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hdf5/release_docs/RELEASE.txt
Allen Byrne cf58730177 Update Windows platforms
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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 HDF5-1.10.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 HDF5-1.10.3
- Bug Fixes since HDF5-1.10.2
- Supported Platforms
- Tested Configuration Features Summary
- More Tested Platforms
- Known Problems
- CMake vs. Autotools installations
New Features
============
Configuration:
-------------
- 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)
- Update CMake tests to use FIXTURES
CMake test fixtures allow setup/cleanup tests and other dependency
requirements as properties for tests. This is more flexible for
modern CMake code.
(ADB - 2019/07/23, HDFFV-10529)
- Windows PDB files are always installed
There are build configuration or flag settings for Windows that may not
generate PDB files. If those files are not generated then the install
utility will fail because those PDB files are not found. An optional
variable, DISABLE_PDB_FILES, was added to not install PDB files.
(ADB - 2019/07/17, HDFFV-10424)
- Add mingw CMake support with a toolchain file
There has been a number of mingw issues that has been linked under
HDFFV-10845. It has been decided to implement the CMake cross-compiling
technique of toolchain files. We will use a linux platform with the mingw
compiler stack for testing. Only the C language is fully supported, and
the error tests are skipped. The C++ language works for static but shared
builds has a shared library issue with the mingw Standard Exception Handling
library, which is not available on Windows. Fortran has a common cross-compile
problem with the fortran configure tests.
(ADB - 2019/07/12, HDFFV-10845, HDFFV-10595)
- Windows PDB files are installed incorrectly
For static builds, the PDB files for windows should be installed next
to the static libraries in the lib folder. Also the debug versions of
libraries and PDB files are now correctly built using the default
CMAKE_DEBUG_POSTFIX setting.
(ADB - 2019/07/09, HDFFV-10581)
- Add option to build only shared libs
A request was made to prevent building static libraries and only build
shared. A new option was added to CMake, ONLY_SHARED_LIBS, which will
skip building static libraries. Certain utility functions will build with
static libs but are not published. Tests are adjusted to use the correct
libraries depending on SHARED/STATIC settings.
(ADB - 2019/06/12, HDFFV-10805)
- Add options to enable or disable building tools and tests
Configure options --enable-tests and --enable-tools were added for
autotools configure. These options are enabled by default, and can be
disabled with either --disable-tests (or tools) or --enable-tests=no
(or --enable-tools=no). Build time is reduced ~20% when tools are
disabled, 35% when tests are disabled, 45% when both are disabled.
Reenabling them after the initial build requires running configure
again with the option(s) enabled.
(LRK - 2019/06/12, HDFFV-9976)
- Change tools test that test the error stack
There are some use cases which can cause the error stack of tools to be
different then the expected output. These tests now use grepTest.cmake,
this was changed to allow the error file to be searched for an expected string.
(ADB - 2019/04/15, HDFFV-10741)
- Keep stderr and stdout separate in tests
Changed test handling of output capture. Tests now keep the stderr
output separate from the stdout output. It is up to the test to decide
which output to check against a reference. Also added the option
to grep for a string in either output.
(ADB - 2018/12/12, HDFFV-10632)
- Add toolchain and cross-compile support
Added info on using a toolchain file to INSTALL_CMAKE.txt. A
toolchain file is also used in cross-compiling, which requires
CMAKE_CROSSCOMPILING_EMULATOR to be set. To help with cross-compiling
the fortran configure process, the HDF5UseFortran.cmake file macros
were improved. Fixed a Fortran configure file issue that incorrectly
used #cmakedefine instead of #define.
(ADB - 2018/10/04, HDFFV-10594)
- Add warning flags for Intel compilers
Identified Intel compiler specific warnings flags that should be used
instead of GNU flags.
(ADB - 2018/10/04, TRILABS-21)
- Add default rpath to targets
Default rpaths should be set in shared executables and
libraries to allow the use of loading dependent libraries
without requiring LD_LIBRARY_PATH to be set. The default
path should be relative using @rpath on osx and $ORIGIN
on linux. Windows is not affected.
(ADB - 2018/09/26, HDFFV-10594)
- Add missing USE_110_API_DEFAULT option.
