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HDF5 History
============
This file contains development history of the HDF5 1.10 branch
03. Release Information for hdf5-1.10.1
02. Release Information for hdf5-1.10.0-patch1
01. Release Information for hdf5-1.10.0
[Search on the string '%%%%' for section breaks of each release.]
%%%%1.10.1%%%%
HDF5 version 1.10.1 released on 2017-04-27
================================================================================
INTRODUCTION
This document describes the differences between HDF5-1.10.0-patch1 and
HDF5 1.10.1, and contains information on the platforms tested and known
problems in HDF5-1.10.1. For more details check the HISTORY*.txt files
in the HDF5 source.
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/
The HDF5 1.10.1 release can be obtained from:
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/
New features in the HDF5-1.10.x release series, including brief general
descriptions of some new and modified APIs, are described in the "New Features
in HDF5 Release 1.10" document:
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
- Major New Features Introduced in HDF5 1.10.1
- Other New Features and Enhancements
- Support for New Platforms, Languages, and Compilers
- Bug Fixes since HDF5-1.10.0-patch1
- Supported Platforms
- Tested Configuration Features Summary
- More Tested Platforms
- Known Problems
Major New Features Introduced in HDF5 1.10.1
============================================
For links to the RFCs and documentation in this section please view
https://support.hdfgroup.org/HDF5/docNewFeatures in a web browser.
________________________________________
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.
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.
________________________________________
Metadata Cache Evict on Close
________________________________________
The HDF5 library's metadata cache is fairly conservative about holding on
to HDF5 object metadata (object headers, chunk index structures, etc.),
which can cause the cache size to grow, resulting in memory pressure on
an application or system. The "evict on close" property will cause all
metadata for an object to be evicted from the cache as long as metadata
is not referenced from any other open object. See the Fine Tuning the
Metadata Cache documentation for information on the APIs.
At present, evict on close is disabled in parallel builds.
________________________________________
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.
At present, page buffering is disabled in parallel builds.
Other New Features and Enhancements
===================================
Library
-------
- Added a mechanism for disabling the SWMR file locking scheme.
The file locking calls used in HDF5 1.10.0 (including patch1)
will fail when the underlying file system does not support file
locking or where locks have been disabled. To disable all file
locking operations, an environment variable named
HDF5_USE_FILE_LOCKING can be set to the five-character string
'FALSE'. This does not fundamentally change HDF5 library
operation (aside from initial file open/create, SWMR is lock-free),
but users will have to be more careful about opening files
to avoid problematic access patterns (i.e.: multiple writers)
that the file locking was designed to prevent.
Additionally, the error message that is emitted when file lock
operations set errno to ENOSYS (typical when file locking has been
disabled) has been updated to describe the problem and potential
resolution better.
(DER, 2016/10/26, HDFFV-9918)
- The return type of H5Pget_driver_info() has been changed from void *
to const void *.
The pointer returned by this function points to internal library
memory and should not be freed by the user.
(DER, 2016/11/04, HDFFV-10017)
- The direct I/O VFD has been removed from the list of VFDs that
support SWMR.
This configuration was never officially tested and several SWMR
tests fail when this VFD is set.
(DER, 2016/11/03, HDFFV-10169)
Configuration:
--------------
- The minimum version of CMake required to build HDF5 is now 3.2.2.
(ADB, 2017/01/10)
- An --enable/disable-developer-warnings option has been added to
configure.
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)
- A bin/restore.sh script was added that reverts autogen.sh processing.
(DER, 2016/11/08)
- CMake: Added NAMESPACE hdf5:: to package configuration files to allow
projects using installed HDF5 binaries built with CMake to link with
them without specifying the HDF5 library location via IMPORTED_LOCATION.
(ABD, 2016/10/17, HDFFV-10003)
- CMake: Changed the CTEST_BUILD_CONFIGURATION option to
CTEST_CONFIGURATION_TYPE as recommended by the CMake documentation.
(ABD, 2016/10/17, HDFFV-9971)
Fortran Library:
----------------
- The HDF5 Fortran library can now be compiled with the NAG compiler.
(MSB, 2017/2/10, HDFFV-9973)
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
// Sets/Gets the file space page size for paged aggregation.
FileCreatPropList::setFileSpacePagesize - H5Pset_file_space_page_size
FileCreatPropList::getFileSpacePagesize - H5Pget_file_space_page_size
// Checks if the given ID is valid.
IdComponent::isValid - H5Iis_valid
// Sets/Gets the number of soft or user-defined links that can be
// traversed before a failure occurs.
LinkAccPropList::setNumLinks - H5Pset_nlinks
LinkAccPropList::getNumLinks - H5Pget_nlinks
// Returns a copy of the creation property list of a datatype.
DataType::getCreatePlist - H5Tget_create_plist
// Opens/Closes an object within a group or a file, regardless of object
// type
Group::getObjId - H5Oopen
Group::closeObjId - H5Oclose
// Maps elements of a virtual dataset to elements of the source dataset.
DSetCreatPropList::setVirtual - H5Pset_virtual
// Gets general information about this file.
H5File::getFileInfo - H5Fget_info2
// Returns the number of members in a type.
IdComponent::getNumMembers - H5Inmembers
// Determines if an element type exists.
IdComponent::typeExists - H5Itype_exists
// Determines if an object exists.
H5Location::exists - H5Lexists.
// Returns the header version of an HDF5 object.
H5Object::objVersion - H5Oget_info for version
(BMR, 2017/03/20, HDFFV-10004, HDFFV-10139, HDFFV-10145)
- New exception: ObjHeaderIException for H5O interface.
(BMR, 2017/03/15, HDFFV-10145)
- New class LinkAccPropList for link access property list, to be used by
wrappers of H5Lexists.
(BMR, 2017/01/04, HDFFV-10145)
- New constructors to open datatypes in ArrayType, CompType, DataType,
EnumType, FloatType, IntType, StrType, and VarLenType.
(BMR, 2016/12/26, HDFFV-10056)
- New member functions:
DSetCreatPropList::setNbit() to setup N-bit compression for a dataset.
ArrayType::getArrayNDims() const
ArrayType::getArrayDims() const
both to replace the non-const versions.
(BMR, 2016/04/25, HDFFV-8623, HDFFV-9725)
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
(QAK, 2017/03/22, PR#361)
High-Level APIs:
---------------
- Added New Fortran 2003 API for h5tbmake_table_f.
(MSB, 2017/02/10, HDFFV-8486)
Support for New Platforms, Languages, and Compilers
===================================================
- Added NAG compiler
Bug Fixes since HDF5-1.10.0-patch1 release
==================================
Library
-------
- Outdated data structure was used in H5D_CHUNK_DEBUG blocks, causing
compilation errors when H5D_CHUNK_DEBUG was defined. This is fixed.
(BMR, 2017/04/04, HDFFV-8089)
- SWMR implementation in the HDF5 1.10.0 and 1.10.0-patch1 releases has a
broken metadata flush dependency that manifested itself with the following
error at the end of the HDF5 error stack:
H5Dint.c line 846 in H5D__swmr_setup(): dataspace chunk index must be 0
for SWMR access, chunkno = 1
major: Dataset
minor: Bad value
It was also reported at https://github.com/areaDetector/ADCore/issues/203
The flush dependency is fixed in this release.
