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authorLarry Knox <lrknox@hdfgroup.org>2018-10-15 17:35:32 (GMT)
committerLarry Knox <lrknox@hdfgroup.org>2018-10-15 17:35:32 (GMT)
commit5eef94f83f4875b64ffe7f9cea05d965bddbd802 (patch)
tree98e19e98333de2fcdf6f8f9a777528dde879733d /release_docs
parent6569f208b8f39ace9e442e94ab110bec94c67d37 (diff)
parentf3f29dc7df5f3cc41a5e9462d8c415e540cda3d6 (diff)
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Merge pull request #1296 in HDFFV/hdf5 from ~LRKNOX/hdf5_lrk:1.10/master to 1.10/master
* commit 'f3f29dc7df5f3cc41a5e9462d8c415e540cda3d6': (42 commits) Commit version string changes for HDF5 1.10.4 release. Merge hdf5_1_10 changes to hdf5_1_10_4. Merge in changes from hdf5_1_10. Commit release date change. Update RELEASE.txt for HDF5 1.10.4 release. Add notes about unsupported options Add contents of HDF5 1.10.3 RELEASE.txt to HISTORY-1_10.txt and update RELEASE.txt for continuing development. Switch maintainer mode to disable, build mode to production, version to 1.10.4, and commit files generated by autogen.sh for release branch hdf5_1_10_4. HDFFV-10568 fix hdf5_java library dependency Fix Java library location for testing Java groups example fix Update system commands with HD prefix and whitespace Merge pull request #1224 in HDFFV/hdf5 from ~JHENDERSON/hdf5:develop to develop Disable failing tests because of execution issue Add testfiles to data copy Same changes needed for examples as test Correct name of test jar Only remove test jars Remove obsolete var Change prefix in example scripts to relative path to bin. This was done for 1.8, and works wherever installed without the need to replace the original prefix. ...
Diffstat (limited to 'release_docs')
-rw-r--r--release_docs/HISTORY-1_10.txt668
-rwxr-xr-xrelease_docs/INSTALL112
-rw-r--r--release_docs/INSTALL_CMake.txt80
-rwxr-xr-xrelease_docs/INSTALL_Cygwin.txt12
-rw-r--r--release_docs/INSTALL_Warnings.txt474
-rwxr-xr-xrelease_docs/RELEASE.txt452
-rw-r--r--release_docs/USING_CMake_Examples.txt2
7 files changed, 1365 insertions, 435 deletions
diff --git a/release_docs/HISTORY-1_10.txt b/release_docs/HISTORY-1_10.txt
index 9887a54..4344482 100644
--- a/release_docs/HISTORY-1_10.txt
+++ b/release_docs/HISTORY-1_10.txt
@@ -3,6 +3,7 @@ HDF5 History
This file contains development history of the HDF5 1.10 branch
+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
@@ -10,6 +11,673 @@ This file contains development history of the HDF5 1.10 branch
[Search on the string '%%%%' for section breaks of each release.]
+%%%%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
diff --git a/release_docs/INSTALL b/release_docs/INSTALL
index baad559..5c54698 100755
--- a/release_docs/INSTALL
+++ b/release_docs/INSTALL
@@ -2,11 +2,11 @@
Instructions for the Installation of HDF5 Software
==================================================
-This file provides instructions for installing the HDF5 software.
+This file provides instructions for installing the HDF5 software.
For help with installing, questions can be posted to the HDF Forum or sent to the HDF Helpdesk:
- HDF Forum: https://forum.hdfgroup.org/
+ HDF Forum: https://forum.hdfgroup.org/
HDF Helpdesk: https://portal.hdfgroup.org/display/support/The+HDF+Help+Desk
CONTENTS
@@ -52,8 +52,8 @@ CONTENTS
1. Obtaining HDF5
The latest supported public release of HDF5 is available from
- https://www.hdfgroup.org/downloads/hdf5/. For Unix and UNIX-like
- platforms, it is available in tar format compressed with gzip.
+ https://www.hdfgroup.org/downloads/hdf5/. For Unix and UNIX-like
+ platforms, it is available in tar format compressed with gzip.
For Microsoft Windows, it is in ZIP format.
@@ -77,14 +77,14 @@ CONTENTS
$ tar zxf hdf5-X.Y.Z.tar.gz
<configure_flags> above refers to the configure flags appropriate
- to your installation. For example, to install HDF5 with the
- Fortran and C++ interfaces and with SZIP compression, the
+ to your installation. For example, to install HDF5 with the
+ Fortran and C++ interfaces and with SZIP compression, the
configure line might read as follows:
-
+
$ ./configure --prefix=/usr/local/hdf5 --enable-fortran \
--enable-cxx --with-szlib=PATH_TO_SZIP
- In this case, PATH_TO_SZIP would be replaced with the path to the
+ In this case, PATH_TO_SZIP would be replaced with the path to the
installed location of the SZIP library.
2.1. Windows
@@ -101,7 +101,7 @@ CONTENTS
3. HDF5 dependencies
3.1. Zlib
- The HDF5 library includes a predefined compression filter that
+ The HDF5 library includes a predefined compression filter that
uses the "deflate" method for chunked datasets. If zlib-1.1.2 or
later is found, HDF5 will use it. Otherwise, HDF5's predefined
compression method will degenerate to a no-op; the compression
@@ -122,17 +122,17 @@ CONTENTS
include the Szip library with the encoder enabled. These can be found
here:
- https://www.hdfgroup.org/downloads/hdf5/
+ https://www.hdfgroup.org/downloads/hdf5/
To configure the HDF5 library with the Szip compression filter, use
the '--with-szlib=/PATH_TO_SZIP' flag. For more information, see
section 4.3.7, "Specifying other libraries and headers."
