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HDF5 History
============
This file contains development history of the HDF5 1.10 branch
09. Release Information for hdf5-1.10.7
08. Release Information for hdf5-1.10.6
07. Release Information for hdf5-1.10.5
06. Release Information for hdf5-1.10.4
05. Release Information for hdf5-1.10.3
04. Release Information for hdf5-1.10.2
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.]
%%%%1.10.7%%%%
HDF5 version 1.10.7 released on 2020-09-11
================================================================================
INTRODUCTION
This document describes the differences between this release and the previous
HDF5 release. It contains information on the platforms tested and known
problems in this release. For more details check the HISTORY*.txt files in the
HDF5 source.
Note that documentation in the links below will be updated at the time of each
final release.
Links to HDF5 documentation can be found on The HDF5 web page:
https://portal.hdfgroup.org/display/HDF5/HDF5
The official HDF5 releases can be obtained from:
https://www.hdfgroup.org/downloads/hdf5/
HDF5 binaries provided are fully tested with ZLIB and the free
Open Source SZIP successor Libaec (with BSD license).
The official ZLIB and SZIP/Libaec pages are at:
ZLIB: http://www.zlib.net/
http://www.zlib.net/zlib_license.html
SZIP/Libaec: https://gitlab.dkrz.de/k202009/libaec
https://gitlab.dkrz.de/k202009/libaec/-/blob/master/Copyright.txt
Changes from Release to Release and New Features in the HDF5-1.10.x release series
can be found at:
https://portal.hdfgroup.org/display/HDF5/HDF5+Application+Developer%27s+Guide
If you have any questions or comments, please send them to the HDF Help Desk:
help@hdfgroup.org
CONTENTS
- New Features
- Support for new platforms and languages
- Bug Fixes since HDF5-1.10.6
- Supported Platforms
- Tested Configuration Features Summary
- More Tested Platforms
- Known Problems
- CMake vs. Autotools installations
New Features
============
Configuration:
-------------
- Disable memory sanity checks in the Autotools in release branches
The library can be configured to use internal memory sanity checking,
which replaces C API calls like malloc(3) and free(3) with our own calls
which add things like heap canaries. These canaries can cause problems
when external filter plugins reallocate canary-marked buffers.
For this reason, the default will be to not use the memory allocation
sanity check feature in release branches (e.g., hdf5_1_10_7).
Debug builds in development branches (e.g., develop, hdf5_1_10) will
still use them by default.
This change only affects Autotools debug builds. Non-debug autotools
builds and all CMake builds do not enable this feature by default.
(DER - 2020/08/19)
- Add file locking configure and CMake options
HDF5 1.10.0 introduced a file locking scheme, primarily to help
enforce SWMR setup. Formerly, the only user-level control of the scheme
was via the HDF5_USE_FILE_LOCKING environment variable.
This change introduces configure-time options that control whether
or not file locking will be used and whether or not the library
ignores errors when locking has been disabled on the file system
(useful on some HPC Lustre installations).
In both the Autotools and CMake, the settings have the effect of changing
the default property list settings (see the H5Pset/get_file_locking()
entry, below).
The yes/no/best-effort file locking configure setting has also been
added to the libhdf5.settings file.
Autotools:
An --enable-file-locking=(yes|no|best-effort) option has been added.
yes: Use file locking.
no: Do not use file locking.
best-effort: Use file locking and ignore "disabled" errors.
CMake:
Two self-explanatory options have been added:
HDF5_USE_FILE_LOCKING
HDF5_IGNORE_DISABLED_FILE_LOCKS
Setting both of these to ON is the equivalent to the Autotools'
best-effort setting.
NOTE:
The precedence order of the various file locking control mechanisms is:
1) HDF5_USE_FILE_LOCKING environment variable (highest)
2) H5Pset_file_locking()
3) configure/CMake options (which set the property list defaults)
4) library defaults (currently best-effort)
(DER - 2020/07/30, HDFFV-11092)
- CMake option to link the generated Fortran MOD files into the include
directory.
The Fortran generation of MOD files by a Fortran compile can produce
different binary files between SHARED and STATIC compiles with different
compilers and/or different platforms. Note that it has been found that
different versions of Fortran compilers will produce incompatible MOD
files. Currently, CMake will locate these MOD files in subfolders of
the include directory and add that path to the Fortran library target
in the CMake config file, which can be used by the CMake find library
process. For other build systems using the binary from a CMake install,
a new CMake configuration can be used to copy the pre-chosen version
of the Fortran MOD files into the install include directory.
The default will depend on the configuration of
BUILD_STATIC_LIBS and BUILD_SHARED_LIBS:
YES YES Default to SHARED
YES NO Default to STATIC
NO YES Default to SHARED
NO NO Default to SHARED
The defaults can be overriden by setting the config option
HDF5_INSTALL_MOD_FORTRAN to one of NO, SHARED, or STATIC
(ADB - 2020/07/09, HDFFV-11116)
- CMake option to use AEC (open source SZip) library instead of SZip
The open source AEC library is a replacement library for SZip. In
order to use it for hdf5, the libaec CMake source was changed to add
"-fPIC" and exclude test files. A new option USE_LIBAEC is required
to compensate for the different files produced by AEC build.
Autotools does not build the compression libraries within hdf5 builds,
but will use an installed libaec when configured as before with the
option --with-libsz=<path to libaec directory>.
(ADB - 2020/04/22, OESS-65)
- CMake ConfigureChecks.cmake file now uses CHECK_STRUCT_HAS_MEMBER
Some handcrafted tests in HDFTests.c have been removed and the CMake
CHECK_STRUCT_HAS_MEMBER module has been used.
(ADB - 2020/03/24, TRILAB-24)
- Both build systems use same set of warnings flags
GNU C, C++ and gfortran warnings flags were moved to files in a config
sub-folder named gnu-warnings. Flags that only are available for a specific
version of the compiler are in files named with that version.
Clang C warnings flags were moved to files in a config sub-folder
named clang-warnings.
Intel C, Fortran warnings flags were moved to files in a config sub-folder
named intel-warnings.
There are flags in named "error-xxx" files with warnings that may
be promoted to errors. Some source files may still need fixes.
There are also pairs of files named "developer-xxx" and "no-developer-xxx"
that are chosen by the CMake option:HDF5_ENABLE_DEV_WARNINGS or the
configure option:--enable-developer-warnings.
In addition, CMake no longer applies these warnings for examples.
(ADB - 2020/03/24, TRILAB-192)
- Update CMake minimum version to 3.12
Updated CMake minimum version to 3.12 and added version checks
for Windows features.
(ADB - 2020/02/05, TRILABS-142)
- Fixed CMake include properties for Fortran libraries
Corrected the library properties for Fortran to use the
correct path for the Fortran module files.
(ADB - 2020/02/04, HDFFV-11012)
- Added common warnings files for gnu and intel
Added warnings files to use one common set of flags
during configure for both autotools and CMake build
systems. The initial implementation only affects a
general set of flags for gnu and intel compilers.
(ADB - 2020/01/17)
- Added new options to CMake for control of testing
Added CMake options (default ON);
HDF5_TEST_SERIAL AND/OR HDF5_TEST_PARALLEL
combined with:
HDF5_TEST_TOOLS
HDF5_TEST_EXAMPLES
HDF5_TEST_SWMR
HDF5_TEST_FORTRAN
HDF5_TEST_CPP
HDF5_TEST_JAVA
(ADB - 2020/01/15, HDFFV-11001)
- Added Clang sanitizers to CMake for analyzer support if compiler is clang.
Added CMake code and files to execute the Clang sanitizers if
HDF5_ENABLE_SANITIZERS is enabled and the USE_SANITIZER option
is set to one of the following:
Address
Memory
MemoryWithOrigins
Undefined
Thread
Leak
'Address;Undefined'
(ADB - 2019/12/12, TRILAB-135)
Library:
--------
- Add metadata cache optimization to reduce skip list usage
On file flush or close, the metadata cache attempts to write out
all dirty entries in increasing address order. To do this, it needs
an address sorted list of metadata entries. Further, since flushing
one metadata cache entry can dirty another, this list must support
efficient insertion and deletion.
The metadata cache uses a skip list of all dirty entries for this
purpose. Before this release, this skip list was maintained at all
times. However, since profiling indicates that this imposes a
significant cost, we now construct and maintain the skip list only
when needed. Specifically, we enable the skip list and load it with
a list of all dirty entries in the metadata cache just before a flush,
and disable it after the flush.
(JRM - 2020/08/17, HDFFV-11034)
- Add BEST_EFFORT value to HDF5_USE_FILE_LOCKING environment variable
This change adds a BEST_EFFORT to the TRUE/FALSE, 1/0 settings that
were previously accepted. This option turns on file locking but
ignores locking errors when the library detects that file locking
has been disabled on a file system (useful on some HPC Lustre
installations).
The capitalization of BEST_EFFORT is mandatory.
See the configure option discussion for HDFFV-11092 (above) for more
information on the file locking feature and how it's controlled.
(DER - 2020/07/30, HDFFV-11092)
- Add H5Pset/get_file_locking() API calls
This change adds new API calls which can be used to set or get the
file locking parameters. The single API call sets both the "use file
locking" flag and the "ignore disabled file locking" flag.
When opening a file multiple times without closing, the file MUST be
opened with the same file locking settings. Opening a file with different
file locking settings will fail (this is similar to the behavior of
H5Pset_fclose_degree()).
See the configure option discussion for HDFFV-11092 (above) for more
information on the file locking feature and how it's controlled.
(DER - 2020/07/30, HDFFV-11092)
- Add Mirror VFD
Use TCP/IP sockets to perform write-only (W/O) file I/O on a remote
machine. Must be used in conjunction with the Splitter VFD.
(JOS - 2020/03/13, TBD)
- Add Splitter VFD
Maintain separate R/W and W/O channels for "concurrent" file writes
to two files using a single HDF5 file handle.
(JOS - 2020/03/13, TBD)
- Fixed an assertion failure in the parallel library when collectively
filling chunks. As it is required that chunks be written in
monotonically non-decreasing order of offset in the file, this assertion
was being triggered when the list of chunk file space allocations being
passed to the collective chunk filling routine was not sorted according
to this particular requirement.
The addition of a sort of the out of order chunks trades a bit of
performance for the elimination of this assertion and of any complaints
from MPI implementations about the file offsets used being out of order.
(JTH - 2019/10/07)
Fortran Library:
----------------
- Add wrappers for H5Pset/get_file_locking() API calls
h5pget_file_locking_f()
h5pset_file_locking_f()
See the configure option discussion for HDFFV-11092 (above) for more
information on the file locking feature and how it's controlled.
(DER - 2020/07/30, HDFFV-11092)
- Added new Fortran parameters:
H5F_LIBVER_ERROR_F
H5F_LIBVER_NBOUNDS_F
H5F_LIBVER_V18_F
H5F_LIBVER_V110_F
- Added new Fortran API: h5pget_libver_bounds_f
(MSB - 2020/02/11, HDFFV-11018)
C++ Library:
------------
- Add wrappers for H5Pset/get_file_locking() API calls
FileAccPropList::setFileLocking()
FileAccPropList::getFileLocking()
See the configure option discussion for HDFFV-11092 (above) for more
information on the file locking feature and how it's controlled.
(DER - 2020/07/30, HDFFV-11092)
Java Library:
----------------
- Add wrappers for H5Pset/get_file_locking() API calls
H5Pset_file_locking()
H5Pget_use_file_locking()
H5Pget_ignore_disabled_file_locking()
Unlike the C++ and Fortran wrappers, there are separate getters for the
two file locking settings, each of which returns a boolean value.
See the configure option discussion for HDFFV-11092 (above) for more
information on the file locking feature and how it's controlled.
(DER - 2020/07/30, HDFFV-11092)
Tools:
------
- h5repack added options to control how external links are handled.
Currently h5repack preserves external links and cannot copy and merge
data from the external files. Two options, merge and prune, were added to
control how to merge data from an external link into the resulting file.
--merge Follow external soft link recursively and merge data.
--prune Do not follow external soft links and remove link.
--merge --prune Follow external link, merge data and remove dangling link.
(ADB - 2020/08/05, HDFFV-9984)
High-Level APIs:
---------------
- None
C Packet Table API
------------------
- None
Internal header file
--------------------
- None
Documentation
-------------
- None
Support for new platforms, languages and compilers.
=======================================
- None
Bug Fixes since HDF5-1.10.6 release
==================================
Library
-------
- Fix bug and simplify collective metadata write operation when some ranks
have no entries to contribute. This fixes parallel regression test
failures with IBM SpectrumScale MPI on the Summit system at ORNL.
(QAK - 2020/09/02)
- Avoid setting up complex MPI types with 0-length vectors, which some
MPI implementations don't handle well. (In particular, IBM
SpectrumScale MPI on the Summit system at ORNL)
(QAK - 2020/08/21)
- Fixed use-of-uninitialized-value error
Appropriate initialization of local structs was added to remove the
use-of-uninitialized-value errors reported by MemorySanitizer.
(BMR - 2020/8/13, HDFFV-11101)
- Creation of dataset with optional filter
When the combination of type, space, etc doesn't work for filter
and the filter is optional, it was supposed to be skipped but it was
not skipped and the creation failed.
A fix is applied to allow the creation of a dataset in such
situation, as specified in the user documentation.
(BMR - 2020/8/13, HDFFV-10933)
- Explicitly declared dlopen to use RTLD_LOCAL
dlopen documentation states that if neither RTLD_GLOBAL nor
RTLD_LOCAL are specified, then the default behavior is unspecified.
The default on linux is usually RTLD_LOCAL while macos will default
to RTLD_GLOBAL.
(ADB - 2020/08/12, HDFFV-11127)
- Fixed issues CVE-2018-13870 and CVE-2018-13869
When a buffer overflow occurred because a name length was corrupted
and became very large, h5dump crashed on memory access violation.
A check for reading past the end of the buffer was added to multiple
locations to prevent the crashes and h5dump now simply fails with an
error message when this error condition occurs.
(BMR - 2020/7/31, HDFFV-11120 and HDFFV-11121)
- H5Sset_extent_none() sets the dataspace class to H5S_NO_CLASS which
causes asserts/errors when passed to other dataspace API calls.
H5S_NO_CLASS is an internal class value that should not have been
exposed via a public API call.
In debug builds of the library, this can cause asserts to trip. In
non-debug builds, it will produce normal library errors.
The new library behavior is for H5Sset_extent_none() to convert
the dataspace into one of type H5S_NULL, which is better handled
by the library and easier for developers to reason about.
(DER - 2020/07/27, HDFFV-11027)
- Fixed the segmentation fault when reading attributes with multiple threads
It was reported that the reading of attributes with variable length string
datatype will crash with segmentation fault particularly when the number
of threads is high (>16 threads). The problem was due to the file pointer
that was set in the variable length string datatype for the attribute.
That file pointer was already closed when the attribute was accessed.
The problem was fixed by setting the file pointer to the current opened
file pointer when the attribute was accessed. Similar patch up was done
before when reading dataset with variable length string datatype.
(VC - 2020/07/13, HDFFV-11080)
- Fixed issue CVE-2018-17438
A division by zero was discovered in H5D__select_io() of H5Dselect.c.
https://security-tracker.debian.org/tracker/CVE-2018-17438
A check was added to protect against division by zero. When such
situation occurs again, the normal HDF5 error handling will be invoked,
instead of segmentation fault.
(BMR, DER - 2020/07/09, HDFFV-10587)
- Fixed CVE-2018-17435
The tool h52gif produced a segfault when the size of an attribute message
was corrupted and caused a buffer overflow.
The problem was fixed by verifying the attribute message's size against the
buffer size before accessing the buffer. h52gif was also fixed to display
the failure instead of silently exiting after the segfault was eliminated.
(BMR - 2020/6/19, HDFFV-10591)
- Don't allocate an empty (0-dimensioned) chunked dataset's chunk
index, until the dataset's dimensions are increased.
(QAK - 2020/05/07)
Configuration
-------------
- Stopped addition of szip header and include directory path for
incompatible libsz
szlib.h is the same for both 32-bit and 64-bit szip, and the header file
and its path were added to the HDF5 binary even though the configure
check of a function in libsz later failed and szip compression was not
enabled. The header file and include path are now added only when the
libsz function passes the configure check.
(LRK - 2020/08/17, HDFFV-10830)
- Added -fsanitize=address autotools configure option for Clang compiler
Clang sanitizer options were also added for Clang compilers with CMake.
(LRK, 2020/08/05, HDFFV-10836)
- Updated testh5cc.sh.in for functions versioned in HDF5 1.10.
testh5cc.sh previously tested that the correct version of a function
versioned in HDF5 1.6 or 1.8 was compiled when one of
H5_NO_DEPRECATED_SYMBOLS or H5_USE_16_API_DEFAULT were defined. This
test was extended for additional testing with H5_USE_18_API_DEFAULT.
(LRK, 2020/06/22, HDFFV-11000)
- Fixed CMake include properties for Fortran libraries
Corrected the library properties for Fortran to use the
correct path for the Fortran module files.
(ADB - 2020/02/04, HDFFV-11012)
Performance
-------------
- None
Java Library:
----------------
- None
Fortran
--------
- Corrected INTERFACE INTENT(IN) to INTENT(OUT) for buf_size in h5fget_file_image_f.
(MSB - 2020/2/18, HDFFV-11029)
- Fixed configure issue when building HDF5 with NAG Fortran 7.0.
HDF5 now accounts for the addition of half-precision floating-point
in NAG 7.0 with a KIND=16.
(MSB - 2020/02/28, HDFFV-11033)
Tools
-----
- The tools library was updated by standardizing the error stack process.
General sequence is:
h5tools_setprogname(PROGRAMNAME);
h5tools_setstatus(EXIT_SUCCESS);
h5tools_init();
... process the command-line (check for error-stack enable) ...
h5tools_error_report();
... (do work) ...
h5diff_exit(ret);
(ADB - 2020/07/20, HDFFV-11066)
- h5diff fixed a command line parsing error.
h5diff would ignore the argument to -d (delta) if it is smaller than DBL_EPSILON.