- Changed the plugins dlopen option from RTLD_NOW to RTLD_LAZY
(ABD, 2016/12/12, PR#201)
- A number of issues were fixed when reading/writing from/to corrupted
files to ensure that the library fails gracefully in these cases:
* Writing to a corrupted file that has an object message which is
incorrectly marked as sharable on disk results in a buffer overflow /
invalid write instead of a clean error message.
* 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.
(NAF, 2016/10/06, HDFFV-9950, HDFFV-9951, HDFFV-9992, HDFFV-9993)
- Fixed an error that would occur when copying an object with an attribute
which is a compound datatype consisting of a variable length string.
(VC, 2016/08/24, HDFFV-7991)
- H5DOappend will no longer fail if a dataset has no append callback
registered.
(VC, 2016/08/14, HDFFV-9960)
- Fixed an issue where H5Pset_alignment could result in misaligned blocks
with some input combinations, causing an assertion failure in debug mode.
(NAF, 2016/08/11, HDFFV-9948)
- 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.
(ABD, 2016/08/01, HDFFV-9706)
- Fixed an error that would occur when calling H5Adelete on an attribute
which is attached to an externally linked object in the target file and
whose datatype is a committed datatype in the main file.
(VC, 2016/07/06, HDFFV-9940)
- (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.
(VC, 2016/05/29, HDFFV-9434)
- 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.
(DER, 2016/04/27, HDFFV-9786)
- 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.
(DER, 2016/12/06, HDFFV-10168)
- Fixed a failure in collective metadata writes.
This failure only appeared when collective metadata writes
were enabled (via H5Pset_coll_metadata_write()).
(JRM, 2017/04/10, HDFFV-10055)
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.
(NAF, 2016/08/11, HDFFV-9969)
Configuration
-------------
- Configuration will check for the strtoll and strtoull functions
before using alternatives
(ABD, 2017/03/17, PR#340)
- CMake uses a Windows pdb directory variable if available and
will generate both static and shared pdb files.
(ABD, 2017/02/06, HDFFV-9875)
- CMake now builds shared versions of tools.
(ABD, 2017/02/01, HDFFV-10123)
- 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.
(LRK, 2017/01/17, HDFFV-10099)
- 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.
(ABD, 2016/10/27, HDFFV-9719)
- 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.
(ABD, 2016/09/19, HDFFV-9431)
- CMake: Fixed a command length overflow error by converting custom
commands inside CMakeTest.cmake files into regular dependencies and
targets.
(ABD, 2016/07/12, HDFFV-9939)
- Fixed a problem preventing HDF5 to be built on 32-bit CYGWIN by
condensing cygwin configuration files into a single file and
removing outdated compiler settings.
(ABD, 2016/07/12, HDFFV-9946)
Fortran
--------
- Changed H5S_ALL_F from INTEGER to INTEGER(HID_T)
(MSB, 2016/10/14, HDFFV-9987)
Tools
-----
- h5diff now correctly ignores strpad in comparing strings.
(ABD, 2017/03/03, HDFFV-10128)
- h5repack now correctly parses the command line filter options.
(ABD, 2017/01/24, HDFFV-10046)
- h5diff now correctly returns an error when it cannot read data due
to an unavailable filter plugin.
(ADB 2017/01/18, HDFFV-9994 )
- Fixed an error in the compiler wrapper scripts (h5cc, h5fc, et al.)
in which they would erroneously drop the file argument specified via
the -o flag when the -o flag was specified before the -c flag on the
command line, resulting in a failure to compile.
(LRK, 2016/11/04, HDFFV-9938, HDFFV-9530)
- 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.
(ABD, 2016/10/19, HDFFV-9996, HDFFV-9974, HDFFV-9515, HDFFV-9039)
- h5repack allows the --enable-error-stack option on the command line.
(ADB, 2016/08/08, HDFFV-9775)
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.
(BMR, 2017/03/17, PR#466)
- Due to the change in the C API, the overloaded functions of
PropList::setProperty now need const for some arguments. They are
planned for deprecation and are replaced by new versions with proper
consts.
(BMR, 2017/03/17, PR#344)
- 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.
(BMR, 2016/10/27, HDFFV-9758)
- The obsolete macros H5_NO_NAMESPACE and H5_NO_STD have been removed from
the HDF5 C++ API library.
(BMR, 2016/10/23, HDFFV-9532)
- The problem where a user-defined function cannot access both, attribute
and dataset, using only one argument is now fixed.
(BMR, 2016/10/11, HDFFV-9920)
- In-memory array information, ArrayType::rank and
ArrayType::dimensions, were removed. This is an implementation
detail and should not affect applications.
(BMR, 2016/04/25, HDFFV-9725)
Testing
-------
- Fixed a problem that caused tests using SWMR to occasionally fail when
running "make check" using parallel make.
(LRK, 2016/03/22, PR#338, PR#346, PR#358)
Supported Platforms
===================
Linux 2.6.32-573.18.1.el6.ppc64 gcc (GCC) 4.4.7 20120313 (Red Hat 4.4.7-4)
#1 SMP ppc64 GNU/Linux g++ (GCC) 4.4.7 20120313 (Red Hat 4.4.7-4)
(ostrich) GNU Fortran (GCC) 4.4.7 20120313
(Red Hat 4.4.7-4)
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 15.0.3.187 Build 20150407
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 Visual Studio 2012 w/ Intel Fortran 15 (cmake)
Visual Studio 2013 w/ Intel Fortran 15 (cmake)
Visual Studio 2015 w/ Intel Fortran 16 (cmake)
Windows 7 x64 Visual Studio 2012 w/ Intel Fortran 15 (cmake)
Visual Studio 2013 w/ Intel Fortran 15 (cmake)
Visual Studio 2015 w/ Intel Fortran 16 (cmake)
Visual Studio 2015 w/ MSMPI 8 (cmake)
Cygwin(CYGWIN_NT-6.1 2.8.0(0.309/5/3)
gcc and gfortran compilers (GCC 5.4.0)
(cmake and autotools)
Windows 10 Visual Studio 2015 w/ Intel Fortran 16 (cmake)
Cygwin(CYGWIN_NT-6.1 2.8.0(0.309/5/3)
gcc and gfortran compilers (GCC 5.4.0)
(cmake and autotools)
Windows 10 x64 Visual Studio 2015 w/ Intel Fortran 16 (cmake)
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
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 y
Mac OS X Yosemite 10.10.5 64-bit n y/y n y y y
Mac OS X El Capitan 10.11.6 64-bit n y/y n y y y
CentOS 7.2 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/y 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 7.2 Linux 2.6.32 x86_64 PGI y y y n
CentOS 7.2 Linux 2.6.32 x86_64 GNU y y y y
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 4.8.4
PGI C, Fortran, C++ for 64-bit target on
x86-64;
Version 16.10-0
Intel(R) C (icc), C++ (icpc), Fortran (icc)
compilers:
Version 15.0.3.187 (Build 20150407)
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)
Intel(R) C (icc) and C++ (icpc) compilers
Version 15.0.3.187 (Build 20150407)
with NAG Fortran Compiler Release 6.1(Tozai)
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
Debian 8.4 3.16.0-4-amd64 #1 SMP Debian 3.16.36-1 x86_64 GNU/Linux
gcc, g++ (Debian 4.9.2-10) 4.9.2
GNU Fortran (Debian 4.9.2-10) 4.9.2
(cmake and autotools)
Fedora 24 4.7.2-201.fc24.x86_64 #1 SMP x86_64 x86_64 x86_64 GNU/Linux
gcc, g++ (GCC) 6.1.1 20160621
(Red Hat 6.1.1-3)
GNU Fortran (GCC) 6.1.1 20160621
(Red Hat 6.1.1-3)
(cmake and autotools)
Ubuntu 16.04.1 4.4.0-38-generic #57-Ubuntu SMP x86_64 GNU/Linux
gcc, g++ (Ubuntu 5.4.0-6ubuntu1~16.04.2)
5.4.0 20160609
GNU Fortran (Ubuntu 5.4.0-6ubuntu1~16.04.2)
5.4.0 20160609
(cmake and autotools)
Known Problems
==============
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.
