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| author | Dana Robinson <43805+derobins@users.noreply.github.com> | 2023-02-13 14:03:11 (GMT) |
|---|---|---|
| committer | GitHub <noreply@github.com> | 2023-02-13 14:03:11 (GMT) |
| commit | 768575225ecfe81e8965c47369576c9befb9d4c1 (patch) | |
| tree | 6bf82693dc0b4f8b8d72f94f6afea1fcc378f444 | |
| parent | b5ddec4554731191f3a7f04c57c87dae61762e74 (diff) | |
| download | hdf5-768575225ecfe81e8965c47369576c9befb9d4c1.zip hdf5-768575225ecfe81e8965c47369576c9befb9d4c1.tar.gz hdf5-768575225ecfe81e8965c47369576c9befb9d4c1.tar.bz2 | |
Update release_docs HISTORY scheme (#2443)
We will no longer maintain HISTORY files for other maintenance branches,
so those have been removed. Adds a README.md explaining the purpose
and procedures of HDF5 HISTORY. Also adds a newsletter template and
updates the RELEASE.txt note part of CONTRIBUTING.md.
Also cleans out RELEASE.txt post-HDF5-1.14.0
| -rw-r--r-- | CONTRIBUTING.md | 31 | ||||
| -rw-r--r-- | doc/release_txt_notes.md | 107 | ||||
| -rw-r--r-- | release_docs/HISTORY-1_0-1_8_0.txt (renamed from release_docs/HISTORY-1_0-1_8_0_rc3.txt) | 0 | ||||
| -rw-r--r-- | release_docs/HISTORY-1_10.txt | 6562 | ||||
| -rw-r--r-- | release_docs/HISTORY-1_12.txt | 628 | ||||
| -rw-r--r-- | release_docs/HISTORY-1_14.txt (renamed from release_docs/HISTORY-1_13.txt) | 2401 | ||||
| -rw-r--r-- | release_docs/HISTORY-1_8.txt | 14439 | ||||
| -rw-r--r-- | release_docs/NEWSLETTER.txt | 25 | ||||
| -rw-r--r-- | release_docs/README.md | 102 | ||||
| -rw-r--r-- | release_docs/RELEASE.txt | 272 |
10 files changed, 1007 insertions, 23560 deletions
diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md index 62b00ea..dc1a200 100644 --- a/CONTRIBUTING.md +++ b/CONTRIBUTING.md @@ -86,36 +86,7 @@ application developers, library developers, and system administrators. # Release Note <A NAME="releasenote"></A> -* **Entry Syntax** -The release note entry syntax is shown below. - -``` - - Title/Problem - - Problem/Solution - - Signature -``` - -* **Entry Elements** - The elements of the entry - title, problem, solution, and signature - are described in more detail in the table -below. Descriptions of the problem and the solution should be clear without any ambiguities and should be short without losing clarity or specifics. - - * **Title** - The title or tag should identify one or more categories that will help readers decide if the entry is something they need to study. Can be combined with the `Problem` element - * **Problem** - Describe the problem and how users might see the problem in a paragraph. -You might also consider the following as you describe the problem: - * Under what specific conditions does this issue arise? - * Under what specific conditions are we sure this issue will not arise? - * For a performance issue, instead of saying something is a performance issue, describe what the performance impact of issue is? - * **Solution** - Describe the solution in another paragraph. -You might also consider the following as you describe the solution: - * What was done to resolve the issue? - * What is the functional impact? - * Is there a workaround – a way for users design their software so as not to encounter the issue? If so, what is the workaround? - * For a performance fix, how has the performance improved? Links to published documentation would be good. - * **Signature** - Each entry must be signed with the initials of the author, the date in YYYY/MM/DD format, and the JIRA ticket number. The -following is an example entry written by developer Xavier Zolo on April 16, 2014 about JIRA ticket HDFFV-5555: (XYZ - 2014/04/16, HDFFV-5555). The -signature is enclosed in parentheses. JIRA or Github numbers should not be used in the description of the problem or the solution. They are like -abbreviations that customers and external users will not be able to interpret. +The use and format of release notes is described in `doc/release_txt_notes.md` in this source code tree # Checklist <A NAME="checklist"></A> diff --git a/doc/release_txt_notes.md b/doc/release_txt_notes.md new file mode 100644 index 0000000..316ba3f --- /dev/null +++ b/doc/release_txt_notes.md @@ -0,0 +1,107 @@ +# Writing Notes in a RELEASE.txt File + +## Introduction + +We have been challenged to write more helpful entries in our RELEASE.txt file +for new features, improvements, and bug fixes. To help users determine the +effects of our software changes on their applications, we have developed a +template that can be used to write release notes. The template is described on +the rest of this page. + +Some of our users face scrutiny from regulatory agencies for their use of +software they did not develop (aka SOUP). When they use our software, they have +to be aware of every change we make. For every change we make, they need to +investigate the effect the change will have on their software. If our change +affects their application, they may have to have their software retested or +re-certified. + +[SOUP](https://en.wikipedia.org/wiki/Software_of_unknown_pedigree) stands for Software Of Unknown/Uncertain Pedigree/Provenance + + +## When to write a RELEASE.txt note + +Generally, a release note must be written for every change that is made to the +code for which users might see a change in the way the software works. In other +words, if a user might see a difference in the way the software works, a note +should be written. By code we mean the text that will be compiled into one of +the company's software products. The code includes configuration changes and +changes to tools users might work with to configure and build our software. + +A release note does not need to be written for changes to the code that users +will not see. + +These things DO require a release note: + +* New features +* Changes in functionality/semantics +* Anything that changes functionality or symbols in a public header file +* Command-line tool option changes +* Adding or dropping support for compilers or operating systems +* Build system (Autotools, CMake) changes that users will encounter + +These things do NOT require a release note: + +* Internal comments +* Refactoring that does not change behavior or public headers (`H5XYpublic.h`) +* Minor build system changes (adding warning flags) + +Notes should also be added for known problems. Known problems are issues that +we know about and have not yet been able to fix. + +## RELEASE.txt entry format + +``` + - Title + + Problem + + Solution + + Signature +``` + +## RELEASE.txt entry elements + +### Title + +The title or tag should identify one or more categories that will help readers +decide if the entry is something they need to study. Categories include problem +areas, tool names, and code file names. Two examples are "Memory Leak" and +"h5repack". A code file such as H5R.c or H5Z.c can be used as the title if the +problem is located in the code file. If both a title and one or more tags are +used, separate each with a period. For example, "Changed Autotools Build Behavior. Fortran." +adds the Fortran tag to the title Changed Autotools Build Behavior. Use +standard capitalization rules. + +### Problem + +Describe the problem and how users might see the problem in a paragraph. + +You might also consider the following as you describe the problem: + +* Under what specific conditions does this issue arise? +* Under what specific conditions are we sure this issue will not arise? +* For a performance issue, instead of saying something is a performance issue, describe what the performance impact of issue is? + +### Solution + +Describe the solution in another paragraph. + +You might also consider the following as you describe the solution: + +* What was done to resolve the issue? +* What is the functional impact? +* Is there a workaround – a way for users design their software so as not to encounter the issue? If so, what is the workaround? +* For a performance fix, how has the performance improved? Links to published documentation would be good. + +### Signature + +Each entry must be signed with the initials of the author, the date in +YYYY/MM/DD format, and the JIRA ticket number. The signature is enclosed in +parentheses. + +Example: + +``` + (ABC - 2023/02/28, JIRA-12345, GitHub #1234) +``` diff --git a/release_docs/HISTORY-1_0-1_8_0_rc3.txt b/release_docs/HISTORY-1_0-1_8_0.txt index 3669f4d..3669f4d 100644 --- a/release_docs/HISTORY-1_0-1_8_0_rc3.txt +++ b/release_docs/HISTORY-1_0-1_8_0.txt diff --git a/release_docs/HISTORY-1_10.txt b/release_docs/HISTORY-1_10.txt deleted file mode 100644 index 1fc3c60..0000000 --- a/release_docs/HISTORY-1_10.txt +++ /dev/null @@ -1,6562 +0,0 @@ -HDF5 History -============ - -This file contains development history of the HDF5 1.10 branch - -09. Release Information for hdf5-1.10.7 -08. Release Information for hdf5-1.10.6 -07. Release Information for hdf5-1.10.5 -06. Release Information for hdf5-1.10.4 -05. Release Information for hdf5-1.10.3 -04. Release Information for hdf5-1.10.2 -03. Release Information for hdf5-1.10.1 -02. Release Information for hdf5-1.10.0-patch1 -01. Release Information for hdf5-1.10.0 - -[Search on the string '%%%%' for section breaks of each release.] - -%%%%1.10.7%%%% - -HDF5 version 1.10.7 released on 2020-09-11 -================================================================================ - - -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/ - - HDF5 binaries provided are fully tested with ZLIB and the free - Open Source SZIP successor Libaec (with BSD license). - The official ZLIB and SZIP/Libaec pages are at: - - ZLIB: http://www.zlib.net/ - http://www.zlib.net/zlib_license.html - SZIP/Libaec: https://gitlab.dkrz.de/k202009/libaec - https://gitlab.dkrz.de/k202009/libaec/-/blob/master/Copyright.txt - -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 HDF5-1.10.6 -- Supported Platforms -- Tested Configuration Features Summary -- More Tested Platforms -- Known Problems -- CMake vs. Autotools installations - - -New Features -============ - - Configuration: - ------------- - - Disable memory sanity checks in the Autotools in release branches - - The library can be configured to use internal memory sanity checking, - which replaces C API calls like malloc(3) and free(3) with our own calls - which add things like heap canaries. These canaries can cause problems - when external filter plugins reallocate canary-marked buffers. - - For this reason, the default will be to not use the memory allocation - sanity check feature in release branches (e.g., hdf5_1_10_7). - Debug builds in development branches (e.g., develop, hdf5_1_10) will - still use them by default. - - This change only affects Autotools debug builds. Non-debug autotools - builds and all CMake builds do not enable this feature by default. - - (DER - 2020/08/19) - - - Add file locking configure and CMake options - - HDF5 1.10.0 introduced a file locking scheme, primarily to help - enforce SWMR setup. Formerly, the only user-level control of the scheme - was via the HDF5_USE_FILE_LOCKING environment variable. - - This change introduces configure-time options that control whether - or not file locking will be used and whether or not the library - ignores errors when locking has been disabled on the file system - (useful on some HPC Lustre installations). - - In both the Autotools and CMake, the settings have the effect of changing - the default property list settings (see the H5Pset/get_file_locking() - entry, below). - - The yes/no/best-effort file locking configure setting has also been - added to the libhdf5.settings file. - - Autotools: - - An --enable-file-locking=(yes|no|best-effort) option has been added. - - yes: Use file locking. - no: Do not use file locking. - best-effort: Use file locking and ignore "disabled" errors. - - CMake: - - Two self-explanatory options have been added: - - HDF5_USE_FILE_LOCKING - HDF5_IGNORE_DISABLED_FILE_LOCKS - - Setting both of these to ON is the equivalent to the Autotools' - best-effort setting. - - NOTE: - The precedence order of the various file locking control mechanisms is: - - 1) HDF5_USE_FILE_LOCKING environment variable (highest) - - 2) H5Pset_file_locking() - - 3) configure/CMake options (which set the property list defaults) - - 4) library defaults (currently best-effort) - - (DER - 2020/07/30, HDFFV-11092) - - - CMake option to link the generated Fortran MOD files into the include - directory. - - The Fortran generation of MOD files by a Fortran compile can produce - different binary files between SHARED and STATIC compiles with different - compilers and/or different platforms. Note that it has been found that - different versions of Fortran compilers will produce incompatible MOD - files. Currently, CMake will locate these MOD files in subfolders of - the include directory and add that path to the Fortran library target - in the CMake config file, which can be used by the CMake find library - process. For other build systems using the binary from a CMake install, - a new CMake configuration can be used to copy the pre-chosen version - of the Fortran MOD files into the install include directory. - - The default will depend on the configuration of - BUILD_STATIC_LIBS and BUILD_SHARED_LIBS: - YES YES Default to SHARED - YES NO Default to STATIC - NO YES Default to SHARED - NO NO Default to SHARED - The defaults can be overridden by setting the config option - HDF5_INSTALL_MOD_FORTRAN to one of NO, SHARED, or STATIC - - (ADB - 2020/07/09, HDFFV-11116) - - - CMake option to use AEC (open source SZip) library instead of SZip - - The open source AEC library is a replacement library for SZip. In - order to use it for hdf5, the libaec CMake source was changed to add - "-fPIC" and exclude test files. A new option USE_LIBAEC is required - to compensate for the different files produced by AEC build. - - Autotools does not build the compression libraries within hdf5 builds, - but will use an installed libaec when configured as before with the - option --with-libsz=<path to libaec directory>. - - (ADB - 2020/04/22, OESS-65) - - - CMake ConfigureChecks.cmake file now uses CHECK_STRUCT_HAS_MEMBER - - Some handcrafted tests in HDFTests.c have been removed and the CMake - CHECK_STRUCT_HAS_MEMBER module has been used. - - (ADB - 2020/03/24, TRILAB-24) - - - Both build systems use same set of warnings flags - - GNU C, C++ and gfortran warnings flags were moved to files in a config - sub-folder named gnu-warnings. Flags that only are available for a specific - version of the compiler are in files named with that version. - Clang C warnings flags were moved to files in a config sub-folder - named clang-warnings. - Intel C, Fortran warnings flags were moved to files in a config sub-folder - named intel-warnings. - - There are flags in named "error-xxx" files with warnings that may - be promoted to errors. Some source files may still need fixes. - - There are also pairs of files named "developer-xxx" and "no-developer-xxx" - that are chosen by the CMake option:HDF5_ENABLE_DEV_WARNINGS or the - configure option:--enable-developer-warnings. - - In addition, CMake no longer applies these warnings for examples. - - (ADB - 2020/03/24, TRILAB-192) - - - Update CMake minimum version to 3.12 - - Updated CMake minimum version to 3.12 and added version checks - for Windows features. - - (ADB - 2020/02/05, TRILABS-142) - - - Fixed CMake include properties for Fortran libraries - - Corrected the library properties for Fortran to use the - correct path for the Fortran module files. - - (ADB - 2020/02/04, HDFFV-11012) - - - Added common warnings files for gnu and intel - - Added warnings files to use one common set of flags - during configure for both autotools and CMake build - systems. The initial implementation only affects a - general set of flags for gnu and intel compilers. - - (ADB - 2020/01/17) - - - Added new options to CMake for control of testing - - Added CMake options (default ON); - HDF5_TEST_SERIAL AND/OR HDF5_TEST_PARALLEL - combined with: - HDF5_TEST_TOOLS - HDF5_TEST_EXAMPLES - HDF5_TEST_SWMR - HDF5_TEST_FORTRAN - HDF5_TEST_CPP - HDF5_TEST_JAVA - - (ADB - 2020/01/15, HDFFV-11001) - - - Added Clang sanitizers to CMake for analyzer support if compiler is clang. - - Added CMake code and files to execute the Clang sanitizers if - HDF5_ENABLE_SANITIZERS is enabled and the USE_SANITIZER option - is set to one of the following: - Address - Memory - MemoryWithOrigins - Undefined - Thread - Leak - 'Address;Undefined' - - (ADB - 2019/12/12, TRILAB-135) - - - Library: - -------- - - Add metadata cache optimization to reduce skip list usage - - On file flush or close, the metadata cache attempts to write out - all dirty entries in increasing address order. To do this, it needs - an address sorted list of metadata entries. Further, since flushing - one metadata cache entry can dirty another, this list must support - efficient insertion and deletion. - - The metadata cache uses a skip list of all dirty entries for this - purpose. Before this release, this skip list was maintained at all - times. However, since profiling indicates that this imposes a - significant cost, we now construct and maintain the skip list only - when needed. Specifically, we enable the skip list and load it with - a list of all dirty entries in the metadata cache just before a flush, - and disable it after the flush. - - (JRM - 2020/08/17, HDFFV-11034) - - - Add BEST_EFFORT value to HDF5_USE_FILE_LOCKING environment variable - - This change adds a BEST_EFFORT to the TRUE/FALSE, 1/0 settings that - were previously accepted. This option turns on file locking but - ignores locking errors when the library detects that file locking - has been disabled on a file system (useful on some HPC Lustre - installations). - - The capitalization of BEST_EFFORT is mandatory. - - See the configure option discussion for HDFFV-11092 (above) for more - information on the file locking feature and how it's controlled. - - (DER - 2020/07/30, HDFFV-11092) - - - - Add H5Pset/get_file_locking() API calls - - This change adds new API calls which can be used to set or get the - file locking parameters. The single API call sets both the "use file - locking" flag and the "ignore disabled file locking" flag. - - When opening a file multiple times without closing, the file MUST be - opened with the same file locking settings. Opening a file with different - file locking settings will fail (this is similar to the behavior of - H5Pset_fclose_degree()). - - See the configure option discussion for HDFFV-11092 (above) for more - information on the file locking feature and how it's controlled. - - (DER - 2020/07/30, HDFFV-11092) - - - Add Mirror VFD - - Use TCP/IP sockets to perform write-only (W/O) file I/O on a remote - machine. Must be used in conjunction with the Splitter VFD. - - (JOS - 2020/03/13, TBD) - - - Add Splitter VFD - - Maintain separate R/W and W/O channels for "concurrent" file writes - to two files using a single HDF5 file handle. - - (JOS - 2020/03/13, TBD) - - - Fixed an assertion failure in the parallel library when collectively - filling chunks. As it is required that chunks be written in - monotonically non-decreasing order of offset in the file, this assertion - was being triggered when the list of chunk file space allocations being - passed to the collective chunk filling routine was not sorted according - to this particular requirement. - - The addition of a sort of the out of order chunks trades a bit of - performance for the elimination of this assertion and of any complaints - from MPI implementations about the file offsets used being out of order. - - (JTH - 2019/10/07) - - Fortran Library: - ---------------- - - Add wrappers for H5Pset/get_file_locking() API calls - - h5pget_file_locking_f() - h5pset_file_locking_f() - - See the configure option discussion for HDFFV-11092 (above) for more - information on the file locking feature and how it's controlled. - - (DER - 2020/07/30, HDFFV-11092) - - - Added new Fortran parameters: - - H5F_LIBVER_ERROR_F - H5F_LIBVER_NBOUNDS_F - H5F_LIBVER_V18_F - H5F_LIBVER_V110_F - - - Added new Fortran API: h5pget_libver_bounds_f - - (MSB - 2020/02/11, HDFFV-11018) - - C++ Library: - ------------ - - Add wrappers for H5Pset/get_file_locking() API calls - - FileAccPropList::setFileLocking() - FileAccPropList::getFileLocking() - - See the configure option discussion for HDFFV-11092 (above) for more - information on the file locking feature and how it's controlled. - - (DER - 2020/07/30, HDFFV-11092) - - Java Library: - ---------------- - - Add wrappers for H5Pset/get_file_locking() API calls - - H5Pset_file_locking() - H5Pget_use_file_locking() - H5Pget_ignore_disabled_file_locking() - - Unlike the C++ and Fortran wrappers, there are separate getters for the - two file locking settings, each of which returns a boolean value. - - See the configure option discussion for HDFFV-11092 (above) for more - information on the file locking feature and how it's controlled. - - (DER - 2020/07/30, HDFFV-11092) - - Tools: - ------ - - h5repack added options to control how external links are handled. - - Currently h5repack preserves external links and cannot copy and merge - data from the external files. Two options, merge and prune, were added to - control how to merge data from an external link into the resulting file. - --merge Follow external soft link recursively and merge data. - --prune Do not follow external soft links and remove link. - --merge --prune Follow external link, merge data and remove dangling link. - - (ADB - 2020/08/05, HDFFV-9984) - - High-Level APIs: - --------------- - - None - - C Packet Table API - ------------------ - - None - - Internal header file - -------------------- - - None - - Documentation - ------------- - - None - - -Support for new platforms, languages and compilers. -======================================= - - None - - -Bug Fixes since HDF5-1.10.6 release -================================== - - Library - ------- - - Fix bug and simplify collective metadata write operation when some ranks - have no entries to contribute. This fixes parallel regression test - failures with IBM SpectrumScale MPI on the Summit system at ORNL. - - (QAK - 2020/09/02) - - - Avoid setting up complex MPI types with 0-length vectors, which some - MPI implementations don't handle well. (In particular, IBM - SpectrumScale MPI on the Summit system at ORNL) - - (QAK - 2020/08/21) - - - Fixed use-of-uninitialized-value error - - Appropriate initialization of local structs was added to remove the - use-of-uninitialized-value errors reported by MemorySanitizer. - - (BMR - 2020/8/13, HDFFV-11101) - - - Creation of dataset with optional filter - - When the combination of type, space, etc doesn't work for filter - and the filter is optional, it was supposed to be skipped but it was - not skipped and the creation failed. - - A fix is applied to allow the creation of a dataset in such - situation, as specified in the user documentation. - - (BMR - 2020/8/13, HDFFV-10933) - - - Explicitly declared dlopen to use RTLD_LOCAL - - dlopen documentation states that if neither RTLD_GLOBAL nor - RTLD_LOCAL are specified, then the default behavior is unspecified. - The default on linux is usually RTLD_LOCAL while macos will default - to RTLD_GLOBAL. - - (ADB - 2020/08/12, HDFFV-11127) - - - Fixed issues CVE-2018-13870 and CVE-2018-13869 - - When a buffer overflow occurred because a name length was corrupted - and became very large, h5dump crashed on memory access violation. - - A check for reading past the end of the buffer was added to multiple - locations to prevent the crashes and h5dump now simply fails with an - error message when this error condition occurs. - - (BMR - 2020/7/31, HDFFV-11120 and HDFFV-11121) - - - H5Sset_extent_none() sets the dataspace class to H5S_NO_CLASS which - causes asserts/errors when passed to other dataspace API calls. - - H5S_NO_CLASS is an internal class value that should not have been - exposed via a public API call. - - In debug builds of the library, this can cause asserts to trip. In - non-debug builds, it will produce normal library errors. - - The new library behavior is for H5Sset_extent_none() to convert - the dataspace into one of type H5S_NULL, which is better handled - by the library and easier for developers to reason about. - - (DER - 2020/07/27, HDFFV-11027) - - - Fixed the segmentation fault when reading attributes with multiple threads - - It was reported that the reading of attributes with variable length string - datatype will crash with segmentation fault particularly when the number - of threads is high (>16 threads). The problem was due to the file pointer - that was set in the variable length string datatype for the attribute. - That file pointer was already closed when the attribute was accessed. - - The problem was fixed by setting the file pointer to the current opened - file pointer when the attribute was accessed. Similar patch up was done - before when reading dataset with variable length string datatype. - - (VC - 2020/07/13, HDFFV-11080) - - - Fixed issue CVE-2018-17438 - - A division by zero was discovered in H5D__select_io() of H5Dselect.c. - https://security-tracker.debian.org/tracker/CVE-2018-17438 - - A check was added to protect against division by zero. When such - situation occurs again, the normal HDF5 error handling will be invoked, - instead of segmentation fault. - - (BMR, DER - 