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1 released on 2017-04-27
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INTRODUCTION
Links to HDF5 1.10.1 source code, documentation, and additional materials can
be found on The HDF5 web page at:
https://support.hdfgroup.org/HDF5/
https://support.hdfgroup.org/HDF5/release/obtain5.html
User documentation for the snapshot can be accessed directly at this location:
https://support.hdfgroup.org/HDF5/doc/
https://support.hdfgroup.org/HDF5/docNewFeatures/index.html
All new and modified APIs are listed in detail in the "HDF5 Software Changes
from Release to Release" document, in the section "Release 10.1 (current
release) versus Release 1.10.0
https://support.hdfgroup.org/HDF5/doc/ADGuide/Changes.html
If you have any questions or comments, please send them to the HDF Help Desk:
help@hdfgroup.org
CONTENTS
For links to the RFCs and documentation in this section please view
https://support.hdfgroup.org/HDF5/docNewFeatures in a web browser.
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Metadata Cache Image
________________________________________
HDF5 metadata is typically small, and scattered throughout the HDF5 file.
This can affect performance, particularly on large HPC systems. The
Metadata Cache Image feature can improve performance by writing the
metadata cache in a single block on file close, and then populating the
cache with the contents of this block on file open, thus avoiding the many
small I/O operations that would otherwise be required on file open and
close. See the RFC for complete details regarding this feature. Also,
see the Fine Tuning the Metadata Cache documentation.
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Metadata Cache Evict on Close
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Paged Aggregation
________________________________________
The current HDF5 file space allocation accumulates small pieces of metadata
and raw data in aggregator blocks which are not page aligned and vary
widely in sizes. The paged aggregation feature was implemented to provide
efficient paged access of these small pieces of metadata and raw data.
See the RFC for details. Also, see the File Space Management documentation.
________________________________________
Page Buffering
________________________________________
Small and random I/O accesses on parallel file systems result in poor
performance for applications. Page buffering in conjunction with paged
aggregation can improve performance by giving an application control of
minimizing HDF5 I/O requests to a specific granularity and alignment.
See the RFC for details. Also, see the Page Buffering documentation.
Library
-------
- Added a mechanism for disabling the SWMR file locking scheme.
- The direct I/O VFD has been removed from the list of VFDs that
support SWMR.
Configuration:
--------------
- The minimum version of CMake required to build HDF5 is now 3.2.2.
(ADB, 2017/01/10)
This disables warnings that do not indicate poor code quality such
as -Winline and gcc's -Wsuggest-attribute. Developer warnings are
disabled by default.
(DER, 2017/01/10)
(DER, 2016/11/08)
Fortran Library:
----------------
- The HDF5 Fortran library can now be compiled with the NAG compiler.
C++ Library:
------------
- The following C++ API wrappers have been added to the C++ Library:
// Sets/Gets the strategy and the threshold value that the library
// will employ in managing file space.
FileCreatPropList::setFileSpaceStrategy - H5Pset_file_space_strategy
FileCreatPropList::getFileSpaceStrategy - H5Pget_file_space_strategy
ArrayType::getArrayNDims() const
ArrayType::getArrayDims() const
both to replace the non-const versions.
Tools:
------
- The following options have been added to h5clear:
-s: clear the status_flags field in the file's superblock
-m: Remove the metadata cache image from the file
High-Level APIs:
---------------
- Added New Fortran 2003 API for h5tbmake_table_f.
* Decoding data from a corrupted file with a dataset encoded with the
H5Z_NBIT decoding can result in a code execution vulnerability under
the context of the application using the HDF5 library.
* When decoding an array datatype from a corrupted file, the HDF5 library
fails to return an error in production if the number of dimensions
decoded is greater than the maximum rank.
* When decoding an "old style" array datatype from a corrupted file, the
HDF5 library fails to return an error in production if the number of
dimensions decoded is greater than the maximum rank.