%%%%1.10.0-patch1%%%%
HDF5 version 1.10.0-patch1 released on 2016-05-23
================================================================================
INTRODUCTION
This document describes the differences between HDF5-1.8 series and
HDF5 1.10.0 releases, and contains information on the platforms
tested.
Links to HDF5 1.10.0 source code can be found on The HDF Group's
development FTP server at the following location:
https://www.hdfgroup.org/HDF5/release/obtain5110.html
User documentation can be accessed directly at this location:
https://www.hdfgroup.org/HDF5/docNewFeatures/
For more information, see the HDF5 home page:
https://www.hdfgroup.org/HDF5/
If you have any questions or comments, please send them to the HDF
Help Desk:
help@hdfgroup.org
CONTENTS
- New Features
- Issues Addressed in this Release
- Supported Platforms
- Tested Configuration Features Summary
- More Tested Platforms
- Known Problems and Limitations
New Features
============
This release supports the following features:
Configuration
-------------
- API Compatibility with HDF5 1.8 Flag Was Added
The 1.10 version of the HDF5 Library can be configured to operate
identically to the 1.8 library with the --with-default-api-version=v18
configure flag. This allows existing code to be compiled with the 1.10
library without requiring immediate changes to the application source
code. For addtional configuration options and other details, see
"API Compatibility Macros in HDF5" at
https://www.hdfgroup.org/HDF5/doc/RM/APICompatMacros.html.
- Autotools Configuration Has Been Extensively Reworked
The autotools configuration options have been updated to allow more
fine-grained control of the build options and to correct some bugs.
See configure --help for comprehensive information on each option.
Specific changes:
* --enable-debug and --enable-production are no longer accepted.
Use --enable-build-mode=(debug | production) instead. These set
appropriate defaults for symbols, optimizations, and other
configuration options. These defaults can be overridden by the
user.
* Extra debug output messages are no longer enabled with
--enable-debug=<package list>. Use --enable-internal-debug=<pkg list>
instead.
* A new --enable-symbols option allows symbols to be generated
independently of the build mode. --disable-symbols can be used
to strip symbols from the binary.
* A new --enable-asserts option sets/unsets NDEBUG. This is
independent of the build mode. This also enables some extra
low-overhead debug checks in the library.
* A new --enable-profiling option sets profiling flags. This is
independent of the build mode.
* A new --enable-optimization option sets the optimization level.
This is independent of the build mode.
* Many of these options can take a flags string that will be used
to build the library. This can be useful for specifying custom
optimization flags such as -Os and -Ofast.
* gnu C++ and Fortran use configure sub-files that update the
build flags and turn on warnings. The increase in warnings when
building these wrapper libraries is due to these flag changes
and not to a decrease in code quality.
* The option to clear file buffers has been removed. Any buffer that
will eventually be written to disk will now always be memset
to zero. This prevents the previous contents of the buffer from
being written to the disk if the buffer contents are not
completely overwritten, which has security implications.
- LFS Changes
The way the autotools handle large file support (LFS) has been
overhauled in this release.
* We assume ftello and fseeko exist
* We no longer explicitly use the *64 I/O functions. Instead, we
rely on a mapping provided by _FILE_OFFSET_BITS or its equivalent.
* _LARGEFILE(64)_SOURCE is no longer exported via AM_CPPFLAGS.
Parallel Library
-----------------
- Collective Metadata I/O
Calls for HDF5 metadata can result in many small reads and writes.
On metadata reads, collective metadata I/O can improve performance
by allowing the library to perform optimizations when reading the
metadata by having one rank read the data and broadcasting it to
all other ranks.
Collective metadata I/O improves metadata write performance through
the construction of an MPI derived datatype that is then written
collectively in a single call. For more information, see
https://www.hdfgroup.org/HDF5/docNewFeatures/NewFeaturesCollectiveMetadataIoDocs.html.
Library
--------
- Concurrent Access to HDF5 Files - Single Writer/ Multple Reader (SWMR)
The Single Writer/ Multiple Reader or SWMR feature enables users to
read data concurrently while writing it. Communications between the
processes and file locking are not required. The processes can run
on the same or on different platforms as long as they share a common
file system that is POSIX compliant. For more information, see the
Single-Writer/Multiple-Reader (SWMR) documentation at
https://www.hdfgroup.org/HDF5/docNewFeatures/NewFeaturesSwmrDocs.html.
- Virtual Dataset (VDS)
The VDS feature enables data to be accessed across HDF5 files
using standard HDF5 objects such as groups and datasets without
rewriting or rearranging the data. An HDF5 virtual dataset (VDS)
is an HDF5 dataset that is composed of source HDF5 datasets in
a predefined mapping. VDS can be used with the SWMR feature. For
documentation, check
https://www.hdfgroup.org/HDF5/docNewFeatures/NewFeaturesVirtualDatasetDocs.html.
- Persistent Free File Space Tracking
Usage patterns when working with an HDF5 file sometimes result in
wasted space within the file. This can also impair access times
when working with the resulting files. The new file space management
feature provides strategies for managing space in a file to improve
performance in both of these areas. For more information, see
https://www.hdfgroup.org/HDF5/docNewFeatures/NewFeaturesFileSpaceMgmtDocs.html.
- Version 3 Metadata Cache
The version 3 metadata cache moves management of metadata I/O from
the clients to the metadata cache proper. This change is essential for
SWMR and other features that have yet to be released.
C++ Library
------------
- New Member Function Added to H5::ArrayType
The assignment operator ArrayType::operator= was added because
ArrayType has pointer data members.
(BMR - 2016/03/07, HDFFV-9562)
Tools
------
- h5watch
The h5watch tool allows users to output new records appended to
a dataset under SWMR access as it grows. The functionality is
similar to the Unix user command "tail" with the follow option,
which outputs appended data as the file grows. For more
information, see
https://www.hdfgroup.org/HDF5/docNewFeatures/NewFeaturesSwmrDocs.html#Tools.
- h5format_convert
The h5format_convert tool allows users to convert the indexing
type of a chunked dataset made with a 1.10.x version of the HDF5
Library when the latest file format is used to the 1.8.x version 1 B-tree indexing
type. For example, datasets created using SWMR access, can be
converted to be accessed by the HDF5 1.18 library and tools. The
tool does not rewrite raw data, but it does rewrite HDF5 metadata.
High-Level APIs
----------------
- H5DOappend
The function appends data to a dataset along a specified dimension.
C Packet Table API
------------------
- Replacement of a Public Function with H5PTcreate
The existing function H5PTcreate_fl limits applications so they
can use the deflate compression only. The public function
H5PTcreate has been added to replace H5PTcreate_fl. H5PTcreate
takes a property list identifier to provide flexibility on
creation properties.