Please notice that if HDF5 configure cannot find a valid Szip library,
- configure will not fail; in this case, the compression filter will
+ configure will not fail; in this case, the compression filter will
not be available to the applications.
- To check if Szip compression was successfully configured in,
+ To check if Szip compression was successfully configured in,
check the "I/O filters (external):" line in the configure output,
summary section, printed to the standard output.
@@ -188,7 +188,7 @@ CONTENTS
detects various features of the host system and creates the
Makefiles. On most systems it should be sufficient to say:
- $ ./configure
+ $ ./configure
Or
$ sh configure
@@ -218,15 +218,15 @@ CONTENTS
before the library and executables are built.
HDF5 can be installed into a different location than the prefix
- specified at configure time; see section 4.6, "Installing HDF5,"
+ specified at configure time; see section 4.6, "Installing HDF5,"
for more details.
4.3.2. Using an alternate C compiler
By default, configure will look for the C compiler by trying
`gcc' and `cc'. However, if the environment variable "CC" is set
- then its value is used as the C compiler. For instance, one would
- use the following line to specify the native C compiler on a system
- that also has the GNU gcc compiler (users of csh and derivatives
+ then its value is used as the C compiler. For instance, one would
+ use the following line to specify the native C compiler on a system
+ that also has the GNU gcc compiler (users of csh and derivatives
will need to prefix the commands below with `env'):
$ CC=cc ./configure
@@ -257,7 +257,7 @@ CONTENTS
$ ./configure --enable-fortran
$ ./configure --enable-cxx
$ ./configure --enable-java
-
+
Configuration will halt if a working Fortran 90 or 95 compiler or
C++ compiler is not found. Currently, the Fortran configure tests
for these compilers in order: f90, pgf90, f95. To use an
@@ -267,7 +267,7 @@ CONTENTS
4.3.5. Specifying other programs
- The build system has been tuned for use with GNU make but also
+ The build system has been tuned for use with GNU make but also
works with other versions of make. If the `make' command runs a
non-GNU version but a GNU version is available under a different
name (perhaps `gmake'), then HDF5 can be configured to use it by
@@ -286,8 +286,8 @@ CONTENTS
during `make install' (described below) with a BSD-compatible
install program detected automatically by configure. If none is
found, the shell script bin/install-sh is used. Configure does not
- check that the install script actually works; if a bad install is
- detected on your system (e.g., on the ASCI blue machine as of
+ check that the install script actually works; if a bad install is
+ detected on your system (e.g., on the ASCI blue machine as of
March 2, 1999) you have two choices:
1. Copy the bin/install-sh program to your $HOME/bin
@@ -310,11 +310,11 @@ CONTENTS
LDFLAGS=-L/home/robb/lib \
./configure
- HDF5 uses the zlib library to support the HDF5 deflate
- data compression filter. Configure searches the standard places
- (plus those specified above with the CPPFLAGS and LDFLAGS variables)
- for the zlib headers and library. The search can be disabled by
- specifying `--without-zlib' or alternate directories can be specified
+ HDF5 uses the zlib library to support the HDF5 deflate
+ data compression filter. Configure searches the standard places
+ (plus those specified above with the CPPFLAGS and LDFLAGS variables)
+ for the zlib headers and library. The search can be disabled by
+ specifying `--without-zlib' or alternate directories can be specified
with `--with-zlib=INCDIR,LIBDIR' or through the CPPFLAGS and LDFLAGS
variables:
@@ -324,8 +324,8 @@ CONTENTS
LDFLAGS=-L/usr/unsup/lib \
./configure
- HDF5 includes Szip as a predefined compression method (see 3.2).
- To enable Szip compression, the HDF5 library must be configured
+ HDF5 includes Szip as a predefined compression method (see 3.2).
+ To enable Szip compression, the HDF5 library must be configured
and built using the Szip library:
$ ./configure --with-szlib=/Szip_Install_Directory
@@ -350,10 +350,10 @@ CONTENTS
The library can be compiled to provide symbolic debugging support
so it can be debugged with gdb, dbx, ddd, etc., or it can be
compiled with various optimizations. To compile for symbolic
- debugging (the default for snapshots), say
- `--enable-build-mode=production'; to compile with optimizations
- (the default for supported public releases),
- say `--enable-build-mode=production'. On some systems the
+ debugging (the default for snapshots), say
+ `--enable-build-mode=production'; to compile with optimizations
+ (the default for supported public releases),
+ say `--enable-build-mode=production'. On some systems the
library can also be compiled for profiling with gprof by saying
`--enable-production=profile'.
@@ -362,13 +362,13 @@ CONTENTS
$ ./configure --enable-production=profile #for use with gprof
Regardless of whether support for symbolic debugging is enabled,
- the library can also perform runtime debugging of certain packages
- (such as type conversion execution times and extensive invariant
- condition checking). To enable this debugging, supply a
- comma-separated list of package names to the `--enable-internal-debug'
- switch.
+ the library can also perform runtime debugging of certain packages
+ (such as type conversion execution times and extensive invariant
+ condition checking). To enable this debugging, supply a
+ comma-separated list of package names to the `--enable-internal-debug'
+ switch.
- Debugging can be disabled by saying `--disable-internal-debug'.
+ Debugging can be disabled by saying `--disable-internal-debug'.
The default debugging level for snapshots is a subset of the
available packages; the default for supported releases is no
debugging (debugging can incur a significant runtime penalty).