2020/07/09, HDFFV-10587) - - - Fixed CVE-2018-17435 - - The tool h52gif produced a segfault when the size of an attribute message - was corrupted and caused a buffer overflow. - - The problem was fixed by verifying the attribute message's size against the - buffer size before accessing the buffer. h52gif was also fixed to display - the failure instead of silently exiting after the segfault was eliminated. - - (BMR - 2020/6/19, HDFFV-10591) - - - Don't allocate an empty (0-dimensioned) chunked dataset's chunk - index, until the dataset's dimensions are increased. - - (QAK - 2020/05/07) - - Configuration - ------------- - - Stopped addition of szip header and include directory path for - incompatible libsz - - szlib.h is the same for both 32-bit and 64-bit szip, and the header file - and its path were added to the HDF5 binary even though the configure - check of a function in libsz later failed and szip compression was not - enabled. The header file and include path are now added only when the - libsz function passes the configure check. - - (LRK - 2020/08/17, HDFFV-10830) - - - Added -fsanitize=address autotools configure option for Clang compiler - - Clang sanitizer options were also added for Clang compilers with CMake. - - (LRK, 2020/08/05, HDFFV-10836) - - - Updated testh5cc.sh.in for functions versioned in HDF5 1.10. - - testh5cc.sh previously tested that the correct version of a function - versioned in HDF5 1.6 or 1.8 was compiled when one of - H5_NO_DEPRECATED_SYMBOLS or H5_USE_16_API_DEFAULT were defined. This - test was extended for additional testing with H5_USE_18_API_DEFAULT. - - (LRK, 2020/06/22, HDFFV-11000) - - - Fixed CMake include properties for Fortran libraries - - Corrected the library properties for Fortran to use the - correct path for the Fortran module files. - - (ADB - 2020/02/04, HDFFV-11012) - - Performance - ------------- - - None - - Java Library: - ---------------- - - None - - Fortran - -------- - - Corrected INTERFACE INTENT(IN) to INTENT(OUT) for buf_size in h5fget_file_image_f. - - (MSB - 2020/2/18, HDFFV-11029) - - - Fixed configure issue when building HDF5 with NAG Fortran 7.0. - - HDF5 now accounts for the addition of half-precision floating-point - in NAG 7.0 with a KIND=16. - - (MSB - 2020/02/28, HDFFV-11033) - - Tools - ----- - - The tools library was updated by standardizing the error stack process. - - General sequence is: - h5tools_setprogname(PROGRAMNAME); - h5tools_setstatus(EXIT_SUCCESS); - h5tools_init(); - ... process the command-line (check for error-stack enable) ... - h5tools_error_report(); - ... (do work) ... - h5diff_exit(ret); - - (ADB - 2020/07/20, HDFFV-11066) - - - h5diff fixed a command line parsing error. - - h5diff would ignore the argument to -d (delta) if it is smaller than DBL_EPSILON. - The macro H5_DBL_ABS_EQUAL was removed and a direct value comparison was used. - - (ADB - 2020/07/20, HDFFV-10897) - - - h5diff added a command line option to ignore attributes. - - h5diff would ignore all objects with a supplied path if the exclude-path argument is used. - Adding the exclude-attribute argument will only eclude attributes, with the supplied path, - from comparison. - - (ADB - 2020/07/20, HDFFV-5935) - - - h5diff added another level to the verbose argument to print filenames. - - Added verbose level 3 that is level 2 plus the filenames. The levels are: - 0 : Identical to '-v' or '--verbose' - 1 : All level 0 information plus one-line attribute status summary - 2 : All level 1 information plus extended attribute status report - 3 : All level 2 information plus file names - - (ADB - 2020/07/20, HDFFV-10005) - - - h5repack was fixed to repack the reference attributes properly. - The code line that checks if the update of reference inside a compound - datatype is misplaced outside the code block loop that carries out the - check. In consequence, the next attribute that is not the reference - type was repacked again as the reference type and caused the failure of - repacking. The fix is to move the corresponding code line to the correct - code block. - - (KY -2020/02/10, HDFFV-11014) - - High-Level APIs: - ------ - - The H5DSis_scale function was updated to return "not a dimension scale" (0) - instead of failing (-1), when CLASS or DIMENSION_SCALE attributes are - not written according to Dimension Scales Specification. - - (EIP - 2020/08/12, HDFFV-10436) - - Fortran High-Level APIs: - ------ - - None - - Documentation - ------------- - - None - - F90 APIs - -------- - - None - - C++ APIs - -------- - - None - - Testing - ------- - - Stopped java/test/junit.sh.in installing libs for testing under ${prefix} - - Lib files needed are now copied to a subdirectory in the java/test - directory, and on Macs the loader path for libhdf5.xxxs.so is changed - in the temporary copy of libhdf5_java.dylib. - - (LRK, 2020/7/2, HDFFV-11063) - - -Supported Platforms -=================== - - Linux 3.10.0-1127.10.1.el7 gcc (GCC) 4.8.5 20150623 (Red Hat 4.8.5-39) - #1 SMP ppc64 GNU/Linux g++ (GCC) 4.8.5 20150623 (Red Hat 4.8.5-39) - (echidna) GNU Fortran (GCC) 4.8.5 20150623 (Red Hat 4.8.5-39) - - Linux 2.6.32-754.31.1.el6 IBM XL C/C++ V13.1 - #1 SMP ppc64 GNU/Linux IBM XL Fortran V15.1 - (ostrich) - - Linux 3.10.0-327.18.2.el7 GNU C (gcc), Fortran (gfortran), C++ (g++) - #1 SMP x86_64 GNU/Linux compilers: - (jelly/kituo/moohan) Version 4.8.5 20150623 (Red Hat 4.8.5-4) - Version 4.9.3, Version 5.3.0, Version 6.3.0, - Version 7.2.0, Version 8.3.0, Version 9.1.0 - Intel(R) C (icc), C++ (icpc), Fortran (icc) - compilers: - Version 17.0.0.098 Build 20160721 - MPICH 3.3 compiled with GCC 7.2.0 - OpenMPI 4.0.0 compiled with GCC 7.2.0 - - SunOS 5.11 11.4.5.12.5.0 Sun C 5.15 SunOS_sparc 2017/05/30 - 32- and 64-bit Studio 12.6 Fortran 95 8.8 SunOS_sparc 2017/05/30 - (hedgehog) Sun C++ 5.15 SunOS_sparc 2017/05/30 - - Windows 7 x64 Visual Studio 2015 w/ Intel C, Fortran 2018 (cmake) - - Windows 10 x64 Visual Studio 2015 w/ Intel Fortran 18 (cmake) - Visual Studio 2017 w/ Intel Fortran 19 (cmake) - Visual Studio 2019 w/ Intel Fortran 19 (cmake) - Visual Studio 2019 w/ MSMPI 10.1 (cmake) - - macOS Mojave 10.14.6 Apple LLVM version 10.0.1 (clang-1001.0.46.4) - 64-bit gfortran GNU Fortran (GCC) 6.3.0 - (swallow) Intel icc/icpc/ifort version 19.0.4.233 20190416 - -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 x64 y y/y y y y y -Windows 10 y y/y n y y y -Windows 10 x64 y y/y n y y y -MacOS Sierra 10.12.6 64-bit n y/y n y y y -MacOS High Sierra 10.13.6 64-bit n y/y n y y y -MacOS Mojave 10.14.6 64-bit 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 2.6.32-754.31.1.el6.ppc64 XL n y/y n y y y - - -Platform Shared Shared Shared Thread- - C libs F90 libs C++ libs safe -Solaris2.11 32-bit y y y y -Solaris2.11 64-bit y y y y -Windows 7 x64 y y y y -Windows 10 y y y y -Windows 10 x64 y y y y -MacOS Sierra 10.12.6 64-bit y n y y -MacOS High Sierra 10.13.6 64-bit y n y y -MacOS Mojave 10.14.6 64-bit y n y y -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 2.6.32-754.31.1.el6.ppc64 XL 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: - (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 19.10-0 - MPICH 3.1.4 compiled with GCC 4.9.3 - - Linux 2.6.32-754.31.1.el6 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) - - 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 2.1.6-GCC-7.2.0-2.29, - 3.1.3-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 3.1.4 compiled with GCC 4.9.3 - #1 SMP x86_64 GNU/Linux - (moohan) - - Linux-3.10.0-1127.0.0.1chaos openmpi-4.0.0 - #1 SMP x86_64 GNU/Linux clang/3.9.0, 8.0.1 - (quartz) gcc/7.3.0, 8.1.0 - intel/16.0.4 - - Linux-4.14.0-115.10.1.1 spectrum-mpi/rolling-release - #1 SMP ppc64le GNU/Linux clang/coral-2018.08.08 - (lassen) gcc/7.3.1 - xl/2019.02.07 - - Linux-4.12.14-150.52-default cray-mpich/7.7.10 - #1 SMP x86_64 GNU/Linux gcc/7.3.0, 8.2.0 - (cori) intel/19.0.3 - - Linux-4.4.180-94.107-default cray-mpich/7.7.6 - # 1SMP x86_64 GNU/Linux gcc/7.2.0, 8.2.0 - (mutrino) intel/17.0.4, 18.0.2, 19.0.4 - - Fedora 32 5.7.15-200.fc32.x86_64 Clang version 10.0.0 (Fedora 10.0.0-2.fc32) - #1 SMP x86_64 GNU/Linux GNU gcc (GCC) 10.2.1 20200723 (Red Hat 10.2.1-1) - GNU Fortran (GCC) 10.2.1 20200723 (Red Hat 10.2.1) - (cmake and autotools) - - Mac OS X El Capitan 10.11.6 Apple clang version 7.3.0 from Xcode 7.3 - 64-bit gfortran GNU Fortran (GCC) 5.2.0 - (osx1011test) Intel icc/icpc/ifort version 16.0.2 - - macOS Sierra 10.12.6 Apple LLVM version 9.0.0 (clang-900.39.2) - 64-bit gfortran GNU Fortran (GCC) 7.4.0 - (kite) Intel icc/icpc/ifort version 17.0.2 - - macOS High Sierra 10.13.6 Apple LLVM version 10.0.0 (clang-1000.10.44.4) - 64-bit gfortran GNU Fortran (GCC) 6.3.0 - (bear) Intel icc/icpc/ifort version 19.0.4.233 20190416 - - SunOS 5.11 11.3 Sun C 5.15 SunOS_sparc - 32- and 64-bit Sun Fortran 95 8.8 SunOS_sparc - (emu) Sun C++ 5.15 SunOS_sparc - - -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. - - Two tests fail attempting collective writes with OpenMPI 3.0.0/GCC-7.2.0-2.29: - testphdf5 (ecdsetw, selnone, cchunk1, cchunk3, cchunk4, and actualio) - t_shapesame (sscontig2) - - CPP ptable test fails on both VS2017 and VS2019 with Intel compiler, JIRA - issue: HDFFV-10628. This test will pass with VS2015 with Intel compiler. - - 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 -the share folder. - -The bin folder contains the tools and the build scripts. Additionally, CMake -places the fortran mod files into separate shared and static subfolders, -while Autotools places one set of mod files into the include folder. Because -CMake produces a tools library, the header files for tools will appear in -the include folder. - -The lib folder contains the library files, and CMake adds the pkgconfig -subfolder with the hdf5*.pc files used by the bin/build scripts created by -the CMake build. CMake separates the C interface code from the fortran code by -creating C-stub libraries for each Fortran library. In addition, only CMake -installs the tools library. The names of the szip libraries are different -between the build systems. - -The share folder will have the most differences because CMake builds include -a number of CMake specific files for support of CMake's find_package and support -for the HDF5 Examples CMake project. - - - -%%%%1.10.6%%%% - -HDF5 version 1.10.6 released on 2019-12-23 -================================================================================ - - -INTRODUCTION - -This document describes the differences between this release and the previous -HDF5 release. It contains information on the platforms tested and known -problems in this release. For more details check the HISTORY*.txt files in the -HDF5 source. - -Note that documentation in the links below will be updated at the time of each -final release. - -Links to HDF5 documentation can be found on The HDF5 web page: - - https://portal.hdfgroup.org/display/HDF5/HDF5 - -The official HDF5 releases can be obtained from: - - https://www.hdfgroup.org/downloads/hdf5/ - -Changes from Release to Release and New Features in the HDF5-1.10.x release series -can be found at: - - https://portal.hdfgroup.org/display/HDF5/HDF5+Application+Developer%27s+Guide - -If you have any questions or comments, please send them to the HDF Help Desk: - - help@hdfgroup.org - - -CONTENTS - -- New Features -- Support for new platforms and languages -- Bug Fixes since HDF5-1.10.5 -- Supported Platforms -- Tested Configuration Features Summary -- More Tested Platforms -- Known Problems -- CMake vs. Autotools installations - - -New Features -============ - - Configuration: - ------------- - - Update CMake for VS2019 support - - CMake added support for VS2019 in version 3.15. Changes to the CMake - generator setting required changes to scripts. Also updated version - references in CMake files as necessary. - - (ADB - 2019/11/18, HDFFV-10962) - - - Update CMake options to match new autotools options - - Add configure options (autotools - CMake): - enable-asserts HDF5_ENABLE_ASSERTS - enable-symbols HDF5_ENABLE_SYMBOLS - enable-profiling HDF5_ENABLE_PROFILING - enable-optimization HDF5_ENABLE_OPTIMIZATION - In addition NDEBUG is no longer forced defined and relies on the CMake - process. - - (ADB - 2019/10/07, HDFFV-100901, HDFFV-10637, TRILAB-97) - - - Update CMake tests to use FIXTURES - - CMake test fixtures allow setup/cleanup tests and other dependency - requirements as properties for tests. This is more flexible for - modern CMake code. - - (ADB - 2019/07/23, HDFFV-10529) - - - Windows PDB files are always installed - - There are build configuration or flag settings for Windows that may not - generate PDB files. If those files are not generated then the install - utility will fail because those PDB files are not found. An optional - variable, DISABLE_PDB_FILES, was added to not install PDB files. - - (ADB - 2019/07/17, HDFFV-10424) - - - Add mingw CMake support with a toolchain file - - There have been a number of mingw issues that have 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 have 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. - Re-enabling them after the initial build requires running configure - again with the option(s) enabled. - - (LRK - 2019/06/12, HDFFV-9976) - - - Change tools tests to search 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) - - - Library: - -------- - - Added S3 and HDFS Virtual File Drivers (VFDs) to HDF5 - - These new VFDs have been introduced in HDF5-1.10.6. Instructions to - enable them when configuring HDF5 on Linux and Mac may be found at - https://portal.hdfgroup.org/display/HDF5/Virtual+File+Drivers+-+S3+and+HDFS. - - Installing on Windows requires CMake 3.13 and the following additional setup. - 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) - - C++ Library: - ------------ - - Added new wrappers for H5Pset/get_create_intermediate_group() - LinkCreatPropList::setCreateIntermediateGroup() - LinkCreatPropList::getCreateIntermediateGroup() - - (BMR - 2019/04/22, HDFFV-10622) - - - Java Library: - ---------------- - - Fixed a failure in JUnit-TestH5P on 32-bit architectures - - (JTH - 2019/04/30) - - -Support for new platforms, languages and compilers. -======================================= - - CMake added support for VS2019 in version 3.15. Updated scripts. - - - macOS 10.13.6 Darwin 17.7.0 with Apple clang LLVM version 10.0.0 - - - macOS 10.14.6 Darwin 18.7.0 with Apple clang LLVM version 10.0.1 - - -Bug Fixes since HDF5-1.10.5 release -================================== - - Library - ------- - - Improved performance when creating a large number of small datasets by - retrieving default property values from the API context instead of doing - skip list searches. More work is required to achieve parity with HDF5 1.8. - - (CJH - 2019/12/10, HDFFV-10658) - - - Fixed user-created data access properties not existing in the property list - returned by H5Dget_access_plist. Thanks to Steven Varga for submitting a - reproducer and a patch. - - (CJH - 2019/12/9, HDFFV-10934) - - - 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) - - - 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) - - - Fixed a bug caused by a bad tag value when condensing object header - messages - - There was an assertion failure when moving messages 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 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 an 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 when creating a file with non-default file space info - together with library high bound setting to H5F_LIBVER_V18. - - When setting non-default file space info in fcpl via - H5Pset_file_space_strategy() and then creating a file with both high and - low library bounds set to H5F_LIBVER_V18 in fapl, the library succeeds in - creating the file. File creation should fail because the feature of - setting non-default file space info does not exist in library release 1.8 - or earlier. - - This was fixed by setting and checking the proper version in the file - space info message based on the library low and high bounds when creating - and opening the HDF5 file. - - (VC - 2019/6/25, HDFFV-10808) - - - Fixed an issue where copying a version 1.8 dataset between files using - H5Ocopy fails due to an incompatible fill version - - When using the HDF5 1.10.x H5Ocopy() API call to copy a version 1.8 - dataset to a file created with both high and low library bounds set to - H5F_LIBVER_V18, the H5Ocopy() call will fail with the error stack indicating - that the fill value version is out of bounds. - - This was fixed by changing the fill value message version to H5O_FILL_VERSION_3 - (from H5O_FILL_VERSION_2) for H5F_LIBVER_V18. - - (VC - 2019/6/14, HDFFV-10800) - - - Fixed a bug that would cause an error or cause fill values to be - incorrectly read from a chunked dataset using the "single chunk" index if - the data was held in cache and there was no data on disk. - - (NAF - 2019/03/06) - - - Fixed a bug that could cause an error or cause fill values to be - incorrectly read from a dataset that was written to using H5Dwrite_chunk - if the dataset was not closed after writing. - - (NAF - 2019/03/06, HDFFV-10716) - - - Fixed memory leak in scale offset filter - - In a special case where the MinBits is the same as the number of bits in - the datatype's precision, the filter's data buffer was not freed, causing - the memory usage to grow. In general the buffer was freed correctly. The - Minbits are the minimal number of bits to store the data values. Please - see the reference manual for H5Pset_scaleoffset for the details. - - (RL - 2019/3/4, HDFFV-10705) - - - 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. - - (ADB - 2019/08/12, HDFFV-10879) - - 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) - - -Supported Platforms -=================== - - Linux 2.6.32-696.20.1.el6.ppc64 gcc (GCC) 4.4.7 20120313 (Red Hat 4.4.7-23) - #1 SMP ppc64 GNU/Linux g++ (GCC) 4.4.7 20120313 (Red Hat 4.4.7-23) - (ostrich) GNU Fortran (GCC) 4.4.7 20120313 (Red Hat 4.4.7-23) - 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: - (jelly/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 18 (cmake) - - Windows 7 x64 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 19 (cmake) - Visual Studio 2019 w/ Intel Fortran 19 (cmake) - - macOS 10.13.6, Darwin, Apple clang LLVM version 10.0.0 - 17.7.0, x86_64 gfortran GNU Fortran (GCC) 6.3.0 - (bear) Intel icc/icpc/ifort version 19.0.4 - - macOS 10.14.6, Darwin Apple clang LLVM version 10.0.1 - 18.7.0, x86_64 gfortran GNU Fortran (GCC) 6.3.0 - (bobcat) Intel icc/icpc/ifort version 19.0.4 - - -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 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 -MacOS High Sierra 10.13.6 64-bit 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 - - -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 Yosemite 10.10.5 64-bit y y y y -Mac OS X El Capitan 10.11.6 64-bit y y y y -MacOS High Sierra 10.13.6 64-bit y y y y -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 -"Supported Platforms" table. - - -More Tested Platforms -===================== -The following configurations are not supported but have been tested for this release. - - Linux 2.6.32-754.11.1.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 6.2(Chiyoda) - GCC Version 7.1.0 - MPICH 3.2-GCC-4.9.3 - MPICH 3.2.1-GCC-7.2.0-2.29 - OpenMPI 2.1.5-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 6.2(Chiyoda) - - Linux 3.10.0-327.10.1.el7 MPICH 3.2 compiled with GCC 5.3.0 - #1 SMP x86_64 GNU/Linux - (moohan) - - Linux 2.6.32-573.18.1.el6.ppc64 MPICH mpich 3.1.4 compiled with - #1 SMP ppc64 GNU/Linux IBM XL C/C++ for Linux, V13.1 - (ostrich) and IBM XL Fortran for Linux, V15.1 - - Fedora30 5.3.11-200.fc30.x86_64 - #1 SMP x86_64 GNU/Linux GNU gcc (GCC) 9.2.1 20190827 (Red Hat 9.2.1 20190827) - GNU Fortran (GCC) 9.2.1 20190827 (Red Hat 9.2.1 20190827) - (cmake and autotools) - - Mac OS X 10.11.6, Darwin, Apple clang version 7.3.0 from Xcode 7.3 - 15.6.0, x86-64 gfortran GNU Fortran (GCC) 5.2.0 - (osx1011test) Intel icc/icpc/ifort version 16.0.2 - - macOS 10.12.6, Darwin, Apple clang LLVM version 8.1.0 from Xcode 8.3 - 16.6.0, x86_64 gfortran GNU Fortran (GCC) 7.1.0 - (kite) Intel icc/icpc/ifort version 17.0.2 - - Windows 7 x64 Visual Studio 2008 - - -Known Problems -============== - CMake files do not behave correctly with paths containing spaces. - Do not use spaces in paths because the required escaping for handling spaces - results in very complex and fragile build files. - ADB - 2019/05/07 - - At present, metadata cache images may not be generated by parallel - applications. Parallel applications can read files with metadata cache - images, but since this is a collective operation, a deadlock is possible - if one or more processes do not participate. - - Three tests fail with OpenMPI 3.0.0/GCC-7.2.0-2.29: - testphdf5 (ecdsetw, selnone, cchunk1, cchunk3, cchunk4, and actualio) - t_shapesame (sscontig2) - t_pflush1/fails on exit - The first two tests fail attempting collective writes. - - Parallel builds using OpenMPI 3.03 or later and romio fail several tests - with collective writes or compression that will not fail when ompio is used - instead of romio. This can be done by adding "--mca io ompio" to the mpirun - command. For example, in autotools builds RUNPARALLEL can be set to - "mpirun --mca io ompio -n 6" provided ompio is installed. - - CPP ptable test fails on VS2017 with Intel compiler, JIRA issue: HDFFV-10628. - This test will pass with VS2015 with Intel compiler. - - Older MPI libraries such as OpenMPI 2.0.1 and MPICH 2.1.5 were tested - while attempting to resolve the Jira issue: HDFFV-10540. - The known problems of reading or writing > 2GBs when using MPI-2 was - partially resolved with the MPICH library. The proposed support recognizes - IO operations > 2GB and if the datatype is not a derived type, the library - breaks the IO into chunks which can be input or output with the existing - MPI 2 limitations, i.e. size reporting and function API size/count - arguments are restricted to be 32 bit integers. For derived types larger - than 2GB, MPICH 2.1.5 fails while attempting to read or write data. - OpenMPI in contrast, implements MPI-3 APIs even in the older releases - and thus does not suffer from the 32 bit size limitation described here. - OpenMPI releases prior to v3.1.3 appear to have other datatype issues however, - e.g. within a single parallel test (testphdf5) the subtests (cdsetr, eidsetr) - report data verification errors before eventually aborting. - The most recent versions of OpenMPI (v3.1.3 or newer) have evidently - resolved these issues and parallel HDF5 testing does not currently report - errors though occasional hangs have been observed. - - Known problems in previous releases can be found in the HISTORY*.txt files - in the HDF5 source. Please report any new problems found to - help@hdfgroup.org. - - -CMake vs. Autotools installations -================================= -While both build systems produce similar results, there are differences. -Each system produces the same set of folders on linux (only CMake works -on standard Windows); bin, include, lib and share. Autotools places the -COPYING and RELEASE.txt file in the root folder, CMake places them in -the share folder. - -The bin folder contains the tools and the build scripts. Additionally, CMake -creates dynamic versions of the tools with the suffix "-shared". Autotools -installs one set of tools depending on the "--enable-shared" configuration -option. - build scripts - ------------- - Autotools: h5c++, h5cc, h5fc - CMake: h5c++, h5cc, h5hlc++, h5hlcc - -The include folder holds the header files and the fortran mod files. CMake -places the fortran mod files into separate shared and static subfolders, -while Autotools places one set of mod files into the include folder. Because -CMake produces a tools library, the header files for tools will appear in -the include folder. - -The lib folder contains the library files, and CMake adds the pkgconfig -subfolder with the hdf5*.pc files used by the bin/build scripts created by -the CMake build. CMake separates the C interface code from the fortran code by -creating C-stub libraries for each Fortran library. In addition, only CMake -installs the tools library. The names of the szip libraries are different -between the build systems. - -The share folder will have the most differences because CMake builds include -a number of CMake specific files for support of CMake's find_package and support -for the HDF5 Examples CMake project. - -%%%%1.10.5%%%% - -HDF5 version 1.10.5 released on 2019-02-25 -================================================================================ - - -INTRODUCTION - -This document describes the differences between this release and the previous -HDF5 release. It contains information on the platforms tested and known -problems in this release. For more details check the HISTORY*.txt files in the -HDF5 source. - -Note that documentation in the links below will be updated at the time of each -final release. - -Links to HDF5 documentation can be found on The HDF5 web page: - - https://portal.hdfgroup.org/display/HDF5/HDF5 - -The official HDF5 releases can be obtained from: - - https://www.hdfgroup.org/downloads/hdf5/ - -Changes from Release to Release and New Features in the HDF5-1.10.x release series -can be found at: - - https://portal.hdfgroup.org/display/HDF5/HDF5+Application+Developer%27s+Guide - -If you