The macro H5_DBL_ABS_EQUAL was removed and a direct value comparision was used.
(ADB - 2020/07/20, HDFFV-10897)
- h5diff added a command line option to ignore attributes.
h5diff would ignore all objects with a supplied path if the exclude-path argument is used.
Adding the exclude-attribute argument will only eclude attributes, with the supplied path,
from comparision.
(ADB - 2020/07/20, HDFFV-5935)
- h5diff added another level to the verbose argument to print filenames.
Added verbose level 3 that is level 2 plus the filenames. The levels are:
0 : Identical to '-v' or '--verbose'
1 : All level 0 information plus one-line attribute status summary
2 : All level 1 information plus extended attribute status report
3 : All level 2 information plus file names
(ADB - 2020/07/20, HDFFV-10005)
- h5repack was fixed to repack the reference attributes properly.
The code line that checks if the update of reference inside a compound
datatype is misplaced outside the code block loop that carries out the
check. In consequence, the next attribute that is not the reference
type was repacked again as the reference type and caused the failure of
repacking. The fix is to move the corresponding code line to the correct
code block.
(KY -2020/02/10, HDFFV-11014)
High-Level APIs:
------
- The H5DSis_scale function was updated to return "not a dimension scale" (0)
instead of failing (-1), when CLASS or DIMENSION_SCALE attributes are
not written according to Dimension Scales Specification.
(EIP - 2020/08/12, HDFFV-10436)
Fortran High-Level APIs:
------
- None
Documentation
-------------
- None
F90 APIs
--------
- None
C++ APIs
--------
- None
Testing
-------
- Stopped java/test/junit.sh.in installing libs for testing under ${prefix}
Lib files needed are now copied to a subdirectory in the java/test
directory, and on Macs the loader path for libhdf5.xxxs.so is changed
in the temporary copy of libhdf5_java.dylib.
(LRK, 2020/7/2, HDFFV-11063)
Supported Platforms
===================
Linux 3.10.0-1127.10.1.el7 gcc (GCC) 4.8.5 20150623 (Red Hat 4.8.5-39)
#1 SMP ppc64 GNU/Linux g++ (GCC) 4.8.5 20150623 (Red Hat 4.8.5-39)
(echidna) GNU Fortran (GCC) 4.8.5 20150623 (Red Hat 4.8.5-39)
Linux 2.6.32-754.31.1.el6 IBM XL C/C++ V13.1
#1 SMP ppc64 GNU/Linux IBM XL Fortran V15.1
(ostrich)
Linux 3.10.0-327.18.2.el7 GNU C (gcc), Fortran (gfortran), C++ (g++)
#1 SMP x86_64 GNU/Linux compilers:
(jelly/kituo/moohan) Version 4.8.5 20150623 (Red Hat 4.8.5-4)
Version 4.9.3, Version 5.3.0, Version 6.3.0,
Version 7.2.0, Version 8.3.0, Version 9.1.0
Intel(R) C (icc), C++ (icpc), Fortran (icc)
compilers:
Version 17.0.0.098 Build 20160721
MPICH 3.3 compiled with GCC 7.2.0
OpenMPI 4.0.0 compiled with GCC 7.2.0
SunOS 5.11 11.4.5.12.5.0 Sun C 5.15 SunOS_sparc 2017/05/30
32- and 64-bit Studio 12.6 Fortran 95 8.8 SunOS_sparc 2017/05/30
(hedgehog) Sun C++ 5.15 SunOS_sparc 2017/05/30
Windows 7 x64 Visual Studio 2015 w/ Intel C, Fortran 2018 (cmake)
Windows 10 x64 Visual Studio 2015 w/ Intel Fortran 18 (cmake)
Visual Studio 2017 w/ Intel Fortran 19 (cmake)
Visual Studio 2019 w/ Intel Fortran 19 (cmake)
Visual Studio 2019 w/ MSMPI 10.1 (cmake)
macOS Mojave 10.14.6 Apple LLVM version 10.0.1 (clang-1001.0.46.4)
64-bit gfortran GNU Fortran (GCC) 6.3.0
(swallow) Intel icc/icpc/ifort version 19.0.4.233 20190416
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 x64 y y/y y y y y
Windows 10 y y/y n y y y
Windows 10 x64 y y/y n y y y
MacOS Sierra 10.12.6 64-bit n y/y n y y y
MacOS High Sierra 10.13.6 64-bit n y/y n y y y
MacOS Mojave 10.14.6 64-bit n y/y n y y y
CentOS 7.2 Linux 3.10.0 x86_64 PGI n y/y n y y y
CentOS 7.2 Linux 3.10.0 x86_64 GNU y y/y y y y y
CentOS 7.2 Linux 3.10.0 x86_64 Intel n y/y n y y y
Linux 2.6.32-754.31.1.el6.ppc64 XL 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 x64 y y y y
Windows 10 y y y y
Windows 10 x64 y y y y
MacOS Sierra 10.12.6 64-bit y n y y
MacOS High Sierra 10.13.6 64-bit y n y y
MacOS Mojave 10.14.6 64-bit y n y y
CentOS 7.2 Linux 3.10.0 x86_64 PGI y y y n
CentOS 7.2 Linux 3.10.0 x86_64 GNU y y y y
CentOS 7.2 Linux 3.10.0 x86_64 Intel y y y n
Linux 2.6.32-754.31.1.el6.ppc64 XL 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:
(platypus) Version 4.4.7 20120313
Version 4.9.3, 5.3.0, 6.2.0
PGI C, Fortran, C++ for 64-bit target on
x86-64;
Version 19.10-0
MPICH 3.1.4 compiled with GCC 4.9.3
Linux 2.6.32-754.31.1.el6 gcc (GCC) 4.4.7 20120313 (Red Hat 4.4.7-18)
#1 SMP ppc64 GNU/Linux g++ (GCC) 4.4.7 20120313 (Red Hat 4.4.7-18)
(ostrich) GNU Fortran (GCC) 4.4.7 20120313 (Red Hat 4.4.7-18)
Linux 3.10.0-327.18.2.el7 GNU C (gcc) and C++ (g++) compilers
#1 SMP x86_64 GNU/Linux Version 4.8.5 20150623 (Red Hat 4.8.5-4)
(jelly) with NAG Fortran Compiler Release 6.1(Tozai)
GCC Version 7.1.0
OpenMPI 2.1.6-GCC-7.2.0-2.29,
3.1.3-GCC-7.2.0-2.29
Intel(R) C (icc) and C++ (icpc) compilers
Version 17.0.0.098 Build 20160721
with NAG Fortran Compiler Release 6.1(Tozai)
Linux 3.10.0-327.10.1.el7 MPICH 3.1.4 compiled with GCC 4.9.3
#1 SMP x86_64 GNU/Linux
(moohan)
Linux-3.10.0-1127.0.0.1chaos openmpi-4.0.0
#1 SMP x86_64 GNU/Linux clang/3.9.0, 8.0.1
(quartz) gcc/7.3.0, 8.1.0
intel/16.0.4
Linux-4.14.0-115.10.1.1 spectrum-mpi/rolling-release
#1 SMP ppc64le GNU/Linux clang/coral-2018.08.08
(lassen) gcc/7.3.1
xl/2019.02.07
Linux-4.12.14-150.52-default cray-mpich/7.7.10
#1 SMP x86_64 GNU/Linux gcc/7.3.0, 8.2.0
(cori) intel/19.0.3
Linux-4.4.180-94.107-default cray-mpich/7.7.6
# 1SMP x86_64 GNU/Linux gcc/7.2.0, 8.2.0
(mutrino) intel/17.0.4, 18.0.2, 19.0.4
Fedora 32 5.7.15-200.fc32.x86_64 Clang version 10.0.0 (Fedora 10.0.0-2.fc32)
#1 SMP x86_64 GNU/Linux GNU gcc (GCC) 10.2.1 20200723 (Red Hat 10.2.1-1)
GNU Fortran (GCC) 10.2.1 20200723 (Red Hat 10.2.1)
(cmake and autotools)
Mac OS X El Capitan 10.11.6 Apple clang version 7.3.0 from Xcode 7.3
64-bit gfortran GNU Fortran (GCC) 5.2.0
(osx1011test) Intel icc/icpc/ifort version 16.0.2
macOS Sierra 10.12.6 Apple LLVM version 9.0.0 (clang-900.39.2)
64-bit gfortran GNU Fortran (GCC) 7.4.0
(kite) Intel icc/icpc/ifort version 17.0.2
macOS High Sierra 10.13.6 Apple LLVM version 10.0.0 (clang-1000.10.44.4)
64-bit gfortran GNU Fortran (GCC) 6.3.0
(bear) Intel icc/icpc/ifort version 19.0.4.233 20190416
SunOS 5.11 11.3 Sun C 5.15 SunOS_sparc
32- and 64-bit Sun Fortran 95 8.8 SunOS_sparc
(emu) Sun C++ 5.15 SunOS_sparc
Known Problems
==============
CMake files do not behave correctly with paths containing spaces.
Do not use spaces in paths because the required escaping for handling spaces
results in very complex and fragile build files.
ADB - 2019/05/07
At present, metadata cache images may not be generated by parallel
applications. Parallel applications can read files with metadata cache
images, but since this is a collective operation, a deadlock is possible
if one or more processes do not participate.
Two tests fail attempting collective writes with OpenMPI 3.0.0/GCC-7.2.0-2.29:
testphdf5 (ecdsetw, selnone, cchunk1, cchunk3, cchunk4, and actualio)
t_shapesame (sscontig2)
CPP ptable test fails on both VS2017 and VS2019 with Intel compiler, JIRA
issue: HDFFV-10628. This test will pass with VS2015 with Intel compiler.
Known problems in previous releases can be found in the HISTORY*.txt files
in the HDF5 source. Please report any new problems found to
help@hdfgroup.org.
CMake vs. Autotools installations
=================================
While both build systems produce similar results, there are differences.
Each system produces the same set of folders on linux (only CMake works
on standard Windows); bin, include, lib and share. Autotools places the
COPYING and RELEASE.txt file in the root folder, CMake places them in
the share folder.
The bin folder contains the tools and the build scripts. Additionally, CMake
creates dynamic versions of the tools with the suffix "-shared". Autotools
installs one set of tools depending on the "--enable-shared" configuration
option.
build scripts
-------------
Autotools: h5c++, h5cc, h5fc
CMake: h5c++, h5cc, h5hlc++, h5hlcc
The include folder holds the header files and the fortran mod files. CMake
the share folder.
The bin folder contains the tools and the build scripts. Additionally, CMake
places the fortran mod files into separate shared and static subfolders,
while Autotools places one set of mod files into the include folder. Because
CMake produces a tools library, the header files for tools will appear in
the include folder.
The lib folder contains the library files, and CMake adds the pkgconfig
subfolder with the hdf5*.pc files used by the bin/build scripts created by
the CMake build. CMake separates the C interface code from the fortran code by
creating C-stub libraries for each Fortran library. In addition, only CMake
installs the tools library. The names of the szip libraries are different
between the build systems.
The share folder will have the most differences because CMake builds include
a number of CMake specific files for support of CMake's find_package and support
for the HDF5 Examples CMake project.
%%%%1.10.6%%%%
HDF5 version 1.10.6 released on 2019-12-23
================================================================================
INTRODUCTION
This document describes the differences between this release and the previous
HDF5 release. It contains information on the platforms tested and known
problems in this release. For more details check the HISTORY*.txt files in the
HDF5 source.
Note that documentation in the links below will be updated at the time of each
final release.
Links to HDF5 documentation can be found on The HDF5 web page:
https://portal.hdfgroup.org/display/HDF5/HDF5
The official HDF5 releases can be obtained from:
https://www.hdfgroup.org/downloads/hdf5/
Changes from Release to Release and New Features in the HDF5-1.10.x release series
can be found at:
https://portal.hdfgroup.org/display/HDF5/HDF5+Application+Developer%27s+Guide
If you have any questions or comments, please send them to the HDF Help Desk:
help@hdfgroup.org
CONTENTS
- New Features
- Support for new platforms and languages
- Bug Fixes since HDF5-1.10.5
- Supported Platforms
- Tested Configuration Features Summary
- More Tested Platforms
- Known Problems
- CMake vs. Autotools installations
New Features
============
Configuration:
-------------
- Update CMake for VS2019 support
CMake added support for VS2019 in version 3.15. Changes to the CMake
generator setting required changes to scripts. Also updated version
references in CMake files as necessary.
(ADB - 2019/11/18, HDFFV-10962)
- Update CMake options to match new autotools options
Add configure options (autotools - CMake):
enable-asserts HDF5_ENABLE_ASSERTS
enable-symbols HDF5_ENABLE_SYMBOLS
enable-profiling HDF5_ENABLE_PROFILING
enable-optimization HDF5_ENABLE_OPTIMIZATION
In addition NDEBUG is no longer forced defined and relies on the CMake
process.
(ADB - 2019/10/07, HDFFV-100901, HDFFV-10637, TRILAB-97)
- Update CMake tests to use FIXTURES
CMake test fixtures allow setup/cleanup tests and other dependency
requirements as properties for tests. This is more flexible for
modern CMake code.
(ADB - 2019/07/23, HDFFV-10529)
- Windows PDB files are always installed
There are build configuration or flag settings for Windows that may not
generate PDB files. If those files are not generated then the install
utility will fail because those PDB files are not found. An optional
variable, DISABLE_PDB_FILES, was added to not install PDB files.
(ADB - 2019/07/17, HDFFV-10424)
- Add mingw CMake support with a toolchain file
There have been a number of mingw issues that have been linked under
HDFFV-10845. It has been decided to implement the CMake cross-compiling
technique of toolchain files. We will use a linux platform with the mingw
compiler stack for testing. Only the C language is fully supported, and
the error tests are skipped. The C++ language works for static but shared
builds have a shared library issue with the mingw Standard Exception Handling
library, which is not available on Windows. Fortran has a common cross-compile
problem with the fortran configure tests.
(ADB - 2019/07/12, HDFFV-10845, HDFFV-10595)
- Windows PDB files are installed incorrectly
For static builds, the PDB files for windows should be installed next
to the static libraries in the lib folder. Also the debug versions of
libraries and PDB files are now correctly built using the default
CMAKE_DEBUG_POSTFIX setting.
(ADB - 2019/07/09, HDFFV-10581)
- Add option to build only shared libs
A request was made to prevent building static libraries and only build
shared. A new option was added to CMake, ONLY_SHARED_LIBS, which will
skip building static libraries. Certain utility functions will build with
static libs but are not published. Tests are adjusted to use the correct
libraries depending on SHARED/STATIC settings.
(ADB - 2019/06/12, HDFFV-10805)
- Add options to enable or disable building tools and tests
Configure options --enable-tests and --enable-tools were added for
autotools configure. These options are enabled by default, and can be
disabled with either --disable-tests (or tools) or --enable-tests=no
(or --enable-tools=no). Build time is reduced ~20% when tools are
disabled, 35% when tests are disabled, 45% when both are disabled.
Re-enabling them after the initial build requires running configure
again with the option(s) enabled.
(LRK - 2019/06/12, HDFFV-9976)
- Change tools tests to search the error stack
There are some use cases which can cause the error stack of tools to be
different then the expected output. These tests now use grepTest.cmake;
this was changed to allow the error file to be searched for an expected string.
(ADB - 2019/04/15, HDFFV-10741)
Library:
--------
- Added S3 and HDFS Virtual File Drivers (VFDs) to HDF5
These new VFDs have been introduced in HDF5-1.10.6. Instructions to
enable them when configuring HDF5 on Linux and Mac may be found at
https://portal.hdfgroup.org/display/HDF5/Virtual+File+Drivers+-+S3+and+HDFS.
Installing on Windows requires CMake 3.13 and the following additional setup.
Install openssl library (with dev files);
from "Shining Light Productions". msi package preferred.
PATH should have been updated with the installation dir.
set ENV variable OPENSSL_ROOT_DIR to the installation dir.
set ENV variable OPENSSL_CONF to the cfg file, likely %OPENSSL_ROOT_DIR%\bin\openssl.cfg
Install libcurl library (with dev files);
download the latest released version using git: https://github.com/curl/curl.git
Open a Visual Studio Command prompt
change to the libcurl root folder
run the "buildconf.bat" batch file
change to the winbuild directory
nmake /f Makefile.vc mode=dll MACHINE=x64
copy libcurl-vc-x64-release-dll-ipv6-sspi-winssl dir to C:\curl (installation dir)
set ENV variable CURL_ROOT to C:\curl (installation dir)
update PATH ENV variable to %CURL_ROOT%\bin (installation bin dir).
the aws credentials file should be in %USERPROFILE%\.aws folder
set the ENV variable "HDF5_ROS3_TEST_BUCKET_URL=https://s3.us-east-2.amazonaws.com/hdf5ros3"
(ADB - 2019/09/12, HDFFV-10854)
C++ Library:
------------
- Added new wrappers for H5Pset/get_create_intermediate_group()
LinkCreatPropList::setCreateIntermediateGroup()
LinkCreatPropList::getCreateIntermediateGroup()
(BMR - 2019/04/22, HDFFV-10622)
Java Library:
----------------
- Fixed a failure in JUnit-TestH5P on 32-bit architectures
(JTH - 2019/04/30)
Support for new platforms, languages and compilers.
=======================================
- CMake added support for VS2019 in version 3.15. Updated scripts.
- macOS 10.13.6 Darwin 17.7.0 with Apple clang LLVM version 10.0.0
- macOS 10.14.6 Darwin 18.7.0 with Apple clang LLVM version 10.0.1
Bug Fixes since HDF5-1.10.5 release
==================================
Library
-------
- Improved performance when creating a large number of small datasets by
retrieving default property values from the API context instead of doing
skip list searches. More work is required to achieve parity with HDF5 1.8.
(CJH - 2019/12/10, HDFFV-10658)
- Fixed user-created data access properties not existing in the property list
returned by H5Dget_access_plist. Thanks to Steven Varga for submitting a
reproducer and a patch.
(CJH - 2019/12/9, HDFFV-10934)
- Inappropriate linking with deprecated MPI C++ libraries
HDF5 does not define *_SKIP_MPICXX in the public headers, so applications
can inadvertently wind up linking to the deprecated MPI C++ wrappers.