Option USE_110_API_DEFAULT sets the default version of
versioned APIs. The bin/makevers perl script did not set
the maxidx variable correctly when the 1.10 branch was
created. This caused the versioning process to always use
the latest version of any API.
(ADB - 2018/08/17, HDFFV-10552)
- Added configuration checks for the following MPI functions:
MPI_Mprobe - Used for the Parallel Compression feature
MPI_Imrecv - Used for the Parallel Compression feature
MPI_Get_elements_x - Used for the "big Parallel I/O" feature
MPI_Type_size_x - Used for the "big Parallel I/O" feature
(JTH - 2018/08/02, HDFFV-10512)
- Added section to the libhdf5.settings file to indicate
the status of the Parallel Compression and "big Parallel I/O"
features.
(JTH - 2018/08/02, HDFFV-10512)
- Add option to execute swmr shell scripts from CMake.
Option TEST_SHELL_SCRIPTS redirects processing into a
separate ShellTests.cmake file for UNIX types. The tests
execute the shell scripts if a SH program is found.
(ADB - 2018/07/16)
Library:
--------
- 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)
- Add S3 and HDFS VFDs to HDF5 maintenance
Fix windows requirements and java tests. Windows requires CMake 3.13.
Install openssl library (with dev files);
from "Shining Light Productions". msi package preferred.
PATH should have been updated with the installation dir.
set ENV variable OPENSSL_ROOT_DIR to the installation dir.
set ENV variable OPENSSL_CONF to the cfg file, likely %OPENSSL_ROOT_DIR%\bin\openssl.cfg
Install libcurl library (with dev files);
download the latest released version using git: https://github.com/curl/curl.git
Open a Visual Studio Command prompt
change to the libcurl root folder
run the "buildconf.bat" batch file
change to the winbuild directory
nmake /f Makefile.vc mode=dll MACHINE=x64
copy libcurl-vc-x64-release-dll-ipv6-sspi-winssl dir to C:\curl (installation dir)
set ENV variable CURL_ROOT to C:\curl (installation dir)
update PATH ENV variable to %CURL_ROOT%\bin (installation bin dir).
the aws credentials file should be in %USERPROFILE%\.aws folder
set the ENV variable "HDF5_ROS3_TEST_BUCKET_URL=https://s3.us-east-2.amazonaws.com/hdf5ros3"
(ADB - 2019/09/12, HDFFV-10854)
- Added new chunk query functions
The following public functions were added to discover information about
the chunks in an HDF5 file.
herr_t H5Dget_num_chunks(dset_id, fspace_id, *nchunks)
herr_t H5Dget_chunk_info_by_coord(dset_id, *coord, *filter_mask, *addr, *size)
herr_t H5Dget_chunk_info(dset_id, fspace_id, index, *coord, *filter_mask, *addr, *size)
(BMR - 2019/06/11, HDFFV-10677)
- Improved the performance of virtual dataset I/O
Refactored the internal dataspace routines used by the virtual dataset
code to improve performance, especially when one of the selections
involved is very long and non-contiguous.
(NAF - 2019/05/31, HDFFV-10693)
- Added the ability to open files with UTF-8 file names on Windows.
The POSIX open(2) API call on Windows is limited to ASCII
file names. The library has been updated to convert incoming file
names to UTF-16 (via MultiByteToWideChar(CP_UTF8, ...) and use
_wopen() instead.
(DER - 2019/03/15, HDFFV-2714, HDFFV-3914, HDFFV-3895, HDFFV-8237, HDFFV-10413, HDFFV-10691)
- Add new API H5M for map objects. Currently not supported by native
library, can be supported by VOL connectors.
(NAF - 2019/03/01)
- Add new H5R_ref_t type for object, dataset region and _attribute_
references. This new type will deprecate the current hobj_ref_t
and hdset_reg_ref_t types for references. Added H5T_REF datatype
to read and write new reference types. As opposed to previous
reference types, reference creation no longer modifies existing
files. New reference types also now support references to external
files.
(JS - 2019/10/08)
- Remove H5I_REFERENCE from the library
This ID class was never used by the library and has been removed.
(DER - 2018/12/08, HDFFV-10252)
- Allow pre-generated H5Tinit.c and H5make_libsettings.c to be used.
