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author | Allen Byrne <byrn@hdfgroup.org> | 2019-10-22 14:55:51 (GMT) |
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committer | Allen Byrne <byrn@hdfgroup.org> | 2019-10-22 14:55:51 (GMT) |
commit | 50b581e08475801fef628132852230987240f337 (patch) | |
tree | fcb35fb8296c54a8dc479c09236c9b7f9e34079f | |
parent | 027cd1ff5b10d10ce2aca5ba4256d5c25bee5e4e (diff) | |
parent | 4bd50505cf4e9ab6a47993a114f149a175178f65 (diff) | |
download | hdf5-50b581e08475801fef628132852230987240f337.zip hdf5-50b581e08475801fef628132852230987240f337.tar.gz hdf5-50b581e08475801fef628132852230987240f337.tar.bz2 |
Merging in latest from upstream (HDFFV/hdf5:refs/heads/hdf5_1_12)
* commit '4bd50505cf4e9ab6a47993a114f149a175178f65':
Update MANIFEST.
Fix typos.
Add HISTORY-1_10_0-1_12_0.txt.
Update RELEASE.txt and add HISTORY-1_10_0-1_12_0.txt file. Set version to 1.12.0-alpha0 for snapshot release.
-rw-r--r-- | MANIFEST | 1 | ||||
-rw-r--r-- | README.txt | 2 | ||||
-rw-r--r-- | c++/src/cpp_doc_config | 2 | ||||
-rw-r--r-- | config/cmake/scripts/HDF5config.cmake | 2 | ||||
-rw-r--r-- | configure.ac | 2 | ||||
-rw-r--r-- | release_docs/HISTORY-1_10_0-1_12_0.txt | 1180 | ||||
-rw-r--r-- | release_docs/RELEASE.txt | 1082 | ||||
-rw-r--r-- | src/H5public.h | 4 |
8 files changed, 1316 insertions, 959 deletions
@@ -459,6 +459,7 @@ ./release_docs/HISTORY-1_8.txt ./release_docs/HISTORY-1_10.txt ./release_docs/HISTORY-1_8_0-1_10_0.txt +./release_docs/HISTORY-1_10_0-1_12_0.txt ./release_docs/INSTALL ./release_docs/INSTALL_CMake.txt ./release_docs/INSTALL_Cygwin.txt @@ -1,4 +1,4 @@ -HDF5 version 1.12.0 currently under development +HDF5 version 1.12.0-alpha0 currently under development ------------------------------------------------------------------------------ Please refer to the release_docs/INSTALL file for installation instructions. diff --git a/c++/src/cpp_doc_config b/c++/src/cpp_doc_config index 1c30292..d91012c 100644 --- a/c++/src/cpp_doc_config +++ b/c++/src/cpp_doc_config @@ -38,7 +38,7 @@ PROJECT_NAME = # could be handy for archiving the generated documentation or if some version # control system is used. -PROJECT_NUMBER = "1.12.0" +PROJECT_NUMBER = "1.12.0-alpha0, currently under development" # Using the PROJECT_BRIEF tag one can provide an optional one line description # for a project that appears at the top of each page and should give viewer a diff --git a/config/cmake/scripts/HDF5config.cmake b/config/cmake/scripts/HDF5config.cmake index 1c04fcc..2f657e1 100644 --- a/config/cmake/scripts/HDF5config.cmake +++ b/config/cmake/scripts/HDF5config.cmake @@ -35,7 +35,7 @@ cmake_minimum_required (VERSION 3.10) ############################################################################## set (CTEST_SOURCE_VERSION "1.12.0") -set (CTEST_SOURCE_VERSEXT "") +set (CTEST_SOURCE_VERSEXT "-alpha0") ############################################################################## # handle input parameters to script. diff --git a/configure.ac b/configure.ac index abfa86e..9898005 100644 --- a/configure.ac +++ b/configure.ac @@ -24,7 +24,7 @@ AC_PREREQ([2.69]) ## NOTE: Do not forget to change the version number here when we do a ## release!!! ## -AC_INIT([HDF5], [1.12.0], [help@hdfgroup.org]) +AC_INIT([HDF5], [1.12.0-alpha0], [help@hdfgroup.org]) AC_CONFIG_SRCDIR([src/H5.c]) AC_CONFIG_HEADERS([src/H5config.h]) diff --git a/release_docs/HISTORY-1_10_0-1_12_0.txt b/release_docs/HISTORY-1_10_0-1_12_0.txt new file mode 100644 index 0000000..b1702b6 --- /dev/null +++ b/release_docs/HISTORY-1_10_0-1_12_0.txt @@ -0,0 +1,1180 @@ +HDF5 version 1.11.6 currently under development +================================================================================ + + +INTRODUCTION + +This document describes the differences between this release and the previous +HDF5 release. It contains information on the platforms tested and known +problems in this release. For more details check the HISTORY*.txt files in the +HDF5 source. + +Note that documentation in the links below will be updated at the time of each +final release. + +Links to HDF5 documentation can be found on The HDF5 web page: + + https://portal.hdfgroup.org/display/HDF5/HDF5 + +The official HDF5 releases can be obtained from: + + https://www.hdfgroup.org/downloads/hdf5/ + +Changes from Release to Release and New Features in the HDF5-1.10.x release series +can be found at: + + https://portal.hdfgroup.org/display/HDF5/HDF5+Application+Developer%27s+Guide + +If you have any questions or comments, please send them to the HDF Help Desk: + + help@hdfgroup.org + + +CONTENTS + +- New Features +- Support for new platforms and languages +- Bug Fixes since HDF5-1.10.3 +- Bug Fixes since HDF5-1.10.2 +- Supported Platforms +- Tested Configuration Features Summary +- More Tested Platforms +- Known Problems +- CMake vs. Autotools installations + + +New Features +============ + + Configuration: + ------------- + - Update CMake tests to use FIXTURES + + CMake test fixtures allow setup/cleanup tests and other dependency + requirements as properties for tests. This is more flexible for + modern CMake code. + + (ADB - 2019/07/23, HDFFV-10529) + + - Windows PDB files are always installed + + There are build configuration or flag settings for Windows that may not + generate PDB files. If those files are not generated then the install + utility will fail because those PDB files are not found. An optional + variable, DISABLE_PDB_FILES, was added to not install PDB files. + + (ADB - 2019/07/17, HDFFV-10424) + + - Add mingw CMake support with a toolchain file + + There has been a number of mingw issues that has been linked under + HDFFV-10845. It has been decided to implement the CMake cross-compiling + technique of toolchain files. We will use a linux platform with the mingw + compiler stack for testing. Only the C language is fully supported, and + the error tests are skipped. The C++ language works for static but shared + builds has a shared library issue with the mingw Standard Exception Handling + library, which is not available on Windows. Fortran has a common cross-compile + problem with the fortran configure tests. + + (ADB - 2019/07/12, HDFFV-10845, HDFFV-10595) + + - Windows PDB files are installed incorrectly + + For static builds, the PDB files for windows should be installed next + to the static libraries in the lib folder. Also the debug versions of + libraries and PDB files are now correctly built using the default + CMAKE_DEBUG_POSTFIX setting. + + (ADB - 2019/07/09, HDFFV-10581) + + - Add option to build only shared libs + + A request was made to prevent building static libraries and only build + shared. A new option was added to CMake, ONLY_SHARED_LIBS, which will + skip building static libraries. Certain utility functions will build with + static libs but are not published. Tests are adjusted to use the correct + libraries depending on SHARED/STATIC settings. + + (ADB - 2019/06/12, HDFFV-10805) + + - Add options to enable or disable building tools and tests + + Configure options --enable-tests and --enable-tools were added for + autotools configure. These options are enabled by default, and can be + disabled with either --disable-tests (or tools) or --enable-tests=no + (or --enable-tools=no). Build time is reduced ~20% when tools are + disabled, 35% when tests are disabled, 45% when both are disabled. + Reenabling them after the initial build requires running configure + again with the option(s) enabled. + + (LRK - 2019/06/12, HDFFV-9976) + + - Change tools test that test the error stack + + There are some use cases which can cause the error stack of tools to be + different then the expected output. These tests now use grepTest.cmake, + this was changed to allow the error file to be searched for an expected string. + + (ADB - 2019/04/15, HDFFV-10741) + + - Keep stderr and stdout separate in tests + + Changed test handling of output capture. Tests now keep the stderr + output separate from the stdout output. It is up to the test to decide + which output to check against a reference. Also added the option + to grep for a string in either output. + + (ADB - 2018/12/12, HDFFV-10632) + + - Add toolchain and cross-compile support + + 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 - 2018/10/04, HDFFV-10594) + + - Add warning flags for Intel compilers + + Identified Intel compiler specific warnings flags that should be used + instead of GNU flags. + + (ADB - 2018/10/04, TRILABS-21) + + - Add default rpath to targets + + 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. + + (ADB - 2018/09/26, HDFFV-10594) + + - 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) + + + Library: + -------- + - Add new H5R_ref_t type for object, dataset region and _attribute_ + references. This new type will deprecate the current hobj_ref_t + and hdset_reg_ref_t types for references. Added H5T_REF datatype + to read and write new reference types. As opposed to previous + reference types, reference creation no longer modifies existing + files. New reference types also now support references to external + files. + + (JS - 2019/10/08) + + - Add S3 and HDFS VFDs to HDF5 maintenance + + Fix windows requirements and java tests. Windows requires CMake 3.13. + Install openssl library (with dev