MPICH_SKIP_MPICXX and OMPI_SKIP_MPICXX have both been defined in H5public.h
so this should no longer be an issue. HDF5 makes no use of the deprecated
MPI C++ wrappers.
(DER - 2019/09/17, HDFFV-10893)
- fcntl(2)-based file locking incorrectly passed the lock argument struct
instead of a pointer to the struct, causing errors on systems where
flock(2) is not available.
File locking is used when files are opened to enforce SWMR semantics. A
lock operation takes place on all file opens unless the
HDF5_USE_FILE_LOCKING environment variable is set to the string "FALSE".
flock(2) is preferentially used, with fcntl(2) locks as a backup if
flock(2) is unavailable on a system (if neither is available, the lock
operation fails). On these systems, the file lock will often fail, which
causes HDF5 to not open the file and report an error.
This bug only affects POSIX systems. Win32 builds on Windows use a no-op
locking call which always succeeds. Systems which exhibit this bug will
have H5_HAVE_FCNTL defined but not H5_HAVE_FLOCK in the configure output.
This bug affects HDF5 1.10.0 through 1.10.5.
fcntl(2)-based file locking now correctly passes the struct pointer.
(DER - 2019/08/27, HDFFV-10892)
- Fixed a bug caused by a bad tag value when condensing object header
messages
There was an assertion failure when moving messages from running a
user test program with library release HDF5 1.10.4. It was because
the tag value (object header's address) was not set up when entering
the library routine H5O__chunk_update_idx(), which eventually
verifies the metadata tag value when protecting the object header.
The problem was fixed by replacing FUNC_ENTER_PACKAGE in H5O__chunk_update_idx()
with FUNC_ENTER_PACKAGE_TAG(oh->cache_info.addr) to set up the metadata tag.
(VC - 2019/08/23, HDFFV-10873)
- Fixed the test failure from test_metadata_read_retry_info() in
test/swmr.c
The test failure is due to an incorrect number of bins returned for
retry info (info.nbins). The # of bins expected for 101 read attempts
is 3 instead of 2. The routine H5F_set_retries() in src/H5Fint.c
calculates the # of bins by first obtaining the log10 value for
(read attempts - 1). For PGI/19, the log10 value for 100 read attempts
is 1.9999999999999998 instead of 2.00000. When casting the log10 value
to unsigned later on, the decimal part is chopped off causing the test
failure.
This was fixed by obtaining the rounded integer value (HDceil) for the
log10 value of read attempts first before casting the result to unsigned.
(VC - 2019/8/14, HDFFV-10813)
- Fixed an issue when creating a file with non-default file space info
together with library high bound setting to H5F_LIBVER_V18.
When setting non-default file space info in fcpl via
H5Pset_file_space_strategy() and then creating a file with both high and
low library bounds set to H5F_LIBVER_V18 in fapl, the library succeeds in
creating the file. File creation should fail because the feature of
setting non-default file space info does not exist in library release 1.8
or earlier.
This was fixed by setting and checking the proper version in the file
space info message based on the library low and high bounds when creating
and opening the HDF5 file.
(VC - 2019/6/25, HDFFV-10808)
- Fixed an issue where copying a version 1.8 dataset between files using
H5Ocopy fails due to an incompatible fill version
When using the HDF5 1.10.x H5Ocopy() API call to copy a version 1.8
dataset to a file created with both high and low library bounds set to
H5F_LIBVER_V18, the H5Ocopy() call will fail with the error stack indicating
that the fill value version is out of bounds.
This was fixed by changing the fill value message version to H5O_FILL_VERSION_3
(from H5O_FILL_VERSION_2) for H5F_LIBVER_V18.
(VC - 2019/6/14, HDFFV-10800)
- Fixed a bug that would cause an error or cause fill values to be
incorrectly read from a chunked dataset using the "single chunk" index if
the data was held in cache and there was no data on disk.
(NAF - 2019/03/06)
- Fixed a bug that could cause an error or cause fill values to be
incorrectly read from a dataset that was written to using H5Dwrite_chunk
if the dataset was not closed after writing.
(NAF - 2019/03/06, HDFFV-10716)
- Fixed memory leak in scale offset filter
In a special case where the MinBits is the same as the number of bits in
the datatype's precision, the filter's data buffer was not freed, causing
the memory usage to grow. In general the buffer was freed correctly. The
Minbits are the minimal number of bits to store the data values. Please
see the reference manual for H5Pset_scaleoffset for the details.
(RL - 2019/3/4, HDFFV-10705)
Configuration
-------------
- Correct option for default API version
CMake options for default API version are not mutually exclusive.
Change the multiple BOOL options to a single STRING option with the
strings; v16, v18, v110.
(ADB - 2019/08/12, HDFFV-10879)
Tools
-----
- h5repack was fixed to repack datasets with external storage
to other types of storage.
New test added to repack files and verify the correct data using h5diff.
(JS - 2019/09/25, HDFFV-10408)
(ADB - 2019/10/02, HDFFV-10918)
Supported Platforms
===================
Linux 2.6.32-696.20.1.el6.ppc64 gcc (GCC) 4.4.7 20120313 (Red Hat 4.4.7-23)
#1 SMP ppc64 GNU/Linux g++ (GCC) 4.4.7 20120313 (Red Hat 4.4.7-23)
(ostrich) GNU Fortran (GCC) 4.4.7 20120313 (Red Hat 4.4.7-23)
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:
(jelly/kituo/moohan) Version 4.8.5 20150623 (Red Hat 4.8.5-4)
Version 4.9.3, Version 5.2.0
Intel(R) C (icc), C++ (icpc), Fortran (icc)
compilers:
Version 17.0.0.098 Build 20160721
MPICH 3.1.4 compiled with GCC 4.9.3
SunOS 5.11 32- and 64-bit Sun C 5.12 SunOS_sparc
(emu) Sun Fortran 95 8.6 SunOS_sparc
Sun C++ 5.12 SunOS_sparc
Windows 7 Visual Studio 2015 w/ Intel Fortran 18 (cmake)
Windows 7 x64 Visual Studio 2015 w/ Intel C, Fortran 2018 (cmake)
Visual Studio 2015 w/ MSMPI 8 (cmake)
Windows 10 Visual Studio 2015 w/ Intel Fortran 18 (cmake)
Windows 10 x64 Visual Studio 2015 w/ Intel Fortran 18 (cmake)
Visual Studio 2017 w/ Intel Fortran 19 (cmake)
Visual Studio 2019 w/ Intel Fortran 19 (cmake)
macOS 10.13.6, Darwin, Apple clang LLVM version 10.0.0
17.7.0, x86_64 gfortran GNU Fortran (GCC) 6.3.0
(bear) Intel icc/icpc/ifort version 19.0.4
macOS 10.14.6, Darwin Apple clang LLVM version 10.0.1
18.7.0, x86_64 gfortran GNU Fortran (GCC) 6.3.0
(bobcat) Intel icc/icpc/ifort version 19.0.4
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 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
MacOS High Sierra 10.13.6 64-bit n y/y n y y y
CentOS 7.2 Linux 3.10.0 x86_64 PGI n y/y n y y y
CentOS 7.2 Linux 3.10.0 x86_64 GNU y y/y y y y y
CentOS 7.2 Linux 3.10.0 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 Yosemite 10.10.5 64-bit y y y y
Mac OS X El Capitan 10.11.6 64-bit y y y y
MacOS High Sierra 10.13.6 64-bit y y y y
CentOS 7.2 Linux 3.10.0 x86_64 PGI y y y n
CentOS 7.2 Linux 3.10.0 x86_64 GNU y y y y
CentOS 7.2 Linux 3.10.0 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 configurations are not supported but have been tested for this release.
Linux 2.6.32-754.11.1.el6 GNU C (gcc), Fortran (gfortran), C++ (g++)
#1 SMP x86_64 GNU/Linux compilers:
(mayll/platypus) Version 4.4.7 20120313
Version 4.9.3, 5.3.0, 6.2.0
PGI C, Fortran, C++ for 64-bit target on
x86-64;
Version 17.10-0
Intel(R) C (icc), C++ (icpc), Fortran (icc)
compilers:
Version 17.0.4.196 Build 20170411
MPICH 3.1.4 compiled with GCC 4.9.3
Linux 3.10.0-327.18.2.el7 GNU C (gcc) and C++ (g++) compilers
#1 SMP x86_64 GNU/Linux Version 4.8.5 20150623 (Red Hat 4.8.5-4)
(jelly) with NAG Fortran Compiler Release 6.2(Chiyoda)
GCC Version 7.1.0
MPICH 3.2-GCC-4.9.3
MPICH 3.2.1-GCC-7.2.0-2.29
OpenMPI 2.1.5-GCC-7.2.0-2.29
Intel(R) C (icc) and C++ (icpc) compilers
Version 17.0.0.098 Build 20160721
with NAG Fortran Compiler Release 6.2(Chiyoda)
Linux 3.10.0-327.10.1.el7 MPICH 3.2 compiled with GCC 5.3.0
#1 SMP x86_64 GNU/Linux
(moohan)
Linux 2.6.32-573.18.1.el6.ppc64 MPICH mpich 3.1.4 compiled with
#1 SMP ppc64 GNU/Linux IBM XL C/C++ for Linux, V13.1
(ostrich) and IBM XL Fortran for Linux, V15.1
Fedora30 5.3.11-200.fc30.x86_64
#1 SMP x86_64 GNU/Linux GNU gcc (GCC) 9.2.1 20190827 (Red Hat 9.2.1 20190827)
GNU Fortran (GCC) 9.2.1 20190827 (Red Hat 9.2.1 20190827)
(cmake and autotools)
Mac OS X 10.11.6, Darwin, Apple clang version 7.3.0 from Xcode 7.3
15.6.0, x86-64 gfortran GNU Fortran (GCC) 5.2.0
(osx1011test) Intel icc/icpc/ifort version 16.0.2
macOS 10.12.6, Darwin, Apple clang LLVM version 8.1.0 from Xcode 8.3
16.6.0, x86_64 gfortran GNU Fortran (GCC) 7.1.0
(kite) Intel icc/icpc/ifort version 17.0.2
Windows 7 x64 Visual Studio 2008
Known Problems
==============
CMake files do not behave correctly with paths containing spaces.
Do not use spaces in paths because the required escaping for handling spaces
results in very complex and fragile build files.
ADB - 2019/05/07
At present, metadata cache images may not be generated by parallel
applications. Parallel applications can read files with metadata cache
images, but since this is a collective operation, a deadlock is possible
if one or more processes do not participate.
Three tests fail with OpenMPI 3.0.0/GCC-7.2.0-2.29:
testphdf5 (ecdsetw, selnone, cchunk1, cchunk3, cchunk4, and actualio)
t_shapesame (sscontig2)
t_pflush1/fails on exit
The first two tests fail attempting collective writes.
Parallel builds using OpenMPI 3.03 or later and romio fail several tests
with collective writes or compression that will not fail when ompio is used
instead of romio. This can be done by adding "--mca io ompio" to the mpirun
command. For example, in autotools builds RUNPARALLEL can be set to
"mpirun --mca io ompio -n 6" provided ompio is installed.
CPP ptable test fails on VS2017 with Intel compiler, JIRA issue: HDFFV-10628.
This test will pass with VS2015 with Intel compiler.
Older MPI libraries such as OpenMPI 2.0.1 and MPICH 2.1.5 were tested
while attempting to resolve the Jira issue: HDFFV-10540.
The known problems of reading or writing > 2GBs when using MPI-2 was
partially resolved with the MPICH library. The proposed support recognizes
IO operations > 2GB and if the datatype is not a derived type, the library
breaks the IO into chunks which can be input or output with the existing
MPI 2 limitations, i.e. size reporting and function API size/count
arguments are restricted to be 32 bit integers. For derived types larger
than 2GB, MPICH 2.1.5 fails while attempting to read or write data.
OpenMPI in contrast, implements MPI-3 APIs even in the older releases
and thus does not suffer from the 32 bit size limitation described here.
OpenMPI releases prior to v3.1.3 appear to have other datatype issues however,
e.g. within a single parallel test (testphdf5) the subtests (cdsetr, eidsetr)
report data verfication errors before eventually aborting.
The most recent versions of OpenMPI (v3.1.3 or newer) have evidently
resolved these isses and parallel HDF5 testing does not currently report
errors though occasional hangs have been observed.
Known problems in previous releases can be found in the HISTORY*.txt files
in the HDF5 source. Please report any new problems found to
help@hdfgroup.org.
CMake vs. Autotools installations
=================================
While both build systems produce similar results, there are differences.
Each system produces the same set of folders on linux (only CMake works
on standard Windows); bin, include, lib and share. Autotools places the
COPYING and RELEASE.txt file in the root folder, CMake places them in
the share folder.
The bin folder contains the tools and the build scripts. Additionally, CMake
creates dynamic versions of the tools with the suffix "-shared". Autotools
installs one set of tools depending on the "--enable-shared" configuration
option.
build scripts
-------------
Autotools: h5c++, h5cc, h5fc
CMake: h5c++, h5cc, h5hlc++, h5hlcc
The include folder holds the header files and the fortran mod files. CMake
places the fortran mod files into separate shared and static subfolders,
while Autotools places one set of mod files into the include folder. Because
CMake produces a tools library, the header files for tools will appear in
the include folder.
The lib folder contains the library files, and CMake adds the pkgconfig
subfolder with the hdf5*.pc files used by the bin/build scripts created by
the CMake build. CMake separates the C interface code from the fortran code by
creating C-stub libraries for each Fortran library. In addition, only CMake
installs the tools library. The names of the szip libraries are different
between the build systems.
The share folder will have the most differences because CMake builds include
a number of CMake specific files for support of CMake's find_package and support
for the HDF5 Examples CMake project.
%%%%1.10.5%%%%
HDF5 version 1.10.5 released on 2019-02-25
================================================================================
INTRODUCTION
This document describes the differences between this release and the previous
HDF5 release. It contains information on the platforms tested and known
problems in this release. For more details check the HISTORY*.txt files in the
HDF5 source.
Note that documentation in the links below will be updated at the time of each
final release.
Links to HDF5 documentation can be found on The HDF5 web page:
https://portal.hdfgroup.org/display/HDF5/HDF5
The official HDF5 releases can be obtained from:
https://www.hdfgroup.org/downloads/hdf5/
Changes from Release to Release and New Features in the HDF5-1.10.x release series
can be found at:
https://portal.hdfgroup.org/display/HDF5/HDF5+Application+Developer%27s+Guide
If you have any questions or comments, please send them to the HDF Help Desk:
help@hdfgroup.org
CONTENTS
- New Features
- Support for new platforms and languages
- Bug Fixes since HDF5-1.10.4
- Supported Platforms
- Tested Configuration Features Summary
- More Tested Platforms
- Known Problems
- CMake vs. Autotools installations
New Features
============
Configuration:
-------------
- Cross compile on mutrino and other Cray XC40 systems.
Added support for CMake options to use CrayLinuxEnvironment, craype-mic-knl
module for building with craype-haswell module for configuration, and
batch scripts in bin/batch for use with sbatch or bsub to run tests in
batch jobs on compute nodes. An instruction file README_HPC describing
the use of these options was added in release_docs.
(LRK - 2019/02/18, TRILABS-34)
- Rework CMake command files to fix MPI testing.
Added setup fixture to remove any test generated files and added DEPENDS
to test properties to execute tests in order expected.
(ADB - 2019/02/14, TRILABS-111)
- Disable SZIP or ZLIB options if TGZ files are not available.
Changed the TGZ option for SZip and ZLib to disable the options
if the source tar.gz files are not found.
(ADB - 2019/02/05, HDFFV-10697)
- Added a new option to enable/disable using pread/pwrite instead of
read/write in the sec2, log, and core VFDs.
This option is enabled by default when pread/pwrite are detected.
Autotools: --enable-preadwrite
CMake: HDF5_ENABLE_PREADWRITE
(DER - 2019/02/03, HDFFV-10696)
- Rework CMake versioning for OSX platforms.
Changed the current_version and compatibility_version flags from optional
with HDF5_BUILD_WITH_INSTALL_NAME to always setting the flags for OSX.
(ADB - 2019/01/22, HDFFV-10685)
- Rework CMake command files to eliminate developer CMP005 warning
Use variables without quotes in if () statements.
(ADB - 2019/01/18, TILABS-105)
- Rework CMake configure files to eliminate developer CMP0075 warning
Renamed varname to HDF5_REQUIRED_LIBRARIES as the contents were not
required for configuration. Also moved check includes calls to top of
files.
(ADB - 2019/01/03, HDFFV-10546)
- Keep stderr and stdout separate in tests
Changed test handling of output capture. Tests now keep the stderr
output separate from the stdout output. It is up to the test to decide
which output to check against a reference. Also added the option
to grep for a string in either output.
(ADB - 2018/12/12, HDFFV-10632)
- Incorrectly installed private header files were removed from
CMake installs.
The CMake build files incorrectly flagged the following header files
as public and installed them. They are private and will no longer be
installed.
HDF5 library private package files (H5Xpkg.h)
H5Edefin.h
H5Einit.h
H5Eterm.h
H5LTparse.h
h5diff.h
h5tools_dump.h
h5tools.h
h5tools_ref.h
h5tools_str.h
h5tools_utils.h
h5trav.h
(DER - 2018/10/26, HDFFV-10614, 10609)
- Autotools installs now install H5FDwindows.h
This is simply to align the installed header files between the
autotools and CMake. H5FDwindows.h has no functionality on
non-Windows systems.
(DER - 2018/10/26, HDFFV-10614)
Library:
--------
- The sec2, log, and core VFDs can now use pread/pwrite instead of
read/write.
pread and pwrite do not change the file offset, a feature that was
requested by a user working with a multi-threaded application.
The option to configure this feature is described above.
(DER - 2019/02/03, HDFFV-10696)
- Add ability to minimze dataset object headers.
Creation of many, very small datasets resulted in extensive file bloat
due to extra space in the dataset object headers -- this space is
allocated by default to allow for the insertion of a small number of
attributes within the object header and not require a continuation
block, an unnecessary provision in the target use case.
