect_shape_same, H5Sselect_adjust,
H5Sselect_intersect_block, H5Sselect_project_intersection,
H5Scombine_hyperslab, H5Smodify_select, H5Scombine_select
wrapper functions added.
(ADB - 2020/10/27, HDFFV-10868)
- Add wrappers for H5Pset/get_file_locking() API calls
H5Pset_file_locking()
H5Pget_use_file_locking()
H5Pget_ignore_disabled_file_locking()
Unlike the C++ and Fortran wrappers, there are separate getters for the
two file locking settings, each of which returns a boolean value.
See the configure option discussion for HDFFV-11092 (above) for more
information on the file locking feature and how it's controlled.
(DER - 2020/07/30, HDFFV-11092)
- Added ability to test java library with VOLs.
Created new CMake script that combines the java and vol test scripts.
(ADB - 2020/02/03, HDFFV-10996)
- Tests fail for non-English locale.
In the JUnit tests with a non-English locale, only the part before
the decimal comma is replaced by XXXX and this leads to a comparison
error. Changed the regex for the Time substitution.
(ADB - 2020/01/09, HDFFV-10995)
Tools:
------
- h5repack added help text for user-defined filters.
Added help text line that states the valid values of the filter flag
for user-defined filters;
filter_flag: 1 is OPTIONAL or 0 is MANDATORY
(ADB - 2021/01/14, HDFFV-11099)
- Added h5delete tool
Deleting HDF5 storage when using the VOL can be tricky when the VOL
does not create files. The h5delete tool is a simple wrapper around
the H5Fdelete() API call that uses the VOL specified in the
HDF5_VOL_CONNECTOR environment variable to delete a "file". If
the call to H5Fdelete() fails, the tool will attempt to use
the POSIX remove(3) call to remove the file.
Note that the HDF5 library does currently have support for
H5Fdelete() in the native VOL connector.
(DER - 2020/12/16)
- h5repack added options to control how external links are handled.
Currently h5repack preserves external links and cannot copy and merge
data from the external files. Two options, merge and prune, were added to
control how to merge data from an external link into the resulting file.
--merge Follow external soft link recursively and merge data.
--prune Do not follow external soft links and remove link.
--merge --prune Follow external link, merge data and remove dangling link.
(ADB - 2020/08/05, HDFFV-9984)
- h5repack was fixed to repack the reference attributes properly.
The code line that checks if the update of reference inside a compound
datatype is misplaced outside the code block loop that carries out the
check. In consequence, the next attribute that is not the reference
type was repacked again as the reference type and caused the failure of
repacking. The fix is to move the corresponding code line to the correct
code block.
(KY -2020/02/07, HDFFV-11014)
- h5diff was updated to use the new reference APIs.
h5diff uses the new reference APIs to compare references.
Attribute references can also be compared.
(ADB - 2019/12/19, HDFFV-10980)
- h5dump and h5ls were updated to use the new reference APIs.
The tools library now use the new reference APIs to inspect a
file. Also the DDL spec was updated to reflect the format
changes produced with the new APIs. The export API and support
functions in the JNI were updated to match.
(ADB - 2019/12/06, HDFFV-10876 and HDFFV-10877)
High-Level APIs:
---------------
-
C Packet Table API
------------------
-
Internal header file
--------------------
-
Documentation
-------------
-
Support for new platforms, languages and compilers.
=======================================
-
Bug Fixes since HDF5-1.12.0 release
==================================
Library
-------
- Fixed problems with vlens and refs inside compound using
H5VLget_file_type()
Modified library to properly ref count H5VL_object_t structs and only
consider file vlen and reference types to be equal if their files are
the same.
(NAF - 2021/01/22)
- Creation of dataset with optional filter
When the combination of type, space, etc doesn't work for filter
and the filter is optional, it was supposed to be skipped but it was
not skipped and the creation failed.
Allowed the creation of the dataset in such situation.
(BMR - 2020/08/13, HDFFV-10933)
- Explicitly declared dlopen to use RTLD_LOCAL
dlopen documentation states that if neither RTLD_GLOBAL nor
RTLD_LOCAL are specified, then the default behavior is unspecified.
The default on linux is usually RTLD_LOCAL while macos will default
to RTLD_GLOBAL.
(ADB - 2020/08/12, HDFFV-11127)
- H5Sset_extent_none() sets the dataspace class to H5S_NO_CLASS which
causes asserts/errors when passed to other dataspace API calls.
H5S_NO_CLASS is an internal class value that should not have been
exposed via a public API call.
In debug builds of the library, this can cause asserts to trip. In
non-debug builds, it will produce normal library errors.
The new library behavior is for H5Sset_extent_none() to convert
the dataspace into one of type H5S_NULL, which is better handled
by the library and easier for developers to reason about.