files); + from "Shining Light Productions". msi package preferred. + + PATH should have been updated with the installation dir. + set ENV variable OPENSSL_ROOT_DIR to the installation dir. + set ENV variable OPENSSL_CONF to the cfg file, likely %OPENSSL_ROOT_DIR%\bin\openssl.cfg + Install libcurl library (with dev files); + download the latest released version using git: https://github.com/curl/curl.git + + Open a Visual Studio Command prompt + change to the libcurl root folder + run the "buildconf.bat" batch file + change to the winbuild directory + nmake /f Makefile.vc mode=dll MACHINE=x64 + copy libcurl-vc-x64-release-dll-ipv6-sspi-winssl dir to C:\curl (installation dir) + set ENV variable CURL_ROOT to C:\curl (installation dir) + update PATH ENV variable to %CURL_ROOT%\bin (installation bin dir). + the aws credentials file should be in %USERPROFILE%\.aws folder + set the ENV variable "HDF5_ROS3_TEST_BUCKET_URL=https://s3.us-east-2.amazonaws.com/hdf5ros3" + + (ADB - 2019/09/12, HDFFV-10854) + + - Added new chunk query functions + + The following public functions were added to discover information about + the chunks in an HDF5 file. + herr_t H5Dget_num_chunks(dset_id, fspace_id, *nchunks) + herr_t H5Dget_chunk_info_by_coord(dset_id, *coord, *filter_mask, *addr, *size) + herr_t H5Dget_chunk_info(dset_id, fspace_id, index, *coord, *filter_mask, *addr, *size) + + (BMR - 2019/06/11, HDFFV-10677) + + - Improved the performance of virtual dataset I/O + + Refactored the internal dataspace routines used by the virtual dataset + code to improve performance, especially when one of the selections + involved is very long and non-contiguous. + + (NAF - 2019/05/31, HDFFV-10693) + + - Added the ability to open files with UTF-8 file names on Windows. + + The POSIX open(2) API call on Windows is limited to ASCII + file names. The library has been updated to convert incoming file + names to UTF-16 (via MultiByteToWideChar(CP_UTF8, ...) and use + _wopen() instead. + + (DER - 2019/03/15, HDFFV-2714, HDFFV-3914, HDFFV-3895, HDFFV-8237, HDFFV-10413, HDFFV-10691) + + - Add new API H5M for map objects. Currently not supported by native + library, can be supported by VOL connectors. + + (NAF - 2019/03/01) + + - Remove H5I_REFERENCE from the library + + This ID class was never used by the library and has been removed. + + (DER - 2018/12/08, HDFFV-10252) + + - Allow pre-generated H5Tinit.c and H5make_libsettings.c to be used. + + 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) + + + Parallel Library: + ----------------- + - Changed the default behavior in parallel when reading the same dataset in its entirely + (i.e. H5S_ALL dataset selection) which is being read by all the processes collectively. + The dataset mush be contiguous, less than 2GB, and of an atomic datatype. + The new behavior is the HDF5 library will use an MPI_Bcast to pass the data read from + the disk by the root process to the remain processes in the MPI communicator associated + with the HDF5 file. + + (MSB - 2019/01/02, HDFFV-10652) + + Fortran Library: + ---------------- + - Added new Fortran derived type, c_h5o_info_t, which is interoperable with + C's h5o_info_t. This is needed for callback functions which + pass C's h5o_info_t data type definition. + + (MSB, 2019/01/08, HDFFV-10443) + + - Added new Fortran API, H5gmtime, which converts (C) 'time_t' structure + to Fortran DATE AND TIME storage format. + + (MSB, 2019/01/08, HDFFV-10443) + + - Added new Fortran 'fields' optional parameter to: h5ovisit_f, h5oget_info_by_name_f, + h5oget_info, h5oget_info_by_idx and h5ovisit_by_name_f. + + (MSB, 2019/01/08, HDFFV-10443) + + C++ Library: + ------------ + - Added new wrappers for H5Pset/get_create_intermediate_group() + LinkCreatPropList::setCreateIntermediateGroup() + LinkCreatPropList::getCreateIntermediateGroup() + + (BMR - 2019/04/22, HDFFV-10622) + + - Added new wrapper for H5Ovisit2() + H5Object::visit() + + (BMR - 2019/02/14, HDFFV-10532) + + + Java Library: + ---------------- + - Fix a failure in JUnit-TestH5P on 32-bit architectures + + (JTH - 2019/04/30) + + - Duplicate the data read/write functions of Datasets for Attributes. + + Region references could not be displayed for attributes as they could + for datasets. Datasets had overloaded read and write functions for different + datatypes that were not available for attributes. After adding similar + functions, attribute region references work normally. + + (ADB - 2018/12/12, HDFVIEW-4) + + - Removed H5I_REFERENCE from the Java wrappers + + This ID class was never used by the library and has been removed + from the Java wrappers. + + (DER - 2018/12/08, HDFFV-10252) + + + Tools: + ------ + - h5repack was fixed to repack datasets with external storage + to other types of storage. + + New test added to repack files and verify the correct data using h5diff. + + (JS - 2019/09/25, HDFFV-10408) + (ADB - 2019/10/02, HDFFV-10918) + + - h5dump was fixed for 128-bit floats, but was missing a test. + + New test greps for the first 15 numbers of the 128-bit value. + + (ADB - 2019/06/23, HDFFV-9407) + + + High-Level APIs: + --------------- + - + + C Packet Table API + ------------------ + - + + Internal header file + -------------------- + - + + Documentation + ------------- + - + +Support for new platforms, languages and compilers. +======================================= + - + +Bug Fixes since HDF5-1.10.3 release +================================== + + Library + ------- + - Fixed the iteration error in test_versionbounds() in test/dtypes.c + + The test was supposed to loop through all valid combinations of + low and high bounds in the array versions[], but they were set to + H5F_LIBVER_EARLIEST always without changing. + + The problem was fixed by indexing low and high into the array versions[]. + + (VC - 2019/09/30) + + - Fixed the slowness of regular hyperslab selection in a chunked dataset + + It was reported that the selection of every 10th element from a 20G + chunked dataset was extremely slow and sometimes could hang the system. + The problem was due to the iteration and the building of the span tree + for all the selected elements in file space. + + As the selected elements are going to a 1-d contiguous single block + memory space, the problem was fixed by building regular hyperslab selections + in memory space for the selected elements in file space. + + (VC - 2019/09/26, HDFFV-10585) + + - Fixed a bug caused by bad tag value when condensing object header + messages + + There was an assertion failure when moving meessages from running a + user test program with library release hdf5.1.10.4. It was because + the tag value (object header's address) was not set up when entering + the library routine H5O__chunk_update_idx(), which will eventually + verifies the metadata tag value when protecting the object header. + + The problem was fixed by replacing FUNC_ENTER_PACKAGE in H5O__chunk_update_idx() + with FUNC_ENTER_PACKAGE_TAG(oh->cache_info.addr) to set up the metadata tag. + + (VC - 2019/08/23, HDFFV-10873) + + - Fixed the test failure from test_metadata_read_retry_info() in + test/swmr.c + + The test failure is due to the incorrect number of bins returned for + retry info (info.nbins). The # of bins expected for 101 read attempts + is 3 instead of 2. The routine H5F_set_retries() in src/H5Fint.c + calculates the # of bins by first obtaining the log10 value for + (read attempts - 1). For PGI/19, the log10 value for 100 read attempts + is 1.9999999999999998 instead of 2.00000. When casting the log10 value + to unsigned later on, the decimal part is chopped off causing the test + failure. + + This was fixed by obtaining the rounded integer value (HDceil) for the + log10 value of read attempts first before casting the result to unsigned. + + (VC - 2019/8/14, HDFFV-10813) + + - Fixed an issue where creating a file with non-default file space info + together with library high bound setting to H5F_LIBVER_V18. + + When setting non-default file space info in fcpl via + H5Pset_file_space_strategy() and then creating a file with + both high and low library bounds set to + H5F_LIBVER_V18 in fapl, the library succeeds in creating the file. + File creation should fail because the feature of setting non-default + file space info does not exist in library release 1.8 or earlier. + + This was fixed by setting and checking the proper version in the + file space info message based on the library low and high bounds + when creating and opening the HDF5 file. + + (VC - 2019/6/25, HDFFV-10808) + + - When iterating over an old-style group (i.e., when not using the latest + file format) of size 0, a NULL pointer representing the empty links + table would be sent to qsort(3) for sorting, which is undefined behavior. + + Iterating over an empty group is explicitly tested in the links test. + This has not caused any failures to date and was flagged by gcc's + -fsanitize=undefined. + + The library no longer attempts to sort an empty array. + + (DER - 2019/06/18, HDFFV-10829) + + - Fixed an issue where copying a version 1.8 dataset between files using + H5Ocopy fails due to an incompatible fill version + + When using the HDF5 1.10.x H5Ocopy() API call to copy a version 1.8 + dataset to a file created with both high and low library bounds set to + H5F_LIBVER_V18, the