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|
HDF5 version 1.10.6-snap1 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 HDF5-1.10.4
- Supported Platforms
- Tested Configuration Features Summary
- More Tested Platforms
- Known Problems
- CMake vs. Autotools installations
New Features
============
Configuration:
-------------
- 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)
- 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 wrappers for H5Pset/get_create_intermediate_group()
LinkCreatPropList::setCreateIntermediateGroup()
LinkCreatPropList::getCreateIntermediateGroup()
(BMR - 2019/04/22, HDFFV-10622)
- Added new function to the C++ interface
Added wrapper for H5Ovisit2:
H5Object::visit()
(BMR - 2019/02/14, HDFFV-10532)
Java Library:
----------------
- Fix a failure in JUnit-TestH5P on 32-bit architectures
(JTH - 2019/04/30)
- 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)
High-Level APIs:
---------------
-
C Packet Table API
------------------
-
Internal header file
--------------------
-
Documentation
-------------
-
Support for new platforms, languages and compilers.
=======================================
-
Bug Fixes since HDF5-1.10.4 release
==================================
Library
-------
- 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)
- 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)
Java Library:
----------------
-
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)
Tools
-----
-
High-Level APIs:
------
-
Fortran High-Level APIs:
------
-
Documentation
-------------
-
F90 APIs
--------
-
C++ APIs
--------
-
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
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.
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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