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Diffstat (limited to 'release_docs/RELEASE.txt')
| -rwxr-xr-x | release_docs/RELEASE.txt | 452 |
1 files changed, 76 insertions, 376 deletions
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 |