@@ -378,10 +378,10 @@ CONTENTS
$ ./configure --enable-internal-debug=all #debug all packages
$ ./configure --disable-internal-debug #no debugging
- HDF5 can also print a trace of all API function calls, their
+ HDF5 can also print a trace of all API function calls, their
arguments, and the return values. To enable or disable the
ability to trace the API say `--enable-trace' (the default for
- snapthots) or `--disable-trace' (the default for public releases).
+ snapthots) or `--disable-trace' (the default for public releases).
The tracing must also be enabled at runtime to see any output.
4.3.9. Parallel versus serial library
@@ -389,25 +389,39 @@ CONTENTS
parallelism on a distributed multi-processor system. Read the
file INSTALL_parallel for detailed information.
+ The threadsafe, C++ and Java interfaces are not compatible
+ with the parallel option.
+ Unless --enable-unsupported has been specified on the configure line,
+ the following options must be disabled:
+ --enable-threadsafe, --enable-cxx, --enable-java
+
+
4.3.10. Threadsafe capability
The HDF5 library can be configured to be thread-safe (on a very
large scale) with the `--enable-threadsafe' flag to the configure
script. Some platforms may also require the '-with-pthread=INC,LIB'
(or '--with-pthread=DIR') flag to the configure script.
- For further information, see:
+ For further information, see:
https://portal.hdfgroup.org/display/knowledge/Questions+about+thread-safety+and+concurrent+access
+ The high-level, C++, Fortran and Java interfaces are not compatible
+ with the thread-safety option because the lock is not hoisted
+ into the higher-level API calls.
+ Unless --enable-unsupported has been specified on the configure line,
+ the following options must be disabled:
+ --enable-hl, --enable-cxx, --enable-fortran, --enable-java
+
4.3.11. Backward compatibility
The 1.10 version of the HDF5 library can be configured to operate
- identically to the v1.8 library with the
+ identically to the v1.8 library with the
--with-default-api-version=v18
- configure flag, or identically to the v1.6 library with the
+ configure flag, or identically to the v1.6 library with the
--with-default-api-version=v16
configure flag. This allows existing code to be compiled with the
- v1.10 library without requiring immediate changes to the application
- source code. For additional configuration options and other details,
+ v1.10 library without requiring immediate changes to the application
+ source code. For additional configuration options and other details,
see "API Compatibility Macros":
https://portal.hdfgroup.org/display/HDF5/API+Compatibility+Macros
@@ -487,7 +501,7 @@ CONTENTS
$ make install prefix=NEW_DIR
- where NEW_DIR is the new directory where you wish to install HDF5.
+ where NEW_DIR is the new directory where you wish to install HDF5.
If you do not use the deploy script, you should run h5redeploy in
NEW_DIR/bin directory. This utility will fix the h5cc, h5fc and
h5c++ scripts to reflect the new NEW_DIR location.
@@ -510,7 +524,7 @@ CONTENTS
The configuration information:
./src/H5pubconf.h
-
+
The support programs that are useful are:
./tools/h5ls/h5ls (list file contents)
./tools/h5dump/h5dump (dump file contents)
@@ -518,12 +532,12 @@ CONTENTS
./tools/misc/h5debug (low-level file debugging)
./tools/h5import/h5import (imports data to HDF5 file)
./tools/h5diff/h5diff (compares two HDF5 files)
- ./tools/gifconv/h52gif (HDF5 to GIF converter)
+ ./tools/gifconv/h52gif (HDF5 to GIF converter)
./tools/gifconv/gif2h5 (GIF to HDF5 converter)
5. Using the Library
-
+
For information on using HDF5 see the documentation, tutorials and examples
found here:
diff --git a/release_docs/INSTALL_CMake.txt b/release_docs/INSTALL_CMake.txt
index 3a69022..edd876a 100644
--- a/release_docs/INSTALL_CMake.txt
+++ b/release_docs/INSTALL_CMake.txt
@@ -12,6 +12,7 @@ Section IV: Further considerations
Section V: Options for building HDF5 Libraries with CMake command line
Section VI: CMake option defaults for HDF5
Section VII: User Defined Options for HDF5 Libraries with CMake
+Section VIII: User Defined Compile Flags for HDF5 Libraries with CMake
************************************************************************
@@ -274,9 +275,14 @@ IV. Further considerations
packages there. Add the following CMake options:
-DZLIB_LIBRARY:FILEPATH=some_location/lib/zlib.lib
-DZLIB_INCLUDE_DIR:PATH=some_location/include
+ -DZLIB_USE_EXTERNAL:BOOL=OFF
-DSZIP_LIBRARY:FILEPATH=some_location/lib/szlib.lib
-DSZIP_INCLUDE_DIR:PATH=some_location/include
+ -DSZIP_USE_EXTERNAL:BOOL=OFF
where "some_location" is the full path to the extlibs folder.
+ Also the appropriate environment variable must be set;
+ set(ENV{ZLIB_ROOT} "some_location")
+ set(ENV{SZIP_ROOT} "some_location")
B. Use source packages from an GIT server by adding the following CMake
options:
@@ -318,6 +324,34 @@ IV. Further considerations
-DHDF5_ENABLE_SZIP_SUPPORT:BOOL=OFF -DHDF5_ENABLE_Z_LIB_SUPPORT:BOOL=OFF \
-DCMAKE_BUILD_TYPE:STRING=Release ..