Rather than always running H5detect and generating H5Tinit.c and
H5make_libsettings.c, supply a location for those files.
(ADB - 2018/09/18, HDFFV-10332)
Parallel Library:
-----------------
- Changed the default behavior in parallel when reading the same dataset in its entirely
(i.e. H5S_ALL dataset selection) which is being read by all the processes collectively.
The dataset mush be contiguous, less than 2GB, and of an atomic datatype.
The new behavior is the HDF5 library will use an MPI_Bcast to pass the data read from
the disk by the root process to the remain processes in the MPI communicator associated
with the HDF5 file.
(MSB - 2019/01/02, HDFFV-10652)
Fortran Library:
----------------
- Added new Fortran derived type, c_h5o_info_t, which is interoperable with
C's h5o_info_t. This is needed for callback functions which
pass C's h5o_info_t data type definition.
(MSB, 2019/01/08, HDFFV-10443)
- Added new Fortran API, H5gmtime, which converts (C) 'time_t' structure
to Fortran DATE AND TIME storage format.
(MSB, 2019/01/08, HDFFV-10443)
- Added new Fortran 'fields' optional parameter to: h5ovisit_f, h5oget_info_by_name_f,
h5oget_info, h5oget_info_by_idx and h5ovisit_by_name_f.
(MSB, 2019/01/08, HDFFV-10443)
C++ Library:
------------
- Added new wrappers for H5Pset/get_create_intermediate_group()
LinkCreatPropList::setCreateIntermediateGroup()
LinkCreatPropList::getCreateIntermediateGroup()
(BMR - 2019/04/22, HDFFV-10622)
- Added new wrapper for H5Ovisit2()
H5Object::visit()
(BMR - 2019/02/14, HDFFV-10532)
Java Library:
----------------
- 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)
- Fix a failure in JUnit-TestH5P on 32-bit architectures
(JTH - 2019/04/30)
- Duplicate the data read/write functions of Datasets for Attributes.
Region references could not be displayed for attributes as they could
for datasets. Datasets had overloaded read and write functions for different
datatypes that were not available for attributes. After adding similar
functions, attribute region references work normally.
(ADB - 2018/12/12, HDFVIEW-4)
- Removed H5I_REFERENCE from the Java wrappers
This ID class was never used by the library and has been removed
from the Java wrappers.
(DER - 2018/12/08, HDFFV-10252)
Tools:
------
- 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)
- h5repack was fixed to repack datasets with external storage
to other types of storage.
New test added to repack files and verify the correct data using h5diff.
(JS - 2019/09/25, HDFFV-10408)
(ADB - 2019/10/02, HDFFV-10918)
- h5dump was fixed for 128-bit floats, but was missing a test.
New test greps for the first 15 numbers of the 128-bit value.
(ADB - 2019/06/23, HDFFV-9407)
High-Level APIs:
---------------
-
C Packet Table API
------------------
-
Internal header file
--------------------
-
Documentation
-------------
-
Support for new platforms, languages and compilers.
=======================================
-
Bug Fixes since HDF5-1.10.3 release
==================================
Library
-------
- Improved peformance when creating a large number of small datasets by
retrieving default property values from the API context instead of doing
skip list searches.
(CJH - 2019/12/10, HDFFV-10658)
- Fixed user-created data access properties not existing in the property list
returned by H5Dget_access_plist. Thanks to Steven Varga for submitting a
reproducer and a patch.
(CJH - 2019/12/9, HDFFV-10934)
- Fixed an assertion failure in the parallel library when collectively
filling chunks. As it is required that chunks be written in
monotonically non-decreasing order of offset in the file, this assertion
was being triggered when the list of chunk file space allocations being
passed to the collective chunk filling routine was not sorted according
to this particular requirement.
The addition of a sort of the out of order chunks trades a bit of
performance for the elimination of this assertion and of any complaints
from MPI implementations about the file offsets used being out of order.
(JTH - 2019/10/07, HDFFV-10792)
- Fixed the iteration error in test_versionbounds() in test/dtypes.c
The test was supposed to loop through all valid combinations of
low and high bounds in the array versions[], but they were set to
H5F_LIBVER_EARLIEST always without changing.