have any questions or comments, please send them to the HDF Help Desk: - - help@hdfgroup.org - - -CONTENTS - -- New Features -- Support for new platforms and languages -- Bug Fixes since HDF5-1.10.4 -- Supported Platforms -- Tested Configuration Features Summary -- More Tested Platforms -- Known Problems -- CMake vs. Autotools installations - - -New Features -============ - - Configuration: - ------------- - - Cross compile on mutrino and other Cray XC40 systems. - - Added support for CMake options to use CrayLinuxEnvironment, craype-mic-knl - module for building with craype-haswell module for configuration, and - batch scripts in bin/batch for use with sbatch or bsub to run tests in - batch jobs on compute nodes. An instruction file README_HPC describing - the use of these options was added in release_docs. - - (LRK - 2019/02/18, TRILABS-34) - - - Rework CMake command files to fix MPI testing. - - Added setup fixture to remove any test generated files and added DEPENDS - to test properties to execute tests in order expected. - - (ADB - 2019/02/14, TRILABS-111) - - - Disable SZIP or ZLIB options if TGZ files are not available. - - Changed the TGZ option for SZip and ZLib to disable the options - if the source tar.gz files are not found. - - (ADB - 2019/02/05, HDFFV-10697) - - - Added a new option to enable/disable using pread/pwrite instead of - read/write in the sec2, log, and core VFDs. - - This option is enabled by default when pread/pwrite are detected. - - Autotools: --enable-preadwrite - CMake: HDF5_ENABLE_PREADWRITE - - (DER - 2019/02/03, HDFFV-10696) - - - Rework CMake versioning for OSX platforms. - - Changed the current_version and compatibility_version flags from optional - with HDF5_BUILD_WITH_INSTALL_NAME to always setting the flags for OSX. - - (ADB - 2019/01/22, HDFFV-10685) - - - Rework CMake command files to eliminate developer CMP005 warning - - Use variables without quotes in if () statements. - - (ADB - 2019/01/18, TILABS-105) - - - Rework CMake configure files to eliminate developer CMP0075 warning - - Renamed varname to HDF5_REQUIRED_LIBRARIES as the contents were not - required for configuration. Also moved check includes calls to top of - files. - - (ADB - 2019/01/03, HDFFV-10546) - - - Keep stderr and stdout separate in tests - - Changed test handling of output capture. Tests now keep the stderr - output separate from the stdout output. It is up to the test to decide - which output to check against a reference. Also added the option - to grep for a string in either output. - - (ADB - 2018/12/12, HDFFV-10632) - - - Incorrectly installed private header files were removed from - CMake installs. - - The CMake build files incorrectly flagged the following header files - as public and installed them. They are private and will no longer be - installed. - - HDF5 library private package files (H5Xpkg.h) - H5Edefin.h - H5Einit.h - H5Eterm.h - H5LTparse.h - h5diff.h - h5tools_dump.h - h5tools.h - h5tools_ref.h - h5tools_str.h - h5tools_utils.h - h5trav.h - - (DER - 2018/10/26, HDFFV-10614, 10609) - - - Autotools installs now install H5FDwindows.h - - This is simply to align the installed header files between the - autotools and CMake. H5FDwindows.h has no functionality on - non-Windows systems. - - (DER - 2018/10/26, HDFFV-10614) - - - Library: - -------- - - The sec2, log, and core VFDs can now use pread/pwrite instead of - read/write. - - pread and pwrite do not change the file offset, a feature that was - requested by a user working with a multi-threaded application. - - The option to configure this feature is described above. - - (DER - 2019/02/03, HDFFV-10696) - - - Add ability to minimize dataset object headers. - - Creation of many, very small datasets resulted in extensive file bloat - due to extra space in the dataset object headers -- this space is - allocated by default to allow for the insertion of a small number of - attributes within the object header and not require a continuation - block, an unnecessary provision in the target use case. - - Inform the library to expect no attributes on created datasets, and to - allocate the least space possible for the object headers. - NOTE: A continuation block is created if attributes are added to a - 'minimized' dataset, which can reduce performance. - NOTE: Some extra space is allocated for attributes essential to the - correct behavior of the object header (store creation times, e.g.). This - does not violate the design principle, as the space is calculated and - allocated as needed at the time of dataset object header creation -- - unused space is not generated. - New API calls: - H5Fget_dset_no_attrs_hint - H5Fset_dset_no_attrs_hint - H5Pget_dset_no_attrs_hint - H5Pset_dset_no_attrs_hint - - (JOS - 2019/01/04, TRILAB-45) - - - Added new chunk query functions - - The following public functions were added to discover information about - the chunks in an HDF5 file. - herr_t H5Dget_num_chunks(dset_id, fspace_id, *nchunks) - herr_t H5Dget_chunk_info_by_coord(dset_id, *coord, *filter_mask, *addr, *size) - herr_t H5Dget_chunk_info(dset_id, fspace_id, index, *coord, *filter_mask, *addr, *size) - - (BMR - 2018/11/07, HDFFV-10615) - - - Several empty public header files where removed from the distribution - - The following files were empty placeholders. They are for internal - packages that are unlikely to ever have public functionality and have - thus been removed. - - H5Bpublic.h - H5B2public.h - H5FSpublic.h - H5HFpublic.h - H5HGpublic.h - H5HLpublic.h - - They were only installed in CMake builds. - - (DER - 2018/10/26, HDFFV-10614) - - - Parallel Library: - ----------------- - - Changed the default behavior in parallel when reading the same dataset in its entirety - (i.e. H5S_ALL dataset selection) which is being read by all the processes collectively. - The dataset must be contiguous, less than 2GB, and of an atomic datatype. - The new behavior is the HDF5 library will use an MPI_Bcast to pass the data read from - the disk by the root process to the remain processes in the MPI communicator associated - with the HDF5 file. - - (MSB - 2019/01/02, HDFFV-10652) - - - All MPI-1 API calls have been replaced with MPI-2 equivalents. - - This was done to better support OpenMPI, as default builds no longer - include MPI-1 support (as of OpenMPI 4.0). - - (DER - 2018/12/30, HDFFV-10566) - - Fortran Library: - ---------------- - - Added wrappers for dataset object header minimization calls. - (see the note for TRILAB-45, above) - - New API calls: - - h5fget_dset_no_attrs_hint_f - h5fset_dset_no_attrs_hint_f - h5pget_dset_no_attrs_hint_f - h5pset_dset_no_attrs_hint_f - - (DER - 2019/01/09, TRILAB-45) - - - Added new Fortran derived type, c_h5o_info_t, which is interoperable with - C's h5o_info_t. This is needed for callback functions which - pass C's h5o_info_t data type definition. - - (MSB, 2019/01/08, HDFFV-10443) - - - Added new Fortran API, H5gmtime, which converts (C) 'time_t' structure - to Fortran DATE AND TIME storage format. - - (MSB, 2019/01/08, HDFFV-10443) - - - Added new Fortran 'fields' optional parameter to: h5ovisit_f, h5oget_info_by_name_f, - h5oget_info, h5oget_info_by_idx and h5ovisit_by_name_f. - - (MSB, 2019/01/08, HDFFV-10443) - - C++ Library: - ------------ - - Added new function to the C++ interface - - Added wrapper for H5Ovisit2: - H5Object::visit() - - (BMR - 2019/02/14, HDFFV-10532) - - - Java Library: - ---------------- - - Rewrote the JNI error handling to be much cleaner - - (JTH - 2019/02/12) - - - Add new functions to java interface - - Added wrappers for: - H5Fset_libver_bounds - H5Fget_dset_no_attrs_hint/H5Fset_dset_no_attrs_hint - H5Pget_dset_no_attrs_hint/H5Pset_dset_no_attrs_hint - - (ADB - 2019/01/07, HDFFV-10664) - - - Fix java unit tests when Time is a natural number - - Time substitution in java/test/junit.sh.in doesn't - handle the case when Time is a natural number. Fixed - the regular expression. - - (ADB - 2019/01/07, HDFFV-10674) - - - Duplicate the data read/write functions of Datasets for Attributes. - - Region references could not be displayed for attributes as they could - for datasets. Datasets had overloaded read and write functions for different - datatypes that were not available for attributes. After adding similar - functions, attribute region references work normally. - - (ADB - 2018/12/12, HDFVIEW-4) - - - Tools: - ------ - - The h5repart -family-to-sec2 argument was changed to -family-to-single - - In order to better support other single-file VFDs which could work with - h5repart, the -family-to-sec2 argument was renamed to -family-to-single. - This is just a name change and the functionality of the argument has not - changed. - - The -family-to-sec2 argument has been kept for backwards-compatibility. - This argument should be considered deprecated. - - (DER - 2018/11/14, HDFFV-10633) - - -Bug Fixes since HDF5-1.10.4 release -================================== - - Library - ------- - - Fix hangs with collective metadata reads during chunked dataset I/O - - In the parallel library, it was discovered that when a particular - sequence of operations following a pattern of: - - "write to chunked dataset" -> "flush file" -> "read from dataset" - - occurred with collective metadata reads enabled, hangs could be - observed due to certain MPI ranks not participating in the collective - metadata reads. - - To fix the issue, collective metadata reads are now disabled during - chunked dataset raw data I/O. - - (JTH - 2019/02/11, HDFFV-10563, HDFFV-10688) - - - Performance issue when closing an object - - The slow down is due to the search of the "tag_list" to find - out the "corked" status of an object and "uncork" it if so. - - Improve performance by skipping the search of the "tag_list" - if there are no "corked" objects when closing an object. - - (VC - 2019/02/06) - - - Uninitialized bytes from a type conversion buffer could be written - to disk in H5Dwrite calls where type conversion takes place - and the type conversion buffer was created by the HDF5 library. - - When H5Dwrite is called and datatype conversion must be performed, - the library will create a temporary buffer for type conversion if - one is not provided by the user via H5Pset_buffer. This internal - buffer is allocated via malloc and contains uninitialized data. In - some datatype conversions (float to long double, possibly others), - some of this uninitialized data could be written to disk. - - This was flagged by valgrind in the dtransform test and does not - appear to be a common occurrence (it is flagged in one test out - of the entire HDF5 test suite). - - Switching to calloc fixed the problem. - - (DER - 2019/02/03, HDFFV-10694) - - - There was missing protection against division by zero reported to - The HDF Group as issue #CVE-2018-17434. - - Protection against division by zero was added to address the issue - #CVE-2018-17434. - - (BMR - 2019/01/29, HDFFV-10586) - - - The issue CVE-2018-17437 was reported to The HDF Group - - Although CVE-2018-17437 reported a memory leak, the actual issue - was invalid read. It was found that the attribute name length - in an attribute message was corrupted, which caused the buffer - pointer to be advanced too far and later caused an invalid read. - - A check was added to detect when the attribute name or its length - was corrupted and report the potential of data corruption. - - (BMR - 2019/01/29, HDFFV-10588) - - - H5Ewalk did not stop when it was supposed to - - H5Ewalk was supposed to stop when the callback function stopped - even though the errors in the stack were not all visited, but it - did not. This problem is now fixed. - - (BMR - 2019/01/29, HDFFV-10684) - - - Revert H5Oget_info* and H5Ovisit* functions - - In 1.10.3 new H5Oget_info*2 and H5Ovisit*2 functions were - added for performance. Inadvertently, the original functions; - H5Oget_info, - H5Oget_info_by_name, - H5Oget_info_by_idx, - H5Ovisit, - H5Ovisit_by_name - were versioned to H5Oget_info*1 and H5Ovisit*1. This - broke the API compatibility for a maintenance release. The - original functions have been restored. - - (ADB - 2019/01/24, HDFFV-10686) - - - Fixed a potential invalid memory access and failure that could occur when - decoding an unknown object header message (from a future version of the - library). - - (NAF - 2019/01/07) - - - Deleting attributes in dense storage - - The library aborts with "infinite loop closing library" after - attributes in dense storage are created and then deleted. - - When deleting the attribute nodes from the name index v2 B-tree, - if an attribute is found in the intermediate B-tree nodes, - which may be merged/redistributed in the process, we need to - free the dynamically allocated spaces for the intermediate - decoded attribute. - - (VC - 2018/12/26, HDFFV-10659) - - - There was missing protection against division by zero reported to - The HDF Group as issue #CVE-2018-17233. - - Protection against division by zero was added to address the issue - #CVE-2018-17233. In addition, several similar occurrences in the same - file were fixed as well. - - (BMR - 2018/12/23, HDFFV-10577) - - - Fixed an issue where the parallel filters tests would fail - if zlib was not available on the system. Until support can - be added in the tests for filters beyond gzip/zlib, the tests - will be skipped if zlib is not available. - - (JTH - 2018/12/05) - - - A bug was discovered in the parallel library where an application - would eventually consume all of the available MPI communicators - when continually writing to a compressed dataset in parallel. This - was due to internal copies of an HDF5 File Access Property List, - which each contained a copy of the MPI communicator, not being - closed at the end of each write operation. This problem was - exacerbated by larger numbers of processors. - - (JTH - 2018/12/05, HDFFV-10629) - - - Fortran - -------- - - Fixed issue with Fortran not returning h5o_info_t field values - meta_size%attr%index_size and meta_size%attr%heap_size. - - (MSB, 2019/01/08, HDFFV-10443) - - - Added symbolic links libhdf5_hl_fortran.so to libhdf5hl_fortran.so and - libhdf5_hl_fortran.a to libhdf5hl_fortran.a in hdf5/lib directory for - autotools installs. These were added to match the name of the files - installed by cmake and the general pattern of hl lib files. We will - change the names of the installed lib files to the matching name in - the next major release. - - (LRK - 2019/01/04, HDFFV-10596) - - - Made Fortran specific subroutines PRIVATE in generic procedures. - - Affected generic procedures were functions in H5A, H5D, H5P, H5R and H5T. - - (MSB, 2018/12/04, HDFFV-10511) - - - Testing - ------- - - Fixed a test failure in testpar/t_dset.c caused by - the test trying to use the parallel filters feature - on MPI-2 implementations. - - (JTH, 2019/2/7) - - -Supported Platforms -=================== - - Linux 2.6.32-696.16.1.el6.ppc64 gcc (GCC) 4.4.7 20120313 (Red Hat 4.4.7-18) - #1 SMP ppc64 GNU/Linux g++ (GCC) 4.4.7 20120313 (Red Hat 4.4.7-18) - (ostrich) GNU Fortran (GCC) 4.4.7 20120313 (Red Hat 4.4.7-18) - IBM XL C/C++ V13.1 - IBM XL Fortran V15.1 - - Linux 3.10.0-327.10.1.el7 GNU C (gcc), Fortran (gfortran), C++ (g++) - #1 SMP x86_64 GNU/Linux compilers: - (kituo/moohan) Version 4.8.5 20150623 (Red Hat 4.8.5-4) - Version 4.9.3, Version 5.2.0 - Intel(R) C (icc), C++ (icpc), Fortran (icc) - compilers: - Version 17.0.0.098 Build 20160721 - MPICH 3.1.4 compiled with GCC 4.9.3 - - SunOS 5.11 32- and 64-bit Sun C 5.12 SunOS_sparc - (emu) Sun Fortran 95 8.6 SunOS_sparc - Sun C++ 5.12 SunOS_sparc - - Windows 7 Visual Studio 2015 w/ Intel Fortran 16 (cmake) - - Windows 7 x64 Visual Studio 2013 - Visual Studio 2015 w/ Intel Fortran 16 (cmake) - Visual Studio 2015 w/ Intel C, Fortran 2018 (cmake) - Visual Studio 2015 w/ MSMPI 8 (cmake) - - Windows 10 Visual Studio 2015 w/ Intel Fortran 18 (cmake) - - Windows 10 x64 Visual Studio 2015 w/ Intel Fortran 18 (cmake) - Visual Studio 2017 w/ Intel Fortran 18 (cmake) - - Mac OS X Yosemite 10.10.5 Apple clang/clang++ version 6.1 from Xcode 7.0 - 64-bit gfortran GNU Fortran (GCC) 4.9.2 - (osx1010dev/osx1010test) Intel icc/icpc/ifort version 15.0.3 - - Mac OS X El Capitan 10.11.6 Apple clang/clang++ version 7.3.0 from Xcode 7.3 - 64-bit gfortran GNU Fortran (GCC) 5.2.0 - (osx1011dev/osx1011test) Intel icc/icpc/ifort version 16.0.2 - - MacOS High Sierra 10.13.6 Apple LLVM version 10.0.0 (clang/clang++-1000.10.44.4) - 64-bit gfortran GNU Fortran (GCC) 8.3.0 - - -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 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 -MacOS High Sierra 10.13.6 64-bit 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 - - -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 Yosemite 10.10.5 64-bit y y y y -Mac OS X El Capitan 10.11.6 64-bit y y y y -MacOS High Sierra 10.13.6 64-bit y y y y -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 -"Supported Platforms" table. - - -More Tested Platforms -===================== -The following configurations 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 - MPICH 3.2-GCC-4.9.3 - MPICH 3.2.1-GCC-7.2.0-2.29 - OpenMPI 2.1.5-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) - - Fedora 29 4.20.10-200.fc29.x86_64 #1 SMP x86_64 x86_64 x86_64 GNU/Linux - gcc, g++ (GCC) 8.2.1 20181215 - (Red Hat 8.2.1-6) - GNU Fortran (GCC) 8.2.1 20181215 - (Red Hat 8.2.1-6) - (cmake and autotools) - - Windows 7 x64 Visual Studio 2008 - - -Known Problems -============== - - At present, metadata cache images may not be generated by parallel - applications. Parallel applications can read files with metadata cache - images, but since this is a collective operation, a deadlock is possible - if one or more processes do not participate. - - Three tests fail with OpenMPI 3.0.0/GCC-7.2.0-2.29: - testphdf5 (ecdsetw, selnone, cchunk1, cchunk3, cchunk4, and actualio) - t_shapesame (sscontig2) - t_pflush1/fails on exit - The first two tests fail attempting collective writes. - - CPP ptable test fails on VS2017 with Intel compiler, JIRA issue: HDFFV-10628. - This test will pass with VS2015 with Intel compiler. - - Older MPI libraries such as OpenMPI 2.0.1 and MPICH 2.1.5 were tested - while attempting to resolve the Jira issue: HDFFV-10540. - The known problems of reading or writing > 2GBs when using MPI-2 was - partially resolved with the MPICH library. The proposed support recognizes - IO operations > 2GB and if the datatype is not a derived type, the library - breaks the IO into chunks which can be input or output with the existing - MPI 2 limitations, i.e. size reporting and function API size/count - arguments are restricted to be 32 bit integers. For derived types larger - than 2GB, MPICH 2.1.5 fails while attempting to read or write data. - OpenMPI in contrast, implements MPI-3 APIs even in the older releases - and thus does not suffer from the 32 bit size limitation described here. - OpenMPI releases prior to v3.1.3 appear to have other datatype issues however, - e.g. within a single parallel test (testphdf5) the subtests (cdsetr, eidsetr) - report data verification errors before eventually aborting. - The most recent versions of OpenMPI (v3.1.3 or newer) have evidently - resolved these issues and parallel HDF5 testing does not currently report - errors though occasional hangs have been observed. - - Known problems in previous releases can be found in the HISTORY*.txt files - in the HDF5 source. Please report any new problems found to - help@hdfgroup.org. - - -CMake vs. Autotools installations -================================= -While both build systems produce similar results, there are differences. -Each system produces the same set of folders on linux (only CMake works -on standard Windows); bin, include, lib and share. Autotools places the -COPYING and RELEASE.txt file in the root folder, CMake places them in -the share folder. - -The bin folder contains the tools and the build scripts. Additionally, CMake -creates dynamic versions of the tools with the suffix "-shared". Autotools -installs one set of tools depending on the "--enable-shared" configuration -option. - build scripts - ------------- - Autotools: h5c++, h5cc, h5fc - CMake: h5c++, h5cc, h5hlc++, h5hlcc - -The include folder holds the header files and the fortran mod files. CMake -places the fortran mod files into separate shared and static subfolders, -while Autotools places one set of mod files into the include folder. Because -CMake produces a tools library, the header files for tools will appear in -the include folder. - -The lib folder contains the library files, and CMake adds the pkgconfig -subfolder with the hdf5*.pc files used by the bin/build scripts created by -the CMake build. CMake separates the C interface code from the fortran code by -creating C-stub libraries for each Fortran library. In addition, only CMake -installs the tools library. The names of the szip libraries are different -between the build systems. - -The share folder will have the most differences because CMake builds include -a number of CMake specific files for support of CMake's find_package and support -for the HDF5 Examples CMake project. - -%%%%1.10.4%%%% - -HDF5 version 1.10.4 released on 2018-10-05 -================================================================================ - - -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 - -- Bug Fixes since HDF5-1.10.3 -- Supported Platforms -- Tested Configuration Features Summary -- More Tested Platforms -- Known Problems -- CMake vs. Autotools installations - - -New Features -============ - - Configuration: - ------------- - - 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) - - Library: - -------- - - 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) - - -Bug Fixes since HDF5-1.10.3 release -================================== - - Library - ------- - - 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) - - 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) - - -Supported Platforms -=================== - - Linux 2.6.32-696.16.1.el6.ppc64 gcc (GCC) 4.4.7 20120313 (Red Hat 4.4.7-18) - #1 SMP ppc64 GNU/Linux g++ (GCC) 4.4.7 20120313 (Red Hat 4.4.7-18) - (ostrich) GNU Fortran (GCC) 4.4.7 20120313 (Red Hat 4.4.7-18) - IBM XL C/C++ V13.1 - IBM XL Fortran V15.1 - - Linux 3.10.0-327.10.1.el7 GNU C (gcc), Fortran (gfortran), C++ (g++) - #1 SMP x86_64 GNU/Linux compilers: - (kituo/moohan) Version 4.8.5 20150623 (Red Hat 4.8.5-4) - Version 4.9.3, Version 5.2.0 - Intel(R) C (icc), C++ (icpc), Fortran (icc) - compilers: - Version 17.0.0.098 Build 20160721 - MPICH 3.1.4 compiled with GCC 4.9.3 - - SunOS 5.11 32- and 64-bit Sun C 5.12 SunOS_sparc - (emu) Sun Fortran 95 8.6 SunOS_sparc - Sun C++ 5.12 SunOS_sparc - - Windows 7 Visual Studio 2015 w/ Intel Fortran 16 (cmake) - - Windows 7 x64 Visual Studio 2012 w/ Intel Fortran 15 (cmake) - Visual Studio 2013 w/ Intel Fortran 15 (cmake) - Visual Studio 2015 w/ Intel Fortran 16 (cmake) - Visual Studio 2015 w/ Intel C, Fortran 2017 (cmake) - Visual Studio 2015 w/ MSMPI 8 (cmake) - - Windows 10 Visual Studio 2015 w/ Intel Fortran 18 (cmake) - - Windows 10 x64 Visual Studio 2015 w/ Intel Fortran 18 (cmake) - Visual Studio 2017 w/ Intel Fortran 18 (cmake) - - Mac OS X Yosemite 10.10.5 Apple clang/clang++ version 6.1 from Xcode 7.0 - 64-bit gfortran GNU Fortran (GCC) 4.9.2 - (osx1010dev/osx1010test) Intel icc/icpc/ifort version 15.0.3 - - Mac OS X El Capitan 10.11.6 Apple clang/clang++ version 7.3.0 from Xcode 7.3 - 64-bit gfortran GNU Fortran (GCC) 5.2.0 - (osx1011dev/osx1011test) Intel icc/icpc/ifort version 16.0.2 - - Mac OS Sierra 10.12.6 Apple LLVM version 8.1.0 (clang/clang++-802.0.42) - 64-bit gfortran GNU Fortran (GCC) 7.1.0 - (kite) Intel icc/icpc/ifort version 17.0.2 - - -Tested Configuration Features Summary -===================================== - - In the tables below - y = tested - n = not tested in this release - C = Cluster - W = Workstation - x = not working in this release - dna = does not apply - ( ) = footnote appears below second table - <blank> = testing incomplete on this feature or platform - -Platform C F90/ F90 C++ zlib SZIP - parallel F2003 parallel -Solaris2.11 32-bit n y/y n y y y -Solaris2.11 64-bit n y/n n y y y -Windows 7 y y/y n y y y -Windows 7 x64 y y/y y y y y -Windows 7 Cygwin n y/n n y y y -Windows 7 x64 Cygwin n y/n n y y y -Windows 10 y y/y n y y y -Windows 10 x64 y y/y n y y y -Mac OS X Mavericks 10.9.5 64-bit n y/y n y y y -Mac OS X Yosemite 10.10.5 64-bit n y/y n y y y -Mac OS X El Capitan 10.11.6 64-bit n y/y n y y y -Mac OS Sierra 10.12.6 64-bit n y/y n y y y -CentOS 7.2 Linux 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 - - -Platform Shared Shared Shared Thread- - C libs F90 libs C++ libs safe -Solaris2.11 32-bit y y y y -Solaris2.11 64-bit y y y y -Windows 7 y y y y -Windows 7 x64 y y y y -Windows 7 Cygwin n n n y -Windows 7 x64 Cygwin n n n y -Windows 10 y y y y -Windows 10 x64 y y y y -Mac OS X Mavericks 10.9.5 64-bit y n y y -Mac OS X Yosemite 10.10.5 64-bit y n y y -Mac OS X El Capitan 10.11.6 64-bit y n y y -Mac OS Sierra 10.12.6 64-bit y n y y -CentOS 7.2 Linux 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 -"Supported Platforms" table. - - -More Tested Platforms -===================== -The following platforms are not supported but have been tested for this release. - - Linux 2.6.32-573.22.1.el6 GNU C (gcc), Fortran (gfortran), C++ (g++) - #1 SMP x86_64 GNU/Linux compilers: - (mayll/platypus) Version 