+ 6. CMake uses a toolchain of utilities to compile, link libraries and
+ create archives, and other tasks to drive the build. The toolchain
+ utilities available are determined by the languages enabled. In normal
+ builds, CMake automatically determines the toolchain for host builds
+ based on system introspection and defaults. In cross-compiling
+ scenarios, a toolchain file may be specified with information about
+ compiler and utility paths.
+ Variables and Properties
+ Several variables relate to the language components of a toolchain which
+ are enabled. CMAKE_<LANG>_COMPILER is the full path to the compiler used
+ for <LANG>. CMAKE_<LANG>_COMPILER_ID is the identifier used by CMake for
+ the compiler and CMAKE_<LANG>_COMPILER_VERSION is the version of the compiler.
+
+ The CMAKE_<LANG>_FLAGS variables and the configuration-specific equivalents
+ contain flags that will be added to the compile command when compiling a
+ file of a particular language.
+
+ As the linker is invoked by the compiler driver, CMake needs a way to
+ determine which compiler to use to invoke the linker. This is calculated
+ by the LANGUAGE of source files in the target, and in the case of static
+ libraries, the language of the dependent libraries. The choice CMake makes
+ may be overridden with the LINKER_LANGUAGE target property.
+
+ See the CMake help for more information on using toolchain files.
+
+ To use a toolchain file with the supplied cmake scripts, see the
+ HDF5options.cmake file under the toolchain section.
+
Notes: CMake and HDF5
1. Using CMake for building and using HDF5 is under active development.
@@ -491,7 +525,7 @@ These five steps are described in detail below.
Release and build the solution.
3.2.1 The external libraries (zlib and szip) can be configured
- to allow building the libraries by downloading from an GIT repository.
+ to allow building the libraries by downloading from a GIT repository.
The option is 'HDF5_ALLOW_EXTERNAL_SUPPORT'; by adding the following
configuration option:
-DHDF5_ALLOW_EXTERNAL_SUPPORT:STRING="GIT"
@@ -508,7 +542,7 @@ These five steps are described in detail below.
adding the following configuration option:
-DHDF5_ALLOW_EXTERNAL_SUPPORT:STRING="TGZ"
- The options to control the SVN URL (config/cmake/cacheinit.cmake
+ The options to control the TGZ URL (config/cmake/cacheinit.cmake
file) are:
ZLIB_TGZ_NAME:STRING="zlib_src.ext"
SZIP_TGZ_NAME:STRING="szip_src.ext"
@@ -590,6 +624,7 @@ HDF5_BUILD_TOOLS "Build HDF5 Tools" ON
---------------- HDF5 Advanced Options ---------------------
ALLOW_UNSUPPORTED "Allow unsupported combinations of configure options" OFF
+HDF5_EXTERNAL_LIB_PREFIX "Use prefix for custom library naming." ""
HDF5_DISABLE_COMPILER_WARNINGS "Disable compiler warnings" OFF
HDF5_ENABLE_ALL_WARNINGS "Enable all warnings" OFF
HDF5_ENABLE_CODESTACK "Enable the function stack tracing (for developer debugging)." OFF
@@ -618,7 +653,8 @@ HDF_TEST_EXPRESS "Control testing framework (0-3)"
HDF5_TEST_VFD "Execute tests with different VFDs" OFF
HDF5_USE_16_API_DEFAULT "Use the HDF5 1.6.x API by default" OFF
HDF5_USE_18_API_DEFAULT "Use the HDF5 1.8.x API by default" OFF
-HDF5_USE_110_API_DEFAULT "Use the HDF5 1.10.x API by default" ON
+HDF5_USE_110_API_DEFAULT "Use the HDF5 1.10.x API by default" OFF
+HDF5_USE_112_API_DEFAULT "Use the HDF5 1.12.x API by default" ON
HDF5_USE_FOLDERS "Enable folder grouping of projects in IDEs." ON
HDF5_WANT_DATA_ACCURACY "IF data accuracy is guaranteed during data conversions" ON
HDF5_WANT_DCONV_EXCEPTION "exception handling functions is checked during data conversions" ON
@@ -650,6 +686,20 @@ NOTE:
flag is not available on windows and some modern linux systems will
ignore the flag.
+ ---------------- Unsupported Library Options ---------------------
+ The threadsafe, C++ and Java interfaces are not compatible
+ with the HDF5_ENABLE_PARALLEL option.
+ Unless ALLOW_UNSUPPORTED has been specified,
+ the following options must be disabled:
+ HDF5_ENABLE_THREADSAFE, HDF5_BUILD_CPP_LIB, HDF5_BUILD_JAVA
+
+ The high-level, C++, Fortran and Java interfaces are not compatible
+ with the HDF5_ENABLE_THREADSAFE option because the lock is not hoisted
+ into the higher-level API calls.
+ Unless ALLOW_UNSUPPORTED has been specified,
+ the following options must be disabled:
+ HDF5_BUILD_HL_LIB, HDF5_BUILD_CPP_LIB, HDF5_BUILD_FORTRAN, HDF5_BUILD_JAVA
+
========================================================================
VII. User Defined Options for HDF5 Libraries with CMake
@@ -664,6 +714,30 @@ Copy the contents of the file, both macro and option, into the
UserMacros.cmake file. Then enable the option to the CMake configuration,
build and test process.
+
+========================================================================
+VIII. User Defined Compile Flags for HDF5 Libraries with CMake
+========================================================================
+
+Custom compiler flags can be added by defining the CMAKE_C_FLAGS and
+CMAKE_CXX_FLAGS variables.
+Using a cmake script:
+ set (CMAKE_C_FLAGS "${CMAKE_C_FLAGS} -O2")
+Defined on the configure line:
+ cmake -G "Visual Studio 12 2013" -DCMAKE_C_FLAGS:STRING=-O2 ..
