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|
HDF5 version 1.11.2 currently under development
================================================================================
INTRODUCTION
This document describes the differences between this release and the previous
HDF5 release. It contains information on the platforms tested and known
problems in this release. For more details check the HISTORY*.txt files in the
HDF5 source.
Note that documentation in the links below will be updated at the time of each
final release.
Links to HDF5 documentation can be found on The HDF5 web page:
https://portal.hdfgroup.org/display/HDF5/HDF5
The official HDF5 releases can be obtained from:
https://www.hdfgroup.org/downloads/hdf5/
Changes from Release to Release and New Features in the HDF5-1.10.x release series
can be found at:
https://portal.hdfgroup.org/display/HDF5/HDF5+Application+Developer%27s+Guide
If you have any questions or comments, please send them to the HDF Help Desk:
help@hdfgroup.org
CONTENTS
- New Features
- Support for new platforms and languages
- Bug Fixes since HDF5-1.10.2
- Supported Platforms
- Tested Configuration Features Summary
- More Tested Platforms
- Known Problems
- CMake vs. Autotools installations
New Features
============
Configuration:
-------------
- Added configuration checks for the following MPI functions:
MPI_Mprobe - Used for the Parallel Compression feature
MPI_Imrecv - Used for the Parallel Compression feature
MPI_Get_elements_x - Used for the "big Parallel I/O" feature
MPI_Type_size_x - Used for the "big Parallel I/O" feature
(JTH - 2018/08/02, HDFFV-10512)
- Added section to the libhdf5.settings file to indicate
the status of the Parallel Compression and "big Parallel I/O"
features.
(JTH - 2018/08/02, HDFFV-10512)
- Add option to execute swmr shell scripts from CMake.
Option TEST_SHELL_SCRIPTS redirects processing into a
separate ShellTests.cmake file for UNIX types. The tests
execute the shell scripts if a SH program is found.
(ADB - 2018/07/16)
Library:
--------
-
Parallel Library:
-----------------
-
Fortran Library:
----------------
-
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 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)
Tools:
------
-
High-Level APIs:
---------------
-
C Packet Table API
------------------
-
Internal header file
--------------------
-
Documentation
-------------
-
Support for new platforms, languages and compilers.
=======================================
-
Bug Fixes since HDF5-1.10.2 release
==================================
Library
-------
- Java HDF5LibraryException class
The error minor and major values would be lost after the
constructor executed.
Created two local class variables to hold the values obtained during
execution of the constructor. Refactored the class functions to retrieve
the class values rather then calling the native functions.
The native functions were renamed and called only during execution
of the constructor.
Added error checking to calling class constructors in JNI classes.
(ADB - 2018/08/06, HDFFV-10544)
- Added checks of the defined MPI_VERSION to guard against usage of
MPI-3 functions in the Parallel Compression and "big Parallel I/O"
features when HDF5 is built with MPI-2. Previously, the configure
step would pass but the build itself would fail when it could not
locate the MPI-3 functions used.
As a result of these new checks, HDF5 can again be built with MPI-2,
but the Parallel Compression feature will be disabled as it relies
on the MPI-3 functions used.
(JTH - 2018/08/02, HDFFV-10512)
- User's patches: CVEs
The following patches have been applied:
CVE-2018-11202 - NULL pointer dereference was discovered in
H5S_hyper_make_spans in H5Shyper.c (HDFFV-10476)
https://security-tracker.debian.org/tracker/CVE-2018-11202
https://cve.mitre.org/cgi-bin/cvename.cgi?name=3DCVE-2018-11202
CVE-2018-11203 - A division by zero was discovered in
H5D__btree_decode_key in H5Dbtree.c (HDFFV-10477)
https://security-tracker.debian.org/tracker/CVE-2018-11203
https://cve.mitre.org/cgi-bin/cvename.cgi?name=3DCVE-2018-11203
CVE-2018-11204 - A NULL pointer dereference was discovered in
H5O__chunk_deserialize in H5Ocache.c (HDFFV-10478)
https://security-tracker.debian.org/tracker/CVE-2018-11204
https://cve.mitre.org/cgi-bin/cvename.cgi?name=3DCVE-2018-11204
CVE-2018-11206 - An out of bound read was discovered in
H5O_fill_new_decode and H5O_fill_old_decode in H5Ofill.c
(HDFFV-10480)
https://security-tracker.debian.org/tracker/CVE-2018-11206
https://cve.mitre.org/cgi-bin/cvename.cgi?name=3DCVE-2018-11206
CVE-2018-11207 - A division by zero was discovered in
H5D__chunk_init in H5Dchunk.c (HDFFV-10481)
https://security-tracker.debian.org/tracker/CVE-2018-11207
https://cve.mitre.org/cgi-bin/cvename.cgi?name=3DCVE-2018-11207
(BMR - 2018/7/22, PR#s: 1134 and 1139,
HDFFV-10476, HDFFV-10477, HDFFV-10478, HDFFV-10480, HDFFV-10481)
- H5Adelete
H5Adelete failed when deleting the last "large" attribute that
is stored densely via fractal heap/v2 b-tree.