Inform the library to expect no attributes on created datasets, and to
allocate the least space possible for the object headers.
NOTE: A continuation block is created if attributes are added to a
'minimized' dataset, which can reduce performance.
NOTE: Some extra space is allocated for attributes essential to the
correct behavior of the object header (store creation times, e.g.). This
does not violate the design principle, as the space is calculated and
allocated as needed at the time of dataset object header creation --
unused space is not generated.
New API calls:
H5Fget_dset_no_attrs_hint
H5Fset_dset_no_attrs_hint
H5Pget_dset_no_attrs_hint
H5Pset_dset_no_attrs_hint
(JOS - 2019/01/04, TRILAB-45)
- Added new chunk query functions
The following public functions were added to discover information about
the chunks in an HDF5 file.
herr_t H5Dget_num_chunks(dset_id, fspace_id, *nchunks)
herr_t H5Dget_chunk_info_by_coord(dset_id, *coord, *filter_mask, *addr, *size)
herr_t H5Dget_chunk_info(dset_id, fspace_id, index, *coord, *filter_mask, *addr, *size)
(BMR - 2018/11/07, HDFFV-10615)
- Several empty public header files where removed from the distribution
The following files were empty placeholders. They are for internal
packages that are unlikely to ever have public functionality and have
thus been removed.
H5Bpublic.h
H5B2public.h
H5FSpublic.h
H5HFpublic.h
H5HGpublic.h
H5HLpublic.h
They were only installed in CMake builds.
(DER - 2018/10/26, HDFFV-10614)
Parallel Library:
-----------------
- Changed the default behavior in parallel when reading the same dataset in its entirety
(i.e. H5S_ALL dataset selection) which is being read by all the processes collectively.
The dataset must be contiguous, less than 2GB, and of an atomic datatype.
The new behavior is the HDF5 library will use an MPI_Bcast to pass the data read from
the disk by the root process to the remain processes in the MPI communicator associated
with the HDF5 file.
(MSB - 2019/01/02, HDFFV-10652)
- All MPI-1 API calls have been replaced with MPI-2 equivalents.
This was done to better support OpenMPI, as default builds no longer
include MPI-1 support (as of OpenMPI 4.0).
(DER - 2018/12/30, HDFFV-10566)
Fortran Library:
----------------
- Added wrappers for dataset object header minimization calls.
(see the note for TRILAB-45, above)
New API calls:
h5fget_dset_no_attrs_hint_f
h5fset_dset_no_attrs_hint_f
h5pget_dset_no_attrs_hint_f
h5pset_dset_no_attrs_hint_f
(DER - 2019/01/09, TRILAB-45)
- Added new Fortran derived type, c_h5o_info_t, which is interoperable with
C's h5o_info_t. This is needed for callback functions which
pass C's h5o_info_t data type definition.
(MSB, 2019/01/08, HDFFV-10443)
- Added new Fortran API, H5gmtime, which converts (C) 'time_t' structure
to Fortran DATE AND TIME storage format.
(MSB, 2019/01/08, HDFFV-10443)
- Added new Fortran 'fields' optional parameter to: h5ovisit_f, h5oget_info_by_name_f,
h5oget_info, h5oget_info_by_idx and h5ovisit_by_name_f.
(MSB, 2019/01/08, HDFFV-10443)
C++ Library:
------------
- Added new function to the C++ interface
Added wrapper for H5Ovisit2:
H5Object::visit()
(BMR - 2019/02/14, HDFFV-10532)
Java Library:
----------------
- Rewrote the JNI error handling to be much cleaner
(JTH - 2019/02/12)
- Add new functions to java interface
Added wrappers for:
H5Fset_libver_bounds
H5Fget_dset_no_attrs_hint/H5Fset_dset_no_attrs_hint
H5Pget_dset_no_attrs_hint/H5Pset_dset_no_attrs_hint
(ADB - 2019/01/07, HDFFV-10664)
- Fix java unit tests when Time is a natural number
Time substitution in java/test/junit.sh.in doesn't
handle the case when Time is a natural number. Fixed
the regular expression.
(ADB - 2019/01/07, HDFFV-10674)
- Duplicate the data read/write functions of Datasets for Attributes.
Region references could not be displayed for attributes as they could
for datasets. Datasets had overloaded read and write functions for different
datatypes that were not available for attributes. After adding similar
functions, attribute region references work normally.
(ADB - 2018/12/12, HDFVIEW-4)
Tools:
------
- The h5repart -family-to-sec2 argument was changed to -family-to-single
In order to better support other single-file VFDs which could work with
h5repart, the -family-to-sec2 argument was renamed to -family-to-single.
This is just a name change and the functionality of the argument has not
changed.
The -family-to-sec2 argument has been kept for backwards-compatibility.
This argument should be considered deprecated.
(DER - 2018/11/14, HDFFV-10633)
Bug Fixes since HDF5-1.10.4 release
==================================
Library
-------
- Fix hangs with collective metadata reads during chunked dataset I/O
In the parallel library, it was discovered that when a particular
sequence of operations following a pattern of:
"write to chunked dataset" -> "flush file" -> "read from dataset"
occurred with collective metadata reads enabled, hangs could be
observed due to certain MPI ranks not participating in the collective
metadata reads.
To fix the issue, collective metadata reads are now disabled during
chunked dataset raw data I/O.
(JTH - 2019/02/11, HDFFV-10563, HDFFV-10688)
- Performance issue when closing an object
The slow down is due to the search of the "tag_list" to find
out the "corked" status of an object and "uncork" it if so.
Improve performance by skipping the search of the "tag_list"
if there are no "corked" objects when closing an object.
(VC - 2019/02/06)
- Uninitialized bytes from a type conversion buffer could be written
to disk in H5Dwrite calls where type conversion takes place
and the type conversion buffer was created by the HDF5 library.
When H5Dwrite is called and datatype conversion must be performed,
the library will create a temporary buffer for type conversion if
one is not provided by the user via H5Pset_buffer. This internal
buffer is allocated via malloc and contains uninitialized data. In
some datatype conversions (float to long double, possibly others),
some of this uninitialized data could be written to disk.
This was flagged by valgrind in the dtransform test and does not
appear to be a common occurrence (it is flagged in one test out
of the entire HDF5 test suite).
Switching to calloc fixed the problem.
(DER - 2019/02/03, HDFFV-10694)
- There was missing protection against division by zero reported to
The HDF Group as issue #CVE-2018-17434.
Protection against division by zero was added to address the issue
#CVE-2018-17434.
(BMR - 2019/01/29, HDFFV-10586)
- The issue CVE-2018-17437 was reported to The HDF Group
Although CVE-2018-17437 reported a memory leak, the actual issue
was invalid read. It was found that the attribute name length
in an attribute message was corrupted, which caused the buffer
pointer to be advanced too far and later caused an invalid read.
A check was added to detect when the attribute name or its length
was corrupted and report the potential of data corruption.
(BMR - 2019/01/29, HDFFV-10588)
- H5Ewalk did not stop when it was supposed to
H5Ewalk was supposed to stop when the callback function stopped
even though the errors in the stack were not all visited, but it
did not. This problem is now fixed.
(BMR - 2019/01/29, HDFFV-10684)
- Revert H5Oget_info* and H5Ovisit* functions
In 1.10.3 new H5Oget_info*2 and H5Ovisit*2 functions were
added for performance. Inadvertently, the original functions;
H5Oget_info,
H5Oget_info_by_name,
H5Oget_info_by_idx,
H5Ovisit,
H5Ovisit_by_name
were versioned to H5Oget_info*1 and H5Ovisit*1. This
broke the API compatibility for a maintenance release. The
original functions have been restored.
(ADB - 2019/01/24, HDFFV-10686)
- Fixed a potential invalid memory access and failure that could occur when
decoding an unknown object header message (from a future version of the
library).
(NAF - 2019/01/07)
- Deleting attributes in dense storage
The library aborts with "infinite loop closing library" after
attributes in dense storage are created and then deleted.
When deleting the attribute nodes from the name index v2 B-tree,
if an attribute is found in the intermediate B-tree nodes,
which may be merged/redistributed in the process, we need to
free the dynamically allocated spaces for the intermediate
decoded attribute.
(VC - 2018/12/26, HDFFV-10659)
- There was missing protection against division by zero reported to
The HDF Group as issue #CVE-2018-17233.
Protection against division by zero was added to address the issue
#CVE-2018-17233. In addition, several similar occurrences in the same
file were fixed as well.
(BMR - 2018/12/23, HDFFV-10577)
- Fixed an issue where the parallel filters tests would fail
if zlib was not available on the system. Until support can
be added in the tests for filters beyond gzip/zlib, the tests
will be skipped if zlib is not available.
(JTH - 2018/12/05)
- A bug was discovered in the parallel library where an application
would eventually consume all of the available MPI communicators
when continually writing to a compressed dataset in parallel. This
was due to internal copies of an HDF5 File Access Property List,
which each contained a copy of the MPI communicator, not being
closed at the end of each write operation. This problem was
exacerbated by larger numbers of processors.
(JTH - 2018/12/05, HDFFV-10629)
Fortran
--------
- Fixed issue with Fortran not returning h5o_info_t field values
meta_size%attr%index_size and meta_size%attr%heap_size.
(MSB, 2019/01/08, HDFFV-10443)
- Added symbolic links libhdf5_hl_fortran.so to libhdf5hl_fortran.so and
libhdf5_hl_fortran.a to libhdf5hl_fortran.a in hdf5/lib directory for
autotools installs. These were added to match the name of the files
installed by cmake and the general pattern of hl lib files. We will
change the names of the installed lib files to the matching name in
the next major release.
(LRK - 2019/01/04, HDFFV-10596)
- Made Fortran specific subroutines PRIVATE in generic procedures.
Affected generic procedures were functions in H5A, H5D, H5P, H5R and H5T.
(MSB, 2018/12/04, HDFFV-10511)
Testing
-------
- Fixed a test failure in testpar/t_dset.c caused by
the test trying to use the parallel filters feature
on MPI-2 implementations.
(JTH, 2019/2/7)
Supported Platforms
===================
Linux 2.6.32-696.16.1.el6.ppc64 gcc (GCC) 4.4.7 20120313 (Red Hat 4.4.7-18)
#1 SMP ppc64 GNU/Linux g++ (GCC) 4.4.7 20120313 (Red Hat 4.4.7-18)
(ostrich) GNU Fortran (GCC) 4.4.7 20120313 (Red Hat 4.4.7-18)
IBM XL C/C++ V13.1
IBM XL Fortran V15.1
Linux 3.10.0-327.10.1.el7 GNU C (gcc), Fortran (gfortran), C++ (g++)
#1 SMP x86_64 GNU/Linux compilers:
(kituo/moohan) Version 4.8.5 20150623 (Red Hat 4.8.5-4)
Version 4.9.3, Version 5.2.0
Intel(R) C (icc), C++ (icpc), Fortran (icc)
compilers:
Version 17.0.0.098 Build 20160721
MPICH 3.1.4 compiled with GCC 4.9.3
SunOS 5.11 32- and 64-bit Sun C 5.12 SunOS_sparc
(emu) Sun Fortran 95 8.6 SunOS_sparc
Sun C++ 5.12 SunOS_sparc
Windows 7 Visual Studio 2015 w/ Intel Fortran 16 (cmake)
Windows 7 x64 Visual Studio 2013
Visual Studio 2015 w/ Intel Fortran 16 (cmake)
Visual Studio 2015 w/ Intel C, Fortran 2018 (cmake)
Visual Studio 2015 w/ MSMPI 8 (cmake)
Windows 10 Visual Studio 2015 w/ Intel Fortran 18 (cmake)
Windows 10 x64 Visual Studio 2015 w/ Intel Fortran 18 (cmake)
Visual Studio 2017 w/ Intel Fortran 18 (cmake)
Mac OS X Yosemite 10.10.5 Apple clang/clang++ version 6.1 from Xcode 7.0
64-bit gfortran GNU Fortran (GCC) 4.9.2
(osx1010dev/osx1010test) Intel icc/icpc/ifort version 15.0.3
Mac OS X El Capitan 10.11.6 Apple clang/clang++ version 7.3.0 from Xcode 7.3
64-bit gfortran GNU Fortran (GCC) 5.2.0
(osx1011dev/osx1011test) Intel icc/icpc/ifort version 16.0.2
MacOS High Sierra 10.13.6 Apple LLVM version 10.0.0 (clang/clang++-1000.10.44.4)
64-bit gfortran GNU Fortran (GCC) 8.3.0
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 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
MacOS High Sierra 10.13.6 64-bit n y/y n y y y
CentOS 7.2 Linux 3.10.0 x86_64 PGI n y/y n y y y
CentOS 7.2 Linux 3.10.0 x86_64 GNU y y/y y y y y
CentOS 7.2 Linux 3.10.0 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 Yosemite 10.10.5 64-bit y y y y
Mac OS X El Capitan 10.11.6 64-bit y y y y
MacOS High Sierra 10.13.6 64-bit y y y y
CentOS 7.2 Linux 3.10.0 x86_64 PGI y y y n
CentOS 7.2 Linux 3.10.0 x86_64 GNU y y y y
CentOS 7.2 Linux 3.10.0 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 configurations are not supported but have been tested for this release.
Linux 2.6.32-573.22.1.el6 GNU C (gcc), Fortran (gfortran), C++ (g++)
#1 SMP x86_64 GNU/Linux compilers:
(mayll/platypus) Version 4.4.7 20120313
Version 4.9.3, 5.3.0, 6.2.0
PGI C, Fortran, C++ for 64-bit target on
x86-64;
Version 17.10-0
Intel(R) C (icc), C++ (icpc), Fortran (icc)
compilers:
Version 17.0.4.196 Build 20170411
MPICH 3.1.4 compiled with GCC 4.9.3
Linux 3.10.0-327.18.2.el7 GNU C (gcc) and C++ (g++) compilers
#1 SMP x86_64 GNU/Linux Version 4.8.5 20150623 (Red Hat 4.8.5-4)
(jelly) with NAG Fortran Compiler Release 6.1(Tozai)
GCC Version 7.1.0
MPICH 3.2-GCC-4.9.3
MPICH 3.2.1-GCC-7.2.0-2.29
OpenMPI 2.1.5-GCC-7.2.0-2.29
Intel(R) C (icc) and C++ (icpc) compilers
Version 17.0.0.098 Build 20160721
with NAG Fortran Compiler Release 6.1(Tozai)
Linux 3.10.0-327.10.1.el7 MPICH 3.2 compiled with GCC 5.3.0
#1 SMP x86_64 GNU/Linux
(moohan)
Fedora 29 4.20.10-200.fc29.x86_64 #1 SMP x86_64 x86_64 x86_64 GNU/Linux
gcc, g++ (GCC) 8.2.1 20181215
(Red Hat 8.2.1-6)
GNU Fortran (GCC) 8.2.1 20181215
(Red Hat 8.2.1-6)
(cmake and autotools)
Windows 7 x64 Visual Studio 2008
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.
Three tests fail with OpenMPI 3.0.0/GCC-7.2.0-2.29:
testphdf5 (ecdsetw, selnone, cchunk1, cchunk3, cchunk4, and actualio)
t_shapesame (sscontig2)
t_pflush1/fails on exit
The first two tests fail attempting collective writes.
CPP ptable test fails on VS2017 with Intel compiler, JIRA issue: HDFFV-10628.
This test will pass with VS2015 with Intel compiler.
Older MPI libraries such as OpenMPI 2.0.1 and MPICH 2.1.5 were tested
while attempting to resolve the Jira issue: HDFFV-10540.
The known problems of reading or writing > 2GBs when using MPI-2 was
partially resolved with the MPICH library. The proposed support recognizes
IO operations > 2GB and if the datatype is not a derived type, the library
breaks the IO into chunks which can be input or output with the existing
MPI 2 limitations, i.e. size reporting and function API size/count
arguments are restricted to be 32 bit integers. For derived types larger
than 2GB, MPICH 2.1.5 fails while attempting to read or write data.
OpenMPI in contrast, implements MPI-3 APIs even in the older releases
and thus does not suffer from the 32 bit size limitation described here.
OpenMPI releases prior to v3.1.3 appear to have other datatype issues however,
e.g. within a single parallel test (testphdf5) the subtests (cdsetr, eidsetr)
report data verfication errors before eventually aborting.
The most recent versions of OpenMPI (v3.1.3 or newer) have evidently
resolved these isses and parallel HDF5 testing does not currently report
errors though occasional hangs have been observed.
Known problems in previous releases can be found in the HISTORY*.txt files
in the HDF5 source. Please report any new problems found to
help@hdfgroup.org.
CMake vs. Autotools installations
=================================
While both build systems produce similar results, there are differences.
Each system produces the same set of folders on linux (only CMake works
on standard Windows); bin, include, lib and share. Autotools places the
COPYING and RELEASE.txt file in the root folder, CMake places them in
the share folder.
The bin folder contains the tools and the build scripts. Additionally, CMake
creates dynamic versions of the tools with the suffix "-shared". Autotools
installs one set of tools depending on the "--enable-shared" configuration
option.
build scripts
-------------
Autotools: h5c++, h5cc, h5fc
CMake: h5c++, h5cc, h5hlc++, h5hlcc
The include folder holds the header files and the fortran mod files. CMake
places the fortran mod files into separate shared and static subfolders,
while Autotools places one set of mod files into the include folder. Because
CMake produces a tools library, the header files for tools will appear in
the include folder.
The lib folder contains the library files, and CMake adds the pkgconfig
subfolder with the hdf5*.pc files used by the bin/build scripts created by
the CMake build. CMake separates the C interface code from the fortran code by
creating C-stub libraries for each Fortran library. In addition, only CMake
installs the tools library. The names of the szip libraries are different
between the build systems.
The share folder will have the most differences because CMake builds include
a number of CMake specific files for support of CMake's find_package and support
for the HDF5 Examples CMake project.