The problem was fixed by indexing low and high into the array versions[].
(VC - 2019/09/30)
- Fixed the slowness of regular hyperslab selection in a chunked dataset
It was reported that the selection of every 10th element from a 20G
chunked dataset was extremely slow and sometimes could hang the system.
The problem was due to the iteration and the building of the span tree
for all the selected elements in file space.
As the selected elements are going to a 1-d contiguous single block
memory space, the problem was fixed by building regular hyperslab selections
in memory space for the selected elements in file space.
(VC - 2019/09/26, HDFFV-10585)
- Fixed a bug caused by bad tag value when condensing object header
messages
There was an assertion failure when moving meessages from running a
user test program with library release hdf5.1.10.4. It was because
the tag value (object header's address) was not set up when entering
the library routine H5O__chunk_update_idx(), which will eventually
verifies the metadata tag value when protecting the object header.
The problem was fixed by replacing FUNC_ENTER_PACKAGE in H5O__chunk_update_idx()
with FUNC_ENTER_PACKAGE_TAG(oh->cache_info.addr) to set up the metadata tag.
(VC - 2019/08/23, HDFFV-10873)
- Fixed the test failure from test_metadata_read_retry_info() in
test/swmr.c
The test failure is due to the incorrect number of bins returned for
retry info (info.nbins). The # of bins expected for 101 read attempts
is 3 instead of 2. The routine H5F_set_retries() in src/H5Fint.c
calculates the # of bins by first obtaining the log10 value for
(read attempts - 1). For PGI/19, the log10 value for 100 read attempts
is 1.9999999999999998 instead of 2.00000. When casting the log10 value
to unsigned later on, the decimal part is chopped off causing the test
failure.
This was fixed by obtaining the rounded integer value (HDceil) for the
log10 value of read attempts first before casting the result to unsigned.
(VC - 2019/8/14, HDFFV-10813)
- Fixed an issue where creating a file with non-default file space info
together with library high bound setting to H5F_LIBVER_V18.
When setting non-default file space info in fcpl via
H5Pset_file_space_strategy() and then creating a file with
both high and low library bounds set to
H5F_LIBVER_V18 in fapl, the library succeeds in creating the file.
File creation should fail because the feature of setting non-default
file space info does not exist in library release 1.8 or earlier.
This was fixed by setting and checking the proper version in the
file space info message based on the library low and high bounds
when creating and opening the HDF5 file.
(VC - 2019/6/25, HDFFV-10808)
- When iterating over an old-style group (i.e., when not using the latest
file format) of size 0, a NULL pointer representing the empty links
table would be sent to qsort(3) for sorting, which is undefined behavior.
Iterating over an empty group is explicitly tested in the links test.
This has not caused any failures to date and was flagged by gcc's
-fsanitize=undefined.
The library no longer attempts to sort an empty array.
(DER - 2019/06/18, HDFFV-10829)
- Fixed an issue where copying a version 1.8 dataset between files using
H5Ocopy fails due to an incompatible fill version
When using the HDF5 1.10.x H5Ocopy() API call to copy a version 1.8
dataset to a file created with both high and low library bounds set to
H5F_LIBVER_V18, the H5Ocopy() call will fail with the error stack indicating
that the fill value version is out of bounds.
This was fixed by changing the fill value message version to H5O_FILL_VERSION_3
(from H5O_FILL_VERSION_2) for H5F_LIBVER_V18.
(VC - 2019/6/14, HDFFV-10800)
- Some oversights in the index iterating area of the library caused
a callback function to continue iterating even though it's supposed
to stop.
Added the returned value check to the for loop's conditions in
H5EA_iterate(), H5FA_iterate(), and H5D__none_idx_iterate(). The
iteration now stops when it should.
(BMR - 2019/06/11, HDFFV-10661)
- Fixed a bug that would cause an error or cause fill values to be
incorrectly read from a chunked dataset using the "single chunk" index if
the data was held in cache and there was no data on disk.
(NAF - 2019/03/06)
- Fixed a bug that could cause an error or cause fill values to be
incorrectly read from a dataset that was written to using H5Dwrite_chunk
if the dataset was not closed after writing.