(BMR - 2016/03/04, HDFFV-8623)
- New Public Functions: H5PTget_dataset and H5PTget_type
Two accessor functions have been added. H5PTget_dataset returns
the identifier of the dataset associated with the packet table,
and H5PTget_type returns the identifier of the datatype used by
the packet table.
(BMR, 2016/03/04, HDFFV-8623)
- Regarding #ifdef VLPT_REMOVED
The #ifdef VLPT_REMOVED blocks have been removed from the packet
table (PT) library source except for the following functions:
+ H5PTis_varlen() has been made available again
+ H5PTfree_vlen_readbuff() is now H5PTfree_vlen_buff()
(BMR - 2016/03/04, HDFFV-442)
C++ Packet Table API
--------------------
- New Constructor Added to FL_PacketTable
An overloaded constructor has been added to FL_PacketTable and
takes a property list identifier to provide flexibility on
creation properties.
(BMR - 2016/03/08, HDFFV-8623)
- New Public Functions
Two accessor wrappers are added to class PacketTable.
PacketTable::GetDataset() returns the identifier of the dataset
associated with the packet table, and PacketTable::GetDatatype()
returns the identifier of the datatype that the packet table uses.
(BMR - 2016/03/04, HDFFV-8623)
- Member Functions with "char*" as an Argument
Overloaded functions were added to provide the "const char*"
argument; the existing version will be deprecated in future
releases.
(BMR - 2016/03/04, HDFFV-8623)
- Regarding #ifdef VLPT_REMOVED
The #ifdef VLPT_REMOVED blocks have been removed from the packet
table library source code except for the following functions:
+ VL_PacketTable::IsVariableLength() was moved to PacketTable
+ VL_PacketTable::FreeReadBuff() is now PacketTable::FreeBuff()
(BMR - 2016/03/04, HDFFV-442)
Java Wrapper Library
--------------------
The Java HDF5 JNI library has been integrated into the HDF5 repository.
The configure option is "--enable-java", and the CMake option is
HDF5_BUILD_JAVA:BOOL=ON. The package hierarchy has changed from the
HDF5 1.8 JNI, which was "ncsa.hdf.hdflib.hdf5", to HDF5 1.10,
"hdf.hdflib.hdf5".
A number of new APIs were added including some for VDS and SWMR.
Other Important Changes
-----------------------
The hid_t type was changed from 32-bit to a 64-bit value.
Issues Addressed in this Release Since 1.10.0
=============================================
- h5diff would return from a compare attributes abnormally if one of the datatypes
was a vlen. This resulted in a memory leak as well as an incorrect report of
attribute comparison.
Fixed.
(ADB - 2016/04/26, HDFFV-9784)
- The JUnit-interface test may fail on Solaris platforms. The result of
a test for verifying the content of the error stack to stdout is
in a different order on Solaris then other platforms.
This test is skipped on Solaris
(ADB - 2016/04/21, HDFFV-9734)
- When building HDF5 with Java using CMake and specifying Debug for CMAKE_BUILD_TYPE,
there was a missing command argument for the tests of the examples.
Fixed.
(ADB - 2016/04/21, HDFFV-9743)
- Changed h5diff to print a warning when a dataset is virtual, enabling
the data to be compared. In addition h5repack failed to copy the data
of a virtual dataset to the new file. Function H5D__get_space_status changed
to correctly determine the H5D_space_status_t allocation value.
CMake added the Fixed Array indexing tests that were only in the autotools
test scripts.
Fixed and tests added for vds issues.
(ADB,NAF - 2016/04/21, HDFFV-9756)
- CMake added the h5format_convert tool and tests that were only in the autotools
build and test scripts. The autotools test script was reworked to allow CMake
to execute the test suite in parallel.
Also, h5clear tool and tests were added to the misc folder.
Fixed.
(ADB - 2016/04/21, HDFFV-9766)
- CMake added the h5watch tool and argument tests that were only in the autotools
build and test scripts. The POSIX only tests were not added to CMake.
CMake HL tools files were refactored to move the CMake test scripts into each tool folder.
Fixed.
(ADB - 2016/04/21, HDFFV-9770)
- Configure fails to detect valid real KINDs on FreeBSD 9.3 (i386) with Fortran enabled.
Fixed. Added the exponential option to SELECTED_REAL_KIND to distinguish
KINDs of same precision
(MSB - 2016/05/14,HDFFV-9912)
- Corrected the f90 H5AWRITE_F integer interface's buf to be INTENT(IN).
(MSB - 2016/05/14)
- Configure fails in sed command on FreeBSD 9.3 (i386) with Fortran enabled.
Fixed.
(MSB - 2016/05/14,HDFFV-9912)
- Compile time error in H5f90global.F90 with IBM XL Fortran 14.1.0.13 on BG/Q with Fortran
enabled.
Fixed.
(MSB - 2016/05/16,HDFFV-9917)
- A cmake build with Fortran enabled does not install module h5fortkit
Fixed.
(MSB - 2016/05/23,HDFFV-9923)
Issues Addressed in this Release Since alpha1
=============================================
- H5Pget_virtual_printf_gap, H5Pget_virtual_view, H5Pget_efile_prefix
The correct access property list settings from the
H5Pget_virtual_printf_gap, H5Pget_virtual_view, and
H5Pget_efile_prefix function calls could not be retrieved
using H5Dget_access_plist().
Fixed.
(DER and NAF - 2016/03/14, HDFFV-9716)
- h5dump
When h5dump was provided with the name of a non-existing file or
when optional arguments were the last option on the command line,
h5dump would segfault.
Fixed.
(ADB 2016/02/28 HDFFV-9639, HDFFV-9684)
- No Error Message for Corrupt Metadata
The HDF5 Library did not propagate an error when it encountered
corrupt metadata in an HDF5 file. The issue was fixed for a
specific file provided by a user. If you still see the problem,
please contact help@hdfgroup.org
Fixed.
(MC - 2016/02/18, HDFFV-9670)
- Problem Reading Chunked Datasets with a String Datatype Larger
Than the Chunk Size in Bytes
When the latest file format was used and when a chunked dataset
was created with a datatype with the size bigger than a chunk
size, the data could not be read back. The issue was reported
for chunked datasets with a string datatype and was confirmed
for other datatypes with the sizes bigger than the chunk size in
bytes.
Fixed.
(JM - 2016/02/13, HDFFV-9672)
- Control over the Location of External Files
Users were unable to specify the locations of external files.
Two APIs - H5Pget_efile_prefix and H5Pset_efile_prefix - were
added so that users could specify the locations of external files.
(DER - 2016/02/04, HDFFV-8740)
Issues Addressed in this Release Since alpha0
=============================================
- h5format_convert
The h5format_convert tool did not downgrade the version of the
superblock.
Fixed. The tool now will downgrade the version of the superblock.
(EIP 2016/01/11)
- Crashes with multiple threads: invalid pointers
It was reported that alpha0 crashed when used with multiple
threads. The issue exists in the HDF5 Library versions 1.8 and
1.9. The problem is related to a shared file pointer used in some
miscellaneous data structures. The thread-safe library exposed
paths in the library where a file pointer became invalid.
The alpha1 release contains the fixes for the specific use case
as described in HDFFV-9643. We will keep working on identifying
and fixing other paths in the library with similar problems.
(EIP - 2016/01/15, HDFFV-9643)
Supported Platforms
===================
The following platforms are supported and have been tested for this release.
They are built with the configure process unless specified otherwise.