After removing the attribute, update the ainfo message. If the
number of attributes goes to zero, remove the message.
(VC - 2018/07/20, HDFFV-9277)
- A bug was discovered in the parallel library which caused partial
parallel reads of filtered datasets to return incorrect data. The
library used the incorrect dataspace for each chunk read, causing
the selection used in each chunk to be wrong.
The bug was not caught during testing because all of the current
tests which do parallel reads of filtered data read all of the data
using an H5S_ALL selection. Several tests were added which exercise
partial parallel reads.
(JTH - 2018/07/16, HDFFV-10467)
- A bug was discovered in the parallel library which caused parallel
writes of filtered datasets to trigger an assertion failure in the
file free space manager.
This occurred when the filter used caused chunks to repeatedly shrink
and grow over the course of several dataset writes. The previous chunk
information, such as the size of the chunk and the offset in the file,
was being cached and not updated after each write, causing the next write
to the chunk to retrieve the incorrect cached information and run into
issues when reallocating space in the file for the chunk.
(JTH - 2018/07/16, HDFFV-10509)
- A bug was discovered in the parallel library which caused the
H5D__mpio_array_gatherv() function to allocate too much memory.
When the function is called with the 'allgather' parameter set
to a non-true value, the function will receive data from all MPI
ranks and gather it to the single rank specied by the 'root'
parameter. However, the bug in the function caused memory for
the received data to be allocated on all MPI ranks, not just the
singular rank specified as the receiver. In some circumstances,
this would cause an application to fail due to the large amounts
of memory being allocated.
(JTH - 2018/07/16, HDFFV-10467)
- Error checks in h5stat and when decoding messages
h5stat exited with seg fault/core dumped when
errors are encountered in the internal library.
Add error checks and --enable-error-stack option to h5stat.
Add range checks when decoding messages: old fill value, old
layout and refcount.
(VC - 2018/07/11, HDFFV-10333)
- If an HDF5 file contains a malformed compound datatype with a
suitably large offset, the type conversion code can run off
the end of the type conversion buffer, causing a segmentation
fault.
This issue was reported to The HDF Group as issue #CVE-2017-17507.
NOTE: The HDF5 C library cannot produce such a file. This condition
should only occur in a corrupt (or deliberately altered) file
or a file created by third-party software.
THE HDF GROUP WILL NOT FIX THIS BUG AT THIS TIME
Fixing this problem would involve updating the publicly visible
H5T_conv_t function pointer typedef and versioning the API calls
which use it. We normally only modify the public API during
major releases, so this bug will not be fixed at this time.
(DER - 2018/02/26, HDFFV-10356)
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
-------------
-
Fortran
--------
-
Tools
-----
-
High-Level APIs:
------
-
Fortran High-Level APIs:
------
-
Documentation
-------------
-
F90 APIs
--------
-
C++ APIs
--------
- Adding default arguments to existing functions
Added the following items:
+ Two more property list arguments are added to H5Location::createDataSet:
const DSetAccPropList& dapl = DSetAccPropList::DEFAULT
const LinkCreatPropList& lcpl = LinkCreatPropList::DEFAULT
+ One more property list argument is added to H5Location::openDataSet:
const DSetAccPropList& dapl = DSetAccPropList::DEFAULT
(BMR - 2018/07/21, PR# 1146)
- Improvement C++ documentation
Replaced the table in main page of the C++ documentation from mht to htm format
for portability.
(BMR - 2018/07/17, PR# 1141)
Testing
-------
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 16 (cmake)
Windows 10 x64 Visual Studio 2015 w/ Intel Fortran 16 (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 Mountain Lion 10.8.5 64-bit n y/y n y y y
Mac OS X Mavericks 10.9.5 64-bit n y/y n y y ?
Mac OS X Yosemite 10.10.5 64-bit n y/y n y y ?
Mac OS X El Capitan 10.11.6 64-bit n y/y n y y ?