%%%%1.10.4%%%%
HDF5 version 1.10.4 released on 2018-10-05
================================================================================
INTRODUCTION
This document describes the differences between this release and the previous
HDF5 release. It contains information on the platforms tested and known
problems in this release. For more details check the HISTORY*.txt files in the
HDF5 source.
Note that documentation in the links below will be updated at the time of each
final release.
Links to HDF5 documentation can be found on The HDF5 web page:
https://portal.hdfgroup.org/display/HDF5/HDF5
The official HDF5 releases can be obtained from:
https://www.hdfgroup.org/downloads/hdf5/
Changes from Release to Release and New Features in the HDF5-1.10.x release series
can be found at:
https://portal.hdfgroup.org/display/HDF5/HDF5+Application+Developer%27s+Guide
If you have any questions or comments, please send them to the HDF Help Desk:
help@hdfgroup.org
CONTENTS
- Bug Fixes since HDF5-1.10.3
- Supported Platforms
- Tested Configuration Features Summary
- More Tested Platforms
- Known Problems
- CMake vs. Autotools installations
New Features
============
Configuration:
-------------
- Add toolchain and cross-compile support
Added info on using a toolchain file to INSTALL_CMAKE.txt. A
toolchain file is also used in cross-compiling, which requires
CMAKE_CROSSCOMPILING_EMULATOR to be set. To help with cross-compiling
the fortran configure process, the HDF5UseFortran.cmake file macros
were improved. Fixed a Fortran configure file issue that incorrectly
used #cmakedefine instead of #define.
(ADB - 2018/10/04, HDFFV-10594)
- Add warning flags for Intel compilers
Identified Intel compiler specific warnings flags that should be used
instead of GNU flags.
(ADB - 2018/10/04, TRILABS-21)
- Add default rpath to targets
Default rpaths should be set in shared executables and
libraries to allow the use of loading dependent libraries
without requiring LD_LIBRARY_PATH to be set. The default
path should be relative using @rpath on osx and $ORIGIN
on linux. Windows is not affected.
(ADB - 2018/09/26, HDFFV-10594)
Library:
--------
- Allow pre-generated H5Tinit.c and H5make_libsettings.c to be used.
Rather than always running H5detect and generating H5Tinit.c and
H5make_libsettings.c, supply a location for those files.
(ADB - 2018/09/18, HDFFV-10332)
Bug Fixes since HDF5-1.10.3 release
==================================
Library
-------
- Allow H5detect and H5make_libsettings to take a file as an argument.
Rather than only writing to stdout, add a command argument to name
the file that H5detect and H5make_libsettings will use for output.
Without an argument, stdout is still used, so backwards compatibility
is maintained.
(ADB - 2018/09/05, HDFFV-9059)
- A bug was discovered in the parallel library where an application
would hang if a collective read/write of a chunked dataset occurred
when collective metadata reads were enabled and some of the ranks
had no selection in the dataset's dataspace. The ranks which had no
selection in the dataset's dataspace called H5D__chunk_addrmap() to
retrieve the lowest chunk address in the dataset. This is because we
require reads/writes to be performed in strictly non-decreasing order
of chunk address in the file.
When the chunk index used was a version 1 or 2 B-tree, these
non-participating ranks would issue a collective MPI_Bcast() call
that the participating ranks would not issue, causing the hang. Since
the non-participating ranks are not actually reading/writing anything,
the H5D__chunk_addrmap() call can be safely removed and the address used
for the read/write can be set to an arbitrary number (0 was chosen).
(JTH - 2018/08/25, HDFFV-10501)
Java Library:
----------------
- JNI native library dependencies
The build for the hdf5_java native library used the wrong
hdf5 target library for CMake builds. Correcting the hdf5_java
library to build with the shared hdf5 library required testing
paths to change also.
(ADB - 2018/08/31, HDFFV-10568)
- Java iterator callbacks
Change global callback object to a small stack structure in order
to fix a runtime crash. This crash was discovered when iterating
through a file with nested group members. The global variable
visit_callback is overwritten when recursion starts. When recursion
completes, visit_callback will be pointing to the wrong callback method.
(ADB - 2018/08/15, HDFFV-10536)
- Java HDFLibraryException class
Change parent class from Exception to RuntimeException.
(ADB - 2018/07/30, HDFFV-10534)
- JNI Read and Write
Refactored variable-length functions, H5DreadVL and H5AreadVL,
to correct dataset and attribute reads. New write functions,
H5DwriteVL and H5AwriteVL, are under construction.
(ADB - 2018/06/02, HDFFV-10519)
Supported Platforms
===================
Linux 2.6.32-696.16.1.el6.ppc64 gcc (GCC) 4.4.7 20120313 (Red Hat 4.4.7-18)
#1 SMP ppc64 GNU/Linux g++ (GCC) 4.4.7 20120313 (Red Hat 4.4.7-18)
(ostrich) GNU Fortran (GCC) 4.4.7 20120313 (Red Hat 4.4.7-18)
IBM XL C/C++ V13.1
IBM XL Fortran V15.1
Linux 3.10.0-327.10.1.el7 GNU C (gcc), Fortran (gfortran), C++ (g++)
#1 SMP x86_64 GNU/Linux compilers:
(kituo/moohan) Version 4.8.5 20150623 (Red Hat 4.8.5-4)
Version 4.9.3, Version 5.2.0
Intel(R) C (icc), C++ (icpc), Fortran (icc)
compilers:
Version 17.0.0.098 Build 20160721
MPICH 3.1.4 compiled with GCC 4.9.3
SunOS 5.11 32- and 64-bit Sun C 5.12 SunOS_sparc
(emu) Sun Fortran 95 8.6 SunOS_sparc
Sun C++ 5.12 SunOS_sparc
Windows 7 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/ Intel C, Fortran 2017 (cmake)
Visual Studio 2015 w/ MSMPI 8 (cmake)
Windows 10 Visual Studio 2015 w/ Intel Fortran 18 (cmake)
Windows 10 x64 Visual Studio 2015 w/ Intel Fortran 18 (cmake)
Visual Studio 2017 w/ Intel Fortran 18 (cmake)
Mac OS X Yosemite 10.10.5 Apple clang/clang++ version 6.1 from Xcode 7.0
64-bit gfortran GNU Fortran (GCC) 4.9.2
(osx1010dev/osx1010test) Intel icc/icpc/ifort version 15.0.3
Mac OS X El Capitan 10.11.6 Apple clang/clang++ version 7.3.0 from Xcode 7.3
64-bit gfortran GNU Fortran (GCC) 5.2.0
(osx1011dev/osx1011test) Intel icc/icpc/ifort version 16.0.2
Mac OS Sierra 10.12.6 Apple LLVM version 8.1.0 (clang/clang++-802.0.42)
64-bit gfortran GNU Fortran (GCC) 7.1.0
(kite) Intel icc/icpc/ifort version 17.0.2
Tested Configuration Features Summary
=====================================
In the tables below
y = tested
n = not tested in this release
C = Cluster
W = Workstation
x = not working in this release
dna = does not apply
( ) = footnote appears below second table
<blank> = testing incomplete on this feature or platform
Platform C F90/ F90 C++ zlib SZIP
parallel F2003 parallel
Solaris2.11 32-bit n y/y n y y y
Solaris2.11 64-bit n y/n n y y y
Windows 7 y y/y n y y y
Windows 7 x64 y y/y y y y y
Windows 7 Cygwin n y/n n y y y
Windows 7 x64 Cygwin n y/n n y y y
Windows 10 y y/y n y y y
Windows 10 x64 y y/y n y y y
Mac OS X 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
Mac OS Sierra 10.12.6 64-bit n y/y n y y y
CentOS 7.2 Linux 3.10.0 x86_64 PGI n y/y n y y y
CentOS 7.2 Linux 3.10.0 x86_64 GNU y y/y y y y y
CentOS 7.2 Linux 3.10.0 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 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
Mac OS Sierra 10.12.6 64-bit y n y y
CentOS 7.2 Linux 3.10.0 x86_64 PGI y y y n
CentOS 7.2 Linux 3.10.0 x86_64 GNU y y y y
CentOS 7.2 Linux 3.10.0 x86_64 Intel y y y n
Linux 2.6.32-573.18.1.el6.ppc64 y y y n
Compiler versions for each platform are listed in the preceding
"Supported Platforms" table.
More Tested Platforms
=====================
The following platforms are not supported but have been tested for this release.
Linux 2.6.32-573.22.1.el6 GNU C (gcc), Fortran (gfortran), C++ (g++)
#1 SMP x86_64 GNU/Linux compilers:
(mayll/platypus) Version 4.4.7 20120313
Version 4.9.3, 5.3.0, 6.2.0
PGI C, Fortran, C++ for 64-bit target on
x86-64;
Version 17.10-0
Intel(R) C (icc), C++ (icpc), Fortran (icc)
compilers:
Version 17.0.4.196 Build 20170411
MPICH 3.1.4 compiled with GCC 4.9.3
Linux 3.10.0-327.18.2.el7 GNU C (gcc) and C++ (g++) compilers
#1 SMP x86_64 GNU/Linux Version 4.8.5 20150623 (Red Hat 4.8.5-4)
(jelly) with NAG Fortran Compiler Release 6.1(Tozai)
GCC Version 7.1.0
OpenMPI 3.0.0-GCC-7.2.0-2.29,
3.1.0-GCC-7.2.0-2.29
Intel(R) C (icc) and C++ (icpc) compilers
Version 17.0.0.098 Build 20160721
with NAG Fortran Compiler Release 6.1(Tozai)
Linux 3.10.0-327.10.1.el7 MPICH 3.2 compiled with GCC 5.3.0
#1 SMP x86_64 GNU/Linux
(moohan)
Linux 2.6.32-573.18.1.el6.ppc64 MPICH mpich 3.1.4 compiled with
#1 SMP ppc64 GNU/Linux IBM XL C/C++ for Linux, V13.1
(ostrich) and IBM XL Fortran for Linux, V15.1
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.
Three tests fail with OpenMPI 3.0.0/GCC-7.2.0-2.29:
testphdf5 (ecdsetw, selnone, cchunk1, cchunk3, cchunk4, and actualio)
t_shapesame (sscontig2)
t_pflush1/fails on exit
The first two tests fail attempting collective writes.
Known problems in previous releases can be found in the HISTORY*.txt files
in the HDF5 source. Please report any new problems found to
help@hdfgroup.org.
CMake vs. Autotools installations
=================================
While both build systems produce similar results, there are differences.
Each system produces the same set of folders on linux (only CMake works
on standard Windows); bin, include, lib and share. Autotools places the
COPYING and RELEASE.txt file in the root folder, CMake places them in
the share folder.
The bin folder contains the tools and the build scripts. Additionally, CMake
creates dynamic versions of the tools with the suffix "-shared". Autotools
installs one set of tools depending on the "--enable-shared" configuration
option.
build scripts
-------------
Autotools: h5c++, h5cc, h5fc
CMake: h5c++, h5cc, h5hlc++, h5hlcc
The include folder holds the header files and the fortran mod files. CMake
places the fortran mod files into separate shared and static subfolders,
while Autotools places one set of mod files into the include folder. Because
CMake produces a tools library, the header files for tools will appear in
the include folder.
The lib folder contains the library files, and CMake adds the pkgconfig
subfolder with the hdf5*.pc files used by the bin/build scripts created by
the CMake build. CMake separates the C interface code from the fortran code by
creating C-stub libraries for each Fortran library. In addition, only CMake
installs the tools library. The names of the szip libraries are different
between the build systems.
The share folder will have the most differences because CMake builds include
a number of CMake specific files for support of CMake's find_package and support
for the HDF5 Examples CMake project.
%%%%1.10.3%%%%
HDF5 version 1.10.3 released on 2018-08-21
================================================================================
INTRODUCTION
This document describes the differences between this release and the previous
HDF5 release. It contains information on the platforms tested and known
problems in this release. For more details check the HISTORY*.txt files in the
HDF5 source.
Note that documentation in the links below will be updated at the time of each
final release.
Links to HDF5 documentation can be found on The HDF5 web page:
https://portal.hdfgroup.org/display/HDF5/HDF5
The official HDF5 releases can be obtained from:
https://www.hdfgroup.org/downloads/hdf5/
Changes from Release to Release and New Features in the HDF5-1.10.x release series
can be found at:
https://portal.hdfgroup.org/display/HDF5/HDF5+Application+Developer%27s+Guide
If you have any questions or comments, please send them to the HDF Help Desk:
help@hdfgroup.org
CONTENTS
- New Features
- Bug Fixes since HDF5-1.10.2
- Supported Platforms
- Tested Configuration Features Summary
- More Tested Platforms
- Known Problems
- CMake vs. Autotools installations
New Features
============
Library
-------
- Moved the H5DOread/write_chunk() API calls to H5Dread/write_chunk()
The functionality of the direct chunk I/O calls in the high-level
library has been moved to the H5D package in the main library. This
will allow using those functions without building the high-level
library. The parameters and functionality of the H5D calls are
identical to the H5DO calls.
The original H5DO high-level API calls have been retained, though
they are now just wrappers for the H5D calls. They are marked as
deprecated and are only available when the library is built with
deprecated functions. New code should use the H5D calls for this
reason.
As a part of this work, the following symbols from H5Dpublic.h are no
longer used:
H5D_XFER_DIRECT_CHUNK_WRITE_FLAG_NAME
H5D_XFER_DIRECT_CHUNK_WRITE_FILTERS_NAME
H5D_XFER_DIRECT_CHUNK_WRITE_OFFSET_NAME
H5D_XFER_DIRECT_CHUNK_WRITE_DATASIZE_NAME
H5D_XFER_DIRECT_CHUNK_READ_FLAG_NAME
H5D_XFER_DIRECT_CHUNK_READ_OFFSET_NAME
H5D_XFER_DIRECT_CHUNK_READ_FILTERS_NAME
And properties with these names are no longer stored in the dataset
transfer property lists. The symbols are still defined in H5Dpublic.h,
but only when the library is built with deprecated symbols.
(DER - 2018/05/04)
Configuration:
-------------
- Add missing USE_110_API_DEFAULT option.
Option USE_110_API_DEFAULT sets the default version of
versioned APIs. The bin/makevers perl script did not set
the maxidx variable correctly when the 1.10 branch was
created. This caused the versioning process to always use
the latest version of any API.
(ADB - 2018/08/17, HDFFV-10552)
- Added configuration checks for the following MPI functions:
MPI_Mprobe - Used for the Parallel Compression feature
MPI_Imrecv - Used for the Parallel Compression feature
MPI_Get_elements_x - Used for the "big Parallel I/O" feature
MPI_Type_size_x - Used for the "big Parallel I/O" feature
(JTH - 2018/08/02, HDFFV-10512)
- Added section to the libhdf5.settings file to indicate
the status of the Parallel Compression and "big Parallel I/O"
features.
(JTH - 2018/08/02, HDFFV-10512)
- Add option to execute swmr shell scripts from CMake.
Option TEST_SHELL_SCRIPTS redirects processing into a
separate ShellTests.cmake file for UNIX types. The tests
execute the shell scripts if a SH program is found.
(ADB - 2018/07/16)
C++ Library:
------------
- New wrappers
Added the following items:
+ Class DSetAccPropList for the dataset access property list.
+ Wrapper for H5Dget_access_plist to class DataSet
// Gets the access property list of this dataset.
DSetAccPropList getAccessPlist() const;
+ Wrappers for H5Pset_chunk_cache and H5Pget_chunk_cache to class DSetAccPropList
// Sets the raw data chunk cache parameters.
void setChunkCache(size_t rdcc_nslots, size_t rdcc_nbytes, double rdcc_w0)
// Retrieves the raw data chunk cache parameters.
void getChunkCache(size_t &rdcc_nslots, size_t &rdcc_nbytes, double &rdcc_w0)
+ New operator!= to class DataType (HDFFV-10472)
// Determines whether two datatypes are not the same.
bool operator!=(const DataType& compared_type)
+ Wrappers for H5Oget_info2, H5Oget_info_by_name2, and H5Oget_info_by_idx2
(HDFFV-10458)
// Retrieves information about an HDF5 object.
void getObjinfo(H5O_info_t& objinfo, unsigned fields = H5O_INFO_BASIC) const;
// Retrieves information about an HDF5 object, given its name.
void getObjinfo(const char* name, H5O_info_t& objinfo,
unsigned fields = H5O_INFO_BASIC,
const LinkAccPropList& lapl = LinkAccPropList::DEFAULT) const;
void getObjinfo(const H5std_string& name, H5O_info_t& objinfo,
unsigned fields = H5O_INFO_BASIC,
const LinkAccPropList& lapl = LinkAccPropList::DEFAULT) const;
// Retrieves information about an HDF5 object, given its index.
void getObjinfo(const char* grp_name, H5_index_t idx_type,
H5_iter_order_t order, hsize_t idx, H5O_info_t& objinfo,
unsigned fields = H5O_INFO_BASIC,
const LinkAccPropList& lapl = LinkAccPropList::DEFAULT) const;
void getObjinfo(const H5std_string& grp_name, H5_index_t idx_type,
H5_iter_order_t order, hsize_t idx, H5O_info_t& objinfo,
unsigned fields = H5O_INFO_BASIC,
const LinkAccPropList& lapl = LinkAccPropList::DEFAULT) const;
(BMR - 2018/07/22, HDFFV-10150, HDFFV-10458, HDFFV-1047)
Java Library:
----------------
- Java HDFLibraryException class
Change parent class from Exception to RuntimeException.
(ADB - 2018/07/30, HDFFV-10534)
- JNI Read and Write
Refactored variable-length functions, H5DreadVL and H5AreadVL,
to correct dataset and attribute reads. New write functions,
H5DwriteVL and H5AwriteVL, are under construction.
(ADB - 2018/06/02, HDFFV-10519)
Bug Fixes since HDF5-1.10.2 release
==================================
Library
-------
- Performance issue with H5Oget_info
H5Oget_info family of routines retrieves information for an object such
as object type, access time, number of attributes, and storage space etc.
Retrieving all such information regardless is an overkill and causes
performance issue when doing so for many objects.