(NAF - 2019/03/06, HDFFV-10716)
- Fixed memory leak in scale offset filter
In a special case where the MinBits is the same as the number of bits in
the datatype's precision, the filter's data buffer was not freed, causing
the memory usage to grow. In general the buffer was freed correctly. The
Minbits are the minimal number of bits to store the data values. Please
see the reference manual for H5Pset_scaleoffset for the detail.
(RL - 2019/3/4, HDFFV-10705)
- Fix hangs with collective metadata reads during chunked dataset I/O
In the parallel library, it was discovered that when a particular
sequence of operations following a pattern of:
"write to chunked dataset" -> "flush file" -> "read from dataset"
occurred with collective metadata reads enabled, hangs could be
observed due to certain MPI ranks not participating in the collective
metadata reads.
To fix the issue, collective metadata reads are now disabled during
chunked dataset raw data I/O.
(JTH - 2019/02/11, HDFFV-10563, HDFFV-10688)
- Performance issue when closing an object
The slow down is due to the search of the "tag_list" to find
out the "corked" status of an object and "uncork" it if so.
Improve porformance by skipping the search of the "tag_list"
if there are no "corked" objects when closing an object.
(VC - 2019/2/6)
- Fixed a potential invalid memory access and failure that could occur when
decoding an unknown object header message (from a future version of the
library).
(NAF - 2019/01/07)
- Deleting attributes in dense storage
The library aborts with "infinite loop closing library" after
attributes in dense storage are created and then deleted.
When deleting the attribute nodes from the name index v2 B-tree,
if an attribute is found in the intermediate B-tree nodes,
which may be merged/redistributed in the process, we need to
free the dynamically allocated spaces for the intermediate
decoded attribute.
(VC - 2018/12/26, HDFFV-10659)
- Allow H5detect and H5make_libsettings to take a file as an argument.
Rather than only writing to stdout, add a command argument to name
the file that H5detect and H5make_libsettings will use for output.
Without an argument, stdout is still used, so backwards compatibility
is maintained.
(ADB - 2018/09/05, HDFFV-9059)
- A bug was discovered in the parallel library where an application
would hang if a collective read/write of a chunked dataset occurred
when collective metadata reads were enabled and some of the ranks
had no selection in the dataset's dataspace. The ranks which had no
selection in the dataset's dataspace called H5D__chunk_addrmap() to
retrieve the lowest chunk address in the dataset. This is because we
require reads/writes to be performed in strictly non-decreasing order
of chunk address in the file.
When the chunk index used was a version 1 or 2 B-tree, these
non-participating ranks would issue a collective MPI_Bcast() call
that the participating ranks would not issue, causing the hang. Since
the non-participating ranks are not actually reading/writing anything,
the H5D__chunk_addrmap() call can be safely removed and the address used
for the read/write can be set to an arbitrary number (0 was chosen).
(JTH - 2018/08/25, HDFFV-10501)
- fcntl(2)-based file locking incorrectly passed the lock argument struct
instead of a pointer to the struct, causing errors on systems where
flock(2) is not available.
File locking is used when files are opened to enforce SWMR semantics. A
lock operation takes place on all file opens unless the
HDF5_USE_FILE_LOCKING environment variable is set to the string "FALSE".
flock(2) is preferentially used, with fcntl(2) locks as a backup if
flock(2) is unavailable on a system (if neither is available, the lock
operation fails). On these systems, the file lock will often fail, which
causes HDF5 to not open the file and report an error.
This bug only affects POSIX systems. Win32 builds on Windows use a no-op
locking call which always succeeds. Systems which exhibit this bug will
have H5_HAVE_FCNTL defined but not H5_HAVE_FLOCK in the configure output.
This bug affects HDF5 1.10.0 through 1.10.5.
fcntl(2)-based file locking now correctly passes the struct pointer.
(DER - 2019/08/27, HDFFV-10892)
- Torn pread/pwrite I/O would result in read and write corruption.
In the sec2, log, and core (with backing store) virtual file drivers
(VFDs), the read and write calls incorrectly reset the offset parameter
on torn pread and pwrite operations (i.e., I/O operations which fail to
be written atomically by the OS). For this bug to occur, pread/pwrite
have to be configured (this is the default if they are present on the
system) and the pread/pwrite operation has to fail to transfer all
the bytes, resulting in a multiple pread/pwrite calls.