CentOS 6.7 Linux 2.6.18 x86_64 GNU n y/y n y y y
CentOS 6.7 Linux 2.6.18 x86_64 Intel n y/y n y y y
CentOS 6.7 Linux 2.6.32 x86_64 PGI n y/y n y y y
CentOS 7.2 Linux 2.6.32 x86_64 GNU y y/y y y y y
CentOS 7.2 Linux 2.6.32 x86_64 Intel n y/y n y y y
Linux 2.6.32-573.18.1.el6.ppc64 n y/n n y y y
Platform Shared Shared Shared Thread-
C libs F90 libs C++ libs safe
Solaris2.11 32-bit y y y y
Solaris2.11 64-bit y y y y
Windows 7 y y y y
Windows 7 x64 y y y y
Windows 7 Cygwin n n n y
Windows 7 x64 Cygwin n n n y
Windows 10 y y y y
Windows 10 x64 y y y y
Mac OS X Mountain Lion 10.8.5 64-bit y n y y
Mac OS X Mavericks 10.9.5 64-bit y n y y
Mac OS X Yosemite 10.10.5 64-bit y n y y
Mac OS X El Capitan 10.11.6 64-bit y n y y
CentOS 6.7 Linux 2.6.18 x86_64 GNU y y y y
CentOS 6.7 Linux 2.6.18 x86_64 Intel y y y n
CentOS 6.7 Linux 2.6.32 x86_64 PGI y y y n
CentOS 7.2 Linux 2.6.32 x86_64 GNU y y y n
CentOS 7.2 Linux 2.6.32 x86_64 Intel y y y n
Linux 2.6.32-573.18.1.el6.ppc64 y y y n
Compiler versions for each platform are listed in the preceding
"Supported Platforms" table.
More Tested Platforms
=====================
The following platforms are not supported but have been tested for this release.
Linux 2.6.32-573.22.1.el6 GNU C (gcc), Fortran (gfortran), C++ (g++)
#1 SMP x86_64 GNU/Linux compilers:
(mayll/platypus) Version 4.4.7 20120313
Version 4.9.3, 5.3.0, 6.2.0
PGI C, Fortran, C++ for 64-bit target on
x86-64;
Version 17.10-0
Intel(R) C (icc), C++ (icpc), Fortran (icc)
compilers:
Version 17.0.4.196 Build 20170411
MPICH 3.1.4 compiled with GCC 4.9.3
Linux 3.10.0-327.18.2.el7 GNU C (gcc) and C++ (g++) compilers
#1 SMP x86_64 GNU/Linux Version 4.8.5 20150623 (Red Hat 4.8.5-4)
(jelly) with NAG Fortran Compiler Release 6.1(Tozai)
GCC Version 7.1.0
OpenMPI 3.0.0-GCC-7.2.0-2.29
Intel(R) C (icc) and C++ (icpc) compilers
Version 17.0.0.098 Build 20160721
with NAG Fortran Compiler Release 6.1(Tozai)
Linux 3.10.0-327.10.1.el7 MPICH 3.2 compiled with GCC 5.3.0
#1 SMP x86_64 GNU/Linux
(moohan)
Linux 2.6.32-573.18.1.el6.ppc64 MPICH mpich 3.1.4 compiled with
#1 SMP ppc64 GNU/Linux IBM XL C/C++ for Linux, V13.1
(ostrich) and IBM XL Fortran for Linux, V15.1
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.
CMake vs. Autotools installations
=================================
While both build systems produce similar results, there are differences.
Each system produces the same set of folders on linux (only CMake works
on standard Windows); bin, include, lib and share. Autotools places the
COPYING and RELEASE.txt file in the root folder, CMake places them in
the share folder.
The bin folder contains the tools and the build scripts. Additionally, CMake
creates dynamic versions of the tools with the suffix "-shared". Autotools
installs one set of tools depending on the "--enable-shared" configuration
option.
build scripts
-------------
Autotools: h5c++, h5cc, h5fc
CMake: h5c++, h5cc, h5hlc++, h5hlcc
The include folder holds the header files and the fortran mod files. CMake
places the fortran mod files into separate shared and static subfolders,
while Autotools places one set of mod files into the include folder. Because
CMake produces a tools library, the header files for tools will appear in
the include folder.
The lib folder contains the library files, and CMake adds the pkgconfig
subfolder with the hdf5*.pc files used by the bin/build scripts created by
the CMake build. CMake separates the C interface code from the fortran code by
creating C-stub libraries for each Fortran library. In addition, only CMake
installs the tools library. The names of the szip libraries are different
between the build systems.
The share folder will have the most differences because CMake builds include
a number of CMake specific files for support of CMake's find_package and support
for the HDF5 Examples CMake project.
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