4.4.7 20120313 - Version 4.9.3, 5.3.0, 6.2.0 - PGI C, Fortran, C++ for 64-bit target on - x86-64; - Version 17.10-0 - Intel(R) C (icc), C++ (icpc), Fortran (icc) - compilers: - Version 17.0.4.196 Build 20170411 - MPICH 3.1.4 compiled with GCC 4.9.3 - - Linux 3.10.0-327.18.2.el7 GNU C (gcc) and C++ (g++) compilers - #1 SMP x86_64 GNU/Linux Version 4.8.5 20150623 (Red Hat 4.8.5-4) - (jelly) with NAG Fortran Compiler Release 6.1(Tozai) - GCC Version 7.1.0 - OpenMPI 3.0.0-GCC-7.2.0-2.29, - 3.1.0-GCC-7.2.0-2.29 - Intel(R) C (icc) and C++ (icpc) compilers - Version 17.0.0.098 Build 20160721 - with NAG Fortran Compiler Release 6.1(Tozai) - - Linux 3.10.0-327.10.1.el7 MPICH 3.2 compiled with GCC 5.3.0 - #1 SMP x86_64 GNU/Linux - (moohan) - - Linux 2.6.32-573.18.1.el6.ppc64 MPICH mpich 3.1.4 compiled with - #1 SMP ppc64 GNU/Linux IBM XL C/C++ for Linux, V13.1 - (ostrich) and IBM XL Fortran for Linux, V15.1 - - Debian 8.4 3.16.0-4-amd64 #1 SMP Debian 3.16.36-1 x86_64 GNU/Linux - gcc, g++ (Debian 4.9.2-10) 4.9.2 - GNU Fortran (Debian 4.9.2-10) 4.9.2 - (cmake and autotools) - - Fedora 24 4.7.2-201.fc24.x86_64 #1 SMP x86_64 x86_64 x86_64 GNU/Linux - gcc, g++ (GCC) 6.1.1 20160621 - (Red Hat 6.1.1-3) - GNU Fortran (GCC) 6.1.1 20160621 - (Red Hat 6.1.1-3) - (cmake and autotools) - - Ubuntu 16.04.1 4.4.0-38-generic #57-Ubuntu SMP x86_64 GNU/Linux - gcc, g++ (Ubuntu 5.4.0-6ubuntu1~16.04.2) - 5.4.0 20160609 - GNU Fortran (Ubuntu 5.4.0-6ubuntu1~16.04.2) - 5.4.0 20160609 - (cmake and autotools) - - -Known Problems -============== - - At present, metadata cache images may not be generated by parallel - applications. Parallel applications can read files with metadata cache - images, but since this is a collective operation, a deadlock is possible - if one or more processes do not participate. - - Three tests fail with OpenMPI 3.0.0/GCC-7.2.0-2.29: - testphdf5 (ecdsetw, selnone, cchunk1, cchunk3, cchunk4, and actualio) - t_shapesame (sscontig2) - t_pflush1/fails on exit - The first two tests fail attempting collective writes. - - Known problems in previous releases can be found in the HISTORY*.txt files - in the HDF5 source. Please report any new problems found to - help@hdfgroup.org. - - -CMake vs. Autotools installations -================================= -While both build systems produce similar results, there are differences. -Each system produces the same set of folders on linux (only CMake works -on standard Windows); bin, include, lib and share. Autotools places the -COPYING and RELEASE.txt file in the root folder, CMake places them in -the share folder. - -The bin folder contains the tools and the build scripts. Additionally, CMake -creates dynamic versions of the tools with the suffix "-shared". Autotools -installs one set of tools depending on the "--enable-shared" configuration -option. - build scripts - ------------- - Autotools: h5c++, h5cc, h5fc - CMake: h5c++, h5cc, h5hlc++, h5hlcc - -The include folder holds the header files and the fortran mod files. CMake -places the fortran mod files into separate shared and static subfolders, -while Autotools places one set of mod files into the include folder. Because -CMake produces a tools library, the header files for tools will appear in -the include folder. - -The lib folder contains the library files, and CMake adds the pkgconfig -subfolder with the hdf5*.pc files used by the bin/build scripts created by -the CMake build. CMake separates the C interface code from the fortran code by -creating C-stub libraries for each Fortran library. In addition, only CMake -installs the tools library. The names of the szip libraries are different -between the build systems. - -The share folder will have the most differences because CMake builds include -a number of CMake specific files for support of CMake's find_package and support -for the HDF5 Examples CMake project. - -%%%%1.10.3%%%% - -HDF5 version 1.10.3 released on 2018-08-21 -================================================================================ - - -INTRODUCTION - -This document describes the differences between this release and the previous -HDF5 release. It contains information on the platforms tested and known -problems in this release. For more details check the HISTORY*.txt files in the -HDF5 source. - -Note that documentation in the links below will be updated at the time of each -final release. - -Links to HDF5 documentation can be found on The HDF5 web page: - - https://portal.hdfgroup.org/display/HDF5/HDF5 - -The official HDF5 releases can be obtained from: - - https://www.hdfgroup.org/downloads/hdf5/ - -Changes from Release to Release and New Features in the HDF5-1.10.x release series -can be found at: - - https://portal.hdfgroup.org/display/HDF5/HDF5+Application+Developer%27s+Guide - -If you have any questions or comments, please send them to the HDF Help Desk: - - help@hdfgroup.org - - -CONTENTS - -- New Features -- Bug Fixes since HDF5-1.10.2 -- Supported Platforms -- Tested Configuration Features Summary -- More Tested Platforms -- Known Problems -- CMake vs. Autotools installations - - -New Features -============ - - Library - ------- - - Moved the H5DOread/write_chunk() API calls to H5Dread/write_chunk() - - The functionality of the direct chunk I/O calls in the high-level - library has been moved to the H5D package in the main library. This - will allow using those functions without building the high-level - library. The parameters and functionality of the H5D calls are - identical to the H5DO calls. - - The original H5DO high-level API calls have been retained, though - they are now just wrappers for the H5D calls. They are marked as - deprecated and are only available when the library is built with - deprecated functions. New code should use the H5D calls for this - reason. - - As a part of this work, the following symbols from H5Dpublic.h are no - longer used: - - H5D_XFER_DIRECT_CHUNK_WRITE_FLAG_NAME - H5D_XFER_DIRECT_CHUNK_WRITE_FILTERS_NAME - H5D_XFER_DIRECT_CHUNK_WRITE_OFFSET_NAME - H5D_XFER_DIRECT_CHUNK_WRITE_DATASIZE_NAME - H5D_XFER_DIRECT_CHUNK_READ_FLAG_NAME - H5D_XFER_DIRECT_CHUNK_READ_OFFSET_NAME - H5D_XFER_DIRECT_CHUNK_READ_FILTERS_NAME - - And properties with these names are no longer stored in the dataset - transfer property lists. The symbols are still defined in H5Dpublic.h, - but only when the library is built with deprecated symbols. - - (DER - 2018/05/04) - - Configuration: - ------------- - - Add missing USE_110_API_DEFAULT option. - - Option USE_110_API_DEFAULT sets the default version of - versioned APIs. The bin/makevers perl script did not set - the maxidx variable correctly when the 1.10 branch was - created. This caused the versioning process to always use - the latest version of any API. - - (ADB - 2018/08/17, HDFFV-10552) - - - Added configuration checks for the following MPI functions: - - MPI_Mprobe - Used for the Parallel Compression feature - MPI_Imrecv - Used for the Parallel Compression feature - - MPI_Get_elements_x - Used for the "big Parallel I/O" feature - MPI_Type_size_x - Used for the "big Parallel I/O" feature - - (JTH - 2018/08/02, HDFFV-10512) - - - Added section to the libhdf5.settings file to indicate - the status of the Parallel Compression and "big Parallel I/O" - features. - - (JTH - 2018/08/02, HDFFV-10512) - - - Add option to execute swmr shell scripts from CMake. - - Option TEST_SHELL_SCRIPTS redirects processing into a - separate ShellTests.cmake file for UNIX types. The tests - execute the shell scripts if a SH program is found. - - (ADB - 2018/07/16) - - - C++ Library: - ------------ - - New wrappers - - Added the following items: - - + Class DSetAccPropList for the dataset access property list. - - + Wrapper for H5Dget_access_plist to class DataSet - // Gets the access property list of this dataset. - DSetAccPropList getAccessPlist() const; - - + Wrappers for H5Pset_chunk_cache and H5Pget_chunk_cache to class DSetAccPropList - // Sets the raw data chunk cache parameters. - void setChunkCache(size_t rdcc_nslots, size_t rdcc_nbytes, double rdcc_w0) - - // Retrieves the raw data chunk cache parameters. - void getChunkCache(size_t &rdcc_nslots, size_t &rdcc_nbytes, double &rdcc_w0) - - + New operator!= to class DataType (HDFFV-10472) - // Determines whether two datatypes are not the same. - bool operator!=(const DataType& compared_type) - - + Wrappers for H5Oget_info2, H5Oget_info_by_name2, and H5Oget_info_by_idx2 - (HDFFV-10458) - - // Retrieves information about an HDF5 object. - void getObjinfo(H5O_info_t& objinfo, unsigned fields = H5O_INFO_BASIC) const; - - // Retrieves information about an HDF5 object, given its name. - void getObjinfo(const char* name, H5O_info_t& objinfo, - unsigned fields = H5O_INFO_BASIC, - const LinkAccPropList& lapl = LinkAccPropList::DEFAULT) const; - void getObjinfo(const H5std_string& name, H5O_info_t& objinfo, - unsigned fields = H5O_INFO_BASIC, - const LinkAccPropList& lapl = LinkAccPropList::DEFAULT) const; - - // Retrieves information about an HDF5 object, given its index. - void getObjinfo(const char* grp_name, H5_index_t idx_type, - H5_iter_order_t order, hsize_t idx, H5O_info_t& objinfo, - unsigned fields = H5O_INFO_BASIC, - const LinkAccPropList& lapl = LinkAccPropList::DEFAULT) const; - void getObjinfo(const H5std_string& grp_name, H5_index_t idx_type, - H5_iter_order_t order, hsize_t idx, H5O_info_t& objinfo, - unsigned fields = H5O_INFO_BASIC, - const LinkAccPropList& lapl = LinkAccPropList::DEFAULT) const; - - (BMR - 2018/07/22, HDFFV-10150, HDFFV-10458, HDFFV-1047) - - - Java Library: - ---------------- - - Java HDFLibraryException class - - Change parent class from Exception to RuntimeException. - - (ADB - 2018/07/30, HDFFV-10534) - - - JNI Read and Write - - Refactored variable-length functions, H5DreadVL and H5AreadVL, - to correct dataset and attribute reads. New write functions, - H5DwriteVL and H5AwriteVL, are under construction. - - (ADB - 2018/06/02, HDFFV-10519) - - -Bug Fixes since HDF5-1.10.2 release -================================== - - Library - ------- - - Performance issue with H5Oget_info - - H5Oget_info family of routines retrieves information for an object such - as object type, access time, number of attributes, and storage space etc. - Retrieving all such information regardless is an overkill and causes - performance issue when doing so for many objects. - - Add an additional parameter "fields" to the the H5Oget_info family of routines - indicating the type of information to be retrieved. The same is done to - the H5Ovisit family of routines which recursively visits an object - returning object information in a callback function. Both sets of routines - are versioned and the corresponding compatibility macros are added. - - The version 2 names of the two sets of routines are: - (1) H5Oget_info2, H5Oget_info_by_idx2, H5Oget_info_by_name2 - (2) H5Ovisit2, H5Ovisit_by_name2 - - (VC - 2018/08/15, HDFFV-10180) - - - Test failure due to metadata size in test/vds.c - - The size of metadata from test_api_get_ex_dcpl() in test/vds.c is not as expected - because the latest format should be used when encoding the layout for VDS. - - Set the latest format in a temporary fapl and pass the setting to the routines that - encode the dataset selection for VDS. - - (VC - 2018/08/14 HDFFV-10469) - - - Java HDF5LibraryException class - - The error minor and major values would be lost after the - constructor executed. - - Created two local class variables to hold the values obtained during - execution of the constructor. Refactored the class functions to retrieve - the class values rather then calling the native functions. - The native functions were renamed and called only during execution - of the constructor. - Added error checking to calling class constructors in JNI classes. - - (ADB - 2018/08/06, HDFFV-10544) - - - Added checks of the defined MPI_VERSION to guard against usage of - MPI-3 functions in the Parallel Compression and "big Parallel I/O" - features when HDF5 is built with MPI-2. Previously, the configure - step would pass but the build itself would fail when it could not - locate the MPI-3 functions used. - - As a result of these new checks, HDF5 can again be built with MPI-2, - but the Parallel Compression feature will be disabled as it relies - on the MPI-3 functions used. - - (JTH - 2018/08/02, HDFFV-10512) - - - User's patches: CVEs - - The following patches have been applied: - - CVE-2018-11202 - NULL pointer dereference was discovered in - H5S_hyper_make_spans in H5Shyper.c (HDFFV-10476) - https://security-tracker.debian.org/tracker/CVE-2018-11202 - https://cve.mitre.org/cgi-bin/cvename.cgi?name=3DCVE-2018-11202 - - CVE-2018-11203 - A division by zero was discovered in - H5D__btree_decode_key in H5Dbtree.c (HDFFV-10477) - https://security-tracker.debian.org/tracker/CVE-2018-11203 - https://cve.mitre.org/cgi-bin/cvename.cgi?name=3DCVE-2018-11203 - - CVE-2018-11204 - A NULL pointer dereference was discovered in - H5O__chunk_deserialize in H5Ocache.c (HDFFV-10478) - https://security-tracker.debian.org/tracker/CVE-2018-11204 - https://cve.mitre.org/cgi-bin/cvename.cgi?name=3DCVE-2018-11204 - - CVE-2018-11206 - An out of bound read was discovered in - H5O_fill_new_decode and H5O_fill_old_decode in H5Ofill.c - (HDFFV-10480) - https://security-tracker.debian.org/tracker/CVE-2018-11206 - https://cve.mitre.org/cgi-bin/cvename.cgi?name=3DCVE-2018-11206 - - CVE-2018-11207 - A division by zero was discovered in - H5D__chunk_init in H5Dchunk.c (HDFFV-10481) - https://security-tracker.debian.org/tracker/CVE-2018-11207 - https://cve.mitre.org/cgi-bin/cvename.cgi?name=3DCVE-2018-11207 - - (BMR - 2018/7/22, PR#s: 1134 and 1139, - HDFFV-10476, HDFFV-10477, HDFFV-10478, HDFFV-10480, HDFFV-10481) - - - H5Adelete - - H5Adelete failed when deleting the last "large" attribute that - is stored densely via fractal heap/v2 b-tree. - - After removing the attribute, update the ainfo message. If the - number of attributes goes to zero, remove the message. - - (VC - 2018/07/20, HDFFV-9277) - - - A bug was discovered in the parallel library which caused partial - parallel reads of filtered datasets to return incorrect data. The - library used the incorrect dataspace for each chunk read, causing - the selection used in each chunk to be wrong. - - The bug was not caught during testing because all of the current - tests which do parallel reads of filtered data read all of the data - using an H5S_ALL selection. Several tests were added which exercise - partial parallel reads. - - (JTH - 2018/07/16, HDFFV-10467) - - - A bug was discovered in the parallel library which caused parallel - writes of filtered datasets to trigger an assertion failure in the - file free space manager. - - This occurred when the filter used caused chunks to repeatedly shrink - and grow over the course of several dataset writes. The previous chunk - information, such as the size of the chunk and the offset in the file, - was being cached and not updated after each write, causing the next write - to the chunk to retrieve the incorrect cached information and run into - issues when reallocating space in the file for the chunk. - - (JTH - 2018/07/16, HDFFV-10509) - - - A bug was discovered in the parallel library which caused the - H5D__mpio_array_gatherv() function to allocate too much memory. - - When the function is called with the 'allgather' parameter set - to a non-true value, the function will receive data from all MPI - ranks and gather it to the single rank specified by the 'root' - parameter. However, the bug in the function caused memory for - the received data to be allocated on all MPI ranks, not just the - singular rank specified as the receiver. In some circumstances, - this would cause an application to fail due to the large amounts - of memory being allocated. - - (JTH - 2018/07/16, HDFFV-10467) - - - Error checks in h5stat and when decoding messages - - h5stat exited with seg fault/core dumped when - errors are encountered in the internal library. - - Add error checks and --enable-error-stack option to h5stat. - Add range checks when decoding messages: old fill value, old - layout and refcount. - - (VC - 2018/07/11, HDFFV-10333) - - - If an HDF5 file contains a malformed compound datatype with a - suitably large offset, the type conversion code can run off - the end of the type conversion buffer, causing a segmentation - fault. - - This issue was reported to The HDF Group as issue #CVE-2017-17507. - - NOTE: The HDF5 C library cannot produce such a file. This condition - should only occur in a corrupt (or deliberately altered) file - or a file created by third-party software. - - THE HDF GROUP WILL NOT FIX THIS BUG AT THIS TIME - - Fixing this problem would involve updating the publicly visible - H5T_conv_t function pointer typedef and versioning the API calls - which use it. We normally only modify the public API during - major releases, so this bug will not be fixed at this time. - - (DER - 2018/02/26, HDFFV-10356) - - - Configuration - ------------- - - Applied patches to address Cywin build issues - - There were three issues for Cygwin builds: - - Shared libs were not built. - - The -std=c99 flag caused a SIG_SETMASK undeclared error. - - Undefined errors when buildbing test shared libraries. - - Patches to address these issues were received and incorporated in this version. - - (LRK - 2018/07/18, HDFFV-10475) - - - The --enable-debug/production configure flags are listed as 'deprecated' - when they should really be listed as 'removed'. - - In the autotools overhaul several years ago, we removed these flags and - implemented a new --enable-build-mode= flag. This was done because we - changed the semantics of the modes and didn't want users to silently - be exposed to them. The newer system is also more flexible and us to - add other modes (like 'clean'). - - The --enable-debug/production flags are now listed as removed. - - (DER - 2018/05/31, HDFFV-10505) - - - Moved the location of gcc attribute. - - The gcc attribute(no_sanitize), named as the macro HDF_NO_UBSAN, - was located after the function name. Builds with GCC 7 did not - indicate any problem, but GCC 8 issued errors. Moved the - attribute before the function name, as required. - - (ADB - 2018/05/22, HDFFV-10473) - - - Reworked java test suite into individual JUnit tests. - - Testing the whole suite of java unit tests in a single JUnit run - made it difficult to determine actual failures when tests would fail. - Running each file set of tests individually, allows individual failures - to be diagnosed easier. A side benefit is that tests for optional components - of the library can be disabled if not configured. - - (ADB - 2018/05/16, HDFFV-9739) - - - Converted CMake global commands ADD_DEFINITIONS and INCLUDE_DIRECTORIES - to use target_* type commands. This change modernizes the CMake usage - in the HDF5 library. - - In addition, there is the intention to convert to generator expressions, - where possible. The exception is Fortran FLAGS on Windows Visual Studio. - The HDF macros TARGET_C_PROPERTIES and TARGET_FORTRAN_PROPERTIES have - been removed with this change in usage. - - The additional language (C++ and Fortran) checks have also been localized - to only be checked when that language is enabled. - - (ADB - 2018/05/08) - - - Performance - ------------- - - Revamped internal use of DXPLs, improving performance - - (QAK - 2018/05/20) - - - Fortran - -------- - - Fixed issue with h5fget_obj_count_f and using a file id of H5F_OBJ_ALL_F not - returning the correct count. - - (MSB - 2018/5/15, HDFFV-10405) - - - C++ APIs - -------- - - Adding default arguments to existing functions - - Added the following items: - + Two more property list arguments are added to H5Location::createDataSet: - const DSetAccPropList& dapl = DSetAccPropList::DEFAULT - const LinkCreatPropList& lcpl = LinkCreatPropList::DEFAULT - - + One more property list argument is added to H5Location::openDataSet: - const DSetAccPropList& dapl = DSetAccPropList::DEFAULT - - (BMR - 2018/07/21, PR# 1146) - - - Improvement C++ documentation - - Replaced the table in main page of the C++ documentation from mht to htm format - for portability. - - (BMR - 2018/07/17, PR# 1141) - - -Supported Platforms -=================== - - Linux 2.6.32-696.16.1.el6.ppc64 gcc (GCC) 4.4.7 20120313 (Red Hat 4.4.7-18) - #1 SMP ppc64 GNU/Linux g++ (GCC) 4.4.7 20120313 (Red Hat 4.4.7-18) - (ostrich) GNU Fortran (GCC) 4.4.7 20120313 (Red Hat 4.4.7-18) - IBM XL C/C++ V13.1 - IBM XL Fortran V15.1 - - Linux 3.10.0-327.10.1.el7 GNU C (gcc), Fortran (gfortran), C++ (g++) - #1 SMP x86_64 GNU/Linux compilers: - (kituo/moohan) Version 4.8.5 20150623 (Red Hat 4.8.5-4) - Version 4.9.3, Version 5.2.0 - Intel(R) C (icc), C++ (icpc), Fortran (icc) - compilers: - Version 17.0.0.098 Build 20160721 - MPICH 3.1.4 compiled with GCC 4.9.3 - - SunOS 5.11 32- and 64-bit Sun C 5.12 SunOS_sparc - (emu) Sun Fortran 95 8.6 SunOS_sparc - Sun C++ 5.12 SunOS_sparc - - Windows 7 Visual Studio 2015 w/ Intel Fortran 16 (cmake) - - Windows 7 x64 Visual Studio 2012 w/ Intel Fortran 15 (cmake) - Visual Studio 2013 w/ Intel Fortran 15 (cmake) - Visual Studio 2015 w/ Intel Fortran 16 (cmake) - Visual Studio 2015 w/ Intel C, Fortran 2017 (cmake) - Visual Studio 2015 w/ MSMPI 8 (cmake) - - Windows 10 Visual Studio 2015 w/ Intel Fortran 18 (cmake) - - Windows 10 x64 Visual Studio 2015 w/ Intel Fortran 18 (cmake) - Visual Studio 2017 w/ Intel Fortran 18 (cmake) - - Mac OS X Yosemite 10.10.5 Apple clang/clang++ version 6.1 from Xcode 7.0 - 64-bit gfortran GNU Fortran (GCC) 4.9.2 - (osx1010dev/osx1010test) Intel icc/icpc/ifort version 15.0.3 - - Mac OS X El Capitan 10.11.6 Apple clang/clang++ version 7.3.0 from Xcode 7.3 - 64-bit gfortran GNU Fortran (GCC) 5.2.0 - (osx1011dev/osx1011test) Intel icc/icpc/ifort version 16.0.2 - - Mac OS Sierra 10.12.6 Apple LLVM version 8.1.0 (clang/clang++-802.0.42) - 64-bit gfortran GNU Fortran (GCC) 7.1.0 - (swallow/kite) Intel icc/icpc/ifort version 17.0.2 - -Tested Configuration Features Summary -===================================== - - In the tables below - y = tested - n = not tested in this release - C = Cluster - W = Workstation - x = not working in this release - dna = does not apply - ( ) = footnote appears below second table - <blank> = testing incomplete on this feature or platform - -Platform C F90/ F90 C++ zlib SZIP - parallel F2003 parallel -Solaris2.11 32-bit n y/y n y y y -Solaris2.11 64-bit n y/n n y y y -Windows 7 y y/y n y y y -Windows 7 x64 y y/y y y y y -Windows 7 Cygwin n y/n n y y y -Windows 7 x64 Cygwin n y/n n y y y -Windows 10 y y/y n y y y -Windows 10 x64 y y/y n y y y -Mac OS X Mavericks 10.9.5 64-bit n y/y n y y y -Mac OS X Yosemite 10.10.5 64-bit n y/y n y y y -Mac OS X El Capitan 10.11.6 64-bit n y/y n y y y -Mac OS Sierra 10.12.6 64-bit n y/y n y y y -CentOS 7.2 Linux 2.6.32 x86_64 PGI n y/y n y y y -CentOS 7.2 Linux 2.6.32 x86_64 GNU y y/y y y y y -CentOS 7.2 Linux 2.6.32 x86_64 Intel n y/y n y y y -Linux 2.6.32-573.18.1.el6.ppc64 n y/y n y y y - - -Platform Shared Shared Shared Thread- - C libs F90 libs C++ libs safe -Solaris2.11 32-bit y y y y -Solaris2.11 64-bit y y y y -Windows 7 y y y y -Windows 7 x64 y y y y -Windows 7 Cygwin n n n y -Windows 7 x64 Cygwin n n n y -Windows 10 y y y y -Windows 10 x64 y y y y -Mac OS X Mavericks 10.9.5 64-bit y n y y -Mac OS X Yosemite 10.10.5 64-bit y n y y -Mac OS X El Capitan 10.11.6 64-bit y n y y -Mac OS Sierra 10.12.6 64-bit y n y y -CentOS 7.2 Linux 2.6.32 x86_64 PGI y y y n -CentOS 7.2 Linux 2.6.32 x86_64 GNU y y y y -CentOS 7.2 Linux 2.6.32 x86_64 Intel y y y n -Linux 2.6.32-573.18.1.el6.ppc64 y y y n - -Compiler versions for each platform are listed in the preceding -"Supported Platforms" table. - - -More Tested Platforms -===================== -The following platforms are not supported but have been tested for this release. - - Linux 2.6.32-573.22.1.el6 GNU C (gcc), Fortran (gfortran), C++ (g++) - #1 SMP x86_64 GNU/Linux compilers: - (mayll/platypus) Version 4.4.7 20120313 - Version 4.9.3, 5.3.0, 6.2.0 - PGI C, Fortran, C++ for 64-bit target on - x86-64; - Version 17.10-0 - Intel(R) C (icc), C++ (icpc), Fortran (icc) - compilers: - Version 17.0.4.196 Build 20170411 - MPICH 3.1.4 compiled with GCC 4.9.3 - - Linux 3.10.0-327.18.2.el7 GNU C (gcc) and C++ (g++) compilers - #1 SMP x86_64 GNU/Linux Version 4.8.5 20150623 (Red Hat 4.8.5-4) - (jelly) with NAG Fortran Compiler Release 6.1(Tozai) - GCC Version 7.1.0 - OpenMPI 3.0.0-GCC-7.2.0-2.29, - 3.1.0-GCC-7.2.0-2.29 - Intel(R) C (icc) and C++ (icpc) compilers - Version 17.0.0.098 Build 20160721 - with NAG Fortran Compiler Release 6.1(Tozai) - - Linux 3.10.0-327.10.1.el7 MPICH 3.2 compiled with GCC 5.3.0 - #1 SMP x86_64 GNU/Linux - (moohan) - - Linux 2.6.32-573.18.1.el6.ppc64 MPICH mpich 3.1.4 compiled with - #1 SMP ppc64 GNU/Linux IBM XL C/C++ for Linux, V13.1 - (ostrich) and IBM XL Fortran for Linux, V15.1 - - Debian 8.4 3.16.0-4-amd64 #1 SMP Debian 3.16.36-1 x86_64 GNU/Linux - gcc, g++ (Debian 4.9.2-10) 4.9.2 - GNU Fortran (Debian 4.9.2-10) 4.9.2 - (cmake and autotools) - - Fedora 24 4.7.2-201.fc24.x86_64 #1 SMP x86_64 x86_64 x86_64 GNU/Linux - gcc, g++ (GCC) 6.1.1 20160621 - (Red Hat 6.1.1-3) - GNU Fortran (GCC) 6.1.1 20160621 - (Red Hat 6.1.1-3) - (cmake and autotools) - - Ubuntu 16.04.1 4.4.0-38-generic #57-Ubuntu SMP x86_64 GNU/Linux - gcc, g++ (Ubuntu 5.4.0-6ubuntu1~16.04.2) - 5.4.0 20160609 - GNU Fortran (Ubuntu 5.4.0-6ubuntu1~16.04.2) - 