AIX 6.1 xlc/xlc_r 10.1.0.5
(NASA G-ADA) xlC/xlC_r 10.1.0.5
xlf90/xlf90_r 12.1.0.6
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 (Red Hat 4.4.7-16)
Version 4.9.3, Version 5.2.0
PGI C, Fortran, C++ for 64-bit target on
x86-64;
Version 15.7-0
Intel(R) C (icc), C++ (icpc), Fortran (icc)
compilers:
Version 15.0.3.187 Build 20150407
MPICH 3.1.4 compiled with GCC 4.9.3
Linux 2.6.32-573.18.1.el6.ppc64 gcc (GCC) 4.4.7 20120313 (Red Hat 4.4.7-11)
#1 SMP ppc64 GNU/Linux g++ (GCC) 4.4.7 20120313 (Red Hat 4.4.7-11)
(ostrich) GNU Fortran (GCC) 4.4.7 20120313 (Red Hat 4.4.7-11)
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 15.0.3.187 Build 20150407
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 Visual Studio 2012 w/ Intel Fortran 15 (cmake)
Visual Studio 2013 w/ Intel Fortran 15 (cmake)
Visual Studio 2015 w/ Intel Fortran 16 (cmake)
Cygwin(CYGWIN_NT-6.1 2.2.1(0.289/5/3) gcc(4.9.3) compiler and gfortran)
(cmake and autotools)
Windows 7 x64 Visual Studio 2012 w/ Intel Fortran 15 (cmake)
Visual Studio 2013 w/ Intel Fortran 15 (cmake)
Visual Studio 2015 w/ Intel Fortran 16 (cmake)
Windows 8.1 Visual Studio 2012 w/ Intel Fortran 15 (cmake)
Visual Studio 2013 w/ Intel Fortran 15 (cmake)
Windows 8.1 x64 Visual Studio 2012 w/ Intel Fortran 15 (cmake)
Visual Studio 2013 w/ Intel Fortran 15 (cmake)
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 6.0 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 10.11.4 Apple clang/clang++ version 7.3.0 from Xcode 7.3
64-bit gfortran GNU Fortran (GCC) 5.2.0
(osx1010dev/osx1010test) Intel icc/icpc/ifort version 15.0.3
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
SunOS 5.11 32-bit n y/y n y y y
SunOS 5.11 64-bit n y/y n y y y
Windows 7 y y/y n y y y
Windows 7 x64 y y/y n y y y
Windows 7 Cygwin n y/y n y y n
Windows 8.1 n y/y n y y y
Windows 8.1 x64 n 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 y
Mac OS X Yosemeti 10.10.5 64-bit n y/y n y y y
AIX 6.1 32- and 64-bit n y/n n y y y
CentOS 6.7 Linux 2.6.32 x86_64 GNU y y/y y y y y
CentOS 6.7 Linux 2.6.32 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 7.1 Linux 3.10.0 x86_64 GNU y y/y y y y y
CentOS 7.1 Linux 3.10.0 x86_64 Intel n y/y n y y y
Linux 2.6.32-431.11.2.el6.ppc64 n y/n n y y y
Platform Shared Shared Shared Thread-
C libs F90 libs C++ libs safe
SunOS 5.11 32-bit y y y y
SunOS 5.11 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 8.1 y y y y
Windows 8.1 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 Yosemeti 10.10.5 64-bit y n y y
AIX 6.1 32- and 64-bit y n n y
CentOS 6.7 Linux 2.6.32 x86_64 GNU y y y y
CentOS 6.7 Linux 2.6.32 x86_64 Intel y y y y
CentOS 6.7 Linux 2.6.32 x86_64 PGI y y y y
CentOS 7.1 Linux 3.10.0 x86_64 GNU y y y y
CentOS 7.1 Linux 3.10.0 x86_64 Intel y y y y
Linux 2.6.32-431.11.2.el6.ppc64 y y y y
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 2.6.18-431.11.2.el6 g95 (GCC 4.0.3 (g95 0.94!)
#1 SMP x86_64 GNU/Linux
(platypus)
Windows 7 Visual Studio 2008 (cmake)
Windows 7 x64 Visual Studio 2008 (cmake)
Windows 7 x64 Visual Studio 2010 (cmake) with SWMR using GPFS
Windows 10 Visual Studio 2013 w/ Intel Fortran 15 (cmake)
Windows 10 x64 Visual Studio 2013 w/ Intel Fortran 15 (cmake)
Debian7.5.0 3.2.0-4-amd64 #1 SMP Debian 3.2.51-1 x86_64 GNU/Linux
gcc (Debian 4.7.2-5) 4.7.2
GNU Fortran (Debian 4.7.2-5) 4.7.2
(cmake and autotools)
Fedora20 3.15.3-200.fc20.x86_64 #1 SMP x86_64 x86_64 x86_64 GNU/Linux
gcc (GCC) 4.8.3 20140624 (Red Hat 4.8.3-1)
GNU Fortran (GCC) 4.8.3 20140624 (Red Hat 4.8.3-1)
(cmake and autotools)
SUSE 13.1 3.11.10-17-desktop #1 SMP PREEMPT x86_64 x86_64 x86_64 GNU/Linux
gcc (SUSE Linux) 4.8.1
GNU Fortran (SUSE Linux) 4.8.1
(cmake and autotools)
Ubuntu 14.04 3.13.0-35-generic #62-Ubuntu SMP x86_64 GNU/Linux
gcc (Ubuntu/Linaro 4.9.1-0ubuntu1) 4.9.1
GNU Fortran (Ubuntu/Linaro 4.9.1-0ubuntu1) 4.9.1
(cmake and autotools)
hopper.nersc.gov PrgEnv-gnu/5.2.40
gcc (GCC) 4.9.2 20141030 (Cray Inc.)
GNU Fortran (GCC) 4.9.2 20141030 (Cray Inc.)
g++ (GCC) 4.9.2 20141030 (Cray Inc.)
Known Problems and Limitations
==============================
This section contains the list of known problems and limitations introduced
in this release of HDF5.
Note: this list is not exhaustive of all known issues discovered in HDF5
software to date. For a list of significant problems and known workarounds
identified in past releases, please refer to:
https://www.hdfgroup.org/HDF5/release/known_problems/
The HDF Group also maintains a JIRA issue-tracking database which is used to
capture all known issues which are too numerous to reasonably list in this
document. The HDF Group is taking steps to make our JIRA issue database
open to the public, and this section will refer to that database in a future
release. In the meantime, please contact help@hdfgroup.org if you come across
an issue not listed here or at the link above, and we will provide any
information about known workarounds that we have or add it to our list of
known issues if it is a new issue.
- The flush/refresh test occasionally fails on OS X platforms. This is
being investigated but no fix or workaround is available at this time.
(DER - 2016/03/22, HDFFV-9731)
- The VDS/SWMR test will fail with a segmentation fault if the library
is built with --enable-using-memchecker. The is due to a VDS shutdown
procedure freeing a shared resource too early when the memory
checker changes are built. This problem does not arise when the
memory checker changes are not used since the internal library free
lists behave differently. The memory checker configure option should
normally only be used under special circumstances so this should not
affect most users. Users should be aware that the --enable-using-memchecker
+ VDS combination may cause a segfault, however, so Valgrind et al. may
have to be used with an HDF5 library built without the feature if this
proves to be a problem.
