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HDF5 History
============
This file contains development history of the HDF5 1.10 branch
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.]
%%%%1.10.0-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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