+
+Debug symbols are enabled with configuration selections Debug or RelWithDebInfo.
+The difference between Debug and RelWithDebInfo configurations is that
+RelWithDebInfo optimizes the code similar to Release. It produces fully optimized
+code, but also creates the symbol table and the debug metadata to give the
+debugger input to map the execution back to the original code.
+RelwithDebInfo configuration should not affect the performance when the code
+is run without a debugger attached.
+
+The HDF5_ENABLE_COVERAGE option will add "-g -O0 -fprofile-arcs -ftest-coverage"
+to CMAKE_C_FLAGS.
+
+
========================================================================
For further assistance, send email to help@hdfgroup.org
========================================================================
diff --git a/release_docs/INSTALL_Cygwin.txt b/release_docs/INSTALL_Cygwin.txt
index ddffcf1..74f494c 100755
--- a/release_docs/INSTALL_Cygwin.txt
+++ b/release_docs/INSTALL_Cygwin.txt
@@ -66,12 +66,11 @@ Preconditions:
2.2.2 Szip
The HDF5 library has a predefined compression filter that uses
the extended-Rice lossless compression algorithm for chunked
- datatsets. For more information about Szip compression and
- license terms see
- http://hdfgroup.org/HDF5/doc_resource/SZIP/index.html.
+ datatsets. For more information on Szip compression, license terms,
+ and obtaining the Szip source code, see:
+
+ https://portal.hdfgroup.org/display/HDF5/Szip+Compression+in+HDF+Products
- The latest supported public release of SZIP is available from
- ftp://ftp.hdfgroup.org/lib-external/szip/2.1.
2.3 Additional Utilities
@@ -266,4 +265,5 @@ Build, Test and Install HDF5 on Cygwin
-----------------------------------------------------------------------
-Need Further assistance, email help@hdfgroup.org
+ HDF Forum: https://forum.hdfgroup.org/
+ HDF Helpdesk: https://portal.hdfgroup.org/display/support/The+HDF+Help+Desk
diff --git a/release_docs/INSTALL_Warnings.txt b/release_docs/INSTALL_Warnings.txt
new file mode 100644
index 0000000..5fde45f
--- /dev/null
+++ b/release_docs/INSTALL_Warnings.txt
@@ -0,0 +1,474 @@
+***********************************************************************
+* COMPILER WARNINGS OPTIONS
+***********************************************************************
+
+ Table of Contents
+
+Section I: Managing Warnings
+Section II: Default Warnings
+Section III: All Warnings
+Section IV: Group 0 Warnings
+Section V: Group 1 Warnings
+Section VI: Group 2 Warnings
+Section VII: Group 3 Warnings
+Section VIII: Group 4 Warnings
+Section IX: Disable Warnings
+
+************************************************************************
+
+
+========================================================================
+I. Managing Warnings
+========================================================================
+Compiler warnings are managed by setting the compiler flags variables.
+
+Autotools uses the H5_CFLAGS and H5_CXXFLAGS, both variables set the flags nearly
+ identical, along with H5_FCFLAGS for Fortran. Autotools uses the type
+ and version of the compiler to determine which warning flags are used.
+ However, there is an option, enable-developer-warnings, to enable extra
+ flags for developers.
+
+CMake uses the CMAKE_C_FLAGS and CMAKE_CXX_FLAGS, both sets are nearly
+ identical, along with CMAKE_Fortran_FLAGS for Fortran. CMake has a
+ minimum set of flags for GNU type compilers and for MSVC compilers. In
+ addition, CMake breaks the list of flags into groups. The groups for
+ GNU are roughly associated with the version of the compiler, while
+ the MSVC groups are associated with the warning levels for the
+ Microsoft compilers. The CMake option for enabling extra developer
+ warnings is HDF5_ENABLE_DEV_WARNINGS.
+
+Custom settings can be used by setting;
+ Environment variables H5_CFLAGS and H5_CXXFLAGS for Autotools
+ CMake defines CMAKE_C_FLAGS and CMAKE_CXX_FLAGS for CMake
+
+
+========================================================================
+II. Default Warnings
+========================================================================
+
+--------------------------------------------------
+Autotools UNIX warnings added to H5_CFLAGS
+--------------------------------------------------
+ -std=c99
+
+ the following warning switches should not raise warnings by the current code
+ -pedantic
+ -Wall
+ -Wextra
+ -Wbad-function-cast
+ -Wc++-compat
+ -Wcast-align
+ -Wcast-qual
+ -Wconversion
+ -Wdeclaration-after-statement
+ -Wdisabled-optimization
+ -Wfloat-equal
+ -Wformat=2
+ -Winit-self
+ -Winvalid-pch
+ -Wmissing-declarations
+ -Wmissing-include-dirs
+ -Wmissing-prototypes
+ -Wnested-externs
+ -Wold-style-definition
+ -Wpacked
+ -Wpointer-arith
+ -Wredundant-decls
+ -Wshadow
+ -Wstrict-prototypes