(DER - 2016/03/21, HDFFV-9732)
- SWMR feature limitations
The SWMR feature will only work if an HDF5 file under SWMR access resides
on a file system that obeys POSIX write() ordering semantics. Because of
this, SWMR will not work on network file systems such as NFS or SMB/Windows
file shares since those systems do not guarantee write odering. SWMR
regression tests are likely to fail if run on a network file system. SWMR
is currently not tested on Windows though it can be tested manually
(some of the SWMR test programs are built by CMake), and there are no
obvious reasons for it to not work on NTFS or GPFS.
(EIP - 2016/03/20, HDFFV-9733)
- VDS feature limitation
Currently, the path to a VDS source file is interpreted as relative to the
directory where the executable program runs and not to the HDF5 file with
the VDS dataset unless a full path to the source file is specified during
the mapping.
(EIP - 2016/03/20, HDFFV-9724)
- The H5Lexists API changed behavior in HDF5-1.10 when used with a file handle
and root group name ("/"):
H5Lexists(fileid, "/")
In HDF5-1.8 it returns false (0) and in HDF5-1.10 it returns true (1).
The documentation will be updated with information regarding this change.
(LRK - 2016/03/30, HDFFV-8746)
%%%%1.10.0%%%%
HDF5 version 1.10.0 released on 2016-03-30
================================================================================
INTRODUCTION
This document describes the differences between HDF5-1.8 series and
HDF5 1.10.0 releases, and contains information on the platforms
tested.
Links to HDF5 1.10.0 source code can be found on The HDF Group's
development FTP server at the following location:
https://www.hdfgroup.org/HDF5/release/obtain5110.html
User documentation can be accessed directly at this location:
https://www.hdfgroup.org/HDF5/docNewFeatures/
For more information, see the HDF5 home page:
https://www.hdfgroup.org/HDF5/
If you have any questions or comments, please send them to the HDF
Help Desk:
help@hdfgroup.org
CONTENTS
- New Features
- Issues Addressed in this Release
- Supported Platforms
- Tested Configuration Features Summary
- More Tested Platforms
- Known Problems and Limitations
New Features
============
This release supports the following features:
Configuration
-------------
- API Compatibility with HDF5 1.8 Flag Was Added
The 1.10 version of the HDF5 Library can be configured to operate
identically to the 1.8 library with the --with-default-api-version=v18
configure flag. This allows existing code to be compiled with the 1.10
library without requiring immediate changes to the application source
code. For addtional configuration options and other details, see
"API Compatibility Macros in HDF5" at
https://www.hdfgroup.org/HDF5/doc/RM/APICompatMacros.html.
- Autotools Configuration Has Been Extensively Reworked
The autotools configuration options have been updated to allow more
fine-grained control of the build options and to correct some bugs.
See configure --help for comprehensive information on each option.
Specific changes:
* --enable-debug and --enable-production are no longer accepted.
Use --enable-build-mode=(debug | production) instead. These set
appropriate defaults for symbols, optimizations, and other
configuration options. These defaults can be overridden by the
user.
* Extra debug output messages are no longer enabled with
--enable-debug=<package list>. Use --enable-internal-debug=<pkg list>
instead.
* A new --enable-symbols option allows symbols to be generated
independently of the build mode. --disable-symbols can be used
to strip symbols from the binary.
* A new --enable-asserts option sets/unsets NDEBUG. This is
independent of the build mode. This also enables some extra
low-overhead debug checks in the library.
* A new --enable-profiling option sets profiling flags. This is
independent of the build mode.
* A new --enable-optimization option sets the optimization level.
This is independent of the build mode.
* Many of these options can take a flags string that will be used
to build the library. This can be useful for specifying custom
optimization flags such as -Os and -Ofast.
* gnu C++ and Fortran use configure sub-files that update the
build flags and turn on warnings. The increase in warnings when
building these wrapper libraries is due to these flag changes
and not to a decrease in code quality.
* The option to clear file buffers has been removed. Any buffer that
will eventually be written to disk will now always be memset
to zero. This prevents the previous contents of the buffer from
being written to the disk if the buffer contents are not
completely overwritten, which has security implications.
- LFS Changes
The way the autotools handle large file support (LFS) has been
overhauled in this release.
* We assume ftello and fseeko exist
* We no longer explicitly use the *64 I/O functions. Instead, we
rely on a mapping provided by _FILE_OFFSET_BITS or its equivalent.
* _LARGEFILE(64)_SOURCE is no longer exported via AM_CPPFLAGS.
Parallel Library
-----------------
- Collective Metadata I/O
Calls for HDF5 metadata can result in many small reads and writes.
On metadata reads, collective metadata I/O can improve performance
by allowing the library to perform optimizations when reading the
metadata by having one rank read the data and broadcasting it to
all other ranks.
Collective metadata I/O improves metadata write performance through
the construction of an MPI derived datatype that is then written
collectively in a single call. For more information, see
https://www.hdfgroup.org/HDF5/docNewFeatures/NewFeaturesCollectiveMetadataIoDocs.html.
Library
--------
- Concurrent Access to HDF5 Files - Single Writer/ Multple Reader (SWMR)
The Single Writer/ Multiple Reader or SWMR feature enables users to
read data concurrently while writing it. Communications between the
processes and file locking are not required. The processes can run
on the same or on different platforms as long as they share a common
file system that is POSIX compliant. For more information, see the
Single-Writer/Multiple-Reader (SWMR) documentation at
https://www.hdfgroup.org/HDF5/docNewFeatures/NewFeaturesSwmrDocs.html.
- Virtual Dataset (VDS)
The VDS feature enables data to be accessed across HDF5 files
using standard HDF5 objects such as groups and datasets without
rewriting or rearranging the data. An HDF5 virtual dataset (VDS)
is an HDF5 dataset that is composed of source HDF5 datasets in
a predefined mapping. VDS can be used with the SWMR feature. For
documentation, check
https://www.hdfgroup.org/HDF5/docNewFeatures/NewFeaturesVirtualDatasetDocs.html.
- Persistent Free File Space Tracking
Usage patterns when working with an HDF5 file sometimes result in
wasted space within the file. This can also impair access times
when working with the resulting files. The new file space management
feature provides strategies for managing space in a file to improve
performance in both of these areas. For more information, see
https://www.hdfgroup.org/HDF5/docNewFeatures/NewFeaturesFileSpaceMgmtDocs.html.
- Version 3 Metadata Cache
The version 3 metadata cache moves management of metadata I/O from
the clients to the metadata cache proper. This change is essential for
SWMR and other features that have yet to be released.
C++ Library
------------
- New Member Function Added to H5::ArrayType
The assignment operator ArrayType::operator= was added because
ArrayType has pointer data members.
(BMR - 2016/03/07, HDFFV-9562)
Tools
------
- h5watch
The h5watch tool allows users to output new records appended to
a dataset under SWMR access as it grows. The functionality is
similar to the Unix user command "tail" with the follow option,
which outputs appended data as the file grows. For more
information, see
https://www.hdfgroup.org/HDF5/docNewFeatures/NewFeaturesSwmrDocs.html#Tools.
- h5format_convert
The h5format_convert tool allows users to convert the indexing
type of a chunked dataset made with a 1.10.x version of the HDF5
Library when the latest file format is used to the 1.8.x version 1 B-tree indexing
type. For example, datasets created using SWMR access, can be
converted to be accessed by the HDF5 1.18 library and tools. The
tool does not rewrite raw data, but it does rewrite HDF5 metadata.
High-Level APIs
----------------
- H5DOappend
The function appends data to a dataset along a specified dimension.