This feature was initially enabled in HDF5 1.10.5 so the bug is
limited to that version.
(DER - 2019/12/09, HDFFV-10945)
Java Library:
----------------
- JNI native library dependencies
The build for the hdf5_java native library used the wrong
hdf5 target library for CMake builds. Correcting the hdf5_java
library to build with the shared hdf5 library required testing
paths to change also.
(ADB - 2018/08/31, HDFFV-10568)
- Java iterator callbacks
Change global callback object to a small stack structure in order
to fix a runtime crash. This crash was discovered when iterating
through a file with nested group members. The global variable
visit_callback is overwritten when recursion starts. When recursion
completes, visit_callback will be pointing to the wrong callback method.
(ADB - 2018/08/15, HDFFV-10536)
- Java HDFLibraryException class
Change parent class from Exception to RuntimeException.
(ADB - 2018/07/30, HDFFV-10534)
- JNI Read and Write
Refactored variable-length functions, H5DreadVL and H5AreadVL,
to correct dataset and attribute reads. New write functions,
H5DwriteVL and H5AwriteVL, are under construction.
(ADB - 2018/06/02, HDFFV-10519)
Configuration
-------------
- Correct option for default API version
CMake options for default API version are not mutually exclusive.
Change the multiple BOOL options to a single STRING option with the
strings; v16, v18, v110, v112.
(ADB - 2019/08/12, HDFFV-10879)
Performance
-------------
-
Fortran
--------
- Added symbolic links libhdf5_hl_fortran.so to libhdf5hl_fortran.so and
libhdf5_hl_fortran.a to libhdf5hl_fortran.a in hdf5/lib directory for
autotools installs. These were added to match the name of the files
installed by cmake and the general pattern of hl lib files. We will
change the names of the installed lib files to the matching name in
the next major release.
(LRK - 2019/01/04, HDFFV-10596)
- Made Fortran specific subroutines PRIVATE in generic procedures.
Effected generic procedures were functions in H5A, H5D, H5P, H5R and H5T.
(MSB, 2018/12/04, HDFFV-10511)
- Fixed issue with Fortran not returning h5o_info_t field values
meta_size%attr%index_size and meta_size%attr%heap_size.
(MSB, 2018/1/8, HDFFV-10443)
- Corrected INTERFACE INTENT(IN) to INTENT(OUT) for buf_size in h5fget_file_image_f.
(MSB - 2020/2/18, HDFFV-11029)
Tools
-----
-
High-Level APIs:
------
-
Fortran High-Level APIs:
------
-
Documentation
-------------
-
F90 APIs
--------
-
C++ APIs
--------
-
Testing
-------
- Fixed a test failure in testpar/t_dset.c caused by
the test trying to use the parallel filters feature
on MPI-2 implementations.
(JTH, 2019/2/7)
Bug Fixes since HDF5-1.10.2 release
==================================
Library
-------
- Java HDF5LibraryException class
The error minor and major values would be lost after the
constructor executed.
Created two local class variables to hold the values obtained during
execution of the constructor. Refactored the class functions to retrieve
the class values rather then calling the native functions.
The native functions were renamed and called only during execution
of the constructor.
Added error checking to calling class constructors in JNI classes.
(ADB - 2018/08/06, HDFFV-10544)
- Added checks of the defined MPI_VERSION to guard against usage of
MPI-3 functions in the Parallel Compression and "big Parallel I/O"
features when HDF5 is built with MPI-2. Previously, the configure
step would pass but the build itself would fail when it could not
locate the MPI-3 functions used.
As a result of these new checks, HDF5 can again be built with MPI-2,
but the Parallel Compression feature will be disabled as it relies
on the MPI-3 functions used.