+ -Wswitch-default
+ -Wswitch-enum
+ -Wundef
+ -Wunused-macros
+ -Wunsafe-loop-optimizations
+ -Wwrite-strings
+
+ enable-developer-warnings=ON
+ -Winline
+ -Waggregate-return
+ -Wmissing-format-attribute
+ -Wmissing-noreturn
+ enable-developer-warnings=OFF
+ -Wno-inline
+ -Wno-aggregate-return
+ -Wno-missing-format-attribute
+ -Wno-missing-noreturn
+
+IF GCC <= 4.3
+ -Wno-long-long
+ -Wvolatile-register-var
+ -Wstrict-overflow
+
+IF GCC <= 4.4
+ -Wno-long-long
+ -Wvolatile-register-var
+ -Wstrict-overflow
+ -Wlogical-op
+ -Wvla
+
+IF GCC <= 4.5
+ -Wno-long-long
+ -Wvolatile-register-var
+ -Wstrict-overflow
+ -Wlogical-op
+ -Wvla
+ -Wlarger-than=2048
+ -Wsync-nand
+ -Wframe-larger-than=16384
+ -Wpacked-bitfield-compat
+
+IF GCC <= 4.6
+ -Wno-long-long
+ -Wlogical-op
+ -Wvla
+ -Wlarger-than=2048
+ -Wsync-nand
+ -Wframe-larger-than=16384
+ -Wpacked-bitfield-compat
+ -Wstrict-aliasing
+ -Wstrict-overflow=5
+ -Wjump-misses-init
+ -Wunsuffixed-float-constants
+
+IF GCC <= 4.7
+ -Wno-long-long
+ -Wlogical-op
+ -Wvla
+ -Wlarger-than=2048
+ -Wsync-nand
+ -Wframe-larger-than=16384
+ -Wpacked-bitfield-compat
+ -Wstrict-aliasing
+ -Wstrict-overflow=5
+ -Wjump-misses-init
+ -Wunsuffixed-float-constants
+ -Wdouble-promotion
+ -Wtrampolines
+ enable-developer-warnings=ON:
+ -Wsuggest-attribute=const
+ enable-developer-warnings=OFF:
+ -Wno-suggest-attribute=const
+
+IF GCC <= 4.8
+ -Wlogical-op
+ -Wvla
+ -Wlarger-than=2048
+ -Wsync-nand
+ -Wframe-larger-than=16384
+ -Wpacked-bitfield-compat
+ -Wstrict-overflow=5
+ -Wjump-misses-init
+ -Wunsuffixed-float-constants
+ -Wdouble-promotion
+ -Wtrampolines
+ -Wstack-usage=8192
+ -Wvector-operation-performance
+ enable-developer-warnings=ON:
+ -Wsuggest-attribute=const
+ -Wsuggest-attribute=pure
+ -Wsuggest-attribute=noreturn
+ enable-developer-warnings=OFF:
+ -Wno-suggest-attribute=const
+ -Wno-suggest-attribute=pure
+ -Wno-suggest-attribute=noreturn
+
+IF GCC <= 4.9
+ -Wlogical-op
+ -Wvla
+ -Wlarger-than=2048
+ -Wsync-nand
+ -Wframe-larger-than=16384
+ -Wpacked-bitfield-compat
+ -Wstrict-overflow=5
+ -Wjump-misses-init
+ -Wdouble-promotion
+ -Wtrampolines
+ -Wstack-usage=8192
+ -Wvector-operation-performance
+ enable-developer-warnings=ON:
+ -Wsuggest-attribute=const
+ -Wsuggest-attribute=pure
+ -Wsuggest-attribute=noreturn
+ -Wsuggest-attribute=format
+ enable-developer-warnings=OFF:
+ -Wno-suggest-attribute=const
+ -Wno-suggest-attribute=pure
+ -Wno-suggest-attribute=noreturn
+ -Wno-suggest-attribute=format
+
+IF GCC < 5
+ -Wlogical-op
+ -Wvla
+ -Wlarger-than=2048
+ -Wsync-nand
+ -Wframe-larger-than=16384
+ -Wpacked-bitfield-compat
+ -Wstrict-overflow=5
+ -Wjump-misses-init
+ -Wunsuffixed-float-constants
+ -Wdouble-promotion
+ -Wtrampolines
+ -Wstack-usage=8192
+ -Wvector-operation-performance
+ -Wdate-time
+ enable-developer-warnings=ON:
+ -Wsuggest-attribute=const
+ -Wsuggest-attribute=pure
+ -Wsuggest-attribute=noreturn
+ -Wsuggest-attribute=format
+ enable-developer-warnings=OFF:
+ -Wno-suggest-attribute=const
+ -Wno-suggest-attribute=pure
+ -Wno-suggest-attribute=noreturn
+ -Wno-suggest-attribute=format
+
+IF GCC < 6
+ -Wlogical-op
+ -Wvla
+ -Wlarger-than=2048
+ -Wsync-nand
+ -Wframe-larger-than=16384
+ -Wpacked-bitfield-compat
+ -Wstrict-overflow=5
+ -Wjump-misses-init
+ -Wunsuffixed-float-constants
+ -Wdouble-promotion
+ -Wtrampolines
+ -Wstack-usage=8192
+ -Wvector-operation-performance
+ -Wdate-time
+ -Warray-bounds=2
+ -Wc99-c11-compat
+ enable-developer-warnings=ON:
+ -Wsuggest-attribute=const
+ -Wsuggest-attribute=pure
+ -Wsuggest-attribute=noreturn
+ -Wsuggest-attribute=format
+ enable-developer-warnings=OFF:
+ -Wno-suggest-attribute=const
+ -Wno-suggest-attribute=pure
+ -Wno-suggest-attribute=noreturn
+ -Wno-suggest-attribute=format
+
+IF GCC < 7
+ -Wlogical-op
+ -Wvla
+ -Wlarger-than=2048
+ -Wsync-nand
+ -Wframe-larger-than=16384
+ -Wpacked-bitfield-compat
+ -Wstrict-overflow=5
+ -Wjump-misses-init
+ -Wunsuffixed-float-constants
+ -Wdouble-promotion
+ -Wtrampolines
+ -Wstack-usage=8192
+ -Wvector-operation-performance
+ -Wdate-time
+ -Warray-bounds=2
+ -Wc99-c11-compat
+ -Wnull-dereference
+ -Wunused-const-variable
+ -Wduplicated-cond -Whsa
+ enable-developer-warnings=ON:
+ -Wsuggest-attribute=const
+ -Wsuggest-attribute=pure
+ -Wsuggest-attribute=noreturn
+ -Wsuggest-attribute=format
+ enable-developer-warnings=OFF:
+ -Wno-suggest-attribute=const
+ -Wno-suggest-attribute=pure
+ -Wno-suggest-attribute=noreturn
+ -Wno-suggest-attribute=format
+
+
+--------------------------------------------
+CMake warnings added to CMAKE_C_FLAGS
+--------------------------------------------
+
+IF GNU GCC
+ -pedantic
+ -Wall
+ -Wextra
+ -Wbad-function-cast
+ -Wc++-compat
+ -Wcast-align
+ -Wcast-qual
+ -Wconversion
+ -Wdeclaration-after-statement
+ -Wdisabled-optimization