C Packet Table API
------------------
- Replacement of a Public Function with H5PTcreate
The existing function H5PTcreate_fl limits applications so they
can use the deflate compression only. The public function
H5PTcreate has been added to replace H5PTcreate_fl. H5PTcreate
takes a property list identifier to provide flexibility on
creation properties.
(BMR - 2016/03/04, HDFFV-8623)
- New Public Functions: H5PTget_dataset and H5PTget_type
Two accessor functions have been added. H5PTget_dataset returns
the identifier of the dataset associated with the packet table,
and H5PTget_type returns the identifier of the datatype used by
the packet table.
(BMR, 2016/03/04, HDFFV-8623)
- Regarding #ifdef VLPT_REMOVED
The #ifdef VLPT_REMOVED blocks have been removed from the packet
table (PT) library source except for the following functions:
+ H5PTis_varlen() has been made available again
+ H5PTfree_vlen_readbuff() is now H5PTfree_vlen_buff()
(BMR - 2016/03/04, HDFFV-442)
C++ Packet Table API
--------------------
- New Constructor Added to FL_PacketTable
An overloaded constructor has been added to FL_PacketTable and
takes a property list identifier to provide flexibility on
creation properties.
(BMR - 2016/03/08, HDFFV-8623)
- New Public Functions
Two accessor wrappers are added to class PacketTable.
PacketTable::GetDataset() returns the identifier of the dataset
associated with the packet table, and PacketTable::GetDatatype()
returns the identifier of the datatype that the packet table uses.
(BMR - 2016/03/04, HDFFV-8623)
- Member Functions with "char*" as an Argument
Overloaded functions were added to provide the "const char*"
argument; the existing version will be deprecated in future
releases.
(BMR - 2016/03/04, HDFFV-8623)
- Regarding #ifdef VLPT_REMOVED
The #ifdef VLPT_REMOVED blocks have been removed from the packet
table library source code except for the following functions:
+ VL_PacketTable::IsVariableLength() was moved to PacketTable
+ VL_PacketTable::FreeReadBuff() is now PacketTable::FreeBuff()
(BMR - 2016/03/04, HDFFV-442)
Java Wrapper Library
--------------------
The Java HDF5 JNI library has been integrated into the HDF5 repository.
The configure option is "--enable-java", and the CMake option is
HDF5_BUILD_JAVA:BOOL=ON. The package hierarchy has changed from the
HDF5 1.8 JNI, which was "ncsa.hdf.hdflib.hdf5", to HDF5 1.10,
"hdf.hdflib.hdf5".
A number of new APIs were added including some for VDS and SWMR.
Other Important Changes
-----------------------
The hid_t type was changed from 32-bit to a 64-bit value.
Issues Addressed in this Release Since alpha1
=============================================
- H5Pget_virtual_printf_gap, H5Pget_virtual_view, H5Pget_efile_prefix
The correct access property list settings from the
H5Pget_virtual_printf_gap, H5Pget_virtual_view, and
H5Pget_efile_prefix function calls could not be retrieved
using H5Dget_access_plist().
Fixed.
(DER and NAF - 2016/03/14, HDFFV-9716)
- h5dump
When h5dump was provided with the name of a non-existing file or
when optional arguments were the last option on the command line,
h5dump would segfault.
Fixed.
(ADB 2016/02/28 HDFFV-9639, HDFFV-9684)
- No Error Message for Corrupt Metadata
The HDF5 Library did not propagate an error when it encountered
corrupt metadata in an HDF5 file. The issue was fixed for a
specific file provided by a user. If you still see the problem,
please contact help@hdfgroup.org
Fixed.
(MC - 2016/02/18, HDFFV-9670)
- Problem Reading Chunked Datasets with a String Datatype Larger
Than the Chunk Size in Bytes
When the latest file format was used and when a chunked dataset
was created with a datatype with the size bigger than a chunk
size, the data could not be read back. The issue was reported
for chunked datasets with a string datatype and was confirmed
for other datatypes with the sizes bigger than the chunk size in
bytes.
Fixed.
(JM - 2016/02/13, HDFFV-9672)
- Control over the Location of External Files
Users were unable to specify the locations of external files.
Two APIs - H5Pget_efile_prefix and H5Pset_efile_prefix - were
added so that users could specify the locations of external files.
(DER - 2016/02/04, HDFFV-8740)
Issues Addressed in this Release Since alpha0
=============================================
- h5format_convert
The h5format_convert tool did not downgrade the version of the
superblock.
Fixed. The tool now will downgrade the version of the superblock.
(EIP 2016/01/11)
- Crashes with multiple threads: invalid pointers
It was reported that alpha0 crashed when used with multiple
threads. The issue exists in the HDF5 Library versions 1.8 and
1.9. The problem is related to a shared file pointer used in some
miscellaneous data structures. The thread-safe library exposed
paths in the library where a file pointer became invalid.
The alpha1 release contains the fixes for the specific use case
as described in HDFFV-9643. We will keep working on identifying
and fixing other paths in the library with similar problems.
(EIP - 2016/01/15, HDFFV-9643)
Supported Platforms
===================
The following platforms are supported and have been tested for this release.
They are built with the configure process unless specified otherwise.
AIX 6.1 xlc/xlc_r 10.1.0.5
(NASA G-ADA) xlC/xlC_r 10.1.0.5
xlf90/xlf90_r 12.1.0.6
Linux 2.6.32-573.18.1.el6 GNU C (gcc), Fortran (gfortran), C++ (g++)
#1 SMP x86_64 GNU/Linux compilers:
(mayll/platypus) Version 4.4.7 20120313 (Red Hat 4.4.7-16)
Version 4.9.3, Version 5.2.0
PGI C, Fortran, C++ for 64-bit target on
x86-64;
Version 15.7-0
Intel(R) C (icc), C++ (icpc), Fortran (icc)
compilers:
Version 15.0.3.187 Build 20150407
MPICH 3.1.4 compiled with GCC 4.9.3
Linux 2.6.32-504.8.1.el6.ppc64 gcc (GCC) 4.4.7 20120313 (Red Hat 4.4.7-11)
#1 SMP ppc64 GNU/Linux g++ (GCC) 4.4.7 20120313 (Red Hat 4.4.7-11)
(ostrich) GNU Fortran (GCC) 4.4.7 20120313 (Red Hat 4.4.7-11)
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 15.0.3.187 Build 20150407
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 Visual Studio 2012 w/ Intel Fortran 15 (cmake)
Visual Studio 2013 w/ Intel Fortran 15 (cmake)
Visual Studio 2015 w/ Intel Fortran 16 (cmake)
Cygwin(CYGWIN_NT-6.1 2.2.1(0.289/5/3) gcc(4.9.3) compiler and gfortran)
(cmake and autotools)
Windows 7 x64 Visual Studio 2012 w/ Intel Fortran 15 (cmake)
Visual Studio 2013 w/ Intel Fortran 15 (cmake)
Visual Studio 2015 w/ Intel Fortran 16 (cmake)
Windows 8.1 Visual Studio 2012 w/ Intel Fortran 15 (cmake)
Visual Studio 2013 w/ Intel Fortran 15 (cmake)
Windows 8.1 x64 Visual Studio 2012 w/ Intel Fortran 15 (cmake)
Visual Studio 2013 w/ Intel Fortran 15 (cmake)
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 6.2.0
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 6.0 from Xcode 7.0.0
64-bit gfortran GNU Fortran (GCC) 4.9.2
(osx1010dev/osx1010test) Intel icc/icpc/ifort version 15.0.3
Mac OS X El Capitan 10.11.3 Apple clang/clang++ version 7.0.2 from Xcode 7.0.2
64-bit gfortran GNU Fortran (GCC) 5.2.0
(osx1010dev/osx1010test) Intel icc/icpc/ifort version 15.0.3
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
SunOS 5.11 32-bit n y/y n y y y
SunOS 5.11 64-bit n y/y n y y y
Windows 7 y y/y n y y y
Windows 7 x64 y y/y n y y y
Windows 7 Cygwin n y/y n y y n
Windows 8.1 n y/y n y y y
Windows 8.1 x64 n 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 y
Mac OS X Yosemeti 10.10.5 64-bit n y/y n y y y
AIX 6.1 32- and 64-bit n y/n n y y y
CentOS 6.7 Linux 2.6.32 x86_64 GNU y y/y y y y y
CentOS 6.7 Linux 2.6.32 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 7.1 Linux 3.10.0 x86_64 GNU y y/y y y y y
CentOS 7.1 Linux 3.10.0 x86_64 Intel n y/y n y y y
Linux 2.6.32-431.11.2.el6.ppc64 n y/n n y y y
Platform Shared Shared Shared Thread-
C libs F90 libs C++ libs safe
SunOS 5.11 32-bit y y y y
SunOS 5.11 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 8.1 y y y y
Windows 8.1 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 Yosemeti 10.10.5 64-bit y n y y
AIX 6.1 32- and 64-bit y n n y
CentOS 6.7 Linux 2.6.32 x86_64 GNU y y y y
CentOS 6.7 Linux 2.6.32 x86_64 Intel y y y y
CentOS 6.7 Linux 2.6.32 x86_64 PGI y y y y
CentOS 7.1 Linux 3.10.0 x86_64 GNU y y y y
CentOS 7.1 Linux 3.10.0 x86_64 Intel y y y y
Linux 2.6.32-431.11.2.el6.ppc64 y y y y
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 2.6.18-431.11.2.el6 g95 (GCC 4.0.3 (g95 0.94!)