H5Ocopy() call will fail with the error stack indicating + that the fill value version is out of bounds. + + This was fixed by changing the fill value message version to H5O_FILL_VERSION_3 + (from H5O_FILL_VERSION_2) for H5F_LIBVER_V18. + + (VC - 2019/6/14, HDFFV-10800) + + - Some oversights in the index iterating area of the library caused + a callback function to continue iterating even though it's supposed + to stop. + + Added the returned value check to the for loop's conditions in + H5EA_iterate(), H5FA_iterate(), and H5D__none_idx_iterate(). The + iteration now stops when it should. + + (BMR - 2019/06/11, HDFFV-10661) + + - Fixed a bug that would cause an error or cause fill values to be + incorrectly read from a chunked dataset using the "single chunk" index if + the data was held in cache and there was no data on disk. + + (NAF - 2019/03/06) + + - Fixed a bug that could cause an error or cause fill values to be + incorrectly read from a dataset that was written to using H5Dwrite_chunk + if the dataset was not closed after writing. + + (NAF - 2019/03/06, HDFFV-10716) + + - Fixed memory leak in scale offset filter + + In a special case where the MinBits is the same as the number of bits in + the datatype's precision, the filter's data buffer was not freed, causing + the memory usage to grow. In general the buffer was freed correctly. The + Minbits are the minimal number of bits to store the data values. Please + see the reference manual for H5Pset_scaleoffset for the detail. + + (RL - 2019/3/4, HDFFV-10705) + + - Fix hangs with collective metadata reads during chunked dataset I/O + + In the parallel library, it was discovered that when a particular + sequence of operations following a pattern of: + + "write to chunked dataset" -> "flush file" -> "read from dataset" + + occurred with collective metadata reads enabled, hangs could be + observed due to certain MPI ranks not participating in the collective + metadata reads. + + To fix the issue, collective metadata reads are now disabled during + chunked dataset raw data I/O. + + (JTH - 2019/02/11, HDFFV-10563, HDFFV-10688) + + - Performance issue when closing an object + + The slow down is due to the search of the "tag_list" to find + out the "corked" status of an object and "uncork" it if so. + + Improve porformance by skipping the search of the "tag_list" + if there are no "corked" objects when closing an object. + + (VC - 2019/2/6) + + - Fixed a potential invalid memory access and failure that could occur when + decoding an unknown object header message (from a future version of the + library). + + (NAF - 2019/01/07) + + - Deleting attributes in dense storage + + The library aborts with "infinite loop closing library" after + attributes in dense storage are created and then deleted. + + When deleting the attribute nodes from the name index v2 B-tree, + if an attribute is found in the intermediate B-tree nodes, + which may be merged/redistributed in the process, we need to + free the dynamically allocated spaces for the intermediate + decoded attribute. + + (VC - 2018/12/26, HDFFV-10659) + + - Allow H5detect and H5make_libsettings to take a file as an argument. + + 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. + + (ADB - 2018/09/05, HDFFV-9059) + + - 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. + + 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). + + (JTH - 2018/08/25, HDFFV-10501) + + - fcntl(2)-based file locking incorrectly passed the lock argument struct + instead of a pointer to the struct, causing errors on systems where + flock(2) is not available. + + File locking is used when files are opened to enforce SWMR semantics. A + lock operation takes place on all file opens unless the + HDF5_USE_FILE_LOCKING environment variable is set to the string "FALSE". + flock(2) is preferentially used, with fcntl(2) locks as a backup if + flock(2) is unavailable on a system (if neither is available, the lock + operation fails). On these systems, the file lock will often fail, which + causes HDF5 to not open the file and report an error. + + This bug only affects POSIX systems. Win32 builds on Windows use a no-op + locking call which always succeeds. Systems which exhibit this bug will + have H5_HAVE_FCNTL defined but not H5_HAVE_FLOCK in the configure output. + + This bug affects HDF5 1.10.0 through 1.10.5. + + fcntl(2)-based file locking now correctly passes the struct pointer. + + (DER - 2019/08/27, HDFFV-10892) + + + 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. + + (ADB - 2018/08/31, HDFFV-10568) + - Java iterator callbacks + + Change global callback object to a small stack structure in order + to fix a runtime crash. This crash was discovered when iterating + through a file with nested group members. The global variable + visit_callback is overwritten when recursion starts. When recursion + completes, visit_callback will be pointing to the wrong callback method. + + (ADB - 2018/08/15, HDFFV-10536) + + - Java HDFLibraryException class + + Change parent class from Exception to RuntimeException. + + (ADB - 2018/07/30, HDFFV-10534) + + - JNI Read and Write + + Refactored variable-length functions, H5DreadVL and H5AreadVL, + to correct dataset and attribute reads. New write functions, + H5DwriteVL and H5AwriteVL, are under construction. + + (ADB - 2018/06/02, HDFFV-10519) + + + Configuration + ------------- + - Correct option for default API version + + CMake options for default API version are not mutually exclusive. + Change the multiple BOOL options to a single STRING option with the + strings; v16, v18, v110, v112. + + (ADB - 2019/08/12, HDFFV-10879) + + + Fortran + -------- + - Added symbolic links libhdf5_hl_fortran.so to libhdf5hl_fortran.so and + libhdf5_hl_fortran.a to libhdf5hl_fortran.a in hdf5/lib directory for + autotools installs. These were added to match the name of the files + installed by cmake and the general pattern of hl lib files. We will + change the names of the installed lib files to the matching name in + the next major release. + + (LRK - 2019/01/04, HDFFV-10596) + + - Made Fortran specific subroutines PRIVATE in generic procedures. + + Effected generic procedures were functions in H5A, H5D, H5P, H5R and H5T. + + (MSB, 2018/12/04, HDFFV-10511) + + - Fixed issue with Fortran not returning h5o_info_t field values + meta_size%attr%index_size and meta_size%attr%heap_size. + + (MSB, 2018/1/8, HDFFV-10443) + + + Tools + ----- + - + + High-Level APIs: + ------ + - + + Fortran High-Level APIs: + ------ + - + + Documentation + ------------- + - + + F90 APIs + -------- + - + + C++ APIs + -------- + - + + Testing + ------- + - Fixed a test failure in testpar/t_dset.c caused by + the test trying to use the parallel filters feature + on MPI-2 implementations. + + (JTH, 2019/2/7) + +Bug Fixes since HDF5-1.10.2 release +================================== + + Library + ------- + - Java HDF5LibraryException class + + The error minor and major values would be lost after the + constructor executed. + + Created two local class variables to hold the values obtained during + execution of the constructor. Refactored the class functions to retrieve + the class values rather then calling the native functions. + The native functions were renamed and called only during execution + of the constructor. + Added error checking to calling class constructors in JNI classes. + + (ADB - 2018/08/06, HDFFV-10544) + + - Added checks of the defined MPI_VERSION to guard against usage of + MPI-3 functions in the Parallel Compression and "big Parallel I/O" + features when HDF5 is built with MPI-2. Previously, the configure + step would pass but the build itself would fail when it could not + locate the MPI-3 functions used. + + As a result of these new checks, HDF5 can again be built with MPI-2, + but the Parallel Compression feature will be disabled as it relies + on the MPI-3 functions used. + + (JTH - 2018/08/02, HDFFV-10512) + + - User's patches: CVEs + + The following patches have been applied: + + CVE-2018-11202 - NULL pointer dereference was discovered in + H5S_hyper_make_spans in H5Shyper.c (HDFFV-10476) + https://security-tracker.debian.org/tracker/CVE-2018-11202 + https://cve.mitre.org/cgi-bin/cvename.cgi?name=3DCVE-2018-11202 + + CVE-2018-11203 - A division by zero was discovered in + H5D__btree_decode_key in H5Dbtree.c (HDFFV-10477) + https://security-tracker.debian.org/tracker/CVE-2018-11203 + https://cve.mitre.org/cgi-bin/cvename.cgi?name=3DCVE-2018-11203 + + CVE-2018-11204 - A NULL pointer dereference was discovered in + H5O__chunk_deserialize in H5Ocache.c (HDFFV-10478) + https://security-tracker.debian.org/tracker/CVE-2018-11204 + https://cve.mitre.org/cgi-bin/cvename.cgi?name=3DCVE-2018-11204 + + CVE-2018-11206 - An out of bound read was discovered in + H5O_fill_new_decode and H5O_fill_old_decode in H5Ofill.c + (HDFFV-10480) + https://security-tracker.debian.org/tracker/CVE-2018-11206 + https://cve.mitre.org/cgi-bin/cvename.cgi?name=3DCVE-2018-11206 + + CVE-2018-11207 - A division by zero was discovered in + H5D__chunk_init in H5Dchunk.c (HDFFV-10481) + https://security-tracker.debian.org/tracker/CVE-2018-11207 + https://cve.mitre.org/cgi-bin/cvename.cgi?name=3DCVE-2018-11207 + + (BMR - 2018/7/22, PR#s: 1134 and 