Add an additional parameter "fields" to the the H5Oget_info family of routines
indicating the type of information to be retrieved. The same is done to
the H5Ovisit family of routines which recursively visits an object
returning object information in a callback function. Both sets of routines
are versioned and the corresponding compatibility macros are added.
The version 2 names of the two sets of routines are:
(1) H5Oget_info2, H5Oget_info_by_idx2, H5Oget_info_by_name2
(2) H5Ovisit2, H5Ovisit_by_name2
(VC - 2018/08/15, HDFFV-10180)
- Test failure due to metadata size in test/vds.c
The size of metadata from test_api_get_ex_dcpl() in test/vds.c is not as expected
because the latest format should be used when encoding the layout for VDS.
Set the latest format in a temporary fapl and pass the setting to the routines that
encode the dataset selection for VDS.
(VC - 2018/08/14 HDFFV-10469)
- Java HDF5LibraryException class
The error minor and major values would be lost after the
constructor executed.
Created two local class variables to hold the values obtained during
execution of the constructor. Refactored the class functions to retrieve
the class values rather then calling the native functions.
The native functions were renamed and called only during execution
of the constructor.
Added error checking to calling class constructors in JNI classes.
(ADB - 2018/08/06, HDFFV-10544)
- Added checks of the defined MPI_VERSION to guard against usage of
MPI-3 functions in the Parallel Compression and "big Parallel I/O"
features when HDF5 is built with MPI-2. Previously, the configure
step would pass but the build itself would fail when it could not
locate the MPI-3 functions used.
As a result of these new checks, HDF5 can again be built with MPI-2,
but the Parallel Compression feature will be disabled as it relies
on the MPI-3 functions used.
(JTH - 2018/08/02, HDFFV-10512)
- User's patches: CVEs
The following patches have been applied:
CVE-2018-11202 - NULL pointer dereference was discovered in
H5S_hyper_make_spans in H5Shyper.c (HDFFV-10476)
https://security-tracker.debian.org/tracker/CVE-2018-11202
https://cve.mitre.org/cgi-bin/cvename.cgi?name=3DCVE-2018-11202
CVE-2018-11203 - A division by zero was discovered in
H5D__btree_decode_key in H5Dbtree.c (HDFFV-10477)
https://security-tracker.debian.org/tracker/CVE-2018-11203
https://cve.mitre.org/cgi-bin/cvename.cgi?name=3DCVE-2018-11203
CVE-2018-11204 - A NULL pointer dereference was discovered in
H5O__chunk_deserialize in H5Ocache.c (HDFFV-10478)
https://security-tracker.debian.org/tracker/CVE-2018-11204
https://cve.mitre.org/cgi-bin/cvename.cgi?name=3DCVE-2018-11204
CVE-2018-11206 - An out of bound read was discovered in
H5O_fill_new_decode and H5O_fill_old_decode in H5Ofill.c
(HDFFV-10480)
https://security-tracker.debian.org/tracker/CVE-2018-11206
https://cve.mitre.org/cgi-bin/cvename.cgi?name=3DCVE-2018-11206
CVE-2018-11207 - A division by zero was discovered in
H5D__chunk_init in H5Dchunk.c (HDFFV-10481)
https://security-tracker.debian.org/tracker/CVE-2018-11207
https://cve.mitre.org/cgi-bin/cvename.cgi?name=3DCVE-2018-11207
(BMR - 2018/7/22, PR#s: 1134 and 1139,
HDFFV-10476, HDFFV-10477, HDFFV-10478, HDFFV-10480, HDFFV-10481)
- H5Adelete
H5Adelete failed when deleting the last "large" attribute that
is stored densely via fractal heap/v2 b-tree.
After removing the attribute, update the ainfo message. If the
number of attributes goes to zero, remove the message.
(VC - 2018/07/20, HDFFV-9277)
- A bug was discovered in the parallel library which caused partial
parallel reads of filtered datasets to return incorrect data. The
library used the incorrect dataspace for each chunk read, causing
the selection used in each chunk to be wrong.
The bug was not caught during testing because all of the current
tests which do parallel reads of filtered data read all of the data
using an H5S_ALL selection. Several tests were added which exercise
partial parallel reads.
(JTH - 2018/07/16, HDFFV-10467)
- A bug was discovered in the parallel library which caused parallel
writes of filtered datasets to trigger an assertion failure in the
file free space manager.
This occurred when the filter used caused chunks to repeatedly shrink
and grow over the course of several dataset writes. The previous chunk
information, such as the size of the chunk and the offset in the file,
was being cached and not updated after each write, causing the next write
to the chunk to retrieve the incorrect cached information and run into
issues when reallocating space in the file for the chunk.
(JTH - 2018/07/16, HDFFV-10509)
- A bug was discovered in the parallel library which caused the
H5D__mpio_array_gatherv() function to allocate too much memory.
When the function is called with the 'allgather' parameter set
to a non-true value, the function will receive data from all MPI
ranks and gather it to the single rank specied by the 'root'
parameter. However, the bug in the function caused memory for
the received data to be allocated on all MPI ranks, not just the
singular rank specified as the receiver. In some circumstances,
this would cause an application to fail due to the large amounts
of memory being allocated.
(JTH - 2018/07/16, HDFFV-10467)
- Error checks in h5stat and when decoding messages
h5stat exited with seg fault/core dumped when
errors are encountered in the internal library.
Add error checks and --enable-error-stack option to h5stat.
Add range checks when decoding messages: old fill value, old
layout and refcount.
(VC - 2018/07/11, HDFFV-10333)
- If an HDF5 file contains a malformed compound datatype with a
suitably large offset, the type conversion code can run off
the end of the type conversion buffer, causing a segmentation
fault.
This issue was reported to The HDF Group as issue #CVE-2017-17507.
NOTE: The HDF5 C library cannot produce such a file. This condition
should only occur in a corrupt (or deliberately altered) file
or a file created by third-party software.
THE HDF GROUP WILL NOT FIX THIS BUG AT THIS TIME
Fixing this problem would involve updating the publicly visible
H5T_conv_t function pointer typedef and versioning the API calls
which use it. We normally only modify the public API during
major releases, so this bug will not be fixed at this time.
(DER - 2018/02/26, HDFFV-10356)
Configuration
-------------
- Applied patches to address Cywin build issues
There were three issues for Cygwin builds:
- Shared libs were not built.
- The -std=c99 flag caused a SIG_SETMASK undeclared error.
- Undefined errors when buildbing test shared libraries.
Patches to address these issues were received and incorporated in this version.
(LRK - 2018/07/18, HDFFV-10475)
- The --enable-debug/production configure flags are listed as 'deprecated'
when they should really be listed as 'removed'.
In the autotools overhaul several years ago, we removed these flags and
implemented a new --enable-build-mode= flag. This was done because we
changed the semantics of the modes and didn't want users to silently
be exposed to them. The newer system is also more flexible and us to
add other modes (like 'clean').
The --enable-debug/production flags are now listed as removed.
(DER - 2018/05/31, HDFFV-10505)
- Moved the location of gcc attribute.
The gcc attribute(no_sanitize), named as the macro HDF_NO_UBSAN,
was located after the function name. Builds with GCC 7 did not
indicate any problem, but GCC 8 issued errors. Moved the
attribute before the function name, as required.
(ADB - 2018/05/22, HDFFV-10473)
- Reworked java test suite into individual JUnit tests.
Testing the whole suite of java unit tests in a single JUnit run
made it difficult to determine actual failures when tests would fail.
Running each file set of tests individually, allows individual failures
to be diagnosed easier. A side benefit is that tests for optional components
of the library can be disabled if not configured.
(ADB - 2018/05/16, HDFFV-9739)
- Converted CMake global commands ADD_DEFINITIONS and INCLUDE_DIRECTORIES
to use target_* type commands. This change modernizes the CMake usage
in the HDF5 library.
In addition, there is the intention to convert to generator expressions,
where possible. The exception is Fortran FLAGS on Windows Visual Studio.
The HDF macros TARGET_C_PROPERTIES and TARGET_FORTRAN_PROPERTIES have
been removed with this change in usage.
The additional language (C++ and Fortran) checks have also been localized
to only be checked when that language is enabled.
(ADB - 2018/05/08)
Performance
-------------
- Revamped internal use of DXPLs, improving performance
(QAK - 2018/05/20)
Fortran
--------
- Fixed issue with h5fget_obj_count_f and using a file id of H5F_OBJ_ALL_F not
returning the correct count.
(MSB - 2018/5/15, HDFFV-10405)
C++ APIs
--------
- Adding default arguments to existing functions
Added the following items:
+ Two more property list arguments are added to H5Location::createDataSet:
const DSetAccPropList& dapl = DSetAccPropList::DEFAULT
const LinkCreatPropList& lcpl = LinkCreatPropList::DEFAULT
+ One more property list argument is added to H5Location::openDataSet:
const DSetAccPropList& dapl = DSetAccPropList::DEFAULT
(BMR - 2018/07/21, PR# 1146)
- Improvement C++ documentation
Replaced the table in main page of the C++ documentation from mht to htm format
for portability.
(BMR - 2018/07/17, PR# 1141)
Supported Platforms
===================
Linux 2.6.32-696.16.1.el6.ppc64 gcc (GCC) 4.4.7 20120313 (Red Hat 4.4.7-18)
#1 SMP ppc64 GNU/Linux g++ (GCC) 4.4.7 20120313 (Red Hat 4.4.7-18)
(ostrich) GNU Fortran (GCC) 4.4.7 20120313 (Red Hat 4.4.7-18)
IBM XL C/C++ V13.1
IBM XL Fortran V15.1
Linux 3.10.0-327.10.1.el7 GNU C (gcc), Fortran (gfortran), C++ (g++)
#1 SMP x86_64 GNU/Linux compilers:
(kituo/moohan) Version 4.8.5 20150623 (Red Hat 4.8.5-4)
Version 4.9.3, Version 5.2.0
Intel(R) C (icc), C++ (icpc), Fortran (icc)
compilers:
Version 17.0.0.098 Build 20160721
MPICH 3.1.4 compiled with GCC 4.9.3
SunOS 5.11 32- and 64-bit Sun C 5.12 SunOS_sparc
(emu) Sun Fortran 95 8.6 SunOS_sparc
Sun C++ 5.12 SunOS_sparc
Windows 7 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/ Intel C, Fortran 2017 (cmake)
Visual Studio 2015 w/ MSMPI 8 (cmake)
Windows 10 Visual Studio 2015 w/ Intel Fortran 18 (cmake)
Windows 10 x64 Visual Studio 2015 w/ Intel Fortran 18 (cmake)
Visual Studio 2017 w/ Intel Fortran 18 (cmake)
Mac OS X Yosemite 10.10.5 Apple clang/clang++ version 6.1 from Xcode 7.0
64-bit gfortran GNU Fortran (GCC) 4.9.2
(osx1010dev/osx1010test) Intel icc/icpc/ifort version 15.0.3
Mac OS X El Capitan 10.11.6 Apple clang/clang++ version 7.3.0 from Xcode 7.3
64-bit gfortran GNU Fortran (GCC) 5.2.0
(osx1011dev/osx1011test) Intel icc/icpc/ifort version 16.0.2
Mac OS Sierra 10.12.6 Apple LLVM version 8.1.0 (clang/clang++-802.0.42)
64-bit gfortran GNU Fortran (GCC) 7.1.0
(swallow/kite) Intel icc/icpc/ifort version 17.0.2
Tested Configuration Features Summary
=====================================
In the tables below
y = tested
n = not tested in this release
C = Cluster
W = Workstation
x = not working in this release
dna = does not apply
( ) = footnote appears below second table
<blank> = testing incomplete on this feature or platform
Platform C F90/ F90 C++ zlib SZIP
parallel F2003 parallel
Solaris2.11 32-bit n y/y n y y y
Solaris2.11 64-bit n y/n n y y y
Windows 7 y y/y n y y y
Windows 7 x64 y y/y y y y y
Windows 7 Cygwin n y/n n y y y
Windows 7 x64 Cygwin n y/n n y y y
Windows 10 y y/y n y y y
Windows 10 x64 y y/y n y y y
Mac OS X 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
Mac OS Sierra 10.12.6 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 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
Mac OS Sierra 10.12.6 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 4.9.3, 5.3.0, 6.2.0
PGI C, Fortran, C++ for 64-bit target on
x86-64;
Version 17.10-0
Intel(R) C (icc), C++ (icpc), Fortran (icc)
compilers:
Version 17.0.4.196 Build 20170411
MPICH 3.1.4 compiled with GCC 4.9.3
Linux 3.10.0-327.18.2.el7 GNU C (gcc) and C++ (g++) compilers
#1 SMP x86_64 GNU/Linux Version 4.8.5 20150623 (Red Hat 4.8.5-4)
(jelly) with NAG Fortran Compiler Release 6.1(Tozai)
GCC Version 7.1.0
OpenMPI 3.0.0-GCC-7.2.0-2.29,
3.1.0-GCC-7.2.0-2.29
Intel(R) C (icc) and C++ (icpc) compilers
Version 17.0.0.098 Build 20160721
with NAG Fortran Compiler Release 6.1(Tozai)
Linux 3.10.0-327.10.1.el7 MPICH 3.2 compiled with GCC 5.3.0
#1 SMP x86_64 GNU/Linux
(moohan)
Linux 2.6.32-573.18.1.el6.ppc64 MPICH mpich 3.1.4 compiled with
#1 SMP ppc64 GNU/Linux IBM XL C/C++ for Linux, V13.1
(ostrich) and IBM XL Fortran for Linux, V15.1
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.
Three tests fail with OpenMPI 3.0.0/GCC-7.2.0-2.29:
testphdf5 (ecdsetw, selnone, cchunk1, cchunk3, cchunk4, and actualio)
t_shapesame (sscontig2)
t_pflush1/fails on exit
The first two tests fail attempting collective writes.
Known problems in previous releases can be found in the HISTORY*.txt files
in the HDF5 source. Please report any new problems found to
help@hdfgroup.org.
CMake vs. Autotools installations
=================================
While both build systems produce similar results, there are differences.
Each system produces the same set of folders on linux (only CMake works
on standard Windows); bin, include, lib and share. Autotools places the
COPYING and RELEASE.txt file in the root folder, CMake places them in
the share folder.
The bin folder contains the tools and the build scripts. Additionally, CMake
creates dynamic versions of the tools with the suffix "-shared". Autotools
installs one set of tools depending on the "--enable-shared" configuration
option.
build scripts
-------------
Autotools: h5c++, h5cc, h5fc
CMake: h5c++, h5cc, h5hlc++, h5hlcc
The include folder holds the header files and the fortran mod files. CMake
places the fortran mod files into separate shared and static subfolders,
while Autotools places one set of mod files into the include folder. Because
CMake produces a tools library, the header files for tools will appear in
the include folder.
The lib folder contains the library files, and CMake adds the pkgconfig
subfolder with the hdf5*.pc files used by the bin/build scripts created by
the CMake build. CMake separates the C interface code from the fortran code by
creating C-stub libraries for each Fortran library. In addition, only CMake
installs the tools library. The names of the szip libraries are different
between the build systems.
The share folder will have the most differences because CMake builds include
a number of CMake specific files for support of CMake's find_package and support
for the HDF5 Examples CMake project.
%%%%1.10.2%%%%
HDF5 version 1.10.2 released on 2018-03-29
================================================================================
INTRODUCTION
This document describes the differences between this release and the previous
HDF5 release. It contains information on the platforms tested and known
problems in this release. For more details check the HISTORY*.txt files in the
HDF5 source.
Note that documentation in the links below will be updated at the time of each
final release.
Links to HDF5 documentation can be found on The HDF5 web page:
https://portal.hdfgroup.org/display/HDF5/HDF5
The official HDF5 releases can be obtained from:
https://www.hdfgroup.org/downloads/hdf5/
Changes from Release to Release and New Features in the HDF5-1.10.x release series
can be found at:
https://portal.hdfgroup.org/display/HDF5/HDF5+Application+Developer%27s+Guide
If you have any questions or comments, please send them to the HDF Help Desk:
help@hdfgroup.org
CONTENTS
- New Features
- Support for new platforms and languages
- Bug Fixes since HDF5-1.10.1
- Supported Platforms
- Tested Configuration Features Summary
- More Tested Platforms
- Known Problems
New Features
============
Configuration and Build Systems:
--------------------------------
- CMake builds
--------------
- Changed minimum CMake required version to 3.10.
This change removed the need to support a copy of the FindMPI.cmake module,
which has been removed, along with its subfolder in the config/cmake_ext_mod
location.
(ADB - 2018/03/09)
- Added pkg-config file generation
Added pkg-config file generation for the C, C++, HL, and HL C++ libraries.
In addition, builds on Linux will create h5cc, h5c++, h5hlcc, and h5hlc++ scripts in the bin
directory that use the pkg-config files. The scripts can be used to build HDF5 C and C++
applications (i.e, similar to the compiler scripts produced by the Autotools builds).
(ADB - 2018/03/08, HDFFV-4359)
- Refactored use of CMAKE_BUILD_TYPE for new variable, which understands
the type of generator in use.
Added new configuration macros to use new HDF_BUILD_TYPE variable. This
variable is set correctly for the type of generator being used for the build.
(ADB - 2018/01/08, HDFFV-10385, HDFFV-10296)
- Autotools builds
------------------
- Removed version-specific gcc/gfortran flags for version 4.0 (inclusive)
and earlier.
The config/gnu-flags file, which is sourced as a part of the configure
process, adds version-specific flags for use when building HDF5. Most of
these flags control warnings and do not affect the final product.
Flags for older versions of the compiler were consolidated into the
common flags section. Moving these flags simplifies maintenance of
the file.
The upshot of this is that building with ancient versions of gcc
(<= 4.0) will possibly no longer work without hand-hacking the file
to remove the flags not understood by that version of the compiler.
Nothing should change when building with gcc >= 4.1.
(DER - 2017/05/31, HDFFV-9937)
- -fno-omit-frame-pointer was added when building with debugging symbols
enabled.
Debugging symbols can be enabled independently of the overall build
mode in both the autotools and CMake. This allows (limited) debugging
of optimized code. Since many debuggers rely on the frame pointer,
we've disabled this optimization when debugging symbols are requested
(e.g.: via building with --enable-symbols).