(DER - 2020/07/27, HDFFV-11027)
- Fixed issues CVE-2018-13870 and CVE-2018-13869
When a buffer overflow occurred because a name length was corrupted
and became very large, h5dump crashed on memory access violation.
A check for reading pass the end of the buffer was added to multiple
locations to prevent the crashes and h5dump now simply fails with an
error message when this error condition occurs.
(BMR - 2020/07/22, HDFFV-11120 and HDFFV-11121)
- Fixed the segmentation fault when reading attributes with multiple threads
It was reported that the reading of attributes with variable length string
datatype will crash with segmentation fault particularly when the number of
threads is high (>16 threads). The problem was due to the file pointer that
was set in the variable length string datatype for the attribute. That file
pointer was already closed when the attribute was accessed.
The problem was fixed by setting the file pointer to the current opened file pointer
when the attribute was accessed. Similar patch up was done before when reading
dataset with variable length string datatype.
(VC - 2020/07/13, HDFFV-11080)
- Fixed CVE-2020-10810
The tool h5clear produced a segfault during an error recovery in
the superblock decoding. An internal pointer was reset to prevent
further accessing when it is not assigned with a value.
(BMR - 2020/06/29, HDFFV-11053)
- Fixed CVE-2018-17435
The tool h52gif produced a segfault when the size of an attribute
message was corrupted and caused a buffer overflow.
The problem was fixed by verifying the attribute message's size
against the buffer size before accessing the buffer. h52gif was
also fixed to display the failure instead of silently exiting
after the segfault was eliminated.
(BMR - 2020/06/19, HDFFV-10591)
Java Library:
----------------
- The H5FArray.java class, in which virtually the entire execution time
is spent using the HDFNativeData method that converts from an array
of bytes to an array of the destination Java type.
1. Convert the entire byte array into a 1-d array of the desired type,
rather than performing 1 conversion per row;
2. Use the Java Arrays method copyOfRange to grab the section of the
array from (1) that is desired to be inserted into the destination array.
(PGT,ADB - 2020/12/13, HDFFV-10865)
- Added ability to test java library with VOLs.
Created new CMake script that combines the java and vol test scripts.
(ADB - 2020/02/03, HDFFV-10996)
- Tests fail for non-English locale.
In the JUnit tests with a non-English locale, only the part before
the decimal comma is replaced by XXXX and this leads to a comparison
error. Changed the regex for the Time substitution.
(ADB - 2020/01/09, HDFFV-10995)
Configuration
-------------
- Reclassify CMake messages, to allow new modes and --log-level option
CMake message commands have a mode argument. By default, STATUS mode
was chosen for any non-error message. CMake version 3.15 added additional
modes, NOTICE, VERBOSE, DEBUG and TRACE. All message commands with a mode
of STATUS were reviewed and most were reclassified as VERBOSE. The new
mode was protected by a check for a CMake version of at least 3.15. If CMake
version 3.17 or above is used, the user can use the command line option
of "--log-level" to further restrict which message commands are displayed.
(ADB - 2021/01/11, HDFFV-11144)
- Fixes Autotools determination of the stat struct having an st_blocks field
A missing parenthesis in an autoconf macro prevented building the test
code used to determine if the stat struct contains the st_blocks field.
Now that the test functions correctly, the H5_HAVE_STAT_ST_BLOCKS #define
found in H5pubconf.h will be defined correctly on both the Autotools and
CMake. This #define is only used in the tests and does not affect the
HDF5 C library.
(DER - 2021/01/07, HDFFV-11201)
Tools
-----
- Fixed tools argument parsing.
Tools parsing used the length of the option from the long array to match
the option from the command line. This incorrectly matched a shorter long
name option that was happened to be a subset of another long option.
Changed to match whole names.
(ADB - 2021/01/19, HDFFV-11106)
- The tools library was updated by standardizing the error stack process.
General sequence is:
h5tools_setprogname(PROGRAMNAME);
h5tools_setstatus(EXIT_SUCCESS);
h5tools_init();
... process the command-line (check for error-stack enable) ...
h5tools_error_report();
... (do work) ...
h5diff_exit(ret);
(ADB - 2020/07/20, HDFFV-11066)
- h5diff fixed a command line parsing error.
h5diff would ignore the argument to -d (delta) if it is smaller than DBL_EPSILON.
The macro H5_DBL_ABS_EQUAL was removed and a direct value comparision was used.
(ADB - 2020/07/20, HDFFV-10897)
- h5diff added a command line option to ignore attributes.
h5diff would ignore all objects with a supplied path if the exclude-path argument is used.
Adding the exclude-attribute argument will only eclude attributes, with the supplied path,
from comparision.