1139, + HDFFV-10476, HDFFV-10477, HDFFV-10478, HDFFV-10480, HDFFV-10481) + + - H5Adelete + + H5Adelete failed when deleting the last "large" attribute that + is stored densely via fractal heap/v2 b-tree. + + After removing the attribute, update the ainfo message. If the + number of attributes goes to zero, remove the message. + + (VC - 2018/07/20, HDFFV-9277) + + - A bug was discovered in the parallel library which caused partial + parallel reads of filtered datasets to return incorrect data. The + library used the incorrect dataspace for each chunk read, causing + the selection used in each chunk to be wrong. + + The bug was not caught during testing because all of the current + tests which do parallel reads of filtered data read all of the data + using an H5S_ALL selection. Several tests were added which exercise + partial parallel reads. + + (JTH - 2018/07/16, HDFFV-10467) + + - A bug was discovered in the parallel library which caused parallel + writes of filtered datasets to trigger an assertion failure in the + file free space manager. + + This occurred when the filter used caused chunks to repeatedly shrink + and grow over the course of several dataset writes. The previous chunk + information, such as the size of the chunk and the offset in the file, + was being cached and not updated after each write, causing the next write + to the chunk to retrieve the incorrect cached information and run into + issues when reallocating space in the file for the chunk. + + (JTH - 2018/07/16, HDFFV-10509) + + - A bug was discovered in the parallel library which caused the + H5D__mpio_array_gatherv() function to allocate too much memory. + + When the function is called with the 'allgather' parameter set + to a non-true value, the function will receive data from all MPI + ranks and gather it to the single rank specied by the 'root' + parameter. However, the bug in the function caused memory for + the received data to be allocated on all MPI ranks, not just the + singular rank specified as the receiver. In some circumstances, + this would cause an application to fail due to the large amounts + of memory being allocated. + + (JTH - 2018/07/16, HDFFV-10467) + + - Error checks in h5stat and when decoding messages + + h5stat exited with seg fault/core dumped when + errors are encountered in the internal library. + + Add error checks and --enable-error-stack option to h5stat. + Add range checks when decoding messages: old fill value, old + layout and refcount. + + (VC - 2018/07/11, HDFFV-10333) + + - If an HDF5 file contains a malformed compound datatype with a + suitably large offset, the type conversion code can run off + the end of the type conversion buffer, causing a segmentation + fault. + + This issue was reported to The HDF Group as issue #CVE-2017-17507. + + NOTE: The HDF5 C library cannot produce such a file. This condition + should only occur in a corrupt (or deliberately altered) file + or a file created by third-party software. + + THE HDF GROUP WILL NOT FIX THIS BUG AT THIS TIME + + Fixing this problem would involve updating the publicly visible + H5T_conv_t function pointer typedef and versioning the API calls + which use it. We normally only modify the public API during + major releases, so this bug will not be fixed at this time. + + (DER - 2018/02/26, HDFFV-10356) + + - Inappropriate linking with deprecated MPI C++ libraries + + HDF5 does not define *_SKIP_MPICXX in the public headers, so applications + can inadvertently wind up linking to the deprecated MPI C++ wrappers. + + MPICH_SKIP_MPICXX and OMPI_SKIP_MPICXX have both been defined in H5public.h + so this should no longer be an issue. HDF5 makes no use of the deprecated + MPI C++ wrappers. + + (DER - 2019/09/17, HDFFV-10893) + + + + 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) + + - Moved the location of gcc attribute. + + The gcc attribute(no_sanitize), named as the macro HDF_NO_UBSAN, + was located after the function name. Builds with GCC 7 did not + indicate any problem, but GCC 8 issued errors. Moved the + attribute before the function name, as required. + + (ADB - 2018/05/22, HDFFV-10473) + + - Reworked java test suite into individual JUnit tests. + + Testing the whole suite of java unit tests in a single JUnit run + made it difficult to determine actual failures when tests would fail. + Running each file set of tests individually, allows individual failures + to be diagnosed easier. A side benefit is that tests for optional components + of the library can be disabled if not configured. + + (ADB - 2018/05/16, HDFFV-9739) + + - Converted CMake global commands ADD_DEFINITIONS and INCLUDE_DIRECTORIES + to use target_* type commands. This change modernizes the CMake usage + in the HDF5 library. + + In addition, there is the intention to convert to generator expressions, + where possible. The exception is Fortran FLAGS on Windows Visual Studio. + The HDF macros TARGET_C_PROPERTIES and TARGET_FORTRAN_PROPERTIES have + been removed with this change in usage. + + The additional language (C++ and Fortran) checks have also been localized + to only be checked when that language is enabled. + + (ADB - 2018/05/08) + + Performance + ------------- + - + + Fortran + -------- + - + + Tools + ----- + - + + High-Level APIs: + ------ + - + + Fortran High-Level APIs: + ------ + - + + Documentation + ------------- + - + + F90 APIs + -------- + - + + C++ APIs + -------- + - Adding default arguments to existing functions + + Added the following items: + + Two more property list arguments are added to H5Location::createDataSet: + const DSetAccPropList& dapl = DSetAccPropList::DEFAULT + const LinkCreatPropList& lcpl = LinkCreatPropList::DEFAULT + + + One more property list argument is added to H5Location::openDataSet: + const DSetAccPropList& dapl = DSetAccPropList::DEFAULT + + (BMR - 2018/07/21, PR# 1146) + + - Improvement C++ documentation + + Replaced the table in main page of the C++ documentation from mht to htm format + for portability. + + (BMR - 2018/07/17, PR# 1141) + + Testing + ------- + - The dt_arith test failed on IBM Power8 and Power9 machines when testing + conversions from or to long double types, especially when special values + such as infinity or NAN were involved. In some cases the results differed + by extremely small amounts from those on other machines, while some other + tests resulted in segmentation faults. These conversion tests with long + double types have been disabled for ppc64 machines until the problems are + better understood and can be properly addressed. + + (SRL - 2019/01/07, TRILAB-98) + +Supported Platforms +=================== + + Linux 2.6.32-696.16.1.el6.ppc64 gcc (GCC) 4.4.7 20120313 (Red Hat 4.4.7-18) + #1 SMP ppc64 GNU/Linux g++ (GCC) 4.4.7 20120313 (Red Hat 4.4.7-18) + (ostrich) GNU Fortran (GCC) 4.4.7 20120313 (Red Hat 4.4.7-18) + IBM XL C/C++ V13.1 + IBM XL Fortran V15.1 + + Linux 3.10.0-327.10.1.el7 GNU C (gcc), Fortran (gfortran), C++ (g++) + #1 SMP x86_64 GNU/Linux compilers: + (kituo/moohan) Version 4.8.5 20150623 (Red Hat 4.8.5-4) + Version 4.9.3, Version 5.2.0, + Intel(R) C (icc), C++ (icpc), Fortran (icc) + compilers: + Version 17.0.0.098 Build 20160721 + MPICH 3.1.4 compiled with GCC 4.9.3 + + SunOS 5.11 32- and 64-bit Sun C 5.12 SunOS_sparc + (emu) Sun Fortran 95 8.6 SunOS_sparc + Sun C++ 5.12 SunOS_sparc + + Windows 7 Visual Studio 2015 w/ Intel Fortran 16 (cmake) + + Windows 7 x64 Visual Studio 2013 + Visual Studio 2015 w/ Intel Fortran 16 (cmake) + Visual Studio 2015 w/ Intel C, Fortran 2018 (cmake) + Visual Studio 2015 w/ MSMPI 8 (cmake) + + Windows 10 Visual Studio 2015 w/ Intel Fortran 18 (cmake) + + Windows 10 x64 Visual Studio 2015 w/ Intel Fortran 18 (cmake) + Visual Studio 2017 w/ Intel Fortran 18 (cmake) + + Mac OS X Yosemite 10.10.5 Apple clang/clang++ version 6.1 from Xcode 7.0 + 64-bit gfortran GNU Fortran (GCC) 4.9.2 + (osx1010dev/osx1010test) Intel icc/icpc/ifort version 15.0.3 + + Mac OS X El Capitan 10.11.6 Apple clang/clang++ version 7.3.0 from Xcode 7.3 + 64-bit gfortran GNU Fortran (GCC) 5.2.0 + (osx1011dev/osx1011test) Intel icc/icpc/ifort version 16.0.2 + + Mac OS Sierra 10.12.6 Apple LLVM version 8.1.0 (clang/clang++-802.0.42) + 64-bit gfortran GNU Fortran (GCC) 7.1.0 + (swallow/kite) Intel icc/icpc/ifort version 17.0.2 + + +Tested Configuration Features Summary +===================================== + + In the tables below + y = tested + n = not tested in this release + C = Cluster + W = Workstation + x = not working in this release + dna = does not apply + ( ) = footnote appears below second table + <blank> = testing incomplete on this feature or platform + +Platform C F90/ F90 C++ zlib SZIP + parallel F2003 parallel +Solaris2.11 32-bit n y/y n y y y +Solaris2.11 64-bit n y/n n y y y +Windows 7 y y/y n y y y +Windows 7 x64 y y/y y y y y +Windows 7 Cygwin n y/n n y y y +Windows 7 x64 Cygwin n y/n n y y y +Windows 10 y y/y n y y y +Windows 10 x64 y y/y n y y y +Mac OS X Mountain Lion 10.8.5 64-bit n y/y n y y y +Mac OS X Mavericks 10.9.5 64-bit n y/y n y y ? +Mac OS X Yosemite 10.10.5 64-bit n y/y n y y ? +Mac OS X El Capitan 10.11.6 64-bit n y/y n y y ? +CentOS 6.7 Linux 2.6.18 x86_64 GNU n y/y n y y y +CentOS 6.7 Linux 2.6.18 x86_64 Intel n y/y n y y y +CentOS 6.7 Linux 2.6.32 x86_64 PGI n y/y n y y y +CentOS 7.2 Linux 2.6.32 x86_64 GNU y