+ -Wfloat-equal
+ -Wformat=2
+ -Winit-self
+ -Winvalid-pch
+ -Wmissing-declarations
+ -Wmissing-include-dirs
+ -Wmissing-prototypes
+ -Wnested-externs
+ -Wold-style-definition
+ -Wpacked
+ -Wpointer-arith
+ -Wredundant-decls
+ -Wshadow
+ -Wstrict-prototypes
+ -Wswitch-default
+ -Wswitch-enum
+ -Wundef
+ -Wunused-macros
+ -Wunsafe-loop-optimizations
+ -Wwrite-strings
+
+ -fmessage-length=0
+ HDF5_ENABLE_DEV_WARNINGS=ON
+ -Winline
+ -Waggregate-return
+ HDF5_ENABLE_DEV_WARNINGS=OFF
+ -Wno-unused-parameter
+ -Wno-inline
+ -Wno-aggregate-return
+
+
+========================================================================
+III. All Warnings in CMake
+========================================================================
+
+Default: HDF5_ENABLE_DEV_WARNINGS:BOOL=OFF
+ For Visual Studio:
+ /W3
+
+HDF5_ENABLE_ALL_WARNINGS:BOOL=ON
+ For Visual Studio:
+ /Wall
+ /wd4668
+
+ For GNU GCC
+ Group 0 flags
+ Group 1 flags
+ Group 2 flags
+
+
+========================================================================
+IV. Group 0 Warnings in CMake
+========================================================================
+
+Default: HDF5_ENABLE_GROUPZERO_WARNINGS:BOOL=OFF
+
+HDF5_ENABLE_GROUPZERO_WARNINGS:BOOL=ON
+ For Visual Studio
+ /W1
+
+ For GNU GCC
+ Default Warnings
+
+
+========================================================================
+V. Group 1 Warnings in CMake
+========================================================================
+
+Default: HDF5_ENABLE_GROUPONE_WARNINGS:BOOL=OFF
+
+HDF5_ENABLE_GROUPONE_WARNINGS:BOOL=ON
+ For Visual Studio
+ /W2
+
+ For GNU GCC
+ IF GCC >= 4.3
+ -Wlogical-op
+ -Wvla
+ -Wlarger-than=2048
+ IF GCC >= 4.4
+ -Wsync-nand
+ -Wframe-larger-than=16384
+ -Wpacked-bitfield-compat
+ IF GCC >= 4.5
+ -Wstrict-overflow=5
+ -Wjump-misses-init
+ -Wunsuffixed-float-constants
+
+
+========================================================================
+VI. Group 2 Warnings in CMake
+========================================================================
+
+Default: HDF5_ENABLE_GROUPTWO_WARNINGS:BOOL=OFF
+
+HDF5_ENABLE_GROUPTWO_WARNINGS:BOOL=ON
+ For Visual Studio
+ /W3
+
+ For GNU GCC
+ IF GCC >= 4.6
+ -Wdouble-promotion
+ -Wtrampolines
+ enable-developer-warnings=ON:
+ -Wsuggest-attribute=const
+ enable-developer-warnings=OFF:
+ -Wno-suggest-attribute=const
+ IF GCC >= 4.7
+ -Wstack-usage=8192
+ -Wvector-operation-performance
+ enable-developer-warnings=ON:
+ -Wsuggest-attribute=pure
+ -Wsuggest-attribute=noreturn
+ enable-developer-warnings=OFF:
+ -Wno-suggest-attribute=pure
+ -Wno-suggest-attribute=noreturn
+ IF GCC >= 4.8
+ enable-developer-warnings=ON:
+ -Wsuggest-attribute=format
+ enable-developer-warnings=OFF:
+ -Wno-suggest-attribute=format
+ IF GCC >= 4.8
+ -Wdate-time
+
+
+========================================================================
+VII. Group 3 Warnings in CMake
+========================================================================
+
+Default: HDF5_ENABLE_GROUPTHREE_WARNINGS:BOOL=OFF
+
+HDF5_ENABLE_GROUPTHREE_WARNINGS:BOOL=ON
+ For Visual Studio
+ /W4
+
+ For GNU GCC
+ IF GCC >= 5.1
+ -Warray-bounds=2
+ -Wc99-c11-compat
+
+
+========================================================================
+VIII. Group 4 Warnings in CMake
+========================================================================
+
+Default: HDF5_ENABLE_GROUPFOUR_WARNINGS:BOOL=OFF
+
+HDF5_ENABLE_GROUPFOUR_WARNINGS:BOOL=ON
+ For GNU GCC
+ IF GCC >= 6.0
+ -Wnull-dereference
+ -Wunused-const-variable
+ -Wduplicated-cond
+ -Whsa
+
+
+========================================================================
+IX. Disable Warnings in CMake
+========================================================================
+
+Default: HDF5_DISABLE_COMPILER_WARNINGS:BOOL=OFF
+
+HDF5_DISABLE_COMPILER_WARNINGS:BOOL=ON
+ For Visual Studio
+ HDF5_WARNINGS_BLOCKED:BOOL=ON
+ /W0
+
+ For GNU GCC
+ -w
+
+
+========================================================================
+For further assistance, send email to help@hdfgroup.org
+========================================================================
+
diff --git a/release_docs/RELEASE.txt b/release_docs/RELEASE.txt
index 8f3c434..7def78e 100755
--- a/release_docs/RELEASE.txt
+++ b/release_docs/RELEASE.txt
@@ -1,4 +1,4 @@
-HDF5 version 1.10.3 released on 2018-08-21
+HDF5 version 1.10.4 released on 2018-10-05
================================================================================
@@ -32,8 +32,7 @@ If you have any questions or comments, please send them to the HDF Help Desk:
CONTENTS
-- New Features
-- Bug Fixes since HDF5-1.10.2
+- Bug Fixes since HDF5-1.10.3
- Supported Platforms
- Tested Configuration Features Summary
- More Tested Platforms
@@ -44,128 +43,99 @@ CONTENTS
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.