(ADB - 2020/07/20, HDFFV-5935)
- h5diff added another level to the verbose argument to print filenames.
Added verbose level 3 that is level 2 plus the filenames. The levels are:
0 : Identical to '-v' or '--verbose'
1 : All level 0 information plus one-line attribute status summary
2 : All level 1 information plus extended attribute status report
3 : All level 2 information plus file names
(ADB - 2020/07/20, HDFFV-10005)
- h5repack was fixed to repack the reference attributes properly.
The code line that checks if the update of reference inside a compound
datatype is misplaced outside the code block loop that carries out the
check. In consequence, the next attribute that is not the reference
type was repacked again as the reference type and caused the failure of
repacking. The fix is to move the corresponding code line to the correct
code block.
(KY -2020/02/10, HDFFV-11014)
- h5diff was updated to use the new reference APIs.
h5diff uses the new reference APIs to compare references.
Attribute references can also be compared.
(ADB - 2019/12/19, HDFFV-10980)
- h5dump and h5ls were updated to use the new reference APIs.
The tools library now use the new reference APIs to inspect a
file. Also the DDL spec was updated to reflect the format
changes produced with the new APIs. The export API and support
functions in the JNI were updated to match.
(ADB - 2019/12/06, HDFFV-10876 and HDFFV-10877)
Performance
-------------
-
Fortran API
--------
- Corrected INTERFACE INTENT(IN) to INTENT(OUT) for buf_size in h5fget_file_image_f.
(MSB - 2020/02/18, HDFFV-11029)
High-Level Library
------
-
Fortran High-Level APIs:
------
-
Documentation
-------------
-
F90 APIs
--------
-
C++ APIs
--------
-
Testing
-------
- Stopped java/test/junit.sh.in installing libs for testing under ${prefix}
Lib files needed are now copied to a subdirectory in the java/test
directory, and on Macs the loader path for libhdf5.xxxs.so is changed
in the temporary copy of libhdf5_java.dylib.
(LRK, 2020/07/02, HDFFV-11063)
Supported Platforms
===================
Linux 2.6.32-696.16.1.el6.ppc64 gcc (GCC) 4.4.7 20120313 (Red Hat 4.4.7-18)
#1 SMP ppc64 GNU/Linux g++ (GCC) 4.4.7 20120313 (Red Hat 4.4.7-18)
(ostrich) GNU Fortran (GCC) 4.4.7 20120313 (Red Hat 4.4.7-18)
IBM XL C/C++ V13.1
IBM XL Fortran V15.1
Linux 3.10.0-327.10.1.el7 GNU C (gcc), Fortran (gfortran), C++ (g++)
#1 SMP x86_64 GNU/Linux compilers:
(kituo/moohan) Version 4.8.5 20150623 (Red Hat 4.8.5-4)
Version 4.9.3, Version 5.2.0,
Intel(R) C (icc), C++ (icpc), Fortran (icc)
compilers:
Version 17.0.0.098 Build 20160721
MPICH 3.1.4 compiled with GCC 4.9.3
SunOS 5.11 32- and 64-bit Sun C 5.12 SunOS_sparc
(emu) Sun Fortran 95 8.6 SunOS_sparc
Sun C++ 5.12 SunOS_sparc
Windows 10 x64 Visual Studio 2015 w/ Intel Fortran 18 (cmake)
Visual Studio 2017 w/ Intel Fortran 19 (cmake)
Visual Studio 2019 w/ Intel Fortran 19 (cmake)
Visual Studio 2019 w/ MSMPI 10.1 (cmake)
Mac OS X Yosemite 10.10.5 Apple clang/clang++ version 6.1 from Xcode 7.0
64-bit gfortran GNU Fortran (GCC) 4.9.2
(osx1010dev/osx1010test) Intel icc/icpc/ifort version 15.0.3
Mac OS X El Capitan 10.11.6 Apple clang/clang++ version 7.3.0 from Xcode 7.3
64-bit gfortran GNU Fortran (GCC) 5.2.0
(osx1011dev/osx1011test) Intel icc/icpc/ifort version 16.0.2
Mac OS Sierra 10.12.6 Apple LLVM version 8.1.0 (clang/clang++-802.0.42)
64-bit gfortran GNU Fortran (GCC) 7.1.0
(swallow/kite) Intel icc/icpc/ifort version 17.0.2
Tested Configuration Features Summary
=====================================
In the tables below
y = tested
n = not tested in this release
C = Cluster
W = Workstation
x = not working in this release
dna = does not apply
( ) = footnote appears below second table
<blank> = testing incomplete on this feature or platform
Platform C F90/ F90 C++ zlib SZIP
parallel F2003 parallel
Solaris2.11 32-bit n y/y n y y y
Solaris2.11 64-bit n y/n n y y y
Windows 10 y y/y n y y y
Windows 10 x64 y y/y n y y y
Mac OS X Mountain Lion 10.8.5 64-bit n y/y n y y y
Mac OS X Mavericks 10.9.5 64-bit n y/y n y y ?