y/y y y y y +CentOS 7.2 Linux 2.6.32 x86_64 Intel n y/y n y y y +Linux 2.6.32-573.18.1.el6.ppc64 n y/n n y y y + + +Platform Shared Shared Shared Thread- + C libs F90 libs C++ libs safe +Solaris2.11 32-bit y y y y +Solaris2.11 64-bit y y y y +Windows 7 y y y y +Windows 7 x64 y y y y +Windows 7 Cygwin n n n y +Windows 7 x64 Cygwin n n n y +Windows 10 y y y y +Windows 10 x64 y y y y +Mac OS X Mountain Lion 10.8.5 64-bit y n y y +Mac OS X Mavericks 10.9.5 64-bit y n y y +Mac OS X Yosemite 10.10.5 64-bit y n y y +Mac OS X El Capitan 10.11.6 64-bit y n y y +CentOS 6.7 Linux 2.6.18 x86_64 GNU y y y y +CentOS 6.7 Linux 2.6.18 x86_64 Intel y y y n +CentOS 6.7 Linux 2.6.32 x86_64 PGI y y y n +CentOS 7.2 Linux 2.6.32 x86_64 GNU y y y n +CentOS 7.2 Linux 2.6.32 x86_64 Intel y y y n +Linux 2.6.32-573.18.1.el6.ppc64 y y y n + +Compiler versions for each platform are listed in the preceding +"Supported Platforms" table. + + +More Tested Platforms +===================== +The following platforms are not supported but have been tested for this release. + + Linux 2.6.32-573.22.1.el6 GNU C (gcc), Fortran (gfortran), C++ (g++) + #1 SMP x86_64 GNU/Linux compilers: + (mayll/platypus) Version 4.4.7 20120313 + Version 4.9.3, 5.3.0, 6.2.0 + PGI C, Fortran, C++ for 64-bit target on + x86-64; + Version 17.10-0 + Intel(R) C (icc), C++ (icpc), Fortran (icc) + compilers: + Version 17.0.4.196 Build 20170411 + MPICH 3.1.4 compiled with GCC 4.9.3 + + Linux 3.10.0-327.18.2.el7 GNU C (gcc) and C++ (g++) compilers + #1 SMP x86_64 GNU/Linux Version 4.8.5 20150623 (Red Hat 4.8.5-4) + (jelly) with NAG Fortran Compiler Release 6.1(Tozai) + GCC Version 7.1.0 + OpenMPI 3.0.0-GCC-7.2.0-2.29 + Intel(R) C (icc) and C++ (icpc) compilers + Version 17.0.0.098 Build 20160721 + with NAG Fortran Compiler Release 6.1(Tozai) + + Linux 3.10.0-327.10.1.el7 MPICH 3.2 compiled with GCC 5.3.0 + #1 SMP x86_64 GNU/Linux + (moohan) + + Linux 2.6.32-573.18.1.el6.ppc64 MPICH mpich 3.1.4 compiled with + #1 SMP ppc64 GNU/Linux IBM XL C/C++ for Linux, V13.1 + (ostrich) and IBM XL Fortran for Linux, V15.1 + + Debian 8.4 3.16.0-4-amd64 #1 SMP Debian 3.16.36-1 x86_64 GNU/Linux + gcc, g++ (Debian 4.9.2-10) 4.9.2 + GNU Fortran (Debian 4.9.2-10) 4.9.2 + (cmake and autotools) + + Fedora 24 4.7.2-201.fc24.x86_64 #1 SMP x86_64 x86_64 x86_64 GNU/Linux + gcc, g++ (GCC) 6.1.1 20160621 + (Red Hat 6.1.1-3) + GNU Fortran (GCC) 6.1.1 20160621 + (Red Hat 6.1.1-3) + (cmake and autotools) + + Ubuntu 16.04.1 4.4.0-38-generic #57-Ubuntu SMP x86_64 GNU/Linux + gcc, g++ (Ubuntu 5.4.0-6ubuntu1~16.04.2) + 5.4.0 20160609 + GNU Fortran (Ubuntu 5.4.0-6ubuntu1~16.04.2) + 5.4.0 20160609 + (cmake and autotools) + + +Known Problems +============== + CMake files do not behave correctly with paths containing spaces. + Do not use spaces in paths because the required escaping for handling spaces + results in very complex and fragile build files. + ADB - 2019/05/07 + + At present, metadata cache images may not be generated by parallel + applications. Parallel applications can read files with metadata cache + images, but since this is a collective operation, a deadlock is possible + if one or more processes do not participate. + + 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. + diff --git a/release_docs/RELEASE.txt b/release_docs/RELEASE.txt index 01b7d6d..0e4a2fd 100644 --- a/release_docs/RELEASE.txt +++ b/release_docs/RELEASE.txt @@ -1,16 +1,15 @@ -HDF5 version 1.12.0 currently under development +HDF5 version 1.12.0-alpha0 currently under development ================================================================================ INTRODUCTION -This document describes the differences between this release and the previous -HDF5 release. It contains information on the platforms tested and known -problems in this release. For more details check the HISTORY*.txt files in the -HDF5 source. +This document describes the new features introduced in the HDF5 1.12.0 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. +Note that documentation in the links below will be updated at the time of the +release. Links to HDF5 documentation can be found on The HDF5 web page: @@ -20,10 +19,9 @@ 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: +More information about the new features can be found at: - https://portal.hdfgroup.org/display/HDF5/HDF5+Application+Developer%27s+Guide + https://portal.hdfgroup.org/display/HDF5/New+Features+in+HDF5+Release+1.12 If you have any questions or comments, please send them to the HDF Help Desk: @@ -34,8 +32,7 @@ CONTENTS - New Features - Support for new platforms and languages -- Bug Fixes since HDF5-1.10.3 -- Bug Fixes since HDF5-1.10.2 +- Major Bug Fixes since HDF5-1.10.0 - Supported Platforms - Tested Configuration Features Summary - More Tested Platforms @@ -46,928 +43,102 @@ CONTENTS New Features ============ - Configuration: - ------------- - - Update CMake tests to use FIXTURES - - CMake test fixtures allow setup/cleanup tests and other dependency - requirements as properties for tests. This is more flexible for - modern CMake code. - - (ADB - 2019/07/23, HDFFV-10529) - - - Windows PDB files are always installed - - There are build configuration or flag settings for Windows that may not - generate PDB files. If those files are not generated then the install - utility will fail because those PDB files are not found. An optional - variable, DISABLE_PDB_FILES, was added to not install PDB files. - - (ADB - 2019/07/17, HDFFV-10424) - - - Add mingw CMake support with a toolchain file - - There has been a number of mingw issues that has been linked under - HDFFV-10845. It has been decided to implement the CMake cross-compiling - technique of toolchain files. We will use a linux platform with the mingw - compiler stack for testing. Only the C language is fully supported, and - the error tests are skipped. The C++ language works for static but shared - builds has a shared library issue with the mingw Standard Exception Handling - library, which is not available on Windows. Fortran has a common cross-compile - problem with the fortran configure tests. - - (ADB - 2019/07/12, HDFFV-10845, HDFFV-10595) - - - Windows PDB files are installed incorrectly - - For static builds, the PDB files for windows should be installed next - to the static libraries in the lib folder. Also the debug versions of - libraries and PDB files are now correctly built using the default - CMAKE_DEBUG_POSTFIX setting. - - (ADB - 2019/07/09, HDFFV-10581) - - - Add option to build only shared libs - - A request was made to prevent building static libraries and only build - shared. A new option was added to CMake, ONLY_SHARED_LIBS, which will - skip building static libraries. Certain utility functions will build with - static libs but are not published. Tests are adjusted to use the correct - libraries depending on SHARED/STATIC settings. - - (ADB - 2019/06/12, HDFFV-10805) - - - Add options to enable or disable building tools and tests - - Configure options --enable-tests and --enable-tools were added for - autotools configure. These options are enabled by default, and can be - disabled with either --disable-tests (or tools) or --enable-tests=no - (or --enable-tools=no). Build time is reduced ~20% when tools are - disabled, 35% when tests are disabled, 45% when both are disabled. - Reenabling them after the initial build requires running configure - again with the option(s) enabled. - - (LRK - 2019/06/12, HDFFV-9976) - - - Change tools test that test the error stack - - There are some use cases which can cause the error stack of tools to be - different then the expected output. These tests now use grepTest.cmake, - this was changed to allow the error file to be searched for an expected string. - - (ADB - 2019/04/15, HDFFV-10741) - - - Keep stderr and stdout separate in tests - - Changed test handling of output capture. Tests now keep the stderr - output separate from the stdout output. It is up to the test to decide - which output to check against a reference. Also added the option - to grep for a string in either output. - - (ADB - 2018/12/12, HDFFV-10632) - - - Add toolchain and cross-compile support - - 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 - 2018/10/04, HDFFV-10594) - - - Add warning flags for Intel compilers - - Identified Intel compiler specific warnings flags that should be used - instead of GNU flags. - - (ADB - 2018/10/04, TRILABS-21) - - - Add default rpath to targets - - 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. - - (ADB - 2018/09/26, HDFFV-10594) - - - 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) - - Library: -------- - - Add S3 and HDFS VFDs to HDF5 maintenance + - Virtual Object Layer (VOL) + + In this major HDF5 release we introduce HDF5 Virtual Object Layer (VOL). + VOL is an abstraction layer within the HDF5 library that enables different + methods for accessing data and objects that conform to the HDF5 data model. + The VOL layer intercepts all HDF5 API calls that potentially modify data + on disk and forwards those calls to a plugin "object driver". The data on + disk can be a different format than the HDF5 format. For more information + about VOL we refer the reader to the following documents (under review): + + VOL HDF5 APIs + https://portal.hdfgroup.org/display/HDF5/Virtual+Object++Layer + + VOL Documentation + https://bitbucket.hdfgroup.org/projects/HDFFV/repos/hdf5doc/browse/RFCs/HDF5/VOL + + Repository with VOL plugins + https://bitbucket.hdfgroup.org/projects/HDF5VOL + + - Enhancements to HDF5 References + + HDF5 references were extended to support attributes, and object and dataset + selections that reside in another HDF5 file. For more information including + a list of new APIs, see + + https://portal.hdfgroup.org/display/HDF5/Update+to+References + + Current known limitations for references in this release: + • HDF5 command-line tools have not been updated to read new references types. + • When reading data with the H5T_STD_REF type, if data is filled with 0s, + H5A/Dread() currently returns an error. This will be fixed in an upcoming + release. + • h5dump will fail to display references on big-endian machines. + + - New S3 and HDFS Virtual File Drivers (VFDs) + + This release has two new VFDs. The S3 VFD allows accessing HDF5 files on + AWS S3 buckets. HDFS VFD allows accessing HDF5 file stored on Apache HDFS. + See https://portal.hdfgroup.org/display/HDF5/H5P_SET_FAPL_ROS3 + and https://portal.hdfgroup.org/display/HDF5/H5P_SET_FAPL_HDFS + for how to use those APIs. + See https://portal.hdfgroup.org/display/HDF5/Virtual+Object+Layer+and+Virtual+File+Drivers + for more information about configuring and setting up either the S3 or HDFS vfd. + Below are specific instructions how to enable S3 VFD on Windows: Fix windows requirements and java tests. Windows requires CMake 3.13. - Install openssl library (with dev files); - from "Shining Light Productions". msi package preferred. - - PATH should have been updated with the installation dir. - set ENV variable OPENSSL_ROOT_DIR to the installation dir. - set ENV variable OPENSSL_CONF to the cfg file, likely %OPENSSL_ROOT_DIR%\bin\openssl.cfg - Install libcurl library (with dev files); - download the latest released version using git: https://github.com/curl/curl.git - - Open a Visual Studio Command prompt - change to the libcurl root folder - run the "buildconf.bat" batch file - change to the winbuild directory - nmake /f Makefile.vc mode=dll MACHINE=x64 - copy libcurl-vc-x64-release-dll-ipv6-sspi-winssl dir to C:\curl (installation dir) - set ENV variable CURL_ROOT to C:\curl (installation dir) - update PATH ENV variable to %CURL_ROOT%\bin (installation bin dir). - the aws credentials file should be in %USERPROFILE%\.aws folder - set the ENV variable "HDF5_ROS3_TEST_BUCKET_URL=https://s3.us-east-2.amazonaws.com/hdf5ros3" - - (ADB - 2019/09/12, HDFFV-10854) - - - Added new chunk query functions - - The following public functions were added to discover information about - the chunks in an HDF5 file. - herr_t H5Dget_num_chunks(dset_id, fspace_id, *nchunks) - herr_t H5Dget_chunk_info_by_coord(dset_id, *coord, *filter_mask, *addr, *size) - herr_t H5Dget_chunk_info(dset_id, fspace_id, index, *coord, *filter_mask, *addr, *size) - - (BMR - 2019/06/11, HDFFV-10677) - - - Improved the performance of virtual dataset I/O - - Refactored the internal dataspace routines used by the virtual dataset - code to improve performance, especially when one of the selections - involved is very long and non-contiguous. - - (NAF - 2019/05/31, HDFFV-10693) - - - Added the ability to open files with UTF-8 file names on Windows. - - The POSIX open(2) API call on Windows is limited to ASCII - file names. The library has been updated to convert incoming file - names to UTF-16 (via MultiByteToWideChar(CP_UTF8, ...) and use - _wopen() instead. - - (DER - 2019/03/15, HDFFV-2714, HDFFV-3914, HDFFV-3895, HDFFV-8237, HDFFV-10413, HDFFV-10691) - - - Add new API H5M for map objects. Currently not supported by native - library, can be supported by VOL connectors. - - (NAF - 2019/03/01) - - - Add new H5R_ref_t type for object, dataset region and _attribute_ - references. This new type will deprecate the current hobj_ref_t - and hdset_reg_ref_t types for references. Added H5T_REF datatype - to read and write new reference types. As opposed to previous - reference types, reference creation no longer modifies existing - files. New reference types also now support references to external - files. - - (JS - 2019/10/08) - - - Remove H5I_REFERENCE from the library - - This ID class was never used by the library and has been removed. - - (DER - 2018/12/08, HDFFV-10252) - - - Allow pre-generated H5Tinit.c and H5make_libsettings.c to be used. - - 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) - - - Parallel Library: - ----------------- - - Changed the default behavior in parallel when reading the same dataset in its entirely - (i.e. H5S_ALL dataset selection) which is being read by all the processes collectively. - The dataset mush be contiguous, less than 2GB, and of an atomic datatype. - The new behavior is the HDF5 library will use an MPI_Bcast to pass the data read from - the disk by the root process to the remain processes in the MPI communicator associated - with the HDF5 file. - - (MSB - 2019/01/02, HDFFV-10652) + - Install openssl library (with dev files); + from "Shining Light Productions". msi package preferred. + - PATH should have been updated with the installation dir. + - set ENV variable OPENSSL_ROOT_DIR to the installation dir. + - set ENV variable OPENSSL_CONF to the cfg file, likely %OPENSSL_ROOT_DIR%\bin\openssl.cfg + - Install libcurl library (with dev files); + - download the latest released version using git: https://github.com/curl/curl.git + - Open a Visual Studio Command prompt + - change to the libcurl root folder + - run the "buildconf.bat" batch file + - change to the winbuild directory + - nmake /f Makefile.vc mode=dll MACHINE=x64 + - copy libcurl-vc-x64-release-dll-ipv6-sspi-winssl dir to C:\curl (installation dir) + - set ENV variable CURL_ROOT to C:\curl (installation dir) + - update PATH ENV variable to %CURL_ROOT%\bin (installation bin dir). + - the aws credentials file should be in %USERPROFILE%\.aws folder + - set the ENV variable HDF5_ROS3_TEST_BUCKET_URL to the s3 url for the + s3 bucket containing the HDF5 files to be accessed. + + Other improvements and changes: + + - Hyperslab selection code was reworked to improve performance, getting more + than 10x speedup in some cases. + + - The HDF5 Library was enhanced to open files with Unicode names on Windows. + + - Deprecated H5Dvlen_reclaim() and replaced it with H5Treclaim(). + This routine is meant to be used when resources are internally allocated + when reading data, i.e. when using either vlen or new reference types. + This is applicable to both attribute and dataset reads. - Fortran Library: - ---------------- - - Added new Fortran derived type, c_h5o_info_t, which is interoperable with - C's h5o_info_t. This is needed for callback functions which - pass C's h5o_info_t data type definition. - - (MSB, 2019/01/08, HDFFV-10443) - - - Added new Fortran API, H5gmtime, which converts (C) 'time_t' structure - to Fortran DATE AND TIME storage format. - - (MSB, 2019/01/08, HDFFV-10443) - - - Added new Fortran 'fields' optional parameter to: h5ovisit_f, h5oget_info_by_name_f, - h5oget_info, h5oget_info_by_idx and h5ovisit_by_name_f. - - (MSB, 2019/01/08, HDFFV-10443) - - C++ Library: - ------------ - - Added new wrappers for H5Pset/get_create_intermediate_group() - LinkCreatPropList::setCreateIntermediateGroup() - LinkCreatPropList::getCreateIntermediateGroup() - - (BMR - 2019/04/22, HDFFV-10622) - - - Added new wrapper for H5Ovisit2() - H5Object::visit() - - (BMR - 2019/02/14, HDFFV-10532) - - - Java Library: - ---------------- - - Fix a failure in JUnit-TestH5P on 32-bit architectures - - (JTH - 2019/04/30) - - - Duplicate the data read/write functions of Datasets for Attributes. - - Region references could not be displayed for attributes as they could - for datasets. Datasets had overloaded read and write functions for different - datatypes that were not available for attributes. After adding similar - functions, attribute region references work normally. - - (ADB - 2018/12/12, HDFVIEW-4) - - - Removed H5I_REFERENCE from the Java wrappers - - This ID class was never used by the library and has been removed - from the Java wrappers. - - (DER - 2018/12/08, HDFFV-10252) - - - Tools: - ------ - h5repack was fixed to repack datasets with external storage to other types of storage. - New test added to repack files and verify the correct data using h5diff. - - (JS - 2019/09/25, HDFFV-10408) - (ADB - 2019/10/02, HDFFV-10918) - - - h5dump was fixed for 128-bit floats, but was missing a test. - - New test greps for the first 15 numbers of the 128-bit value. - - (ADB - 2019/06/23, HDFFV-9407) - - - High-Level APIs: - --------------- - - - - C Packet Table API - ------------------ - - - - Internal header file - -------------------- - - - - Documentation - ------------- - - Support for new platforms, languages and compilers. ======================================= - - - -Bug Fixes since HDF5-1.10.3 release -================================== - - Library - ------- - - Fixed the iteration error in test_versionbounds() in test/dtypes.c - - The test was supposed to loop through all valid combinations of - low and high bounds in the array versions[], but they were set to - H5F_LIBVER_EARLIEST always without changing. - - The problem