+ - Add toolchain and cross-compile support
- 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.
+ 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 - 2018/08/17, HDFFV-10552)
+ (ADB - 2018/10/04, HDFFV-10594)
- - Added configuration checks for the following MPI functions:
+ - Add warning flags for Intel compilers
- MPI_Mprobe - Used for the Parallel Compression feature
- MPI_Imrecv - Used for the Parallel Compression feature
+ Identified Intel compiler specific warnings flags that should be used
+ instead of GNU flags.
- MPI_Get_elements_x - Used for the "big Parallel I/O" feature
- MPI_Type_size_x - Used for the "big Parallel I/O" feature
+ (ADB - 2018/10/04, TRILABS-21)
- (JTH - 2018/08/02, HDFFV-10512)
+ - Add default rpath to targets
- - Added section to the libhdf5.settings file to indicate
- the status of the Parallel Compression and "big Parallel I/O"
- features.
+ 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.
- (JTH - 2018/08/02, HDFFV-10512)
+ (ADB - 2018/09/26, HDFFV-10594)
- - 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.
+ Library:
+ --------
+ - Allow pre-generated H5Tinit.c and H5make_libsettings.c to be used.
- (ADB - 2018/07/16)
+ 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)
- C++ Library:
- ------------
- - New wrappers
- Added the following items:
+Bug Fixes since HDF5-1.10.3 release
+==================================
- + Class DSetAccPropList for the dataset access property list.
+ Library
+ -------
+ - Allow H5detect and H5make_libsettings to take a file as an argument.
- + Wrapper for H5Dget_access_plist to class DataSet
- // Gets the access property list of this dataset.
- DSetAccPropList getAccessPlist() const;
+ 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.
- + 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)
+ (ADB - 2018/09/05, HDFFV-9059)
- // Retrieves the raw data chunk cache parameters.
- void getChunkCache(size_t &rdcc_nslots, size_t &rdcc_nbytes, double &rdcc_w0)
+ - 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.
- + New operator!= to class DataType (HDFFV-10472)
- // Determines whether two datatypes are not the same.
- bool operator!=(const DataType& compared_type)
+ 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).
- + Wrappers for H5Oget_info2, H5Oget_info_by_name2, and H5Oget_info_by_idx2
- (HDFFV-10458)
+ (JTH - 2018/08/25, HDFFV-10501)
- // Retrieves information about an HDF5 object.
- void getObjinfo(H5O_info_t& objinfo, unsigned fields = H5O_INFO_BASIC) const;
+ 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.
- // 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;
+ (ADB - 2018/08/31, HDFFV-10568)
- // 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;
+ - Java iterator callbacks
- (BMR - 2018/07/22, HDFFV-10150, HDFFV-10458, HDFFV-1047)
+ 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 Library:
- ----------------
- Java HDFLibraryException class
Change parent class from Exception to RuntimeException.
@@ -181,277 +151,6 @@ New Features
(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
===================
@@ -497,7 +196,8 @@ Supported Platforms
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
+ (kite) Intel icc/icpc/ifort version 17.0.2
+
Tested Configuration Features Summary
=====================================
@@ -526,9 +226,9 @@ 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
+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
@@ -546,9 +246,9 @@ 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
+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
diff --git a/release_docs/USING_CMake_Examples.txt b/release_docs/USING_CMake_Examples.txt
index 6f744d9..d5fae39 100644
--- a/release_docs/USING_CMake_Examples.txt
+++ b/release_docs/USING_CMake_Examples.txt
@@ -46,7 +46,7 @@ Default installation process:
Copy HDF5_Examples.cmake to this directory.
The default source folder is defined as "HDF5Examples". It can be changed
with the CTEST_SOURCE_NAME script option.
- The default installation folder is defined as "@CMAKE_INSTALL_PREFIX@".
+ The default installation folder is defined for the platform.
It can be changed with the INSTALLDIR script option.
(Note: Windows has issues with spaces and paths -The path will need to
be set correctly.)