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|
HDF5 version 1.10.7-1 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 HDF5-1.10.5
- Supported Platforms
- Tested Configuration Features Summary
- More Tested Platforms
- Known Problems
- CMake vs. Autotools installations
New Features
============
Configuration:
-------------
- 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 - 2020/07/9, 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. Autotools does not build the
compression libraries within hdf5 builds. New option USE_LIBAEC is
required to compensate for the different files produced by AEC build.
(ADB - 2020/04/22, OESS-65)
- CMake ConfigureChecks.cmake file now uses CHECK_STRUCT_HAS_MEMBER
Some handcrafted tests in HDFTests.c has 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)
- 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 has been a number of mingw issues that has 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 has 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.
Reenabling them after the initial build requires running configure
again with the option(s) enabled.
(LRK - 2019/06/12, HDFFV-9976)
- Change tools test that test 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)
- 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)
Library:
--------
- 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)
- Add S3 and HDFS VFDs to HDF5 maintenance
Fix windows requirements and java tests. Windows requires CMake 3.13.
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)
- 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)
- 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.
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)
Parallel Library:
-----------------
-
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)
C++ Library:
------------
- Added new wrappers for H5Pset/get_create_intermediate_group()
LinkCreatPropList::setCreateIntermediateGroup()
LinkCreatPropList::getCreateIntermediateGroup()
(BMR - 2019/04/22, HDFFV-10622)
- 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:
----------------
- Fix a failure in JUnit-TestH5P on 32-bit architectures
(JTH - 2019/04/30)
- 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:
------
-
High-Level APIs:
---------------
-
C Packet Table API
------------------
-
Internal header file
--------------------
-
Documentation
-------------
-
Support for new platforms, languages and compilers.
=======================================
-
Bug Fixes since HDF5-1.10.5 release
==================================
Library
-------
- 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)
- 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 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)
- Improved peformance when creating a large number of small datasets by
retrieving default property values from the API context instead of doing
skip list searches.
(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)
- Fixed a bug caused by bad tag value when condensing object header
messages
There was an assertion failure when moving meessages 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 will 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 the 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 where 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 detail.
(RL - 2019/3/4, HDFFV-10705)
- 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)
- 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)
- Don't allocate an empty (0-dimensioned) chunked dataset's chunk
index, until the dataset's dimensions are increased.
(QAK - 2020/05/07)
- 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)
Java Library:
----------------
-
Configuration
-------------
- 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)
- 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)
Performance
-------------
-
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)
- 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)
High-Level APIs:
------
-
Fortran High-Level APIs:
------
-
Documentation
-------------
-
F90 APIs
--------
-
C++ APIs
--------
-
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 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 x64 Visual Studio 2015 w/ Intel C, Fortran 2018 (cmake)
Visual Studio 2015 w/ MSMPI 10 (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)
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
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)
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.
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.
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