was fixed by indexing low and high into the array versions[]. - - (VC - 2019/09/30) - - - Fixed the slowness of regular hyperslab selection in a chunked dataset - - It was reported that the selection of every 10th element from a 20G - chunked dataset was extremely slow and sometimes could hang the system. - The problem was due to the iteration and the building of the span tree - for all the selected elements in file space. - - As the selected elements are going to a 1-d contiguous single block - memory space, the problem was fixed by building regular hyperslab selections - in memory space for the selected elements in file space. - - (VC - 2019/09/26, HDFFV-10585) - - - Fixed a bug caused by bad tag value when condensing object header - messages - - There was an assertion failure when moving meessages from running a - user test program with library release hdf5.1.10.4. It was because - the tag value (object header's address) was not set up when entering - the library routine H5O__chunk_update_idx(), which will eventually - verifies the metadata tag value when protecting the object header. - - The problem was fixed by replacing FUNC_ENTER_PACKAGE in H5O__chunk_update_idx() - with FUNC_ENTER_PACKAGE_TAG(oh->cache_info.addr) to set up the metadata tag. - - (VC - 2019/08/23, HDFFV-10873) - - - Fixed the test failure from test_metadata_read_retry_info() in - test/swmr.c - - The test failure is due to the incorrect number of bins returned for - retry info (info.nbins). The # of bins expected for 101 read attempts - is 3 instead of 2. The routine H5F_set_retries() in src/H5Fint.c - calculates the # of bins by first obtaining the log10 value for - (read attempts - 1). For PGI/19, the log10 value for 100 read attempts - is 1.9999999999999998 instead of 2.00000. When casting the log10 value - to unsigned later on, the decimal part is chopped off causing the test - failure. - - This was fixed by obtaining the rounded integer value (HDceil) for the - log10 value of read attempts first before casting the result to unsigned. - - (VC - 2019/8/14, HDFFV-10813) - - - Fixed an issue where creating a file with non-default file space info - together with library high bound setting to H5F_LIBVER_V18. - - When setting non-default file space info in fcpl via - H5Pset_file_space_strategy() and then creating a file with - both high and low library bounds set to - H5F_LIBVER_V18 in fapl, the library succeeds in creating the file. - File creation should fail because the feature of setting non-default - file space info does not exist in library release 1.8 or earlier. - - This was fixed by setting and checking the proper version in the - file space info message based on the library low and high bounds - when creating and opening the HDF5 file. - - (VC - 2019/6/25, HDFFV-10808) - - - When iterating over an old-style group (i.e., when not using the latest - file format) of size 0, a NULL pointer representing the empty links - table would be sent to qsort(3) for sorting, which is undefined behavior. - - Iterating over an empty group is explicitly tested in the links test. - This has not caused any failures to date and was flagged by gcc's - -fsanitize=undefined. - - The library no longer attempts to sort an empty array. - - (DER - 2019/06/18, HDFFV-10829) - - - Fixed an issue where copying a version 1.8 dataset between files using - H5Ocopy fails due to an incompatible fill version - - When using the HDF5 1.10.x H5Ocopy() API call to copy a version 1.8 - dataset to a file created with both high and low library bounds set to - H5F_LIBVER_V18, the H5Ocopy() call will fail with the error stack indicating - that the fill value version is out of bounds. - - This was fixed by changing the fill value message version to H5O_FILL_VERSION_3 - (from H5O_FILL_VERSION_2) for H5F_LIBVER_V18. - - (VC - 2019/6/14, HDFFV-10800) - - - Some oversights in the index iterating area of the library caused - a callback function to continue iterating even though it's supposed - to stop. - - Added the returned value check to the for loop's conditions in - H5EA_iterate(), H5FA_iterate(), and H5D__none_idx_iterate(). The - iteration now stops when it should. - - (BMR - 2019/06/11, HDFFV-10661) - - - Fixed a bug that would cause an error or cause fill values to be - incorrectly read from a chunked dataset using the "single chunk" index if - the data was held in cache and there was no data on disk. - - (NAF - 2019/03/06) - - - Fixed a bug that could cause an error or cause fill values to be - incorrectly read from a dataset that was written to using H5Dwrite_chunk - if the dataset was not closed after writing. - - (NAF - 2019/03/06, HDFFV-10716) - - - Fixed memory leak in scale offset filter - - In a special case where the MinBits is the same as the number of bits in - the datatype's precision, the filter's data buffer was not freed, causing - the memory usage to grow. In general the buffer was freed correctly. The - Minbits are the minimal number of bits to store the data values. Please - see the reference manual for H5Pset_scaleoffset for the detail. - - (RL - 2019/3/4, HDFFV-10705) - - - Fix hangs with collective metadata reads during chunked dataset I/O + - Added spectrum-mpi with clang, gcc and xl compilers on Linux 3.10.0 + - Added OpenMPI 3.1 and 4.0 with clang, gcc and Intel compilers on Linux 3.10.0 + - Added cray-mpich/PrgEnv with gcc and Intel compilers on Linux 4.14.180 + - Added spectrum mpi with clang, gcc and xl compilers on Linux 4.14.0 + - In the parallel library, it was discovered that when a particular - sequence of operations following a pattern of: - - "write to chunked dataset" -> "flush file" -> "read from dataset" - - occurred with collective metadata reads enabled, hangs could be - observed due to certain MPI ranks not participating in the collective - metadata reads. - - To fix the issue, collective metadata reads are now disabled during - chunked dataset raw data I/O. - - (JTH - 2019/02/11, HDFFV-10563, HDFFV-10688) - - - Performance issue when closing an object - - The slow down is due to the search of the "tag_list" to find - out the "corked" status of an object and "uncork" it if so. - - Improve porformance by skipping the search of the "tag_list" - if there are no "corked" objects when closing an object. - - (VC - 2019/2/6) - - - Fixed a potential invalid memory access and failure that could occur when - decoding an unknown object header message (from a future version of the - library). - - (NAF - 2019/01/07) - - - Deleting attributes in dense storage - - The library aborts with "infinite loop closing library" after - attributes in dense storage are created and then deleted. - - When deleting the attribute nodes from the name index v2 B-tree, - if an attribute is found in the intermediate B-tree nodes, - which may be merged/redistributed in the process, we need to - free the dynamically allocated spaces for the intermediate - decoded attribute. - - (VC - 2018/12/26, HDFFV-10659) - - - Allow H5detect and H5make_libsettings to take a file as an argument. - - 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. - - (ADB - 2018/09/05, HDFFV-9059) - - - 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. - - 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). - - (JTH - 2018/08/25, HDFFV-10501) - - - fcntl(2)-based file locking incorrectly passed the lock argument struct - instead of a pointer to the struct, causing errors on systems where - flock(2) is not available. - - File locking is used when files are opened to enforce SWMR semantics. A - lock operation takes place on all file opens unless the - HDF5_USE_FILE_LOCKING environment variable is set to the string "FALSE". - flock(2) is preferentially used, with fcntl(2) locks as a backup if - flock(2) is unavailable on a system (if neither is available, the lock - operation fails). On these systems, the file lock will often fail, which - causes HDF5 to not open the file and report an error. - - This bug only affects POSIX systems. Win32 builds on Windows use a no-op - locking call which always succeeds. Systems which exhibit this bug will - have H5_HAVE_FCNTL defined but not H5_HAVE_FLOCK in the configure output. - - This bug affects HDF5 1.10.0 through 1.10.5. - - fcntl(2)-based file locking now correctly passes the struct pointer. - - (DER - 2019/08/27, HDFFV-10892) - - - 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. - - (ADB - 2018/08/31, HDFFV-10568) - - Java iterator callbacks - - Change global callback object to a small stack structure in order - to fix a runtime crash. This crash was discovered when iterating - through a file with nested group members. The global variable - visit_callback is overwritten when recursion starts. When recursion - completes, visit_callback will be pointing to the wrong callback method. - - (ADB - 2018/08/15, HDFFV-10536) - - - Java HDFLibraryException class - - Change parent class from Exception to RuntimeException. - - (ADB - 2018/07/30, HDFFV-10534) - - - JNI Read and Write - - Refactored variable-length functions, H5DreadVL and H5AreadVL, - to correct dataset and attribute reads. New write functions, - H5DwriteVL and H5AwriteVL, are under construction. - - (ADB - 2018/06/02, HDFFV-10519) - - Configuration - ------------- - - Correct option for default API version - - CMake options for default API version are not mutually exclusive. - Change the multiple BOOL options to a single STRING option with the - strings; v16, v18, v110, v112. - - (ADB - 2019/08/12, HDFFV-10879) - - Performance - ------------- - - - - Fortran - -------- - - Added symbolic links libhdf5_hl_fortran.so to libhdf5hl_fortran.so and - libhdf5_hl_fortran.a to libhdf5hl_fortran.a in hdf5/lib directory for - autotools installs. These were added to match the name of the files - installed by cmake and the general pattern of hl lib files. We will - change the names of the installed lib files to the matching name in - the next major release. - - (LRK - 2019/01/04, HDFFV-10596) - - - Made Fortran specific subroutines PRIVATE in generic procedures. - - Effected generic procedures were functions in H5A, H5D, H5P, H5R and H5T. - - (MSB, 2018/12/04, HDFFV-10511) - - - Fixed issue with Fortran not returning h5o_info_t field values - meta_size%attr%index_size and meta_size%attr%heap_size. - - (MSB, 2018/1/8, HDFFV-10443) - - - Tools - ----- - - - - High-Level APIs: - ------ - - - - Fortran High-Level APIs: - ------ - - - - Documentation - ------------- - - - - F90 APIs - -------- - - - - C++ APIs - -------- - - - - Testing - ------- - - Fixed a test failure in testpar/t_dset.c caused by - the test trying to use the parallel filters feature - on MPI-2 implementations. - - (JTH, 2019/2/7) - -Bug Fixes since HDF5-1.10.2 release +Major Bug Fixes since HDF5-1.10.0 release ================================== - Library - ------- - - Java HDF5LibraryException class - - The error minor and major values would be lost after the - constructor executed. - - Created two local class variables to hold the values obtained during - execution of the constructor. Refactored the class functions to retrieve - the class values rather then calling the native functions. - The native functions were renamed and called only during execution - of the constructor. - Added error checking to calling class constructors in JNI classes. - - (ADB - 2018/08/06, HDFFV-10544) - - - Added checks of the defined MPI_VERSION to guard against usage of - MPI-3 functions in the Parallel Compression and "big Parallel I/O" - features when HDF5 is built with MPI-2. Previously, the configure - step would pass but the build itself would fail when it could not - locate the MPI-3 functions used. - - As a result of these new checks, HDF5 can again be built with MPI-2, - but the Parallel Compression feature will be disabled as it relies - on the MPI-3 functions used. - - (JTH - 2018/08/02, HDFFV-10512) - - - User's patches: CVEs - - The following patches have been applied: - - CVE-2018-11202 - NULL pointer dereference was discovered in - H5S_hyper_make_spans in H5Shyper.c (HDFFV-10476) - https://security-tracker.debian.org/tracker/CVE-2018-11202 - https://cve.mitre.org/cgi-bin/cvename.cgi?name=3DCVE-2018-11202 + - For major bug fixes please see HISTORY-1_10_0-1_12_0.txt file - 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) - - - Inappropriate linking with deprecated MPI C++ libraries - - HDF5 does not define *_SKIP_MPICXX in the public headers, so applications - can inadvertently wind up linking to the deprecated MPI C++ wrappers. - - MPICH_SKIP_MPICXX and OMPI_SKIP_MPICXX have both been defined in H5public.h - so this should no longer be an issue. HDF5 makes no use of the deprecated - MPI C++ wrappers. - - (DER - 2019/09/17, HDFFV-10893) - - - - 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) - - - Moved the location of gcc attribute. - - The gcc attribute(no_sanitize), named as the macro HDF_NO_UBSAN, - was located after the function name. Builds with GCC 7 did not - indicate any problem, but GCC 8 issued errors. Moved the - attribute before the function name, as required. - - (ADB - 2018/05/22, HDFFV-10473) - - - Reworked java test suite into individual JUnit tests. - - Testing the whole suite of java unit tests in a single JUnit run - made it difficult to determine actual failures when tests would fail. - Running each file set of tests individually, allows individual failures - to be diagnosed easier. A side benefit is that tests for optional components - of the library can be disabled if not configured. - - (ADB - 2018/05/16, HDFFV-9739) - - - Converted CMake global commands ADD_DEFINITIONS and INCLUDE_DIRECTORIES - to use target_* type commands. This change modernizes the CMake usage - in the HDF5 library. - - In addition, there is the intention to convert to generator expressions, - where possible. The exception is Fortran FLAGS on Windows Visual Studio. - The HDF macros TARGET_C_PROPERTIES and TARGET_FORTRAN_PROPERTIES have - been removed with this change in usage. - - The additional language (C++ and Fortran) checks have also been localized - to only be checked when that language is enabled. - - (ADB - 2018/05/08) - - Performance - ------------- - - - - Fortran - -------- - - - - Tools - ----- - - - - High-Level APIs: - ------ - - - - Fortran High-Level APIs: - ------ - - - - Documentation - ------------- - - - - F90 APIs - -------- - - - - C++ APIs - -------- - - Adding default arguments to existing functions - - Added the following items: - + Two more property list arguments are added to H5Location::createDataSet: - const DSetAccPropList& dapl = DSetAccPropList::DEFAULT - const LinkCreatPropList& lcpl = LinkCreatPropList::DEFAULT - - + One more property list argument is added to H5Location::openDataSet: - const DSetAccPropList& dapl = DSetAccPropList::DEFAULT - - (BMR - 2018/07/21, PR# 1146) - - - Improvement C++ documentation - - Replaced the table in main page of the C++ documentation from mht to htm format - for portability. - - (BMR - 2018/07/17, PR# 1141) - - Testing - ------- - - The dt_arith test failed on IBM Power8 and Power9 machines when testing - conversions from or to long double types, especially when special values - such as infinity or NAN were involved. In some cases the results differed - by extremely small amounts from those on other machines, while some other - tests resulted in segmentation faults. These conversion tests with long - double types have been disabled for ppc64 machines until the problems are - better understood and can be properly addressed. - - (SRL - 2019/01/07, TRILAB-98) Supported Platforms =================== @@ -981,11 +152,35 @@ Supported Platforms 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, + Version 4.9.3, 5.2.0, 7.1.0 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 + MPICH 3.1.4 + + Linux-3.10.0- spectrum-mpi/rolling-release with cmake>3.10 and + 862.14.4.1chaos.ch6.ppc64le clang/3.9,8.0 + #1 SMP ppc64le GNU/Linux gcc/7.3 + (ray) xl/2016,2019 + + Linux 3.10.0- openmpi/3.1,4.0 with cmake>3.10 and + 957.12.2.1chaos.ch6.x86_64 clang 5.0 + #1 SMP x86_64 GNU/Linux gcc/7.3,8.2 + (serrano) intel/17.0,18.0/19.0 + + Linux 3.10.0- openmpi/3.1/4.0 with cmake>3.10 and + 1062.1.1.1chaos.ch6.x86_64 clang/3.9,5.0,8.0 + #1 SMP x86_64 GNU/Linux gcc/7.3,8.1,8.2 + (chama,quartz) intel/16.0,18.0,19.0 + + Linux 4.4.180-94.100-default cray-mpich/7.7.6 with PrgEnv-*/6.0.5, cmake>3.10 and + #1 SMP x86_64 GNU/Linux gcc/7.2.0,8.2.0 + (mutrino) intel/17.0,18.0 + + Linux 4.14.0- spectrum-mpi/rolling-release with cmake>3.10 and + 49.18.1.bl6.ppc64le clang/6.0,8.0 + #1 SMP ppc64le GNU/Linux gcc/7.3 + (lassen) xl/2019 SunOS 5.11 32- and 64-bit Sun C 5.12 SunOS_sparc (emu) Sun Fortran 95 8.6 SunOS_sparc @@ -993,8 +188,7 @@ Supported Platforms Windows 7 Visual Studio 2015 w/ Intel Fortran 16 (cmake) - Windows 7 x64 Visual Studio 2013 - Visual Studio 2015 w/ Intel Fortran 16 (cmake) + Windows 7 x64 Visual Studio 2015 w/ Intel Fortran 16 (cmake) Visual Studio 2015 w/ Intel C, Fortran 2018 (cmake) Visual Studio 2015 w/ MSMPI 8 (cmake) @@ -1011,9 +205,13 @@ Supported Platforms 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 + Mac OS High Sierra 10.13.6 Apple LLVM version 10.0.0 (clang/clang++-1000.10.44.4) + 64-bit gfortran GNU Fortran (GCC) 6.3.0 + (bear) Intel icc/icpc/ifort version 19.0.4 + + Mac OS Mojave 10.14.6 Apple LLVM version 10.0.1 (clang/clang++-1001.0.46.4) + 64-bit gfortran GNU Fortran (GCC) 6.3.0 + (bobcat) Intel icc/icpc/ifort version 19.0.4 Tested Configuration Features Summary @@ -1100,33 +298,11 @@ The following platforms are not supported but have been tested for this release. 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) + PGI C (pgcc), C++ (pgc++), Fortran (pgf90) + compilers: + Version 18.4, 19.4 + MPICH 3.3 + OpenMPI 2.1.5, 3.1.3, 4.0.0 Known Problems diff --git a/src/H5public.h b/src/H5public.h index ce108f9..c151ead 100644 --- a/src/H5public.h +++ b/src/H5public.h @@ -97,9 +97,9 @@ extern "C" { #define H5_VERS_MAJOR 1 /* For major interface/format changes */ #define H5_VERS_MINOR 12 /* For minor interface/format changes */ #define H5_VERS_RELEASE 0 /* For tweaks, bug-fixes, or development */ -#define H5_VERS_SUBRELEASE "" /* For pre-releases like snap0 */ +#define H5_VERS_SUBRELEASE "alpha0" /* For pre-releases like snap0 */ /* Empty string for real releases. */ -#define H5_VERS_INFO "HDF5 library version: 1.12.0" /* Full version string */ +#define H5_VERS_INFO "HDF5 library version: 1.12.0-alpha0" /* Full version string */ #define H5check() H5check_version(H5_VERS_MAJOR,H5_VERS_MINOR, \ H5_VERS_RELEASE) |