- Fixed an error that would occur when copying an object with an attribute
which is a compound datatype consisting of a variable length string.
- Fixed a problem where a plugin compiled into a DLL in the default plugin
directory could not be found by the HDF5 library at runtime on Windows
when the HDF5_PLUGIN_PATH environment variable was not set.
- (a) Throw an error instead of assertion when v1 btree level hits the 1
byte limit.
(b) Modifications to better handle error recovery when conversion by
h5format_convert fails.
- Fixed a memory leak where an array used by the library to track SWMR
read retries was unfreed.
The leaked memory was small (on the order of a few tens of ints) and
allocated per-file. The memory was allocated (and lost) only when a
file was opened for SWMR access.
- Fixed a memory leak that could occur when opening a file for the first
time (including creating) and the call fails.
This occurred when the file-driver-specific info was not cleaned up.
The amount of memory leaked varied with the file driver, but would
normally be less than 1 kB.
Parallel Library
----------------
- Fixed a bug that could occur when allocating a chunked dataset in parallel
with an alignment set and an alignment threshold greater than the chunk
size but less than or equal to the raw data aggregator size.
Configuration
-------------
- Configuration will check for the strtoll and strtoull functions
before using alternatives
- Makefiles and test scripts have been updated to correctly remove files
created when running "make check" and to avoid removing any files under
source control. In-source builds followed by "make clean" and "make
distclean" should result in the original source files.
- The tools directory has been divided into two separate source and test
directories. This resolves a build dependency and, as a result,
'make check' will no longer fail in the tools directory if 'make' was
not executed first.
- CMake: Fixed a timeout error that would occasionally occur when running
the virtual file driver tests simultaneously due to test directory
and file name collisions.
Fortran
--------
- Changed H5S_ALL_F from INTEGER to INTEGER(HID_T)
Tools
-----
- h5diff now correctly ignores strpad in comparing strings.
- h5diff now correctly returns an error when it cannot read data due
to an unavailable filter plugin.
- h5repack User Defined (UD) filter parameters were not parsed correctly.
The UD filter parameters were not being parsed correctly. Reworked coding
section to parse the correct values and verify number of parameters.
C++ APIs
--------
- The member function H5Location::getNumObjs() is moved to
class Group because the objects are in a group or a file only,
and H5Object::getNumAttrs to H5Location to get the number of
attributes at a given location.
- The high-level API Packet Table (PT) did not write data correctly when
the datatype is a compound type that has string type as one of the
members. This problem started in 1.8.15, after the fix of HDFFV-9042
was applied, which caused the Packet Table to use native type to access
the data. It should be up to the application to specify whether the
buffer to be read into memory is in the machine's native architecture.
Thus, the PT is fixed to not use native type but to make a copy of the
user's provided datatype during creation or the packet table's datatype
during opening. If an application wishes to use native type to read the
data, then the application will request that. However, the Packet Table
doesn't provide a way to specify memory datatype in this release. This
feature will be available in future releases.
Testing
-------
- Fixed a problem that caused tests using SWMR to occasionally fail when
running "make check" using parallel make.
Supported Platforms
===================
Mac OS X Mt. Lion 10.8.5 Apple clang/clang++ version 5.1 from Xcode 5.1
64-bit gfortran GNU Fortran (GCC) 4.8.2
(swallow/kite) Intel icc/icpc/ifort version 15.0.3
Mac OS X Mavericks 10.9.5 Apple clang/clang++ version 6.0 from Xcode 6.2
64-bit gfortran GNU Fortran (GCC) 4.9.2
(wren/quail) Intel icc/icpc/ifort version 15.0.3
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 from Xcode 7.3
64-bit gfortran GNU Fortran (GCC) 5.2.0
(osx1010dev/osx1010test) Intel icc/icpc/ifort version 16.0.2
The following platforms are not supported but have been tested for this release.
Known Problems
==============