5.4.0 20160609 - (cmake and autotools) - - -Known Problems -============== - - At present, metadata cache images may not be generated by parallel - applications. Parallel applications can read files with metadata cache - images, but since this is a collective operation, a deadlock is possible - if one or more processes do not participate. - - Three tests fail with OpenMPI 3.0.0/GCC-7.2.0-2.29: - testphdf5 (ecdsetw, selnone, cchunk1, cchunk3, cchunk4, and actualio) - t_shapesame (sscontig2) - t_pflush1/fails on exit - The first two tests fail attempting collective writes. - - Known problems in previous releases can be found in the HISTORY*.txt files - in the HDF5 source. Please report any new problems found to - help@hdfgroup.org. - - -CMake vs. Autotools installations -================================= -While both build systems produce similar results, there are differences. -Each system produces the same set of folders on linux (only CMake works -on standard Windows); bin, include, lib and share. Autotools places the -COPYING and RELEASE.txt file in the root folder, CMake places them in -the share folder. - -The bin folder contains the tools and the build scripts. Additionally, CMake -creates dynamic versions of the tools with the suffix "-shared". Autotools -installs one set of tools depending on the "--enable-shared" configuration -option. - build scripts - ------------- - Autotools: h5c++, h5cc, h5fc - CMake: h5c++, h5cc, h5hlc++, h5hlcc - -The include folder holds the header files and the fortran mod files. CMake -places the fortran mod files into separate shared and static subfolders, -while Autotools places one set of mod files into the include folder. Because -CMake produces a tools library, the header files for tools will appear in -the include folder. - -The lib folder contains the library files, and CMake adds the pkgconfig -subfolder with the hdf5*.pc files used by the bin/build scripts created by -the CMake build. CMake separates the C interface code from the fortran code by -creating C-stub libraries for each Fortran library. In addition, only CMake -installs the tools library. The names of the szip libraries are different -between the build systems. - -The share folder will have the most differences because CMake builds include -a number of CMake specific files for support of CMake's find_package and support -for the HDF5 Examples CMake project. - - -%%%%1.10.2%%%% - -HDF5 version 1.10.2 released on 2018-03-29 -================================================================================ - - -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 HDF5-1.10.1 -- Supported Platforms -- Tested Configuration Features Summary -- More Tested Platforms -- Known Problems - - -New Features -============ - - Configuration and Build Systems: - -------------------------------- - - CMake builds - -------------- - - - Changed minimum CMake required version to 3.10. - - This change removed the need to support a copy of the FindMPI.cmake module, - which has been removed, along with its subfolder in the config/cmake_ext_mod - location. - - (ADB - 2018/03/09) - - - Added pkg-config file generation - - Added pkg-config file generation for the C, C++, HL, and HL C++ libraries. - In addition, builds on Linux will create h5cc, h5c++, h5hlcc, and h5hlc++ scripts in the bin - directory that use the pkg-config files. The scripts can be used to build HDF5 C and C++ - applications (i.e, similar to the compiler scripts produced by the Autotools builds). - - (ADB - 2018/03/08, HDFFV-4359) - - - Refactored use of CMAKE_BUILD_TYPE for new variable, which understands - the type of generator in use. - - Added new configuration macros to use new HDF_BUILD_TYPE variable. This - variable is set correctly for the type of generator being used for the build. - - (ADB - 2018/01/08, HDFFV-10385, HDFFV-10296) - - - Autotools builds - ------------------ - - - Removed version-specific gcc/gfortran flags for version 4.0 (inclusive) - and earlier. - - The config/gnu-flags file, which is sourced as a part of the configure - process, adds version-specific flags for use when building HDF5. Most of - these flags control warnings and do not affect the final product. - - Flags for older versions of the compiler were consolidated into the - common flags section. Moving these flags simplifies maintenance of - the file. - - The upshot of this is that building with ancient versions of gcc - (<= 4.0) will possibly no longer work without hand-hacking the file - to remove the flags not understood by that version of the compiler. - Nothing should change when building with gcc >= 4.1. - - (DER - 2017/05/31, HDFFV-9937) - - - -fno-omit-frame-pointer was added when building with debugging symbols - enabled. - - Debugging symbols can be enabled independently of the overall build - mode in both the autotools and CMake. This allows (limited) debugging - of optimized code. Since many debuggers rely on the frame pointer, - we've disabled this optimization when debugging symbols are requested - (e.g.: via building with --enable-symbols). - - (DER - 2017/05/31, HDFFV-10226) - - - Library: - -------- - - Added an enumerated value to H5F_libver_t for H5Pset_libver_bounds(). - - Currently, the library defines two values for H5F_libver_t and supports - only two pairs of (low, high) combinations as derived from these values. - Thus the bounds setting via H5Pset_libver_bounds() is rather restricted. - - Added an enumerated value (H5F_LIBVER_V18) to H5F_libver_t and - H5Pset_libver_bounds() now supports five pairs of (low, high) combinations - as derived from these values. This addition provides the user more - flexibility in setting bounds for object creation. - - (VC - 2018/03/14) - - - Added prefix option to VDS files. - - Currently, VDS source files must be in the active directory to be - found by the virtual file. Adding the option of a prefix to be set - on the virtual file, using a data access property list (DAPL), - allows the source files to locate at an absolute or relative path - to the virtual file. - Private utility functions in H5D and H5L packages merged into single - function in H5F package. - - New public APIs: - herr_t H5Pset_virtual_prefix(hid_t dapl_id, const char* prefix); - ssize_t H5Pget_virtual_prefix(hid_t dapl_id, char* prefix /*out*/, size_t size); - The prefix can also be set with an environment variable, HDF5_VDS_PREFIX. - - (ADB - 2017/12/12, HDFFV-9724, HDFFV-10361) - - - H5FDdriver_query() API call added to the C library. - - This new library call allows the user to query a virtual file driver - (VFD) for the feature flags it supports (listed in H5FDpublic.h). - This can be useful to determine if a VFD supports SWMR, for example. - - Note that some VFDs have feature flags that may only be present - after a file has been created or opened (e.g.: the core VFD will - have the H5FD_FEAT_POSIX_COMPAT_HANDLE flag set if the backing - store is switched on). Since the new API call queries a generic VFD - unassociated with a file, these flags will never be returned. - - (DER - 2017/05/31, HDFFV-10215) - - - H5FD_FEAT_DEFAULT_VFD_COMPATIBLE VFD feature flag added to the C library. - - This new feature flag indicates that the VFD is compatible with the - default VFD. VFDs that set this flag create single files that follow - the canonical HDF5 file format. - - (DER - 2017/05/31, HDFFV-10214) - - - The H5I_REFERENCE value in the H5I_type_t enum (defined in H5Ipublic.h) - has been marked as deprecated. - - This ID type value is not used in the C library. i.e.: There are no - hid_t values that are of ID type H5I_REFERENCE. - - This enum value will be removed in a future major version of the library. - The code will remain unchanged in the HDF5 1.10.x releases and branches. - - (DER - 2017/04/05, HDFFV-10252) - - - Parallel Library: - ----------------- - - Enabled compression for parallel applications. - - With this release parallel applications can create and write compressed - datasets (or the datasets with the filters such as Fletcher32 applied). - - (EIP - 2018/03/29) - - - Addressed slow file close on some Lustre file systems. - - Slow file close has been reported on some Lustre file systems. - While the ultimate cause is not understood fully, the proximate - cause appears to be long delays in MPI_File_set_size() calls at - file close and flush. - - To minimize this problem pending a definitive diagnosis and fix, - PHDF5 has been modified to avoid MPI_File_set_size() calls when - possible. This is done by comparing the library's EOA (End of - Allocation) with the file systems EOF, and skipping the - MPI_File_set_size() call if the two match. - - (JRM - 2018/03/29) - - - Optimized parallel open/location of the HDF5 super-block. - - Previous releases of PHDF5 required all parallel ranks to - search for the HDF5 superblock signature when opening the - file. As this is accomplished more or less as a synchronous - operation, a large number of processes can experience a - slowdown in the file open due to filesystem contention. - - As a first step in improving the startup/file-open performance, - we allow MPI rank 0 of the associated MPI communicator to locate - the base offset of the super-block and then broadcast that result - to the remaining ranks in the parallel group. Note that this - approach is utilized ONLY during file opens which employ the MPIO - file driver in HDF5 by previously having called H5Pset_fapl_mpio(). - - HDF5 parallel file operations which do not employ multiple ranks - e.g. specifying MPI_COMM_SELF (whose MPI_Comm_size == 1) - as opposed to MPI_COMM_WORLD, will not be affected by this - optimization. Conversely, parallel file operations on subgroups - of MPI_COMM_WORLD are allowed to be run in parallel with each - subgroup operating as an independent collection of processes. - - (RAW - 2017/10/10, HDFFV-10294) - - - Added large (>2GB) MPI-IO transfers. - - Previous releases of PHDF5 would fail when attempting to - read or write greater than 2GB of data in a single IO operation. - This issue stems principally from an MPI API whose definitions - utilize 32 bit integers to describe the number of data elements - and datatype that MPI should use to effect a data transfer. - Historically, HDF5 has invoked MPI-IO with the number of - elements in a contiguous buffer represented as the length - of that buffer in bytes. - - Resolving the issue and thus enabling larger MPI-IO transfers - is accomplished first, by detecting when a user IO request would - exceed the 2GB limit as described above. Once a transfer request - is identified as requiring special handling, PHDF5 now creates a - derived datatype consisting of a vector of fixed sized blocks - which is in turn wrapped within a single MPI_Type_struct to - contain the vector and any remaining data. The newly created - datatype is then used in place of MPI_BYTE and can be used to - fulfill the original user request without encountering API - errors. - - (RAW - 2017/09/10, HDFFV-8839) - - - C++ Library: - ------------ - - The following C++ API wrappers have been added to the C++ Library: - + H5Lcreate_soft: - // Creates a soft link from link_name to target_name. - void link(const char *target_name, const char *link_name,...) - void link(const H5std_string& target_name,...) - - + H5Lcreate_hard: - // Creates a hard link from new_name to curr_name. - void link(const char *curr_name, const Group& new_loc,...) - void link(const H5std_string& curr_name, const Group& new_loc,...) - - // Creates a hard link from new_name to curr_name in same location. - void link(const char *curr_name, const hid_t same_loc,...) - void link(const H5std_string& curr_name, const hid_t same_loc,...) - - Note: previous version of H5Location::link will be deprecated. - - + H5Lcopy: - // Copy an object from a group of file to another. - void copyLink(const char *src_name, const Group& dst,...) - void copyLink(const H5std_string& src_name, const Group& dst,...) - - // Copy an object from a group of file to the same location. - void copyLink(const char *src_name, const char *dst_name,...) - void copyLink(const H5std_string& src_name,...) - - + H5Lmove: - // Rename an object in a group or file to a new location. - void moveLink(const char* src_name, const Group& dst,...) - void moveLink(const H5std_string& src_name, const Group& dst,...) - - // Rename an object in a group or file to the same location. - void moveLink(const char* src_name, const char* dst_name,...) - void moveLink(const H5std_string& src_name,...) - - Note: previous version H5Location::move will be deprecated. - - + H5Ldelete: - // Removes the specified link from this location. - void unlink(const char *link_name, - const LinkAccPropList& lapl = LinkAccPropList::DEFAULT) - void unlink(const H5std_string& link_name, - const LinkAccPropList& lapl = LinkAccPropList::DEFAULT) - - Note: additional parameter is added to previous H5Location::unlink. - - + H5Tencode and H5Tdecode: - // Creates a binary object description of this datatype. - void DataType::encode() - C API H5Tencode() - - // Returns the decoded type from the binary object description. - DataType::decode() - C API H5Tdecode() - ArrayType::decode() - C API H5Tdecode() - CompType::decode() - C API H5Tdecode() - DataType::decode() - C API H5Tdecode() - EnumType::decode() - C API H5Tdecode() - FloatType::decode() - C API H5Tdecode() - IntType::decode() - C API H5Tdecode() - StrType::decode() - C API H5Tdecode() - VarLenType::decode() - C API H5Tdecode() - - + H5Lget_info: - // Returns the information of the named link. - H5L_info_t getLinkInfo(const H5std_string& link_name,...) - - (BMR - 2018/03/11, HDFFV-10149) - - - Added class LinkCreatPropList for link create property list. - - (BMR - 2018/03/11, HDFFV-10149) - - - Added overloaded functions H5Location::createGroup to take a link - creation property list. - Group createGroup(const char* name, const LinkCreatPropList& lcpl) - Group createGroup(const H5std_string& name, const LinkCreatPropList& lcpl) - - (BMR - 2018/03/11, HDFFV-10149) - - - A document is added to the HDF5 C++ API Reference Manual to show the - mapping from a C API to C++ wrappers. It can be found from the main - page of the C++ API Reference Manual. - - (BMR - 2017/10/17, HDFFV-10151) - - - Java Library: - ---------------- - - Wrapper added for enabling the error stack. - - H5error_off would disable the error stack reporting. In order - to re-enable the reporting, the error stack info needs to be - saved so that H5error_on can revert state. - - (ADB - 2018/03/13, HDFFV-10412) - - - Wrappers were added for the following C APIs: - H5Pset_evict_on_close - H5Pget_evict_on_close - H5Pset_chunk_opts - H5Pget_chunk_opts - H5Pset_efile_prefix - H5Pget_efile_prefix - H5Pset_virtual_prefix - H5Pget_virtual_prefix - - (ADB - 2017/12/20) - - - The H5I_REFERENCE value in the H5I_type_t enum (defined in H5Ipublic.h) - has been marked as deprecated. - - JNI code which refers to this value will be removed in a future - major version of the library. The code will remain unchanged in the - 1.10.x releases and branches. - - See the C library section, above, for further information. - - (HDFFV-10252, DER, 2017/04/05) - - - Tools: - ------ - - h5diff has a new option to display error stack. - - Updated h5diff with the --enable-error-stack argument, which - enables the display of the hdf5 error stack. This completes the - improvement to the main tools: h5copy, h5diff, h5dump, h5ls and - h5repack. - - (ADB - 2017/08/30, HDFFV-9774) - - -Support for new platforms, languages and compilers. -======================================= - - None - -Bug Fixes since HDF5-1.10.1 release -================================== - - Library - ------- - - The data read after a direct chunk write to a chunked dataset with - one chunk was incorrect. - - The problem was due to the passing of a null dataset pointer to - the insert callback for the chunk index in the routine - H5D__chunk_direct_write() in H5Dchunk.c - The dataset was a single-chunked dataset which will use the - single chunk index when latest format was enabled on file creation. - The single chunk index was the only index that used this pointer - in the insert callback. - - Passed the dataset pointer to the insert callback for the chunk - index in H5D__chunk_direct_write(). - - (VC - 2018/03/20, HDFFV-10425) - - - Added public routine H5DOread_chunk to the high-level C library. - - The patch for H5DOwrite_chunk() to write an entire chunk to the file - directly was contributed by GE Healthcare and integrated by The HDF Group - developers. - - (VC - 2017/05/19, HDFFV-9934) - - - Freeing of object header after failed checksum verification. - - It was discovered that the object header (in H5Ocache.c) was not released properly - when the checksum verification failed and a re-load of the object - header was needed. - - Freed the object header that failed the chksum verification only - after the new object header is reloaded, deserialized and set up. - - (VC - 2018/03/14, HDFFV-10209) - - - Updated H5Pset_evict_on_close in H5Pfapl.c - - Changed the minor error number from H5E_CANTSET to H5E_UNSUPPORTED for - parallel library. - - (ADB - 2018/03/06, HDFFV-10414) - - - Fixed the problems with the utility function that could not handle lowercase - Windows drive letters. - - Added call to upper function for drive letter. - - (ADB - 2017/12/18, HDFFV-10307) - - - Fixed H5Sencode() bug when the number of elements selected was > 2^32. - - H5Sencode() incorrectly encodes dataspace selection with number of - elements exceeding 2^32. When decoding such selection via H5Sdecode(), - the number of elements in the decoded dataspace is not the same as - what is encoded. This problem exists for H5S_SEL_HYPER and - H5S_SEL_POINTS encoding. - - The cause of the problem is due to the fact that the library uses 32 bits to - encode counts and block offsets for the selection. - The solution is to use the original 32 bit encodings if possible, - but use a different way to encode selection if more that 32 bits is needed. - See details in the RFC: H5Sencode/H5Sdecode Format Change i - https://bitbucket.hdfgroup.org/projects/HDFFV/repos/hdf5doc/browse/RFCs/HDF5_Library/H5SencodeFormatChange. - - (VC - 2017/11/28, HDFFV-9947) - - - Fixed filter plugin handling in H5PL.c and H5Z.c to not require i availability of - dependent libraries (e.g., szip or zlib). - - It was discovered that the dynamic loading process used by - filter plugins had issues with library dependencies. - - CMake build process changed to use LINK INTERFACE keywords, which - allowed HDF5 C library to make dependent libraries private. The - filter plugin libraries no longer require dependent libraries - (such as szip or zlib) to be available. - - (ADB - 2017/11/16, HDFFV-10328) - - - Fixed rare object header corruption bug. - - In certain cases, such as when converting large attributes to dense - storage, an error could occur which would either fail an assertion or - cause file corruption. Fixed and added test. - - (NAF - 2017/11/14, HDFFV-10274) - - - Updated H5Zfilter_avail in H5Z.c. - - The public function checked for plugins, while the private - function did not. - - Modified H5Zfilter_avail and private function, H5Z_filter_avail. - Moved check for plugin from public to private function. Updated - H5P__set_filter due to change in H5Z_filter_avail. Updated tests. - - (ADB - 2017/10/10, HDFFV-10297, HDFFV-10319) - - - h5dump produced SEGFAULT when dumping corrypted file. - - The behavior was due to the error in the internal function H5HL_offset_into(). - - (1) Fixed H5HL_offset_into() to return error when offset exceeds heap data - block size. - (2) Fixed other places in the library that call this routine to detect - error routine. - - (VC - 2017/08/30, HDFFV-10216) - - - Fixes for paged aggregation feature. - - Skip test in test/fheap.c when: - (1) multi/split drivers and - (2) persisting free-space or using paged aggregation strategy - - (VC, 2017/07/10) - - Changes made based on RFC review comments: - (1) Added maximum value for file space page size - (2) Dropped check for page end metadata threshold - (3) Removed "can_shrink" and "shrink" callbacks for small section class - - (VC - 2017/06/09) - - - Fixed for infinite loop in H5VM_power2up(). - - The function H5VM_power2up() returns the next power of 2 - for n. When n exceeds 2^63, it overflows and becomes 0 causing - the infinite looping. - - The fix ensures that the function checks for n >= 2^63 - and returns 0. - - (VC - 2017/07/10, HDFFV-10217) - - - Fixed for H5Ocopy doesn't work with open identifiers. - - Changes made so that raw data for dataset objects are copied from - cached info when possible instead of flushing objects to file and - read them back in again. - - (VC - 2017/07/05, HDFFV-7853) - - - An uninitialized struct could cause a memory access error when using - variable-length or reference types in a compressed, chunked dataset. - - A struct containing a callback function pointer and a pointer to some - associated data was used before initialization. This could cause a - memory access error and system crash. This could only occur under - unusual conditions when using variable-lenth and reference types in - a compressed, chunked dataset. - - On recent versions of Visual Studio, when built in debug mode, the - debug heap will complain and cause a crash if the code in question - is executed (this will cause the objcopy test to fail). - - (DER - 2017/11/21, HDFFV-10330) - - - Fixed collective metadata writes on file close. - - It was discovered that metadata was being written twice as part of - the parallel file close behavior, once independently and once - collectively. - - A fix for this error was included as part of the parallel compression - feature but remained undocumented here. - - (RAW - 2017/12/01, HDFFV-10272) - - - If an HDF5 file contains a filter pipeline message with a 'number of - filters' field that exceeds the maximum number of allowed filters, - the error handling code will attempt to dereference a NULL pointer. - - This issue was reported to The HDF Group as issue #CVE-2017-17505. - https://security-tracker.debian.org/tracker/CVE-2017-17505 - https://cve.mitre.org/cgi-bin/cvename.cgi?name=3DCVE-2017-17505 - - 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. - - This problem arose because the error handling code assumed that - the 'number of filters' field implied that a dynamic array of that - size had already been created and that the cleanup code should - iterate over that array and clean up each element's resources. If - an error occurred before the array has been allocated, this will - not be true. - - This has been changed so that the number of filters is set to - zero on errors. Additionally, the filter array traversal in the - error handling code now requires that the filter array not be NULL. - - (DER - 2018/02/06, HDFFV-10354) - - - If an HDF5 file contains a filter pipeline message which contains - a 'number of filters' field that exceeds the actual number of - filters in the message, the HDF5 C library will read off the end of - the read buffer. - - This issue was reported to The HDF Group as issue #CVE-2017-17506. - https://security-tracker.debian.org/tracker/CVE-2017-17506 - https://cve.mitre.org/cgi-bin/cvename.cgi?name=3DCVE-2017-17506 - - 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 problem was fixed by passing the buffer size with the buffer - and ensuring that the pointer cannot be incremented off the end - of the buffer. A mismatch between the number of filters declared - and the actual number of filters will now invoke normal HDF5 - error handling. - - (DER - 2018/02/26, HDFFV-10355) - - - 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. - https://security-tracker.debian.org/tracker/CVE-2017-17506 - https://cve.mitre.org/cgi-bin/cvename.cgi?name=3DCVE-2017-17506 - - 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) - - - If an HDF5 file contains a malformed compound type which contains - a member of size zero, a division by zero error will occur while - processing the type. - - This issue was reported to The HDF Group as issue #CVE-2017-17508. - https://security-tracker.debian.org/tracker/CVE-2017-17508 - https://cve.mitre.org/cgi-bin/cvename.cgi?name=3DCVE-2017-17508 - - 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. - - Checking for zero before dividing fixes the problem. Instead of the - division by zero, the normal HDF5 error handling is invoked. - - (DER - 2018/02/26, HDFFV-10357) - - - If an HDF5 file contains a malformed symbol table node that declares - it contains more symbols than it actually contains, the library - can run off the end of the metadata cache buffer while processing - the symbol table node. - - This issue was reported to The HDF Group as issue #CVE-2017-17509. - https://security-tracker.debian.org/tracker/CVE-2017-17509 - https://cve.mitre.org/cgi-bin/cvename.cgi?name=3DCVE-2017-17509 - - 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. - - Performing bounds checks on the buffer while processing fixes the - problem. Instead of the segmentation fault, the normal HDF5 error - handling is invoked. - - (DER - 2018/03/12, HDFFV-10358) - - - Fixed permissions passed to open(2) on file create. - - On Windows, the POSIX permissions passed to open(2) when creating files - were only incidentally correct. They are now set to the correct value of - (_S_IREAD | _S_IWRITE). - - On other