Mac OS X Yosemite 10.10.5 64-bit n y/y n y y ?
Mac OS X El Capitan 10.11.6 64-bit n y/y n y y ?
CentOS 6.7 Linux 2.6.18 x86_64 GNU n y/y n y y y
CentOS 6.7 Linux 2.6.18 x86_64 Intel n y/y n y y y
CentOS 6.7 Linux 2.6.32 x86_64 PGI n y/y n y y y
CentOS 7.2 Linux 2.6.32 x86_64 GNU y y/y y y y y
CentOS 7.2 Linux 2.6.32 x86_64 Intel n y/y n y y y
Linux 2.6.32-573.18.1.el6.ppc64 n y/n n y y y
Platform Shared Shared Shared Thread-
C libs F90 libs C++ libs safe
Solaris2.11 32-bit y y y y
Solaris2.11 64-bit y y y y
Windows 10 y y y y
Windows 10 x64 y y y y
Mac OS X Mountain Lion 10.8.5 64-bit y n y y
Mac OS X Mavericks 10.9.5 64-bit y n y y
Mac OS X Yosemite 10.10.5 64-bit y n y y
Mac OS X El Capitan 10.11.6 64-bit y n y y
CentOS 6.7 Linux 2.6.18 x86_64 GNU y y y y
CentOS 6.7 Linux 2.6.18 x86_64 Intel y y y n
CentOS 6.7 Linux 2.6.32 x86_64 PGI y y y n
CentOS 7.2 Linux 2.6.32 x86_64 GNU y y y n
CentOS 7.2 Linux 2.6.32 x86_64 Intel y y y n
Linux 2.6.32-573.18.1.el6.ppc64 y y y n
Compiler versions for each platform are listed in the preceding
"Supported Platforms" table.
More Tested Platforms
=====================
The following platforms are not supported but have been tested for this release.
Linux 2.6.32-573.22.1.el6 GNU C (gcc), Fortran (gfortran), C++ (g++)
#1 SMP x86_64 GNU/Linux compilers:
(mayll/platypus) Version 4.4.7 20120313
Version 4.9.3, 5.3.0, 6.2.0
PGI C, Fortran, C++ for 64-bit target on
x86-64;
Version 17.10-0
Intel(R) C (icc), C++ (icpc), Fortran (icc)
compilers:
Version 17.0.4.196 Build 20170411
MPICH 3.1.4 compiled with GCC 4.9.3
Linux 3.10.0-327.18.2.el7 GNU C (gcc) and C++ (g++) compilers
#1 SMP x86_64 GNU/Linux Version 4.8.5 20150623 (Red Hat 4.8.5-4)
(jelly) with NAG Fortran Compiler Release 6.1(Tozai)
GCC Version 7.1.0
OpenMPI 3.0.0-GCC-7.2.0-2.29
Intel(R) C (icc) and C++ (icpc) compilers
Version 17.0.0.098 Build 20160721
with NAG Fortran Compiler Release 6.1(Tozai)
Linux 3.10.0-327.10.1.el7 MPICH 3.2 compiled with GCC 5.3.0
#1 SMP x86_64 GNU/Linux
(moohan)
Linux 2.6.32-573.18.1.el6.ppc64 MPICH mpich 3.1.4 compiled with
#1 SMP ppc64 GNU/Linux IBM XL C/C++ for Linux, V13.1
(ostrich) and IBM XL Fortran for Linux, V15.1
Fedora32 5.8.18-200.fc32.x86_64
#1 SMP x86_64 GNU/Linux GNU gcc (GCC) 10.2.1 20201016 (Red Hat 10.2.1-6)
GNU Fortran (GCC) 10.2.1 20201016 (Red Hat 10.2.1-6)
clang version 10.0.1 (Fedora 10.0.1-3.fc32)
(cmake and autotools)
Ubuntu20.10 -5.8.0-29-generic-x86_64
#31-Ubuntu SMP x86_64 GNU/Linux GNU gcc (GCC) 10.2.0-13ubuntu1
GNU Fortran (GCC) 10.2.0-13ubuntu1
(cmake and autotools)
Known Problems
==============
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.
ADB - 2019/05/07
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.
CPP ptable test fails on both VS2017 and VS2019 with Intel compiler, JIRA
issue: HDFFV-10628. This test will pass with VS2015 with Intel compiler.
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
COPYING 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.
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