(JTH - 2018/08/02, HDFFV-10512)
- User's patches: CVEs
The following patches have been applied:
CVE-2018-11202 - NULL pointer dereference was discovered in
H5S_hyper_make_spans in H5Shyper.c (HDFFV-10476)
https://security-tracker.debian.org/tracker/CVE-2018-11202
https://cve.mitre.org/cgi-bin/cvename.cgi?name=3DCVE-2018-11202
CVE-2018-11203 - A division by zero was discovered in
H5D__btree_decode_key in H5Dbtree.c (HDFFV-10477)
https://security-tracker.debian.org/tracker/CVE-2018-11203
https://cve.mitre.org/cgi-bin/cvename.cgi?name=3DCVE-2018-11203
CVE-2018-11204 - A NULL pointer dereference was discovered in
H5O__chunk_deserialize in H5Ocache.c (HDFFV-10478)
https://security-tracker.debian.org/tracker/CVE-2018-11204
https://cve.mitre.org/cgi-bin/cvename.cgi?name=3DCVE-2018-11204
CVE-2018-11206 - An out of bound read was discovered in
H5O_fill_new_decode and H5O_fill_old_decode in H5Ofill.c
(HDFFV-10480)
https://security-tracker.debian.org/tracker/CVE-2018-11206
https://cve.mitre.org/cgi-bin/cvename.cgi?name=3DCVE-2018-11206
CVE-2018-11207 - A division by zero was discovered in
H5D__chunk_init in H5Dchunk.c (HDFFV-10481)
https://security-tracker.debian.org/tracker/CVE-2018-11207
https://cve.mitre.org/cgi-bin/cvename.cgi?name=3DCVE-2018-11207
(BMR - 2018/7/22, PR#s: 1134 and 1139,
HDFFV-10476, HDFFV-10477, HDFFV-10478, HDFFV-10480, HDFFV-10481)
- H5Adelete
H5Adelete failed when deleting the last "large" attribute that
is stored densely via fractal heap/v2 b-tree.
After removing the attribute, update the ainfo message. If the
number of attributes goes to zero, remove the message.
(VC - 2018/07/20, HDFFV-9277)
- A bug was discovered in the parallel library which caused partial
parallel reads of filtered datasets to return incorrect data. The
library used the incorrect dataspace for each chunk read, causing
the selection used in each chunk to be wrong.
The bug was not caught during testing because all of the current
tests which do parallel reads of filtered data read all of the data
using an H5S_ALL selection. Several tests were added which exercise
partial parallel reads.
(JTH - 2018/07/16, HDFFV-10467)
- A bug was discovered in the parallel library which caused parallel
writes of filtered datasets to trigger an assertion failure in the
file free space manager.
This occurred when the filter used caused chunks to repeatedly shrink
and grow over the course of several dataset writes. The previous chunk
information, such as the size of the chunk and the offset in the file,
was being cached and not updated after each write, causing the next write
to the chunk to retrieve the incorrect cached information and run into
issues when reallocating space in the file for the chunk.
(JTH - 2018/07/16, HDFFV-10509)
- A bug was discovered in the parallel library which caused the
H5D__mpio_array_gatherv() function to allocate too much memory.
When the function is called with the 'allgather' parameter set
to a non-true value, the function will receive data from all MPI
ranks and gather it to the single rank specied by the 'root'
parameter. However, the bug in the function caused memory for
the received data to be allocated on all MPI ranks, not just the
singular rank specified as the receiver. In some circumstances,
this would cause an application to fail due to the large amounts
of memory being allocated.
(JTH - 2018/07/16, HDFFV-10467)
- Error checks in h5stat and when decoding messages
h5stat exited with seg fault/core dumped when
errors are encountered in the internal library.
Add error checks and --enable-error-stack option to h5stat.
Add range checks when decoding messages: old fill value, old
layout and refcount.
(VC - 2018/07/11, HDFFV-10333)
- If an HDF5 file contains a malformed compound datatype with a
suitably large offset, the type conversion code can run off
the end of the type conversion buffer, causing a segmentation
fault.
This issue was reported to The HDF Group as issue #CVE-2017-17507.
NOTE: The HDF5 C library cannot produce such a file. This condition
should only occur in a corrupt (or deliberately altered) file
or a file created by third-party software.
THE HDF GROUP WILL NOT FIX THIS BUG AT THIS TIME
Fixing this problem would involve updating the publicly visible
H5T_conv_t function pointer typedef and versioning the API calls
which use it. We normally only modify the public API during
major releases, so this bug will not be fixed at this time.