platforms, the permissions were set to a mix of 666, 644, and - 000. They are now set uniformly to 666. - - (DER - 2017/04/28, HDFFV-9877) - - - The H5FD_FEAT_POSIX_COMPAT_HANDLE flag is no longer used to determine - if a virtual file driver (VFD) is compatible with SWMR. - - Use of this VFD feature flag was not in line with the documentation in - the public H5FDpublic.h file. In particular, it was being used as a - proxy for determining if SWMR I/O is allowed. This is unnecessary as we - already have a feature flag for this (H5FD_SUPPORTS_SWMR_IO). - - (DER - 2017/05/31, HDFFV-10214) - - - Configuration - ------------- - - CMake changes - - - Updated CMake commands configuration. - - A number of improvements were made to the CMake commands. Most - changes simplify usage or eliminate unused constructs. Also, - some changes support better cross-platform support. - - (ADB - 2018/02/01, HDFFV-10398) - - - Corrected usage of CMAKE_BUILD_TYPE variable. - - The use of the CMAKE_BUILD_TYPE is incorrect for multi-config - generators (Visual Studio and XCode) and is optional for single - config generators. Created a new macro to check - GLOBAL PROPERTY -> GENERATOR_IS_MULTI_CONFIG - Created two new HDF variable, HDF_BUILD_TYPE and HDF_CFG_BUILD_TYPE. - Defaults for these variables is "Release". - - (ADB - 2018/01/10, HDFFV-10385) - - - Added replacement of fortran flags if using static CRT. - - Added TARGET_STATIC_CRT_FLAGS call to HDFUseFortran.cmake file in - config/cmake_ext_mod folder. - - (ADB - 2018/01/08, HDFFV-10334) - - - - The hdf5 library used shared szip and zlib, which needlessly required - applications to link with the same szip and zlib libraries. - - Changed the target_link_libraries commands to use the static libs. - Removed improper link duplication of szip and zlib. - Adjusted the link dependencies and the link interface values of - the target_link_libraries commands. - - (ADB - 2017/11/14, HDFFV-10329) - - - CMake MPI - - CMake implementation for MPI was problematic and would create incorrect - MPI library references in the hdf5 libraries. - - Reworked the CMake MPI code to properly create CMake targets. Also merged - the latest CMake FindMPI.cmake changes to the local copy. This is necessary - until HDF changes the CMake minimum to 3.9 or greater. - - (ADB - 2017/11/02, HDFFV-10321) - - - Corrected FORTRAN_HAVE_C_LONG_DOUBLE processing in the autotools. - - A bug in the autotools Fortran processing code always set the - FORTRAN_HAVE_C_LONG_DOUBLE variable to be true regardless of - whether or not a C long double type was present. - - This would cause compilation failures on platforms where a C - long double type was not available and the Fortran wrappers - were being built. - - (DER - 2017/07/05, HDFFV-10247) - - - The deprecated --enable-production and --enable-debug configure options - failed to emit errors when passed an empty string - (e.g.: --enable-debug=""). - - Due to the way we checked for these options being set, it was possible - to avoid the error message and continue configuration if an empty string - was passed to the option. - - Any use of --enable-production or --enable-debug will now halt the - configuration step and emit a helpful error message - (use --enable-build-mode=debug|production instead). - - (DER - 2017/07/05, HDFFV-10248) - - - CMake - - Too many commands for POST_BUILD step caused command line to be - too big on windows. - - Changed foreach of copy command to use a custom command with the - use of the HDFTEST_COPY_FILE macro. - - (ADB - 2017/07/12, HDFFV-10254) - - - CMake test execution environment - - The parallel HDF5 test: 't_pread' assumed the use of autotools - and the directory structure associated with that testing approach. - Modified the test code to check whether the 'h5jam' utility can be - found in the same directory as the test executable (which is - preferred directory structure utilized by cmake) and if found - will invoke the tool directly rather than utilizing a relative path. - - (RAW - 2017/11/03, HDFFV-10318) - - - Fortran compilation fails for xlf and CMake builds. - - Fixed CMake shared library build for H5match_types and modules - - (MSB - 2017/12/19, HDFFV-10363) - - - Shared libraries fail test on OSX with Fortran enabled with CMake. - - Fixed by removing the F77 use of EQUIVALENCE and COMMON, replaced - using MODULES. Updated CMake. - - (MSB - 2017/12/07, HDFFV-10223) - - - The bin/trace script now emits an error code on problems and autogen.sh - will fail if bin/trace fails. - - The bin/trace script adds tracing functionality to public HDF5 API calls. - It is only of interest to developers who modify the HDF5 source code. - Previously, bin/trace just wrote an error message to stdout when it - encountered problems, so autogen.sh processing did not halt and a broken - version of the library could be built. The script will now return an - error code when it encounters problems, and autogen.sh will fail. - - This only affects users who run autogen.sh to rebuild the Autotools files, - which is not necessary to build HDF5 from source in official releases of the - library. CMake users are unaffected as bin/trace is not run via CMake - at this time. - - (DER - 2017/04/25, HDFFV-10178) - - - FC_BASENAME was changed from gfortran40 to gfortran in a few places. - - In the autotools, FC_BASENAME was set to gfortran40 in a few locations - (config/gnu-fflags and config/freebsd). This was probably a historical - artifact and did not seem to affect many users. - - The value is now correctly set to gfortran. - - (DER - 2017/05/26, HDFFV-10249) - - - The ar flags were changed to -cr (was: -cru) - - The autotools set the flags for ar to -cru by default. The -u flag, - which allows selective replacement of only the members which have - changed, raises warnings on some platforms, so the flags are now set to - -cr via AR_FLAGS in configure.ac. This causes the static library to - always be completely recreated from the object files on each build. - - (DER - 2017/11/15, HDFFV-10428) - - - Fortran - -------- - - Fixed compilation errors when using Intel 18 Fortran compilers - (MSB - 2017/11/3, HDFFV-10322) - - Tools - ----- - - h5clear - - An enhancement to the tool in setting a file's stored EOA. - - It was discovered that a crashed file's stored EOA in the superblock - was smaller than the actual file's EOF. When the file was reopened - and closed, the library truncated the file to the stored EOA. - - Added an option to the tool in setting the file's stored EOA in the - superblock to the maximum of (EOA, EOF) + increment. - An option was also added to print the file's EOA and EOF. - - (VC - 2018/03/14, HDFFV-10360) - - - h5repack - - h5repack changes the chunk parameters when a change of layout is not - specified and a filter is applied. - - HDFFV-10297, HDFFV-10319 reworked code for h5repack and h5diff code - in the tools library. The check for an existing layout was incorrectly - placed into an if block and not executed. The check was moved into - the normal path of the function. - - (ADB - 2018/02/21, HDFFV-10412) - - - h5dump - - The tools library will hide the error stack during file open. - - While this is preferable almost always, there are reasons to enable - display of the error stack when a tool will not open a file. Adding an - optional argument to the --enable-error-stack will provide this use case. - As an optional argument it will not affect the operation of the - --enable-error-stack. h5dump is the only tool to implement this change. - - (ADB - 2018/02/15, HDFFV-10384) - - - h5dump - - h5dump would output an indented blank line in the filters section. - - h5dump overused the h5tools_simple_prefix function, which is a - function intended to account for the data index (x,y,z) option. - Removed the function call for header information. - - (ADB - 2018/01/25, HDFFV-10396) - - - h5repack - - h5repack incorrectly searched internal object table for name. - - h5repack would search the table of objects for a name, if the - name did not match it tried to determine if the name without a - leading slash would match. The logic was flawed! The table - stored names(paths) without a leading slash and did a strstr - of the table path to the name. - The assumption was that if there was a difference of one then - it was a match, however "pressure" would match "/pressure" as - well as "/pressure1", "/pressure2", etc. Changed logic to remove - any leading slash and then do a full compare of the name. - - (ADB - 2018/01/18, HDFFV-10393) - - - h5repack - - h5repack failed to handle command line parameters for customer filters. - - User defined filter parameter conversions would fail when integers were - represented on the command line with character string - larger then 9 characters. Increased local variable array for storing - the current command line parameter to prevent buffer overflows. - - (ADB - 2018/01/17, HDFFV-10392) - - - h5diff - - h5diff seg faulted if comparing VL strings against fixed strings. - - Reworked solution for HDFFV-8625 and HDFFV-8639. Implemented the check - for string objects of same type in the diff_can_type function by - adding an if(tclass1 == H5T_STRING) block. This "if block" moves the - same check that was added for attributes to this function, which is - used by all object types. This function handles complex type structures. - Also added a new test file in h5diffgenttest for testing this issue - and removed the temporary files used in the test scripts. - - (ADB - 2018/01/04, HDFFV-8745) - - - h5repack - - h5repack failed to copy a dataset with existing filter. - - Reworked code for h5repack and h5diff code in the tools library. Added - improved error handling, cleanup of resources and checks of calls. - Modified H5Zfilter_avail and private function, H5Z_filter_avail. - Moved check for plugin from public to private function. Updated - H5P__set_filter due to change in H5Z_filter_avail. Updated tests. - Note, h5repack output display has changed to clarify the individual - steps of the repack process. The output indicates if an operation - applies to all objects. Lines with notation and no information - have been removed. - - (ADB - 2017/10/10, HDFFV-10297, HDFFV-10319) - - - h5repack - - h5repack always set the User Defined filter flag to H5Z_FLAG_MANDATORY. - - Added another parameter to the 'UD=' option to set the flag by default - to '0' or H5Z_FLAG_MANDATORY, the other choice is '1' or H5Z_FLAG_OPTIONAL. - - (ADB - 2017/08/31, HDFFV-10269) - - - h5ls - - h5ls generated error on stack when it encountered a H5S_NULL - dataspace. - - Adding checks for H5S_NULL before calling H5Sis_simple (located - in the h5tools_dump_mem function) fixed the issue. - - (ADB - 2017/08/17, HDFFV-10188) - - - h5repack - - Added tests to h5repack.sh.in to verify options added for paged - aggregation work as expected. - - (VC - 2017/08/03) - - - h5dump - - h5dump segfaulted on output of XML file. - - Function that escape'd strings used the full buffer length - instead of just the length of the replacement string in a - strncpy call. Using the correct length fixed the issue. - - (ADB - 2017/08/01, HDFFV-10256) - - - h5diff - - h5diff segfaulted on compare of a NULL variable length string. - - Improved h5diff compare of strings by adding a check for - NULL strings and setting the lengths to zero. - - (ADB - 2017/07/25, HDFFV-10246) - - - h5import - - h5import crashed trying to import data from a subset of a dataset. - - Improved h5import by adding the SUBSET keyword. h5import understands - to use the Count times the Block as the size of the dimensions. - Added INPUT_B_ORDER keyword to old-style configuration files. - The import from h5dump function expects the binary files to use native - types (FILE '-b' option) in the binary file. - - (ADB - 2017/06/15, HDFFV-10219) - - - h5repack - - h5repack did not maintain the creation order flag of the root - group. - - Improved h5repack by reading the creation order and applying the - flag to the new root group. Also added arguments to set the - order and index direction, which applies to the traversing of the - original file, on the command line. - - (ADB - 2017/05/26, HDFFV-8611) - - - h5diff - - h5diff failed to account for strpad type and null terminators - of char strings. Also, h5diff failed to account for string length - differences and would give a different result depending on file - order in the command line. - - Improved h5diff compare of strings and arrays by adding a check for - string lengths and if the strpad was null filled. - - (ADB - 2017/05/18, HDFFV-9055, HDFFV-10128) - - High-Level APIs: - ------ - - H5DOwrite_chunk() problems when overwriting an existing chunk with - no filters enabled. - - When overwriting chunks and no filters were being used, the library would - fail (when asserts are enabled, e.g. debug builds) or incorrectly - insert additional chunks instead of overwriting (when asserts are not - enabled, e.g. production builds). - - This has been fixed and a test was added to the hl/test_dset_opt test. - - (DER - 2017/05/11, HDFFV-10187) - - C++ APIs - -------- - - Removal of memory leaks. - - A private function was inadvertently called, causing memory leaks. This - is now fixed. - - (BMR - 2018/03/12 - User's reported in email) - - Testing - ------- - - Memory for three variables in testphdf5's coll_write_test was malloced - but not freed, leaking memory when running the test. - - The variables' memory is now freed. - - (LRK - 2018/03/12, HDFFV-10397) - - - Refactored the testpar/t_bigio.c test to include ALARM macros - - Changed the test to include the ALARM_ON and ALARM_OFF macros which - are intended to prevent nightly test hangs that have been observed - with this particular parallel test example. The code was also modified to - simplify status reporting (only from MPI rank 0) and additional - status checking added. - - (RAW - 2017/11/08, HDFFV-10301) - - -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 2012 w/ Intel Fortran 15 (cmake) - Visual Studio 2013 w/ Intel Fortran 15 (cmake) - Visual Studio 2015 w/ Intel Fortran 16 (cmake) - - Windows 7 x64 Visual Studio 2012 w/ Intel Fortran 15 (cmake) - Visual Studio 2013 w/ Intel Fortran 15 (cmake) - Visual Studio 2015 w/ Intel Fortran 16 (cmake) - Visual Studio 2015 w/ Intel C, Fortran 2017 (cmake) - Visual Studio 2015 w/ MSMPI 8 (cmake) - Cygwin(CYGWIN_NT-6.1 2.8.0(0.309/5/3) - gcc and gfortran compilers (GCC 5.4.0) - (cmake and autotools) - - Windows 10 Visual Studio 2015 w/ Intel Fortran 16 (cmake) - Cygwin(CYGWIN_NT-6.1 2.8.0(0.309/5/3) - gcc and gfortran compilers (GCC 5.4.0) - (cmake and autotools) - - Windows 10 x64 Visual Studio 2015 w/ Intel Fortran 16 (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 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 -CentOS 7.2 Linux 2.6.32 x86_64 PGI n y/y n y y y -CentOS 7.2 Linux 2.6.32 x86_64 GNU y y/y y y y y -CentOS 7.2 Linux 2.6.32 x86_64 Intel n y/y n y y y -Linux 2.6.32-573.18.1.el6.ppc64 n y/y n y y y - - -Platform Shared Shared Shared Thread- - C libs F90 libs C++ libs safe -Solaris2.11 32-bit y y y y -Solaris2.11 64-bit y y y y -Windows 7 y y y y -Windows 7 x64 y y y y -Windows 7 Cygwin n n n y -Windows 7 x64 Cygwin n n n y -Windows 10 y y y y -Windows 10 x64 y y y y -Mac OS X 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 7.2 Linux 2.6.32 x86_64 PGI y y y n -CentOS 7.2 Linux 2.6.32 x86_64 GNU y y y y -CentOS 7.2 Linux 2.6.32 x86_64 Intel y y y n -Linux 2.6.32-573.18.1.el6.ppc64 y y y n - -Compiler versions for each platform are listed in the preceding -"Supported Platforms" table. - - -More Tested Platforms -===================== -The following platforms are not supported but have been tested for this release. - - Linux 2.6.32-573.22.1.el6 GNU C (gcc), Fortran (gfortran), C++ (g++) - #1 SMP x86_64 GNU/Linux compilers: - (mayll/platypus) Version 4.4.7 20120313 - Version 4.9.3, 5.3.0, 6.2.0 - PGI C, Fortran, C++ for 64-bit target on - x86-64; - Version 17.10-0 - Intel(R) C (icc), C++ (icpc), Fortran (icc) - compilers: - Version 17.0.4.196 Build 20170411 - MPICH 3.1.4 compiled with GCC 4.9.3 - - Linux 3.10.0-327.18.2.el7 GNU C (gcc) and C++ (g++) compilers - #1 SMP x86_64 GNU/Linux Version 4.8.5 20150623 (Red Hat 4.8.5-4) - (jelly) with NAG Fortran Compiler Release 6.1(Tozai) - GCC Version 7.1.0 - OpenMPI 3.0.0-GCC-7.2.0-2.29 - Intel(R) C (icc) and C++ (icpc) compilers - Version 17.0.0.098 Build 20160721 - with NAG Fortran Compiler Release 6.1(Tozai) - - Linux 3.10.0-327.10.1.el7 MPICH 3.2 compiled with GCC 5.3.0 - #1 SMP x86_64 GNU/Linux - (moohan) - - Linux 2.6.32-573.18.1.el6.ppc64 MPICH mpich 3.1.4 compiled with - #1 SMP ppc64 GNU/Linux IBM XL C/C++ for Linux, V13.1 - (ostrich) and IBM XL Fortran for Linux, V15.1 - - Debian 8.4 3.16.0-4-amd64 #1 SMP Debian 3.16.36-1 x86_64 GNU/Linux - gcc, g++ (Debian 4.9.2-10) 4.9.2 - GNU Fortran (Debian 4.9.2-10) 4.9.2 - (cmake and autotools) - - Fedora 24 4.7.2-201.fc24.x86_64 #1 SMP x86_64 x86_64 x86_64 GNU/Linux - gcc, g++ (GCC) 6.1.1 20160621 - (Red Hat 6.1.1-3) - GNU Fortran (GCC) 6.1.1 20160621 - (Red Hat 6.1.1-3) - (cmake and autotools) - - Ubuntu 16.04.1 4.4.0-38-generic #57-Ubuntu SMP x86_64 GNU/Linux - gcc, g++ (Ubuntu 5.4.0-6ubuntu1~16.04.2) - 5.4.0 20160609 - GNU Fortran (Ubuntu 5.4.0-6ubuntu1~16.04.2) - 5.4.0 20160609 - (cmake and autotools) - - -Known Problems -============== - - At present, metadata cache images may not be generated by parallel - applications. Parallel applications can read files with metadata cache - images, but since this is a collective operation, a deadlock is possible - if one or more processes do not participate. - - Three tests fail with OpenMPI 3.0.0/GCC-7.2.0-2.29: - testphdf5 (ecdsetw, selnone, cchunk1, cchunk3, cchunk4, and actualio) - t_shapesame (sscontig2) - t_pflush1/fails on exit - The first two tests fail attempting collective writes. - - Known problems in previous releases can be found in the HISTORY*.txt files - in the HDF5 source. Please report any new problems found to - help@hdfgroup.org. - - -%%%%1.10.1%%%% - -HDF5 version 1.10.1 released on 2017-04-27 -================================================================================ - -INTRODUCTION - -This document describes the differences between HDF5-1.10.0-patch1 and -HDF5 1.10.1, and contains information on the platforms tested and known -problems in HDF5-1.10.1. For more details check the HISTORY*.txt files -in the HDF5 source. - -Links to HDF5 1.10.1 source code, documentation, and additional materials can -be found on The HDF5 web page at: - - https://support.hdfgroup.org/HDF5/ - -The HDF5 1.10.1 release can be obtained from: - - https://support.hdfgroup.org/HDF5/release/obtain5.html - -User documentation for the snapshot can be accessed directly at this location: - - https://support.hdfgroup.org/HDF5/doc/ - -New features in the HDF5-1.10.x release series, including brief general -descriptions of some new and modified APIs, are described in the "New Features -in HDF5 Release 1.10" document: - - https://support.hdfgroup.org/HDF5/docNewFeatures/index.html - -All new and modified APIs are listed in detail in the "HDF5 Software Changes -from Release to Release" document, in the section "Release 10.1 (current -release) versus Release 1.10.0 - - https://support.hdfgroup.org/HDF5/doc/ADGuide/Changes.html - -If you have any questions or comments, please send them to the HDF Help Desk: - - help@hdfgroup.org - - -CONTENTS - -- Major New Features Introduced in HDF5 1.10.1 -- Other New Features and Enhancements -- Support for New Platforms, Languages, and Compilers -- Bug Fixes since HDF5-1.10.0-patch1 -- Supported Platforms -- Tested Configuration Features Summary -- More Tested Platforms -- Known Problems - - -Major New Features Introduced in HDF5 1.10.1 -============================================ - -For links to the RFCs and documentation in this section please view -https://support.hdfgroup.org/HDF5/docNewFeatures in a web browser. - -________________________________________ -Metadata Cache Image -________________________________________ - - HDF5 metadata is typically small, and scattered throughout the HDF5 file. - This can affect performance, particularly on large HPC systems. The - Metadata Cache Image feature can improve performance by writing the - metadata cache in a single block on file close, and then populating the - cache with the contents of this block on file open, thus avoiding the many - small I/O operations that would otherwise be required on file open and - close. See the RFC for complete details regarding this feature. Also, - see the Fine Tuning the Metadata Cache documentation. - - 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. - -________________________________________ -Metadata Cache Evict on Close -________________________________________ - - The HDF5 library's metadata cache is fairly conservative about holding on - to HDF5 object metadata (object headers, chunk index structures, etc.), - which can cause the cache size to grow, resulting in memory pressure on - an application or system. The "evict on close" property will cause all - metadata for an object to be evicted from the cache as long as metadata - is not referenced from any other open object. See the Fine Tuning the - Metadata Cache documentation for information on the APIs. - - At present, evict on close is disabled in parallel builds. - -________________________________________ -Paged Aggregation -________________________________________ - - The current HDF5 file space allocation accumulates small pieces of metadata - and raw data in aggregator blocks which are not page aligned and vary - widely in sizes. The paged aggregation feature was implemented to provide - efficient paged access of these small pieces of metadata and raw data. - See the RFC for details. Also, see the File Space Management documentation. - -________________________________________ -Page Buffering -________________________________________ - - Small and random I/O accesses on parallel file systems result in poor - performance for applications. Page buffering in conjunction with paged - aggregation can improve performance by giving an application control of - minimizing HDF5 I/O requests to a specific granularity and alignment. - See the RFC for details. Also, see the Page Buffering documentation. - - At present, page buffering is disabled in parallel builds. - - - -Other New Features and Enhancements -=================================== - - Library - ------- - - Added a mechanism for disabling the SWMR file locking scheme. - - The file locking calls used in HDF5 1.10.0 (including patch1) - will fail when the underlying file system does not support file - locking or where locks have been disabled. To disable all file - locking operations, an environment variable named - HDF5_USE_FILE_LOCKING can be set to the five-character string - 'FALSE'. This does not fundamentally change HDF5 library - operation (aside from initial file open/create, SWMR is lock-free), - but users will have to be more careful about opening files - to avoid problematic access patterns (i.e.: multiple writers) - that the file locking was designed to prevent. - - Additionally, the error message that is emitted when file lock - operations set errno to ENOSYS (typical when file locking has been - disabled) has been updated to describe the problem and potential - resolution better. - - (DER, 2016/10/26, HDFFV-9918) - - - The return type of H5Pget_driver_info() has been changed from void * - to const void *. - - The pointer returned by this function points to internal library - memory and should not be freed by the user. - - (DER, 2016/11/04, HDFFV-10017) - - - The direct I/O VFD has been removed from the list of VFDs that - support SWMR. - - This configuration was never officially tested and several SWMR - tests fail when this VFD is set. - - (DER, 2016/11/03, HDFFV-10169) - - Configuration: - -------------- - - The minimum version of CMake required to build HDF5 is now 3.2.2. - - (ADB, 2017/01/10) - - - An --enable/disable-developer-warnings option has been added to - configure. - - This disables warnings that do not indicate poor code quality such - as -Winline and gcc's -Wsuggest-attribute. Developer warnings are - disabled by default. - - (DER, 2017/01/10) - - - A bin/restore.sh script was added that reverts autogen.sh processing. - - (DER, 2016/11/08) - - - CMake: Added NAMESPACE hdf5:: to package configuration files to allow - projects using installed HDF5 binaries built with CMake to link with - them without specifying the HDF5 library location via IMPORTED_LOCATION. - - (ABD, 2016/10/17, HDFFV-10003) - - - CMake: Changed the CTEST_BUILD_CONFIGURATION option to - CTEST_CONFIGURATION_TYPE as recommended by the CMake documentation. - - (ABD, 2016/10/17, HDFFV-9971) - - - Fortran Library: - ---------------- - - - The HDF5 Fortran library can now be compiled with the NAG compiler. - - (MSB, 2017/2/10, HDFFV-9973) - - - C++ Library: - ------------ - - - The following C++ API wrappers have been added to the C++ Library: - - // Sets/Gets the strategy and the threshold value that the library - // will employ in managing file space. - FileCreatPropList::setFileSpaceStrategy - H5Pset_file_space_strategy - FileCreatPropList::getFileSpaceStrategy - H5Pget_file_space_strategy - - // Sets/Gets the file space page size for paged aggregation. - FileCreatPropList::setFileSpacePagesize - H5Pset_file_space_page_size - FileCreatPropList::getFileSpacePagesize - H5Pget_file_space_page_size - - // Checks if the given ID is valid. - IdComponent::isValid - H5Iis_valid - - // Sets/Gets the number of soft or user-defined links that can be - // traversed before a failure occurs. - LinkAccPropList::setNumLinks - H5Pset_nlinks - LinkAccPropList::getNumLinks - H5Pget_nlinks - - // Returns a copy of the creation property list of a datatype. - DataType::getCreatePlist - H5Tget_create_plist - - // Opens/Closes an object within a group or a file, regardless of object - // type - Group::getObjId - H5Oopen - Group::closeObjId - H5Oclose - - // Maps elements of a virtual dataset to elements of the source dataset. - DSetCreatPropList::setVirtual - H5Pset_virtual - - // Gets general information about this file. - H5File::getFileInfo - H5Fget_info2 - - // Returns the number of members in a type. - IdComponent::getNumMembers - H5Inmembers - - // Determines if an element type exists. - IdComponent::typeExists - H5Itype_exists - - // Determines if an object exists. - H5Location::exists - H5Lexists. - - // Returns the header version of an HDF5 object. - H5Object::objVersion - H5Oget_info for version - - (BMR, 2017/03/20, HDFFV-10004, HDFFV-10139, HDFFV-10145) - - - New exception: ObjHeaderIException for H5O interface. - - (BMR, 2017/03/15, HDFFV-10145) - - - New class LinkAccPropList for link access property list, to be used by - wrappers of H5Lexists. - - (BMR, 2017/01/04, HDFFV-10145) - - - New constructors to open datatypes in ArrayType, CompType, DataType, - EnumType, FloatType, IntType, StrType, and VarLenType. - - (BMR, 2016/12/26, HDFFV-10056) - - - New member functions: - - DSetCreatPropList::setNbit() to setup N-bit compression for a dataset. - - ArrayType::getArrayNDims() const - ArrayType::getArrayDims() const - both to replace the non-const versions. - - (BMR, 2016/04/25, HDFFV-8623, HDFFV-9725) - - - Tools: - ------ - - The following options have been added to h5clear: - -s: clear the status_flags field in the file's superblock - -m: Remove the metadata cache image from the file - - (QAK, 2017/03/22, PR#361) - - - High-Level APIs: - --------------- - - Added New Fortran 2003 API for h5tbmake_table_f. - - (MSB, 2017/02/10, HDFFV-8486) - - - -Support for New Platforms, Languages, and Compilers -=================================================== - - - Added NAG compiler - - - -Bug Fixes since HDF5-1.10.0-patch1 release -================================== - - Library - ------- - - Outdated data structure was used in H5D_CHUNK_DEBUG blocks, causing - compilation errors when H5D_CHUNK_DEBUG was defined. This is fixed. - - (BMR, 2017/04/04, HDFFV-8089) - - - SWMR implementation in the HDF5 1.10.0 and 1.10.0-patch1 releases has a - broken metadata flush dependency that manifested itself with the following - error at the end of the HDF5 error stack: - - H5Dint.c line 846 in H5D__swmr_setup(): dataspace chunk index must be 0 - for SWMR access, chunkno = 1 - major: Dataset - minor: Bad value - - It was also reported at https://github.com/areaDetector/ADCore/issues/203 - - The flush dependency is fixed in this release. - - - Changed the plugins dlopen option from RTLD_NOW to RTLD_LAZY - - (ABD, 2016/12/12, PR#201) - - - A number of issues were fixed when reading/writing from/to corrupted - files to ensure that the library fails gracefully in these cases: - - * Writing to a corrupted file that has an object message which is - incorrectly marked as shareable on disk results in a buffer overflow / - invalid write instead of a clean error message. - - * Decoding data from a corrupted file with a dataset encoded with the - H5Z_NBIT decoding can result in a code execution vulnerability under - the context of the application using the HDF5 library. - - * When decoding an array datatype from a corrupted file, the HDF5 library - fails to return an error in production if the number of dimensions - decoded is greater than the maximum rank. - - * When decoding an "old style" array datatype from a corrupted file, the - HDF5 library fails to return an error in production if the number of - dimensions decoded is greater than the maximum rank. - - (NAF, 2016/10/06, HDFFV-9950, HDFFV-9951, HDFFV-9992, HDFFV-9993) - - - Fixed an error that would occur when copying an object with an attribute - which is a compound datatype consisting of a variable length string. - - (VC, 2016/08/24, HDFFV-7991) - - - H5DOappend will no longer fail if a dataset has no append callback - registered. - - (VC, 2016/08/14, HDFFV-9960) - - - Fixed an issue where H5Pset_alignment could result in misaligned blocks - with some input combinations, causing an assertion failure in debug mode. - - (NAF, 2016/08/11, HDFFV-9948) - - - Fixed a problem where a plugin compiled into a DLL in the default plugin - directory could not be found by the HDF5 library at runtime on Windows - when the HDF5_PLUGIN_PATH environment variable was not set. - - (ABD, 2016/08/01, HDFFV-9706) - - - Fixed an error that would occur when calling H5Adelete on an attribute - which is attached to an externally linked object in the target file and - whose datatype is a committed datatype in the main file. - - (VC, 2016/07/06, HDFFV-9940) - - - (a) Throw an error instead of assertion when v1 btree level hits the 1 - byte limit. - (b) Modifications to better handle error recovery when conversion by - h5format_convert fails. - - (VC, 2016/05/29, HDFFV-9434) - - - Fixed a memory leak where an array used by the library to track SWMR - read retries was unfreed. - - The leaked memory was small (on the order of a few tens of ints) and - allocated per-file. The memory was allocated (and lost) only when a - file was opened for SWMR access. - - (DER, 2016/04/27, HDFFV-9786) - - - Fixed a memory leak that could occur when opening a file for the first - time (including creating) and the call fails. - - This occurred when the file-driver-specific info was not cleaned up. - The amount of memory leaked varied with the file driver, but would - normally be less than 1 kB. - - (DER, 2016/12/06, HDFFV-10168) - - - Fixed a failure in collective metadata writes. - - This failure only appeared when collective metadata writes - were enabled (via H5Pset_coll_metadata_write()). - - (JRM, 2017/04/10, HDFFV-10055) - - - Parallel Library - ---------------- - - Fixed a bug that could occur when allocating a chunked dataset in parallel - with an alignment set and an alignment threshold greater than the chunk - size but less than or equal to the raw data aggregator size. - - (NAF, 2016/08/11, HDFFV-9969) - - - Configuration - ------------- - - Configuration will check for the strtoll and strtoull functions - before using alternatives - - (ABD, 2017/03/17, PR#340) - - - CMake uses a Windows pdb directory variable if available and - will generate both static and shared pdb files. - - (ABD, 2017/02/06, HDFFV-9875) - - - CMake now builds shared versions of tools. - - (ABD, 2017/02/01, HDFFV-10123) - - - Makefiles and test scripts have been updated to correctly remove files - created when running "make check" and to avoid removing any files under - source control. In-source builds followed by "make clean" and "make - distclean" should result in the original source files. - (LRK, 2017/01/17, HDFFV-10099) - - - The tools directory has been divided into two separate source and test - directories. This resolves a build dependency and, as a result, - 'make check' will no longer fail in the tools directory if 'make' was - not executed first. - - (ABD, 2016/10/27, HDFFV-9719) - - - CMake: Fixed a timeout error that would occasionally occur when running - the virtual file driver tests simultaneously due to test directory - and file name collisions. - - (ABD, 2016/09/19, HDFFV-9431) - - - CMake: Fixed a command length overflow error by converting custom - commands inside CMakeTest.cmake files into regular dependencies and - targets. - - (ABD, 2016/07/12, HDFFV-9939) - - - Fixed a problem preventing HDF5 to be built on 32-bit CYGWIN by - condensing cygwin configuration files into a single file and - removing outdated compiler settings. - - (ABD, 2016/07/12, HDFFV-9946) - - - Fortran - -------- - - Changed H5S_ALL_F from INTEGER to INTEGER(HID_T) - - (MSB, 2016/10/14, HDFFV-9987) - - - Tools - ----- - - h5diff now correctly ignores strpad in comparing strings. - - (ABD, 2017/03/03, HDFFV-10128) - - - h5repack now correctly parses the command line filter options. - - (ABD, 2017/01/24, HDFFV-10046) - - - h5diff now correctly returns an error when it cannot read data due - to an unavailable filter plugin. - - (ADB 2017/01/18, HDFFV-9994 ) - - - Fixed an error in the compiler wrapper scripts (h5cc, h5fc, et al.) - in which they would erroneously drop the file argument specified via - the -o flag when the -o flag was specified before the -c flag on the - command line, resulting in a failure to compile. - - (LRK, 2016/11/04, HDFFV-9938, HDFFV-9530) - - - h5repack User Defined (UD) filter parameters were not parsed correctly. - - The UD filter parameters were not being parsed correctly. Reworked coding - section to parse the correct values and verify number of parameters. - - (ABD, 2016/10/19, HDFFV-9996, HDFFV-9974, HDFFV-9515, HDFFV-9039) - - - h5repack allows the --enable-error-stack option on the command line. - - (ADB, 2016/08/08, HDFFV-9775) - - - C++ APIs - -------- - - The member function H5Location::getNumObjs() is moved to - class Group because the objects are in a group or a file only, - and H5Object::getNumAttrs to H5Location to get the number of - attributes at a given location. - - (BMR, 2017/03/17, PR#466) - - - Due to the change in the C API, the overloaded functions of - PropList::setProperty now need const for some arguments. They are - planned for deprecation and are replaced by new versions with proper - consts. - - (BMR, 2017/03/17, PR#344) - - - The high-level API Packet Table (PT) did not write data correctly when - the datatype is a compound type that has string type as one of the - members. This problem started in 1.8.15, after the fix of HDFFV-9042 - was applied, which caused the Packet Table to use native type to access - the data. It should be up to the application to specify whether the - buffer to be read into memory is in the machine's native architecture. - Thus, the PT is fixed to not use native type but to make a copy of the - user's provided datatype during creation or the packet table's datatype - during opening. If an application wishes to use native type to read the - data, then the application will request that. However, the Packet Table - doesn't provide a way to specify memory datatype in this release. This - feature will be available in future releases. - - (BMR, 2016/10/27, HDFFV-9758) - - - The obsolete macros H5_NO_NAMESPACE and H5_NO_STD have been removed from - the HDF5 C++ API library. - - (BMR, 2016/10/23, HDFFV-9532) - - - The problem where a user-defined function cannot access both, attribute - and dataset, using only one argument is now fixed. - - (BMR, 2016/10/11, HDFFV-9920) - - - In-memory array information, ArrayType::rank and - ArrayType::dimensions, were removed. This is an implementation - detail and should not affect applications. - - (BMR, 2016/04/25, HDFFV-9725) - - - Testing - ------- - - Fixed a problem that caused tests using SWMR to occasionally fail when - running "make check" using parallel make. - - (LRK, 2016/03/22, PR#338, PR#346, PR#358) - - -Supported Platforms -=================== - - Linux 2.6.32-573.18.1.el6.ppc64 gcc (GCC) 4.4.7 20120313 (Red Hat 4.4.7-4) - #1 SMP ppc64 GNU/Linux g++ (GCC) 4.4.7 20120313 (Red Hat 4.4.7-4) - (ostrich) GNU Fortran (GCC) 4.4.7 20120313 - (Red Hat 4.4.7-4) - 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 15.0.3.187 Build 20150407 - 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 2012 w/ Intel Fortran 15 (cmake) - Visual Studio 2013 w/ Intel Fortran 15 (cmake) - Visual Studio 2015 w/ Intel Fortran 16 (cmake) - - Windows 7 x64 Visual Studio 2012 w/ Intel Fortran 15 (cmake) - Visual Studio 2013 w/ Intel Fortran 15 (cmake) - Visual Studio 2015 w/ Intel Fortran 16 (cmake) - Visual Studio 2015 w/ MSMPI 8 (cmake) - Cygwin(CYGWIN_NT-6.1 2.8.0(0.309/5/3) - gcc and gfortran compilers (GCC 5.4.0) - (cmake and autotools) - - Windows 10 Visual Studio 2015 w/ Intel Fortran 16 (cmake) - Cygwin(CYGWIN_NT-6.1 2.8.0(0.309/5/3) - gcc and gfortran compilers (GCC 5.4.0) - (cmake and autotools) - - Windows 10 x64 Visual Studio 2015 w/ Intel Fortran 16 (cmake) - - Mac OS X Mt. Lion 10.8.5 Apple clang/clang++ version 5.1 from Xcode 5.1 - 64-bit gfortran GNU Fortran (GCC) 4.8.2 - (swallow/kite) Intel icc/icpc/ifort version 15.0.3 - - Mac OS X Mavericks 10.9.5 Apple clang/clang++ version 6.0 from Xcode 6.2 - 64-bit gfortran GNU Fortran (GCC) 4.9.2 - (wren/quail) Intel icc/icpc/ifort version 15.0.3 - - 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 from Xcode 7.3 - 64-bit gfortran GNU Fortran (GCC) 5.2.0 - (osx1010dev/osx1010test) Intel icc/icpc/ifort version 16.0.2 - - -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 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 -CentOS 7.2 Linux 2.6.32 x86_64 PGI n y/y n y y y -CentOS 7.2 Linux 2.6.32 x86_64 GNU y y/y y y y y -CentOS 7.2 Linux 2.6.32 x86_64 Intel n y/y n y y y -Linux 2.6.32-573.18.1.el6.ppc64 n y/y n y y y - - -Platform Shared Shared Shared Thread- - C libs F90 libs C++ libs safe -Solaris2.11 32-bit y y y y -Solaris2.11 64-bit y y y y -Windows 7 y y y y -Windows 7 x64 y y y y -Windows 7 Cygwin n n n y -Windows 7 x64 Cygwin n n n y -Windows 10 y y y y -Windows 10 x64 y y y y -Mac OS X 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 7.2 Linux 2.6.32 x86_64 PGI y y y n -CentOS 7.2 Linux 2.6.32 x86_64 GNU y y y y -CentOS 7.2 Linux 2.6.32 x86_64 Intel y y y n -Linux 2.6.32-573.18.1.el6.ppc64 y y y n - -Compiler versions for each platform are listed in the preceding -"Supported Platforms" table. - - -More Tested Platforms -===================== - -The following platforms are not supported but have been tested for this release. - - Linux 2.6.32-573.22.1.el6 GNU C (gcc), Fortran (gfortran), C++ (g++) - #1 SMP x86_64 GNU/Linux compilers: - (mayll/platypus) Version 4.4.7 20120313 - Version 4.8.4 - PGI C, Fortran, C++ for 64-bit target on - x86-64; - Version 16.10-0 - Intel(R) C (icc), C++ (icpc), Fortran (icc) - compilers: - Version 15.0.3.187 (Build 20150407) - 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) - Intel(R) C (icc) and C++ (icpc) compilers - Version 15.0.3.187 (Build 20150407) - with NAG Fortran Compiler Release 6.1(Tozai) - - Linux 2.6.32-573.18.1.el6.ppc64 MPICH mpich 3.1.4 compiled with - #1 SMP ppc64 GNU/Linux IBM XL C/C++ for Linux, V13.1 - (ostrich) and IBM XL Fortran for Linux, V15.1 - - Debian 8.4 3.16.0-4-amd64 #1 SMP Debian 3.16.36-1 x86_64 GNU/Linux - gcc, g++ (Debian 4.9.2-10) 4.9.2 - GNU Fortran (Debian 4.9.2-10) 4.9.2 - (cmake and autotools) - - Fedora 24 4.7.2-201.fc24.x86_64 #1 SMP x86_64 x86_64 x86_64 GNU/Linux - gcc, g++ (GCC) 6.1.1 20160621 - (Red Hat 6.1.1-3) - GNU Fortran (GCC) 6.1.1 20160621 - (Red Hat 6.1.1-3) - (cmake and autotools) - - Ubuntu 16.04.1 4.4.0-38-generic #57-Ubuntu SMP x86_64 GNU/Linux - gcc, g++ (Ubuntu 5.4.0-6ubuntu1~16.04.2) - 5.4.0 20160609 - GNU Fortran (Ubuntu 5.4.0-6ubuntu1~16.04.2) - 5.4.0 20160609 - (cmake and autotools) - - -Known Problems -============== - - At present, metadata cache images may not be generated by parallel - applications. Parallel applications can read files with metadata cache - images, but since this is a collective operation, a deadlock is possible - if one or more processes do not participate. - - 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. - - -%%%%1.10.0-patch1%%%% - - -HDF5 version 1.10.0-patch1 released on 2016-05-23 -================================================================================ - -INTRODUCTION - -This document describes the differences between HDF5-1.8 series and -HDF5 1.10.0 releases, and contains information on the platforms -tested. - -Links to HDF5 1.10.0 source code can be found on The HDF Group's -development FTP server at the following location: - - https://www.hdfgroup.org/HDF5/release/obtain5110.html - -User documentation can be accessed directly at this location: - - https://www.hdfgroup.org/HDF5/docNewFeatures/ - -For more information, see the HDF5 home page: - - https://www.hdfgroup.org/HDF5/ - -If you have any questions or comments, please send them to the HDF -Help Desk: - - help@hdfgroup.org - - - -CONTENTS - -- New Features -- Issues Addressed in this Release -- Supported Platforms -- Tested Configuration Features Summary -- More Tested Platforms -- Known Problems and Limitations - - - -New Features -============ -This release supports the following features: - - Configuration - ------------- - - API Compatibility with HDF5 1.8 Flag Was Added - - The 1.10 version of the HDF5 Library can be configured to operate - identically to the 1.8 library with the --with-default-api-version=v18 - configure flag. This allows existing code to be compiled with the 1.10 - library without requiring immediate changes to the application source - code. For additional configuration options and other details, see - "API Compatibility Macros in HDF5" at - https://www.hdfgroup.org/HDF5/doc/RM/APICompatMacros.html. - - - Autotools Configuration Has Been Extensively Reworked - - The autotools configuration options have been updated to allow more - fine-grained control of the build options and to correct some bugs. - See configure --help for comprehensive information on each option. - - Specific changes: - - * --enable-debug and --enable-production are no longer accepted. - Use --enable-build-mode=(debug | production) instead. These set - appropriate defaults for symbols, optimizations, and other - configuration options. These defaults can be overridden by the - user. - - * Extra debug output messages are no longer enabled with - --enable-debug=<package list>. Use --enable-internal-debug=<pkg list> - instead. - - * A new --enable-symbols option allows symbols to be generated - independently of the build mode. --disable-symbols can be used - to strip symbols from the binary. - - * A new --enable-asserts option sets/unsets NDEBUG. This is - independent of the build mode. This also enables some extra - low-overhead debug checks in the library. - - * A new --enable-profiling option sets profiling flags. This is - independent of the build mode. - - * A new --enable-optimization option sets the optimization level. - This is independent of the build mode. - - * Many of these options can take a flags string that will be used - to build the library. This can be useful for specifying custom - optimization flags such as -Os and -Ofast. - - * gnu C++ and Fortran use configure sub-files that update the - build flags and turn on warnings. The increase in warnings when - building these wrapper libraries is due to these flag changes - and not to a decrease in code quality. - - * The option to clear file buffers has been removed. Any buffer that - will eventually be written to disk will now always be memset - to zero. This prevents the previous contents of the buffer from - being written to the disk if the buffer contents are not - completely overwritten, which has security implications. - - - LFS Changes - - The way the autotools handle large file support (LFS) has been - overhauled in this release. - - * We assume ftello and fseeko exist - - * We no longer explicitly use the *64 I/O functions. Instead, we - rely on a mapping provided by _FILE_OFFSET_BITS or its equivalent. - - * _LARGEFILE(64)_SOURCE is no longer exported via AM_CPPFLAGS. - - - - Parallel Library - ----------------- - - Collective Metadata I/O - - Calls for HDF5 metadata can result in many small reads and writes. - On metadata reads, collective metadata I/O can improve performance - by allowing the library to perform optimizations when reading the - metadata by having one rank read the data and broadcasting it to - all other ranks. - - Collective metadata I/O improves metadata write performance through - the construction of an MPI derived datatype that is then written - collectively in a single call. For more information, see - https://www.hdfgroup.org/HDF5/docNewFeatures/NewFeaturesCollectiveMetadataIoDocs.html. - - - - Library - -------- - - Concurrent Access to HDF5 Files - Single Writer/ Multiple Reader (SWMR) - - The Single Writer/ Multiple Reader or SWMR feature enables users to - read data concurrently while writing it. Communications between the - processes and file locking are not required. The processes can run - on the same or on different platforms as long as they share a common - file system that is POSIX compliant. For more information, see the - Single-Writer/Multiple-Reader (SWMR) documentation at - https://www.hdfgroup.org/HDF5/docNewFeatures/NewFeaturesSwmrDocs.html. - - - Virtual Dataset (VDS) - - The VDS feature enables data to be accessed across HDF5 files - using standard HDF5 objects such as groups and datasets without - rewriting or rearranging the data. An HDF5 virtual dataset (VDS) - is an HDF5 dataset that is composed of source HDF5 datasets in - a predefined mapping. VDS can be used with the SWMR feature. For - documentation, check - https://www.hdfgroup.org/HDF5/docNewFeatures/NewFeaturesVirtualDatasetDocs.html. - - - Persistent Free File Space Tracking - - Usage patterns when working with an HDF5 file sometimes result in - wasted space within the file. This can also impair access times - when working with the resulting files. The new file space management - feature provides strategies for managing space in a file to improve - performance in both of these areas. For more information, see - https://www.hdfgroup.org/HDF5/docNewFeatures/NewFeaturesFileSpaceMgmtDocs.html. - - - Version 3 Metadata Cache - - The version 3 metadata cache moves management of metadata I/O from - the clients to the metadata cache proper. This change is essential for - SWMR and other features that have yet to be released. - - - - C++ Library - ------------ - - New Member Function Added to H5::ArrayType - - The assignment operator ArrayType::operator= was added because - ArrayType has pointer data members. - - (BMR - 2016/03/07, HDFFV-9562) - - - - Tools - ------ - - h5watch - - The h5watch tool allows users to output new records appended to - a dataset under SWMR access as it grows. The functionality is - similar to the Unix user command "tail" with the follow option, - which outputs appended data as the file grows. For more - information, see - https://www.hdfgroup.org/HDF5/docNewFeatures/NewFeaturesSwmrDocs.html#Tools. - - - h5format_convert - - The h5format_convert tool allows users to convert the indexing - type of a chunked dataset made with a 1.10.x version of the HDF5 - Library when the latest file format is used to the 1.8.x version 1 B-tree indexing - type. For example, datasets created using SWMR access, can be - converted to be accessed by the HDF5 1.18 library and tools. The - tool does not rewrite raw data, but it does rewrite HDF5 metadata. - - - - High-Level APIs - ---------------- - - H5DOappend - - The function appends data to a dataset along a specified dimension. - - - C Packet Table API - ------------------ - - Replacement of a Public Function with H5PTcreate - - The existing function H5PTcreate_fl limits applications so they - can use the deflate compression only. The public function - H5PTcreate has been added to replace H5PTcreate_fl. H5PTcreate - takes a property list identifier to provide flexibility on - creation properties. - - (BMR - 2016/03/04, HDFFV-8623) - - - New Public Functions: H5PTget_dataset and H5PTget_type - - Two accessor functions have been added. H5PTget_dataset returns - the identifier of the dataset associated with the packet table, - and H5PTget_type returns the identifier of the datatype used by - the packet table. - - (BMR, 2016/03/04, HDFFV-8623) - - - Regarding #ifdef VLPT_REMOVED - - The #ifdef VLPT_REMOVED blocks have been removed from the packet - table (PT) library source except for the following functions: - + H5PTis_varlen() has been made available again - + H5PTfree_vlen_readbuff() is now H5PTfree_vlen_buff() - - (BMR - 2016/03/04, HDFFV-442) - - C++ Packet Table API - -------------------- - - New Constructor Added to FL_PacketTable - - An overloaded constructor has been added to FL_PacketTable and - takes a property list identifier to provide flexibility on - creation properties. - - (BMR - 2016/03/08, HDFFV-8623) - - - New Public Functions - - Two accessor wrappers are added to class PacketTable. - PacketTable::GetDataset() returns the identifier of the dataset - associated with the packet table, and PacketTable::GetDatatype() - returns the identifier of the datatype that the packet table uses. - - (BMR - 2016/03/04, HDFFV-8623) - - - Member Functions with "char*" as an Argument - - Overloaded functions were added to provide the "const char*" - argument; the existing version will be deprecated in future - releases. - - (BMR - 2016/03/04, HDFFV-8623) - - - Regarding #ifdef VLPT_REMOVED - - The #ifdef VLPT_REMOVED blocks have been removed from the packet - table library source code except for the following functions: - + VL_PacketTable::IsVariableLength() was moved to PacketTable - + VL_PacketTable::FreeReadBuff() is now PacketTable::FreeBuff() - - (BMR - 2016/03/04, HDFFV-442) - - - - Java Wrapper Library - -------------------- - - The