#1 SMP x86_64 GNU/Linux
(platypus)
Windows 7 Visual Studio 2008 (cmake)
Windows 7 x64 Visual Studio 2008 (cmake)
Windows 7 x64 Visual Studio 2010 (cmake) with SWMR using GPFS
Windows 10 Visual Studio 2013 w/ Intel Fortran 15 (cmake)
Windows 10 x64 Visual Studio 2013 w/ Intel Fortran 15 (cmake)
Debian7.5.0 3.2.0-4-amd64 #1 SMP Debian 3.2.51-1 x86_64 GNU/Linux
gcc (Debian 4.7.2-5) 4.7.2
GNU Fortran (Debian 4.7.2-5) 4.7.2
(cmake and autotools)
Fedora20 3.15.3-200.fc20.x86_64 #1 SMP x86_64 x86_64 x86_64 GNU/Linux
gcc (GCC) 4.8.3 20140624 (Red Hat 4.8.3-1)
GNU Fortran (GCC) 4.8.3 20140624 (Red Hat 4.8.3-1)
(cmake and autotools)
SUSE 13.1 3.11.10-17-desktop #1 SMP PREEMPT x86_64 x86_64 x86_64 GNU/Linux
gcc (SUSE Linux) 4.8.1
GNU Fortran (SUSE Linux) 4.8.1
(cmake and autotools)
Ubuntu 14.04 3.13.0-35-generic #62-Ubuntu SMP x86_64 GNU/Linux
gcc (Ubuntu/Linaro 4.9.1-0ubuntu1) 4.9.1
GNU Fortran (Ubuntu/Linaro 4.9.1-0ubuntu1) 4.9.1
(cmake and autotools)
hopper.nersc.gov PrgEnv-gnu/5.2.40
gcc (GCC) 4.9.2 20141030 (Cray Inc.)
GNU Fortran (GCC) 4.9.2 20141030 (Cray Inc.)
g++ (GCC) 4.9.2 20141030 (Cray Inc.)
Known Problems and Limitations
==============================
This section contains the list of known problems and limitations introduced
in this release of HDF5.
Note: this list is not exhaustive of all known issues discovered in HDF5
software to date. For a list of significant problems and known workarounds
identified in past releases, please refer to:
https://www.hdfgroup.org/HDF5/release/known_problems/
The HDF Group also maintains a JIRA issue-tracking database which is used to
capture all known issues which are too numerous to reasonably list in this
document. The HDF Group is taking steps to make our JIRA issue database
open to the public, and this section will refer to that database in a future
release. In the meantime, please contact help@hdfgroup.org if you come across
an issue not listed here or at the link above, and we will provide any
information about known workarounds that we have or add it to our list of
known issues if it is a new issue.
- The JUnit-interface test may fail on Solaris platforms. The result of
a test for verifying the content of the error stack to stdout is
in a different order on Solaris then other platforms. Use make -i option
to test beyond the java/test folder.
(ADB - 2016/03/22, HDFFV-9734)
- The flush/refresh test occasionally fails on OS X platforms. This is
being investigated but no fix or workaround is available at this time.
(DER - 2016/03/22, HDFFV-9731)
- The VDS/SWMR test will fail with a segmentation fault if the library
is built with --enable-using-memchecker. The is due to a VDS shutdown
procedure freeing a shared resource too early when the memory
checker changes are built. This problem does not arise when the
memory checker changes are not used since the internal library free
lists behave differently. The memory checker configure option should
normally only be used under special circumstances so this should not
affect most users. Users should be aware that the --enable-using-memchecker
+ VDS combination may cause a segfault, however, so Valgrind et al. may
have to be used with an HDF5 library built without the feature if this
proves to be a problem.
(DER - 2016/03/21, HDFFV-9732)
- SWMR feature limitations
The SWMR feature will only work if an HDF5 file under SWMR access resides
on a file system that obeys POSIX write() ordering semantics. Because of
this, SWMR will not work on network file systems such as NFS or SMB/Windows
file shares since those systems do not guarantee write odering. SWMR
regression tests are likely to fail if run on a network file system. SWMR
is currently not tested on Windows though it can be tested manually
(some of the SWMR test programs are built by CMake), and there are no
obvious reasons for it to not work on NTFS or GPFS.
(EIP - 2016/03/20, HDFFV-9733)
- VDS feature limitation
Currently, the path to a VDS source file is interpreted as relative to the
directory where the executable program runs and not to the HDF5 file with
the VDS dataset unless a full path to the source file is specified during
the mapping.
(EIP - 2016/03/20, HDFFV-9724)
- When building HDF5 with Java using CMake and specifying Debug for CMAKE_BUILD_TYPE,
there is a missing command argument for the tests of the examples.
This error can be avoided by not building Java with Debug, HDF5_BUILD_JAVA:BOOL=OFF,
or not building Examples, HDF5_BUILD_EXAMPLES:BOOL=OFF.
(LRK - 2016/03/30, HDFFV-9743)
- The H5Lexists API changed behavior in HDF5-1.10 when used with a file handle
and root group name ("/"):
H5Lexists(fileid, "/")
In HDF5-1.8 it returns false (0) and in HDF5-1.10 it returns true (1).
The documentation will be updated with information regarding this change.
(LRK - 2016/03/30, HDFFV-8746)
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