(DER - 2017/05/31, HDFFV-10226)
Library:
--------
- Added an enumerated value to H5F_libver_t for H5Pset_libver_bounds().
Currently, the library defines two values for H5F_libver_t and supports
only two pairs of (low, high) combinations as derived from these values.
Thus the bounds setting via H5Pset_libver_bounds() is rather restricted.
Added an enumerated value (H5F_LIBVER_V18) to H5F_libver_t and
H5Pset_libver_bounds() now supports five pairs of (low, high) combinations
as derived from these values. This addition provides the user more
flexibility in setting bounds for object creation.
(VC - 2018/03/14)
- Added prefix option to VDS files.
Currently, VDS source files must be in the active directory to be
found by the virtual file. Adding the option of a prefix to be set
on the virtual file, using a data access property list (DAPL),
allows the source files to locate at an absolute or relative path
to the virtual file.
Private utility functions in H5D and H5L packages merged into single
function in H5F package.
New public APIs:
herr_t H5Pset_virtual_prefix(hid_t dapl_id, const char* prefix);
ssize_t H5Pget_virtual_prefix(hid_t dapl_id, char* prefix /*out*/, size_t size);
The prefix can also be set with an environment variable, HDF5_VDS_PREFIX.
(ADB - 2017/12/12, HDFFV-9724, HDFFV-10361)
- H5FDdriver_query() API call added to the C library.
This new library call allows the user to query a virtual file driver
(VFD) for the feature flags it supports (listed in H5FDpublic.h).
This can be useful to determine if a VFD supports SWMR, for example.
Note that some VFDs have feature flags that may only be present
after a file has been created or opened (e.g.: the core VFD will
have the H5FD_FEAT_POSIX_COMPAT_HANDLE flag set if the backing
store is switched on). Since the new API call queries a generic VFD
unassociated with a file, these flags will never be returned.
(DER - 2017/05/31, HDFFV-10215)
- H5FD_FEAT_DEFAULT_VFD_COMPATIBLE VFD feature flag added to the C library.
This new feature flag indicates that the VFD is compatible with the
default VFD. VFDs that set this flag create single files that follow
the canonical HDF5 file format.
(DER - 2017/05/31, HDFFV-10214)
- The H5I_REFERENCE value in the H5I_type_t enum (defined in H5Ipublic.h)
has been marked as deprecated.
This ID type value is not used in the C library. i.e.: There are no
hid_t values that are of ID type H5I_REFERENCE.
This enum value will be removed in a future major version of the library.
The code will remain unchanged in the HDF5 1.10.x releases and branches.
(DER - 2017/04/05, HDFFV-10252)
Parallel Library:
-----------------
- Enabled compression for parallel applications.
With this release parallel applications can create and write compressed
datasets (or the datasets with the filters such as Fletcher32 applied).
(EIP - 2018/03/29)
- Addressed slow file close on some Lustre file systems.
Slow file close has been reported on some Lustre file systems.
While the ultimate cause is not understood fully, the proximate
cause appears to be long delays in MPI_File_set_size() calls at
file close and flush.
To minimize this problem pending a definitive diagnosis and fix,
PHDF5 has been modified to avoid MPI_File_set_size() calls when
possible. This is done by comparing the library's EOA (End of
Allocation) with the file systems EOF, and skipping the
MPI_File_set_size() call if the two match.
(JRM - 2018/03/29)
- Optimized parallel open/location of the HDF5 super-block.
Previous releases of PHDF5 required all parallel ranks to
search for the HDF5 superblock signature when opening the
file. As this is accomplished more or less as a synchronous
operation, a large number of processes can experience a
slowdown in the file open due to filesystem contention.
As a first step in improving the startup/file-open performance,
we allow MPI rank 0 of the associated MPI communicator to locate
the base offset of the super-block and then broadcast that result
to the remaining ranks in the parallel group. Note that this
approach is utilized ONLY during file opens which employ the MPIO
file driver in HDF5 by previously having called H5Pset_fapl_mpio().
HDF5 parallel file operations which do not employ multiple ranks
e.g. specifiying MPI_COMM_SELF (whose MPI_Comm_size == 1)
as opposed to MPI_COMM_WORLD, will not be affected by this
optimization. Conversely, parallel file operations on subgroups
of MPI_COMM_WORLD are allowed to be run in parallel with each
subgroup operating as an independant collection of processes.
(RAW - 2017/10/10, HDFFV-10294)
- Added large (>2GB) MPI-IO transfers.
Previous releases of PHDF5 would fail when attempting to
read or write greater than 2GB of data in a single IO operation.
This issue stems principally from an MPI API whose definitions
utilize 32 bit integers to describe the number of data elements
and datatype that MPI should use to effect a data transfer.
Historically, HDF5 has invoked MPI-IO with the number of
elements in a contiguous buffer represented as the length
of that buffer in bytes.
Resolving the issue and thus enabling larger MPI-IO transfers
is accomplished first, by detecting when a user IO request would
exceed the 2GB limit as described above. Once a transfer request
is identified as requiring special handling, PHDF5 now creates a
derived datatype consisting of a vector of fixed sized blocks
which is in turn wrapped within a single MPI_Type_struct to
contain the vector and any remaining data. The newly created
datatype is then used in place of MPI_BYTE and can be used to
fulfill the original user request without encountering API
errors.
(RAW - 2017/09/10, HDFFV-8839)
C++ Library:
------------
- The following C++ API wrappers have been added to the C++ Library:
+ H5Lcreate_soft:
// Creates a soft link from link_name to target_name.
void link(const char *target_name, const char *link_name,...)
void link(const H5std_string& target_name,...)
+ H5Lcreate_hard:
// Creates a hard link from new_name to curr_name.
void link(const char *curr_name, const Group& new_loc,...)
void link(const H5std_string& curr_name, const Group& new_loc,...)
// Creates a hard link from new_name to curr_name in same location.
void link(const char *curr_name, const hid_t same_loc,...)
void link(const H5std_string& curr_name, const hid_t same_loc,...)
Note: previous version of H5Location::link will be deprecated.
+ H5Lcopy:
// Copy an object from a group of file to another.
void copyLink(const char *src_name, const Group& dst,...)
void copyLink(const H5std_string& src_name, const Group& dst,...)
// Copy an object from a group of file to the same location.
void copyLink(const char *src_name, const char *dst_name,...)
void copyLink(const H5std_string& src_name,...)
+ H5Lmove:
// Rename an object in a group or file to a new location.
void moveLink(const char* src_name, const Group& dst,...)
void moveLink(const H5std_string& src_name, const Group& dst,...)
// Rename an object in a group or file to the same location.
void moveLink(const char* src_name, const char* dst_name,...)
void moveLink(const H5std_string& src_name,...)
Note: previous version H5Location::move will be deprecated.
+ H5Ldelete:
// Removes the specified link from this location.
void unlink(const char *link_name,
const LinkAccPropList& lapl = LinkAccPropList::DEFAULT)
void unlink(const H5std_string& link_name,
const LinkAccPropList& lapl = LinkAccPropList::DEFAULT)
Note: additional parameter is added to previous H5Location::unlink.
+ H5Tencode and H5Tdecode:
// Creates a binary object description of this datatype.
void DataType::encode() - C API H5Tencode()
// Returns the decoded type from the binary object description.
DataType::decode() - C API H5Tdecode()
ArrayType::decode() - C API H5Tdecode()
CompType::decode() - C API H5Tdecode()
DataType::decode() - C API H5Tdecode()
EnumType::decode() - C API H5Tdecode()
FloatType::decode() - C API H5Tdecode()
IntType::decode() - C API H5Tdecode()
StrType::decode() - C API H5Tdecode()
VarLenType::decode() - C API H5Tdecode()
+ H5Lget_info:
// Returns the information of the named link.
H5L_info_t getLinkInfo(const H5std_string& link_name,...)
(BMR - 2018/03/11, HDFFV-10149)
- Added class LinkCreatPropList for link create property list.
(BMR - 2018/03/11, HDFFV-10149)
- Added overloaded functions H5Location::createGroup to take a link
creation property list.
Group createGroup(const char* name, const LinkCreatPropList& lcpl)
Group createGroup(const H5std_string& name, const LinkCreatPropList& lcpl)
(BMR - 2018/03/11, HDFFV-10149)
- A document is added to the HDF5 C++ API Reference Manual to show the
mapping from a C API to C++ wrappers. It can be found from the main
page of the C++ API Reference Manual.
(BMR - 2017/10/17, HDFFV-10151)
Java Library:
----------------
- Wrapper added for enabling the error stack.
H5error_off would disable the error stack reporting. In order
to re-enable the reporting, the error stack info needs to be
saved so that H5error_on can revert state.
(ADB - 2018/03/13, HDFFV-10412)
- Wrappers were added for the following C APIs:
H5Pset_evict_on_close
H5Pget_evict_on_close
H5Pset_chunk_opts
H5Pget_chunk_opts
H5Pset_efile_prefix
H5Pget_efile_prefix
H5Pset_virtual_prefix
H5Pget_virtual_prefix
(ADB - 2017/12/20)
- The H5I_REFERENCE value in the H5I_type_t enum (defined in H5Ipublic.h)
has been marked as deprectated.
JNI code which refers to this value will be removed in a future
major version of the library. The code will remain unchanged in the
1.10.x releases and branches.
See the C library section, above, for further information.
(HDFFV-10252, DER, 2017/04/05)
Tools:
------
- h5diff has a new option to display error stack.
Updated h5diff with the --enable-error-stack argument, which
enables the display of the hdf5 error stack. This completes the
improvement to the main tools: h5copy, h5diff, h5dump, h5ls and
h5repack.
(ADB - 2017/08/30, HDFFV-9774)
Support for new platforms, languages and compilers.
=======================================
- None
Bug Fixes since HDF5-1.10.1 release
==================================
Library
-------
- The data read after a direct chunk write to a chunked dataset with
one chunk was incorrect.
The problem was due to the passing of a null dataset pointer to
the insert callback for the chunk index in the routine
H5D__chunk_direct_write() in H5Dchunk.c
The dataset was a single-chunked dataset which will use the
single chunk index when latest format was enabled on file creation.
The single chunk index was the only index that used this pointer
in the insert callback.
Passed the dataset pointer to the insert callback for the chunk
index in H5D__chunk_direct_write().
(VC - 2018/03/20, HDFFV-10425)
- Added public routine H5DOread_chunk to the high-level C library.
The patch for H5DOwrite_chunk() to write an entire chunk to the file
directly was contributed by GE Healthcare and integrated by The HDF Group
developers.
(VC - 2017/05/19, HDFFV-9934)
- Freeing of object header after failed checksum verification.
It was discovered that the object header (in H5Ocache.c) was not released properly
when the checksum verification failed and a re-load of the object
header was needed.
Freed the object header that failed the chksum verification only
after the new object header is reloaded, deserialized and set up.
(VC - 2018/03/14, HDFFV-10209)
- Updated H5Pset_evict_on_close in H5Pfapl.c
Changed the minor error number from H5E_CANTSET to H5E_UNSUPPORTED for
parallel library.
(ADB - 2018/03/06, HDFFV-10414)
- Fixed the problems with the utility function that could not handle lowercase
Windows drive letters.
Added call to upper function for drive letter.
(ADB - 2017/12/18, HDFFV-10307)
- Fixed H5Sencode() bug when the number of elements selected was > 2^32.
H5Sencode() incorrectly encodes dataspace selection with number of
elements exceeding 2^32. When decoding such selection via H5Sdecode(),
the number of elements in the decoded dataspace is not the same as
what is encoded. This problem exists for H5S_SEL_HYPER and
H5S_SEL_POINTS encoding.
The cause of the problem is due to the fact that the library uses 32 bits to
encode counts and block offsets for the selection.
The solution is to use the original 32 bit encodings if possible,
but use a different way to encode selection if more that 32 bits is needed.
See details in the RFC: H5Sencode/H5Sdecode Format Change i
https://bitbucket.hdfgroup.org/projects/HDFFV/repos/hdf5doc/browse/RFCs/HDF5_Library/H5SencodeFormatChange.
(VC - 2017/11/28, HDFFV-9947)
- Fixed filter plugin handling in H5PL.c and H5Z.c to not require i availability of
dependent libraries (e.g., szip or zlib).
It was discovered that the dynamic loading process used by
filter plugins had issues with library dependencies.
CMake build process changed to use LINK INTERFACE keywords, which
allowed HDF5 C library to make dependent libraries private. The
filter plugin libraries no longer require dependent libraries
(such as szip or zlib) to be available.
(ADB - 2017/11/16, HDFFV-10328)
- Fixed rare object header corruption bug.
In certain cases, such as when converting large attributes to dense
storage, an error could occur which would either fail an assertion or
cause file corruption. Fixed and added test.
(NAF - 2017/11/14, HDFFV-10274)
- Updated H5Zfilter_avail in H5Z.c.
The public function checked for plugins, while the private
function did not.
Modified H5Zfilter_avail and private function, H5Z_filter_avail.
Moved check for plugin from public to private function. Updated
H5P__set_filter due to change in H5Z_filter_avail. Updated tests.
(ADB - 2017/10/10, HDFFV-10297, HDFFV-10319)
- h5dump produced SEGFAULT when dumping corrypted file.
The behavior was due to the error in the internal function H5HL_offset_into().
(1) Fixed H5HL_offset_into() to return error when offset exceeds heap data
block size.
(2) Fixed other places in the library that call this routine to detect
error routine.
(VC - 2017/08/30, HDFFV-10216)
- Fixes for paged aggregation feature.
Skip test in test/fheap.c when:
(1) multi/split drivers and
(2) persisting free-space or using paged aggregation strategy
(VC, 2017/07/10)
Changes made based on RFC review comments:
(1) Added maximum value for file space page size
(2) Dropped check for page end metadata threshold
(3) Removed "can_shrink" and "shrink" callbacks for small section class
(VC - 2017/06/09)
- Fixed for infinite loop in H5VM_power2up().
The function H5VM_power2up() returns the next power of 2
for n. When n exceeds 2^63, it overflows and becomes 0 causing
the infinite looping.
The fix ensures that the function checks for n >= 2^63
and returns 0.
(VC - 2017/07/10, HDFFV-10217)
- Fixed for H5Ocopy doesn't work with open identifiers.
Changes made so that raw data for dataset objects are copied from
cached info when possible instead of flushing objects to file and
read them back in again.
(VC - 2017/07/05, HDFFV-7853)
- An uninitialized struct could cause a memory access error when using
variable-length or reference types in a compressed, chunked dataset.
A struct containing a callback function pointer and a pointer to some
associated data was used before initialization. This could cause a
memory access error and system crash. This could only occur under
unusual conditions when using variable-lenth and reference types in
a compressed, chunked dataset.
On recent versions of Visual Studio, when built in debug mode, the
debug heap will complain and cause a crash if the code in question
is executed (this will cause the objcopy test to fail).
(DER - 2017/11/21, HDFFV-10330)
- Fixed collective metadata writes on file close.
It was discovered that metadata was being written twice as part of
the parallel file close behavior, once independently and once
collectively.
A fix for this error was included as part of the parallel compression
feature but remained undocumented here.
(RAW - 2017/12/01, HDFFV-10272)
- If an HDF5 file contains a filter pipeline message with a 'number of
filters' field that exceeds the maximum number of allowed filters,
the error handling code will attempt to dereference a NULL pointer.
This issue was reported to The HDF Group as issue #CVE-2017-17505.
https://security-tracker.debian.org/tracker/CVE-2017-17505
https://cve.mitre.org/cgi-bin/cvename.cgi?name=3DCVE-2017-17505
NOTE: The HDF5 C library cannot produce such a file. This condition
should only occur in a corrupt (or deliberately altered) file
or a file created by third-party software.
This problem arose because the error handling code assumed that
the 'number of filters' field implied that a dynamic array of that
size had already been created and that the cleanup code should
iterate over that array and clean up each element's resources. If
an error occurred before the array has been allocated, this will
not be true.
This has been changed so that the number of filters is set to
zero on errors. Additionally, the filter array traversal in the
error handling code now requires that the filter array not be NULL.
(DER - 2018/02/06, HDFFV-10354)
- If an HDF5 file contains a filter pipeline message which contains
a 'number of filters' field that exceeds the actual number of
filters in the message, the HDF5 C library will read off the end of
the read buffer.
This issue was reported to The HDF Group as issue #CVE-2017-17506.
https://security-tracker.debian.org/tracker/CVE-2017-17506
https://cve.mitre.org/cgi-bin/cvename.cgi?name=3DCVE-2017-17506
NOTE: The HDF5 C library cannot produce such a file. This condition
should only occur in a corrupt (or deliberately altered) file
or a file created by third-party software.
The problem was fixed by passing the buffer size with the buffer
and ensuring that the pointer cannot be incremented off the end
of the buffer. A mismatch between the number of filters declared
and the actual number of filters will now invoke normal HDF5
error handling.
(DER - 2018/02/26, HDFFV-10355)
- If an HDF5 file contains a malformed compound datatype with a
suitably large offset, the type conversion code can run off
the end of the type conversion buffer, causing a segmentation
fault.
This issue was reported to The HDF Group as issue #CVE-2017-17507.
https://security-tracker.debian.org/tracker/CVE-2017-17506
https://cve.mitre.org/cgi-bin/cvename.cgi?name=3DCVE-2017-17506
NOTE: The HDF5 C library cannot produce such a file. This condition
should only occur in a corrupt (or deliberately altered) file
or a file created by third-party software.
THE HDF GROUP WILL NOT FIX THIS BUG AT THIS TIME
Fixing this problem would involve updating the publicly visible
H5T_conv_t function pointer typedef and versioning the API calls
which use it. We normally only modify the public API during
major releases, so this bug will not be fixed at this time.
(DER - 2018/02/26, HDFFV-10356)
- If an HDF5 file contains a malformed compound type which contains
a member of size zero, a division by zero error will occur while
processing the type.