(DER - 2018/02/26, HDFFV-10356)
- Inappropriate linking with deprecated MPI C++ libraries
HDF5 does not define *_SKIP_MPICXX in the public headers, so applications
can inadvertently wind up linking to the deprecated MPI C++ wrappers.
MPICH_SKIP_MPICXX and OMPI_SKIP_MPICXX have both been defined in H5public.h
so this should no longer be an issue. HDF5 makes no use of the deprecated
MPI C++ wrappers.
(DER - 2019/09/17, HDFFV-10893)
Configuration
-------------
- Applied patches to address Cywin build issues
There were three issues for Cygwin builds:
- Shared libs were not built.
- The -std=c99 flag caused a SIG_SETMASK undeclared error.
- Undefined errors when buildbing test shared libraries.
Patches to address these issues were received and incorporated in this version.
(LRK - 2018/07/18, HDFFV-10475)
- Moved the location of gcc attribute.
The gcc attribute(no_sanitize), named as the macro HDF_NO_UBSAN,
was located after the function name. Builds with GCC 7 did not
indicate any problem, but GCC 8 issued errors. Moved the
attribute before the function name, as required.
(ADB - 2018/05/22, HDFFV-10473)
- Reworked java test suite into individual JUnit tests.
Testing the whole suite of java unit tests in a single JUnit run
made it difficult to determine actual failures when tests would fail.
Running each file set of tests individually, allows individual failures
to be diagnosed easier. A side benefit is that tests for optional components
of the library can be disabled if not configured.
(ADB - 2018/05/16, HDFFV-9739)
- Converted CMake global commands ADD_DEFINITIONS and INCLUDE_DIRECTORIES
to use target_* type commands. This change modernizes the CMake usage
in the HDF5 library.
In addition, there is the intention to convert to generator expressions,
where possible. The exception is Fortran FLAGS on Windows Visual Studio.
The HDF macros TARGET_C_PROPERTIES and TARGET_FORTRAN_PROPERTIES have
been removed with this change in usage.
The additional language (C++ and Fortran) checks have also been localized
to only be checked when that language is enabled.
(ADB - 2018/05/08)
Performance
-------------
-
Fortran
--------
-
Tools
-----
-
High-Level APIs:
------
-
Fortran High-Level APIs:
------
-
Documentation
-------------
-
F90 APIs
--------
-
C++ APIs
--------
- Adding default arguments to existing functions
Added the following items:
+ Two more property list arguments are added to H5Location::createDataSet:
const DSetAccPropList& dapl = DSetAccPropList::DEFAULT
const LinkCreatPropList& lcpl = LinkCreatPropList::DEFAULT
+ One more property list argument is added to H5Location::openDataSet:
const DSetAccPropList& dapl = DSetAccPropList::DEFAULT
(BMR - 2018/07/21, PR# 1146)
- Improvement C++ documentation
Replaced the table in main page of the C++ documentation from mht to htm format
for portability.
(BMR - 2018/07/17, PR# 1141)
Testing
-------
- The dt_arith test failed on IBM Power8 and Power9 machines when testing
conversions from or to long double types, especially when special values
such as infinity or NAN were involved. In some cases the results differed
by extremely small amounts from those on other machines, while some other
tests resulted in segmentation faults. These conversion tests with long
double types have been disabled for ppc64 machines until the problems are
better understood and can be properly addressed.
(SRL - 2019/01/07, TRILAB-98)
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 7 x64 Visual Studio 2015 w/ Intel C, Fortran 2018 (cmake)
Visual Studio 2015 w/ MSMPI 10 (cmake)
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)
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 7 y y/y n y y y
Windows 7 x64 y y/y y y y y
Windows 7 Cygwin n y/n n y y y
Windows 7 x64 Cygwin 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 7 y y y y
Windows 7 x64 y y y y
Windows 7 Cygwin n n n y
Windows 7 x64 Cygwin n n n 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
Fedora30 5.3.11-200.fc30.x86_64
#1 SMP x86_64 GNU/Linux GNU gcc (GCC) 9.2.1 20190827 (Red Hat 9.2.1 20190827)
GNU Fortran (GCC) 9.2.1 20190827 (Red Hat 9.2.1 20190827)
(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.
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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