This issue was reported to The HDF Group as issue #CVE-2017-17508.
https://security-tracker.debian.org/tracker/CVE-2017-17508
https://cve.mitre.org/cgi-bin/cvename.cgi?name=3DCVE-2017-17508
NOTE: The HDF5 C library cannot produce such a file. This condition
should only occur in a corrupt (or deliberately altered) file
or a file created by third-party software.
Checking for zero before dividing fixes the problem. Instead of the
division by zero, the normal HDF5 error handling is invoked.
(DER - 2018/02/26, HDFFV-10357)
- If an HDF5 file contains a malformed symbol table node that declares
it contains more symbols than it actually contains, the library
can run off the end of the metadata cache buffer while processing
the symbol table node.
This issue was reported to The HDF Group as issue #CVE-2017-17509.
https://security-tracker.debian.org/tracker/CVE-2017-17509
https://cve.mitre.org/cgi-bin/cvename.cgi?name=3DCVE-2017-17509
NOTE: The HDF5 C library cannot produce such a file. This condition
should only occur in a corrupt (or deliberately altered) file
or a file created by third-party software.
Performing bounds checks on the buffer while processing fixes the
problem. Instead of the segmentation fault, the normal HDF5 error
handling is invoked.
(DER - 2018/03/12, HDFFV-10358)
- Fixed permissions passed to open(2) on file create.
On Windows, the POSIX permissions passed to open(2) when creating files
were only incidentally correct. They are now set to the correct value of
(_S_IREAD | _S_IWRITE).
On other platforms, the permissions were set to a mix of 666, 644, and
000. They are now set uniformly to 666.
(DER - 2017/04/28, HDFFV-9877)
- The H5FD_FEAT_POSIX_COMPAT_HANDLE flag is no longer used to determine
if a virtual file driver (VFD) is compatible with SWMR.
Use of this VFD feature flag was not in line with the documentation in
the public H5FDpublic.h file. In particular, it was being used as a
proxy for determining if SWMR I/O is allowed. This is unecessary as we
already have a feature flag for this (H5FD_SUPPORTS_SWMR_IO).
(DER - 2017/05/31, HDFFV-10214)
Configuration
-------------
- CMake changes
- Updated CMake commands configuration.
A number of improvements were made to the CMake commands. Most
changes simplify usage or eliminate unused constructs. Also,
some changes support better cross-platform support.
(ADB - 2018/02/01, HDFFV-10398)
- Corrected usage of CMAKE_BUILD_TYPE variable.
The use of the CMAKE_BUILD_TYPE is incorrect for multi-config
generators (Visual Studio and XCode) and is optional for single
config generators. Created a new macro to check
GLOBAL PROPERTY -> GENERATOR_IS_MULTI_CONFIG
Created two new HDF variable, HDF_BUILD_TYPE and HDF_CFG_BUILD_TYPE.
Defaults for these variables is "Release".
(ADB - 2018/01/10, HDFFV-10385)
- Added replacement of fortran flags if using static CRT.
Added TARGET_STATIC_CRT_FLAGS call to HDFUseFortran.cmake file in
config/cmake_ext_mod folder.
(ADB - 2018/01/08, HDFFV-10334)
- The hdf5 library used shared szip and zlib, which needlessly required
applications to link with the same szip and zlib libraries.
Changed the target_link_libraries commands to use the static libs.
Removed improper link duplication of szip and zlib.
Adjusted the link dependencies and the link interface values of
the target_link_libraries commands.
(ADB - 2017/11/14, HDFFV-10329)
- CMake MPI
CMake implementation for MPI was problematic and would create incorrect
MPI library references in the hdf5 libraries.
Reworked the CMake MPI code to properly create CMake targets. Also merged
the latest CMake FindMPI.cmake changes to the local copy. This is necessary
until HDF changes the CMake minimum to 3.9 or greater.
(ADB - 2017/11/02, HDFFV-10321)
- Corrected FORTRAN_HAVE_C_LONG_DOUBLE processing in the autotools.
A bug in the autotools Fortran processing code always set the
FORTRAN_HAVE_C_LONG_DOUBLE variable to be true regardless of
whether or not a C long double type was present.
This would cause compilation failures on platforms where a C
long double type was not available and the Fortran wrappers
were being built.
(DER - 2017/07/05, HDFFV-10247)
- The deprecated --enable-production and --enable-debug configure options
failed to emit errors when passed an empty string
(e.g.: --enable-debug="").
Due to the way we checked for these options being set, it was possible
to avoid the error message and continue configuration if an empty string
was passed to the option.
Any use of --enable-production or --enable-debug will now halt the
configuration step and emit a helpful error message
(use --enable-build-mode=debug|production instead).
(DER - 2017/07/05, HDFFV-10248)
- CMake
Too many commands for POST_BUILD step caused command line to be
too big on windows.
Changed foreach of copy command to use a custom command with the
use of the HDFTEST_COPY_FILE macro.
(ADB - 2017/07/12, HDFFV-10254)
- CMake test execution environment
The parallel HDF5 test: 't_pread' assumed the use of autotools
and the directory structure associated with that testing approach.
Modified the test code to check whether the 'h5jam' utility can be
found in the same directory as the test executable (which is
preferred directory structure utilized by cmake) and if found
will invoke the tool directly rather than utilizing a relative path.
(RAW - 2017/11/03, HDFFV-10318)
- Fortran compilation fails for xlf and CMake builds.
Fixed CMake shared library build for H5match_types and modules
(MSB - 2017/12/19, HDFFV-10363)
- Shared libraries fail test on OSX with Fortran enabled with CMake.
Fixed by removing the F77 use of EQUIVALENCE and COMMON, replaced
using MODULES. Updated CMake.
(MSB - 2017/12/07, HDFFV-10223)
- The bin/trace script now emits an error code on problems and autogen.sh
will fail if bin/trace fails.
The bin/trace script adds tracing functionality to public HDF5 API calls.
It is only of interest to developers who modify the HDF5 source code.
Previously, bin/trace just wrote an error message to stdout when it
encountered problems, so autogen.sh processing did not halt and a broken
version of the library could be built. The script will now return an
error code when it encounters problems, and autogen.sh will fail.
This only affects users who run autogen.sh to rebuild the Autotools files,
which is not necessary to build HDF5 from source in official releases of the
library. CMake users are unaffected as bin/trace is not run via CMake
at this time.
(DER - 2017/04/25, HDFFV-10178)
- FC_BASENAME was changed from gfortran40 to gfortran in a few places.
In the autotools, FC_BASENAME was set to gfortran40 in a few locations
(config/gnu-fflags and config/freebsd). This was probably a historical
artifact and did not seem to affect many users.
The value is now correctly set to gfortran.
(DER - 2017/05/26, HDFFV-10249)
- The ar flags were changed to -cr (was: -cru)
The autotools set the flags for ar to -cru by default. The -u flag,
which allows selective replacement of only the members which have
changed, raises warnings on some platforms, so the flags are now set to
-cr via AR_FLAGS in configure.ac. This causes the static library to
always be completely recreated from the object files on each build.
(DER - 2017/11/15, HDFFV-10428)
Fortran
--------
- Fixed compilation errors when using Intel 18 Fortran compilers
(MSB - 2017/11/3, HDFFV-10322)
Tools
-----
- h5clear
An enhancement to the tool in setting a file's stored EOA.
It was discovered that a crashed file's stored EOA in the superblock
was smaller than the actual file's EOF. When the file was reopened
and closed, the library truncated the file to the stored EOA.
Added an option to the tool in setting the file's stored EOA in the
superblock to the maximum of (EOA, EOF) + increment.
An option was also added to print the file's EOA and EOF.
(VC - 2018/03/14, HDFFV-10360)
- h5repack
h5repack changes the chunk parameters when a change of layout is not
specified and a filter is applied.
HDFFV-10297, HDFFV-10319 reworked code for h5repack and h5diff code
in the tools library. The check for an existing layout was incorrectly
placed into an if block and not executed. The check was moved into
the normal path of the function.
(ADB - 2018/02/21, HDFFV-10412)
- h5dump
The tools library will hide the error stack during file open.
While this is preferable almost always, there are reasons to enable
display of the error stack when a tool will not open a file. Adding an
optional argument to the --enable-error-stack will provide this use case.
As an optional argument it will not affect the operation of the
--enable-error-stack. h5dump is the only tool to implement this change.
(ADB - 2018/02/15, HDFFV-10384)
- h5dump
h5dump would output an indented blank line in the filters section.
h5dump overused the h5tools_simple_prefix function, which is a
function intended to account for the data index (x,y,z) option.
Removed the function call for header information.
(ADB - 2018/01/25, HDFFV-10396)
- h5repack
h5repack incorrectly searched internal object table for name.
h5repack would search the table of objects for a name, if the
name did not match it tried to determine if the name without a
leading slash would match. The logic was flawed! The table
stored names(paths) without a leading slash and did a strstr
of the table path to the name.
The assumption was that if there was a difference of one then
it was a match, however "pressure" would match "/pressure" as
well as "/pressure1", "/pressure2", etc. Changed logic to remove
any leading slash and then do a full compare of the name.
(ADB - 2018/01/18, HDFFV-10393)
- h5repack
h5repack failed to handle command line parameters for customer filters.
User defined filter parameter conversions would fail when integers were
represented on the command line with character string
larger then 9 characters. Increased local variable array for storing
the current command line parameter to prevent buffer overflows.
(ADB - 2018/01/17, HDFFV-10392)
- h5diff
h5diff seg faulted if comparing VL strings against fixed strings.
Reworked solution for HDFFV-8625 and HDFFV-8639. Implemented the check
for string objects of same type in the diff_can_type function by
adding an if(tclass1 == H5T_STRING) block. This "if block" moves the
same check that was added for attributes to this function, which is
used by all object types. This function handles complex type structures.
Also added a new test file in h5diffgenttest for testing this issue
and removed the temporary files used in the test scripts.
(ADB - 2018/01/04, HDFFV-8745)
- h5repack
h5repack failed to copy a dataset with existing filter.
Reworked code for h5repack and h5diff code in the tools library. Added
improved error handling, cleanup of resources and checks of calls.
Modified H5Zfilter_avail and private function, H5Z_filter_avail.
Moved check for plugin from public to private function. Updated
H5P__set_filter due to change in H5Z_filter_avail. Updated tests.
Note, h5repack output display has changed to clarify the individual
steps of the repack process. The output indicates if an operation
applies to all objects. Lines with notation and no information
have been removed.
(ADB - 2017/10/10, HDFFV-10297, HDFFV-10319)
- h5repack
h5repack always set the User Defined filter flag to H5Z_FLAG_MANDATORY.
Added another parameter to the 'UD=' option to set the flag by default
to '0' or H5Z_FLAG_MANDATORY, the other choice is '1' or H5Z_FLAG_OPTIONAL.
(ADB - 2017/08/31, HDFFV-10269)
- h5ls
h5ls generated error on stack when it encountered a H5S_NULL
dataspace.
Adding checks for H5S_NULL before calling H5Sis_simple (located
in the h5tools_dump_mem function) fixed the issue.
(ADB - 2017/08/17, HDFFV-10188)
- h5repack
Added tests to h5repack.sh.in to verify options added for paged
aggregation work as expected.
(VC - 2017/08/03)
- h5dump
h5dump segfaulted on output of XML file.
Function that escape'd strings used the full buffer length
instead of just the length of the replacement string in a
strncpy call. Using the correct length fixed the issue.
(ADB - 2017/08/01, HDFFV-10256)
- h5diff
h5diff segfaulted on compare of a NULL variable length string.
Improved h5diff compare of strings by adding a check for
NULL strings and setting the lengths to zero.
(ADB - 2017/07/25, HDFFV-10246)
- h5import
h5import crashed trying to import data from a subset of a dataset.
Improved h5import by adding the SUBSET keyword. h5import understands
to use the Count times the Block as the size of the dimensions.
Added INPUT_B_ORDER keyword to old-style configuration files.
The import from h5dump function expects the binary files to use native
types (FILE '-b' option) in the binary file.
(ADB - 2017/06/15, HDFFV-10219)
- h5repack
h5repack did not maintain the creation order flag of the root
group.
Improved h5repack by reading the creation order and applying the
flag to the new root group. Also added arguments to set the
order and index direction, which applies to the traversing of the
original file, on the command line.
(ADB - 2017/05/26, HDFFV-8611)
- h5diff
h5diff failed to account for strpad type and null terminators
of char strings. Also, h5diff failed to account for string length
differences and would give a different result depending on file
order in the command line.
Improved h5diff compare of strings and arrays by adding a check for
string lengths and if the strpad was null filled.
(ADB - 2017/05/18, HDFFV-9055, HDFFV-10128)
High-Level APIs:
------
- H5DOwrite_chunk() problems when overwriting an existing chunk with
no filters enabled.
When overwriting chunks and no filters were being used, the library would
fail (when asserts are enabled, e.g. debug builds) or incorrectly
insert additional chunks instead of overwriting (when asserts are not
enabled, e.g. production builds).
This has been fixed and a test was added to the hl/test_dset_opt test.
(DER - 2017/05/11, HDFFV-10187)
C++ APIs
--------
- Removal of memory leaks.
A private function was inadvertently called, causing memory leaks. This
is now fixed.
(BMR - 2018/03/12 - User's reported in email)
Testing
-------
- Memory for three variables in testphdf5's coll_write_test was malloced
but not freed, leaking memory when running the test.
The variables' memory is now freed.
(LRK - 2018/03/12, HDFFV-10397)
- Refactored the testpar/t_bigio.c test to include ALARM macros
Changed the test to include the ALARM_ON and ALARM_OFF macros which
are intended to prevent nightly test hangs that have been observed
with this particular parallel test example. The code was also modified to
simplify status reporting (only from MPI rank 0) and additional
status checking added.
(RAW - 2017/11/08, HDFFV-10301)
Supported Platforms
===================
Linux 2.6.32-696.16.1.el6.ppc64 gcc (GCC) 4.4.7 20120313 (Red Hat 4.4.7-18)
#1 SMP ppc64 GNU/Linux g++ (GCC) 4.4.7 20120313 (Red Hat 4.4.7-18)
(ostrich) GNU Fortran (GCC) 4.4.7 20120313 (Red Hat 4.4.7-18)
IBM XL C/C++ V13.1
IBM XL Fortran V15.1
Linux 3.10.0-327.10.1.el7 GNU C (gcc), Fortran (gfortran), C++ (g++)
#1 SMP x86_64 GNU/Linux compilers:
(kituo/moohan) Version 4.8.5 20150623 (Red Hat 4.8.5-4)
Version 4.9.3, Version 5.2.0,
Intel(R) C (icc), C++ (icpc), Fortran (icc)
compilers:
Version 17.0.0.098 Build 20160721
MPICH 3.1.4 compiled with GCC 4.9.3
SunOS 5.11 32- and 64-bit Sun C 5.12 SunOS_sparc
(emu) Sun Fortran 95 8.6 SunOS_sparc
Sun C++ 5.12 SunOS_sparc
Windows 7 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/ Intel C, Fortran 2017 (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 Yosemite 10.10.5 Apple clang/clang++ version 6.1 from Xcode 7.0
64-bit gfortran GNU Fortran (GCC) 4.9.2
(osx1010dev/osx1010test) Intel icc/icpc/ifort version 15.0.3
Mac OS X El Capitan 10.11.6 Apple clang/clang++ version 7.3.0 from Xcode 7.3
64-bit gfortran GNU Fortran (GCC) 5.2.0
(osx1011dev/osx1011test) Intel icc/icpc/ifort version 16.0.2
Mac OS Sierra 10.12.6 Apple LLVM version 8.1.0 (clang/clang++-802.0.42)
64-bit gfortran GNU Fortran (GCC) 7.1.0
(swallow/kite) Intel icc/icpc/ifort version 17.0.2
Tested Configuration Features Summary
=====================================
In the tables below
y = tested
n = not tested in this release
C = Cluster
W = Workstation
x = not working in this release
dna = does not apply
( ) = footnote appears below second table
<blank> = testing incomplete on this feature or platform
Platform C F90/ F90 C++ zlib SZIP
parallel F2003 parallel
Solaris2.11 32-bit n y/y n y y y
Solaris2.11 64-bit n y/n n y y y
Windows 7 y y/y n y y y
Windows 7 x64 y y/y y y y y
Windows 7 Cygwin n y/n n y y y
Windows 7 x64 Cygwin n y/n n y y y
Windows 10 y y/y n y y y
Windows 10 x64 y y/y n y y y
Mac OS X Mountain Lion 10.8.5 64-bit n y/y n y y y
Mac OS X Mavericks 10.9.5 64-bit n y/y n y y 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 4.9.3, 5.3.0, 6.2.0
PGI C, Fortran, C++ for 64-bit target on
x86-64;
Version 17.10-0
Intel(R) C (icc), C++ (icpc), Fortran (icc)
compilers:
Version 17.0.4.196 Build 20170411
MPICH 3.1.4 compiled with GCC 4.9.3
Linux 3.10.0-327.18.2.el7 GNU C (gcc) and C++ (g++) compilers
#1 SMP x86_64 GNU/Linux Version 4.8.5 20150623 (Red Hat 4.8.5-4)
(jelly) with NAG Fortran Compiler Release 6.1(Tozai)
GCC Version 7.1.0
OpenMPI 3.0.0-GCC-7.2.0-2.29
Intel(R) C (icc) and C++ (icpc) compilers
Version 17.0.0.098 Build 20160721
with NAG Fortran Compiler Release 6.1(Tozai)
Linux 3.10.0-327.10.1.el7 MPICH 3.2 compiled with GCC 5.3.0
#1 SMP x86_64 GNU/Linux
(moohan)
Linux 2.6.32-573.18.1.el6.ppc64 MPICH mpich 3.1.4 compiled with
#1 SMP ppc64 GNU/Linux IBM XL C/C++ for Linux, V13.1
(ostrich) and IBM XL Fortran for Linux, V15.1
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.
Three tests fail with OpenMPI 3.0.0/GCC-7.2.0-2.29:
testphdf5 (ecdsetw, selnone, cchunk1, cchunk3, cchunk4, and actualio)
t_shapesame (sscontig2)
t_pflush1/fails on exit
The first two tests fail attempting collective writes.
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.
%%%%1.10.1%%%%
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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