Java HDF5 JNI library has been integrated into the HDF5 repository. - The configure option is "--enable-java", and the CMake option is - HDF5_BUILD_JAVA:BOOL=ON. The package hierarchy has changed from the - HDF5 1.8 JNI, which was "ncsa.hdf.hdflib.hdf5", to HDF5 1.10, - "hdf.hdflib.hdf5". - - A number of new APIs were added including some for VDS and SWMR. - - - - Other Important Changes - ----------------------- - - The hid_t type was changed from 32-bit to a 64-bit value. - - - -Issues Addressed in this Release Since 1.10.0 -============================================= - - - h5diff would return from a compare attributes abnormally if one of the datatypes - was a vlen. This resulted in a memory leak as well as an incorrect report of - attribute comparison. - - Fixed. - (ADB - 2016/04/26, HDFFV-9784) - - - The JUnit-interface test may fail on Solaris platforms. The result of - a test for verifying the content of the error stack to stdout is - in a different order on Solaris then other platforms. - - This test is skipped on Solaris - (ADB - 2016/04/21, HDFFV-9734) - - - When building HDF5 with Java using CMake and specifying Debug for CMAKE_BUILD_TYPE, - there was a missing command argument for the tests of the examples. - - Fixed. - (ADB - 2016/04/21, HDFFV-9743) - - - Changed h5diff to print a warning when a dataset is virtual, enabling - the data to be compared. In addition h5repack failed to copy the data - of a virtual dataset to the new file. Function H5D__get_space_status changed - to correctly determine the H5D_space_status_t allocation value. - - CMake added the Fixed Array indexing tests that were only in the autotools - test scripts. - - Fixed and tests added for vds issues. - (ADB,NAF - 2016/04/21, HDFFV-9756) - - - CMake added the h5format_convert tool and tests that were only in the autotools - build and test scripts. The autotools test script was reworked to allow CMake - to execute the test suite in parallel. - - Also, h5clear tool and tests were added to the misc folder. - - Fixed. - (ADB - 2016/04/21, HDFFV-9766) - - - CMake added the h5watch tool and argument tests that were only in the autotools - build and test scripts. The POSIX only tests were not added to CMake. - - CMake HL tools files were refactored to move the CMake test scripts into each tool folder. - - Fixed. - (ADB - 2016/04/21, HDFFV-9770) - - - Configure fails to detect valid real KINDs on FreeBSD 9.3 (i386) with Fortran enabled. - - Fixed. Added the exponential option to SELECTED_REAL_KIND to distinguish - KINDs of same precision - (MSB - 2016/05/14,HDFFV-9912) - - - - Corrected the f90 H5AWRITE_F integer interface's buf to be INTENT(IN). - (MSB - 2016/05/14) - - - Configure fails in sed command on FreeBSD 9.3 (i386) with Fortran enabled. - - Fixed. - (MSB - 2016/05/14,HDFFV-9912) - - - Compile time error in H5f90global.F90 with IBM XL Fortran 14.1.0.13 on BG/Q with Fortran - enabled. - - Fixed. - (MSB - 2016/05/16,HDFFV-9917) - - - A cmake build with Fortran enabled does not install module h5fortkit - - Fixed. - (MSB - 2016/05/23,HDFFV-9923) - - -Issues Addressed in this Release Since alpha1 -============================================= - - - H5Pget_virtual_printf_gap, H5Pget_virtual_view, H5Pget_efile_prefix - - The correct access property list settings from the - H5Pget_virtual_printf_gap, H5Pget_virtual_view, and - H5Pget_efile_prefix function calls could not be retrieved - using H5Dget_access_plist(). - - Fixed. - - (DER and NAF - 2016/03/14, HDFFV-9716) - - - h5dump - - When h5dump was provided with the name of a non-existing file or - when optional arguments were the last option on the command line, - h5dump would segfault. - - Fixed. - - (ADB 2016/02/28 HDFFV-9639, HDFFV-9684) - - - No Error Message for Corrupt Metadata - - The HDF5 Library did not propagate an error when it encountered - corrupt metadata in an HDF5 file. The issue was fixed for a - specific file provided by a user. If you still see the problem, - please contact help@hdfgroup.org - - Fixed. - - (MC - 2016/02/18, HDFFV-9670) - - - Problem Reading Chunked Datasets with a String Datatype Larger - Than the Chunk Size in Bytes - - When the latest file format was used and when a chunked dataset - was created with a datatype with the size bigger than a chunk - size, the data could not be read back. The issue was reported - for chunked datasets with a string datatype and was confirmed - for other datatypes with the sizes bigger than the chunk size in - bytes. - - Fixed. - - (JM - 2016/02/13, HDFFV-9672) - - - Control over the Location of External Files - - Users were unable to specify the locations of external files. - - Two APIs - H5Pget_efile_prefix and H5Pset_efile_prefix - were - added so that users could specify the locations of external files. - - (DER - 2016/02/04, HDFFV-8740) - - - -Issues Addressed in this Release Since alpha0 -============================================= - - h5format_convert - - The h5format_convert tool did not downgrade the version of the - superblock. - - Fixed. The tool now will downgrade the version of the superblock. - - (EIP 2016/01/11) - - - Crashes with multiple threads: invalid pointers - - It was reported that alpha0 crashed when used with multiple - threads. The issue exists in the HDF5 Library versions 1.8 and - 1.9. The problem is related to a shared file pointer used in some - miscellaneous data structures. The thread-safe library exposed - paths in the library where a file pointer became invalid. - - The alpha1 release contains the fixes for the specific use case - as described in HDFFV-9643. We will keep working on identifying - and fixing other paths in the library with similar problems. - - (EIP - 2016/01/15, HDFFV-9643) - - - -Supported Platforms -=================== -The following platforms are supported and have been tested for this release. -They are built with the configure process unless specified otherwise. - - AIX 6.1 xlc/xlc_r 10.1.0.5 - (NASA G-ADA) xlC/xlC_r 10.1.0.5 - xlf90/xlf90_r 12.1.0.6 - - 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 (Red Hat 4.4.7-16) - Version 4.9.3, Version 5.2.0 - PGI C, Fortran, C++ for 64-bit target on - x86-64; - Version 15.7-0 - Intel(R) C (icc), C++ (icpc), Fortran (icc) - compilers: - Version 15.0.3.187 Build 20150407 - MPICH 3.1.4 compiled with GCC 4.9.3 - - Linux 2.6.32-573.18.1.el6.ppc64 gcc (GCC) 4.4.7 20120313 (Red Hat 4.4.7-11) - #1 SMP ppc64 GNU/Linux g++ (GCC) 4.4.7 20120313 (Red Hat 4.4.7-11) - (ostrich) GNU Fortran (GCC) 4.4.7 20120313 (Red Hat 4.4.7-11) - 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 15.0.3.187 Build 20150407 - 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 2012 w/ Intel Fortran 15 (cmake) - Visual Studio 2013 w/ Intel Fortran 15 (cmake) - Visual Studio 2015 w/ Intel Fortran 16 (cmake) - Cygwin(CYGWIN_NT-6.1 2.2.1(0.289/5/3) gcc(4.9.3) compiler and gfortran) - (cmake and autotools) - - Windows 7 x64 Visual Studio 2012 w/ Intel Fortran 15 (cmake) - Visual Studio 2013 w/ Intel Fortran 15 (cmake) - Visual Studio 2015 w/ Intel Fortran 16 (cmake) - - Windows 8.1 Visual Studio 2012 w/ Intel Fortran 15 (cmake) - Visual Studio 2013 w/ Intel Fortran 15 (cmake) - - Windows 8.1 x64 Visual Studio 2012 w/ Intel Fortran 15 (cmake) - Visual Studio 2013 w/ Intel Fortran 15 (cmake) - - Mac OS X Mt. Lion 10.8.5 Apple clang/clang++ version 5.1 from Xcode 5.1 - 64-bit gfortran GNU Fortran (GCC) 4.8.2 - (swallow/kite) Intel icc/icpc/ifort version 15.0.3 - - Mac OS X Mavericks 10.9.5 Apple clang/clang++ version 6.0 from Xcode 6.2 - 64-bit gfortran GNU Fortran (GCC) 4.9.2 - (wren/quail) Intel icc/icpc/ifort version 15.0.3 - - Mac OS X Yosemite 10.10.5 Apple clang/clang++ version 6.0 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 10.11.4 Apple clang/clang++ version 7.3.0 from Xcode 7.3 - 64-bit gfortran GNU Fortran (GCC) 5.2.0 - (osx1010dev/osx1010test) Intel icc/icpc/ifort version 15.0.3 - - - -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 -SunOS 5.11 32-bit n y/y n y y y -SunOS 5.11 64-bit n y/y n y y y -Windows 7 y y/y n y y y -Windows 7 x64 y y/y n y y y -Windows 7 Cygwin n y/y n y y n -Windows 8.1 n y/y n y y y -Windows 8.1 x64 n 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 y -Mac OS X Yosemeti 10.10.5 64-bit n y/y n y y y -AIX 6.1 32- and 64-bit n y/n n y y y -CentOS 6.7 Linux 2.6.32 x86_64 GNU y y/y y y y y -CentOS 6.7 Linux 2.6.32 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 7.1 Linux 3.10.0 x86_64 GNU y y/y y y y y -CentOS 7.1 Linux 3.10.0 x86_64 Intel n y/y n y y y -Linux 2.6.32-431.11.2.el6.ppc64 n y/n n y y y - -Platform Shared Shared Shared Thread- - C libs F90 libs C++ libs safe -SunOS 5.11 32-bit y y y y -SunOS 5.11 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 8.1 y y y y -Windows 8.1 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 Yosemeti 10.10.5 64-bit y n y y -AIX 6.1 32- and 64-bit y n n y -CentOS 6.7 Linux 2.6.32 x86_64 GNU y y y y -CentOS 6.7 Linux 2.6.32 x86_64 Intel y y y y -CentOS 6.7 Linux 2.6.32 x86_64 PGI y y y y -CentOS 7.1 Linux 3.10.0 x86_64 GNU y y y y -CentOS 7.1 Linux 3.10.0 x86_64 Intel y y y y -Linux 2.6.32-431.11.2.el6.ppc64 y y y y - -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 2.6.18-431.11.2.el6 g95 (GCC 4.0.3 (g95 0.94!) - #1 SMP x86_64 GNU/Linux - (platypus) - - Windows 7 Visual Studio 2008 (cmake) - - Windows 7 x64 Visual Studio 2008 (cmake) - - Windows 7 x64 Visual Studio 2010 (cmake) with SWMR using GPFS - - Windows 10 Visual Studio 2013 w/ Intel Fortran 15 (cmake) - - Windows 10 x64 Visual Studio 2013 w/ Intel Fortran 15 (cmake) - - Debian7.5.0 3.2.0-4-amd64 #1 SMP Debian 3.2.51-1 x86_64 GNU/Linux - gcc (Debian 4.7.2-5) 4.7.2 - GNU Fortran (Debian 4.7.2-5) 4.7.2 - (cmake and autotools) - - Fedora20 3.15.3-200.fc20.x86_64 #1 SMP x86_64 x86_64 x86_64 GNU/Linux - gcc (GCC) 4.8.3 20140624 (Red Hat 4.8.3-1) - GNU Fortran (GCC) 4.8.3 20140624 (Red Hat 4.8.3-1) - (cmake and autotools) - - SUSE 13.1 3.11.10-17-desktop #1 SMP PREEMPT x86_64 x86_64 x86_64 GNU/Linux - gcc (SUSE Linux) 4.8.1 - GNU Fortran (SUSE Linux) 4.8.1 - (cmake and autotools) - - Ubuntu 14.04 3.13.0-35-generic #62-Ubuntu SMP x86_64 GNU/Linux - gcc (Ubuntu/Linaro 4.9.1-0ubuntu1) 4.9.1 - GNU Fortran (Ubuntu/Linaro 4.9.1-0ubuntu1) 4.9.1 - (cmake and autotools) - - hopper.nersc.gov PrgEnv-gnu/5.2.40 - gcc (GCC) 4.9.2 20141030 (Cray Inc.) - GNU Fortran (GCC) 4.9.2 20141030 (Cray Inc.) - g++ (GCC) 4.9.2 20141030 (Cray Inc.) - - - -Known Problems and Limitations -============================== -This section contains the list of known problems and limitations introduced -in this release of HDF5. - -Note: this list is not exhaustive of all known issues discovered in HDF5 -software to date. For a list of significant problems and known workarounds -identified in past releases, please refer to: - -https://www.hdfgroup.org/HDF5/release/known_problems/ - -The HDF Group also maintains a JIRA issue-tracking database which is used to -capture all known issues which are too numerous to reasonably list in this -document. The HDF Group is taking steps to make our JIRA issue database -open to the public, and this section will refer to that database in a future -release. In the meantime, please contact help@hdfgroup.org if you come across -an issue not listed here or at the link above, and we will provide any -information about known workarounds that we have or add it to our list of -known issues if it is a new issue. - - - The flush/refresh test occasionally fails on OS X platforms. This is - being investigated but no fix or workaround is available at this time. - (DER - 2016/03/22, HDFFV-9731) - - - The VDS/SWMR test will fail with a segmentation fault if the library - is built with --enable-using-memchecker. The is due to a VDS shutdown - procedure freeing a shared resource too early when the memory - checker changes are built. This problem does not arise when the - memory checker changes are not used since the internal library free - lists behave differently. The memory checker configure option should - normally only be used under special circumstances so this should not - affect most users. Users should be aware that the --enable-using-memchecker - + VDS combination may cause a segfault, however, so Valgrind et al. may - have to be used with an HDF5 library built without the feature if this - proves to be a problem. - (DER - 2016/03/21, HDFFV-9732) - - - SWMR feature limitations - The SWMR feature will only work if an HDF5 file under SWMR access resides - on a file system that obeys POSIX write() ordering semantics. Because of - this, SWMR will not work on network file systems such as NFS or SMB/Windows - file shares since those systems do not guarantee write odering. SWMR - regression tests are likely to fail if run on a network file system. SWMR - is currently not tested on Windows though it can be tested manually - (some of the SWMR test programs are built by CMake), and there are no - obvious reasons for it to not work on NTFS or GPFS. - (EIP - 2016/03/20, HDFFV-9733) - - - VDS feature limitation - Currently, the path to a VDS source file is interpreted as relative to the - directory where the executable program runs and not to the HDF5 file with - the VDS dataset unless a full path to the source file is specified during - the mapping. - (EIP - 2016/03/20, HDFFV-9724) - - - The H5Lexists API changed behavior in HDF5-1.10 when used with a file handle - and root group name ("/"): - - H5Lexists(fileid, "/") - - In HDF5-1.8 it returns false (0) and in HDF5-1.10 it returns true (1). - The documentation will be updated with information regarding this change. - (LRK - 2016/03/30, HDFFV-8746) - - -%%%%1.10.0%%%% - -HDF5 version 1.10.0 released on 2016-03-30 -================================================================================ - - - -INTRODUCTION - -This document describes the differences between HDF5-1.8 series and -HDF5 1.10.0 releases, and contains information on the platforms -tested. - -Links to HDF5 1.10.0 source code can be found on The HDF Group's -development FTP server at the following location: - - https://www.hdfgroup.org/HDF5/release/obtain5110.html - -User documentation can be accessed directly at this location: - - https://www.hdfgroup.org/HDF5/docNewFeatures/ - -For more information, see the HDF5 home page: - - https://www.hdfgroup.org/HDF5/ - -If you have any questions or comments, please send them to the HDF -Help Desk: - - help@hdfgroup.org - - - -CONTENTS - -- New Features -- Issues Addressed in this Release -- Supported Platforms -- Tested Configuration Features Summary -- More Tested Platforms -- Known Problems and Limitations - - - -New Features -============ -This release supports the following features: - - Configuration - ------------- - - API Compatibility with HDF5 1.8 Flag Was Added - - The 1.10 version of the HDF5 Library can be configured to operate - identically to the 1.8 library with the --with-default-api-version=v18 - configure flag. This allows existing code to be compiled with the 1.10 - library without requiring immediate changes to the application source - code. For additional configuration options and other details, see - "API Compatibility Macros in HDF5" at - https://www.hdfgroup.org/HDF5/doc/RM/APICompatMacros.html. - - - Autotools Configuration Has Been Extensively Reworked - - The autotools configuration options have been updated to allow more - fine-grained control of the build options and to correct some bugs. - See configure --help for comprehensive information on each option. - - Specific changes: - - * --enable-debug and --enable-production are no longer accepted. - Use --enable-build-mode=(debug | production) instead. These set - appropriate defaults for symbols, optimizations, and other - configuration options. These defaults can be overridden by the - user. - - * Extra debug output messages are no longer enabled with - --enable-debug=<package list>. Use --enable-internal-debug=<pkg list> - instead. - - * A new --enable-symbols option allows symbols to be generated - independently of the build mode. --disable-symbols can be used - to strip symbols from the binary. - - * A new --enable-asserts option sets/unsets NDEBUG. This is - independent of the build mode. This also enables some extra - low-overhead debug checks in the library. - - * A new --enable-profiling option sets profiling flags. This is - independent of the build mode. - - * A new --enable-optimization option sets the optimization level. - This is independent of the build mode. - - * Many of these options can take a flags string that will be used - to build the library. This can be useful for specifying custom - optimization flags such as -Os and -Ofast. - - * gnu C++ and Fortran use configure sub-files that update the - build flags and turn on warnings. The increase in warnings when - building these wrapper libraries is due to these flag changes - and not to a decrease in code quality. - - * The option to clear file buffers has been removed. Any buffer that - will eventually be written to disk will now always be memset - to zero. This prevents the previous contents of the buffer from - being written to the disk if the buffer contents are not - completely overwritten, which has security implications. - - - LFS Changes - - The way the autotools handle large file support (LFS) has been - overhauled in this release. - - * We assume ftello and fseeko exist - - * We no longer explicitly use the *64 I/O functions. Instead, we - rely on a mapping provided by _FILE_OFFSET_BITS or its equivalent. - - * _LARGEFILE(64)_SOURCE is no longer exported via AM_CPPFLAGS. - - - - Parallel Library - ----------------- - - Collective Metadata I/O - - Calls for HDF5 metadata can result in many small reads and writes. - On metadata reads, collective metadata I/O can improve performance - by allowing the library to perform optimizations when reading the - metadata by having one rank read the data and broadcasting it to - all other ranks. - - Collective metadata I/O improves metadata write performance through - the construction of an MPI derived datatype that is then written - collectively in a single call. For more information, see - https://www.hdfgroup.org/HDF5/docNewFeatures/NewFeaturesCollectiveMetadataIoDocs.html. - - - - Library - -------- - - Concurrent Access to HDF5 Files - Single Writer/ Multiple Reader (SWMR) - - The Single Writer/ Multiple Reader or SWMR feature enables users to - read data concurrently while writing it. Communications between the - processes and file locking are not required. The processes can run - on the same or on different platforms as long as they share a common - file system that is POSIX compliant. For more information, see the - Single-Writer/Multiple-Reader (SWMR) documentation at - https://www.hdfgroup.org/HDF5/docNewFeatures/NewFeaturesSwmrDocs.html. - - - Virtual Dataset (VDS) - - The VDS feature enables data to be accessed across HDF5 files - using standard HDF5 objects such as groups and datasets without - rewriting or rearranging the data. An HDF5 virtual dataset (VDS) - is an HDF5 dataset that is composed of source HDF5 datasets in - a predefined mapping. VDS can be used with the SWMR feature. For - documentation, check - https://www.hdfgroup.org/HDF5/docNewFeatures/NewFeaturesVirtualDatasetDocs.html. - - - Persistent Free File Space Tracking - - Usage patterns when working with an HDF5 file sometimes result in - wasted space within the file. This can also impair access times - when working with the resulting files. The new file space management - feature provides strategies for managing space in a file to improve - performance in both of these areas. For more information, see - https://www.hdfgroup.org/HDF5/docNewFeatures/NewFeaturesFileSpaceMgmtDocs.html. - - - Version 3 Metadata Cache - - The version 3 metadata cache moves management of metadata I/O from - the clients to the metadata cache proper. This change is essential for - SWMR and other features that have yet to be released. - - - - C++ Library - ------------ - - New Member Function Added to H5::ArrayType - - The assignment operator ArrayType::operator= was added because - ArrayType has pointer data members. - - (BMR - 2016/03/07, HDFFV-9562) - - - - Tools - ------ - - h5watch - - The h5watch tool allows users to output new records appended to - a dataset under SWMR access as it grows. The functionality is - similar to the Unix user command "tail" with the follow option, - which outputs appended data as the file grows. For more - information, see - https://www.hdfgroup.org/HDF5/docNewFeatures/NewFeaturesSwmrDocs.html#Tools. - - - h5format_convert - - The h5format_convert tool allows users to convert the indexing - type of a chunked dataset made with a 1.10.x version of the HDF5 - Library when the latest file format is used to the 1.8.x version 1 B-tree indexing - type. For example, datasets created using SWMR access, can be - converted to be accessed by the HDF5 1.18 library and tools. The - tool does not rewrite raw data, but it does rewrite HDF5 metadata. - - - - High-Level APIs - ---------------- - - H5DOappend - - The function appends data to a dataset along a specified dimension. - - - C Packet Table API - ------------------ - - Replacement of a Public Function with H5PTcreate - - The existing function H5PTcreate_fl limits applications so they - can use the deflate compression only. The public function - H5PTcreate has been added to replace H5PTcreate_fl. H5PTcreate - takes a property list identifier to provide flexibility on - creation properties. - - (BMR - 2016/03/04, HDFFV-8623) - - - New Public Functions: H5PTget_dataset and H5PTget_type - - Two accessor functions have been added. H5PTget_dataset returns - the identifier of the dataset associated with the packet table, - and H5PTget_type returns the identifier of the datatype used by - the packet table. - - (BMR, 2016/03/04, HDFFV-8623) - - - Regarding #ifdef VLPT_REMOVED - - The #ifdef VLPT_REMOVED blocks have been removed from the packet - table (PT) library source except for the following functions: - + H5PTis_varlen() has been made available again - + H5PTfree_vlen_readbuff() is now H5PTfree_vlen_buff() - - (BMR - 2016/03/04, HDFFV-442) - - C++ Packet Table API - -------------------- - - New Constructor Added to FL_PacketTable - - An overloaded constructor has been added to FL_PacketTable and - takes a property list identifier to provide flexibility on - creation properties. - - (BMR - 2016/03/08, HDFFV-8623) - - - New Public Functions - - Two accessor wrappers are added to class PacketTable. - PacketTable::GetDataset() returns the identifier of the dataset - associated with the packet table, and PacketTable::GetDatatype() - returns the identifier of the datatype that the packet table uses. - - (BMR - 2016/03/04, HDFFV-8623) - - - Member Functions with "char*" as an Argument - - Overloaded functions were added to provide the "const char*" - argument; the existing version will be deprecated in future - releases. - - (BMR - 2016/03/04, HDFFV-8623) - - - Regarding #ifdef VLPT_REMOVED - - The #ifdef VLPT_REMOVED blocks have been removed from the packet - table library source code except for the following functions: - + VL_PacketTable::IsVariableLength() was moved to PacketTable - + VL_PacketTable::FreeReadBuff() is now PacketTable::FreeBuff() - - (BMR - 2016/03/04, HDFFV-442) - - - - Java Wrapper Library - -------------------- - - The Java HDF5 JNI library has been integrated into the HDF5 repository. - The configure option is "--enable-java", and the CMake option is - HDF5_BUILD_JAVA:BOOL=ON. The package hierarchy has changed from the - HDF5 1.8 JNI, which was "ncsa.hdf.hdflib.hdf5", to HDF5 1.10, - "hdf.hdflib.hdf5". - - A number of new APIs were added including some for VDS and SWMR. - - - - Other Important Changes - ----------------------- - - The hid_t type was changed from 32-bit to a 64-bit value. - - - -Issues Addressed in this Release Since alpha1 -============================================= - - - H5Pget_virtual_printf_gap, H5Pget_virtual_view, H5Pget_efile_prefix - - The correct access property list settings from the - H5Pget_virtual_printf_gap, H5Pget_virtual_view, and - H5Pget_efile_prefix function calls could not be retrieved - using H5Dget_access_plist(). - - Fixed. - - (DER and NAF - 2016/03/14, HDFFV-9716) - - - h5dump - - When h5dump was provided with the name of a non-existing file or - when optional arguments were the last option on the command line, - h5dump would segfault. - - Fixed. - - (ADB 2016/02/28 HDFFV-9639, HDFFV-9684) - - - No Error Message for Corrupt Metadata - - The HDF5 Library did not propagate an error when it encountered - corrupt metadata in an HDF5 file. The issue was fixed for a - specific file provided by a user. If you still see the problem, - please contact help@hdfgroup.org - - Fixed. - - (MC - 2016/02/18, HDFFV-9670) - - - Problem Reading Chunked Datasets with a String Datatype Larger - Than the Chunk Size in Bytes - - When the latest file format was used and when a chunked dataset - was created with a datatype with the size bigger than a chunk - size, the data could not be read back. The issue was reported - for chunked datasets with a string datatype and was confirmed - for other datatypes with the sizes bigger than the chunk size in - bytes. - - Fixed. - - (JM - 2016/02/13, HDFFV-9672) - - - Control over the Location of External Files - - Users were unable to specify the locations of external files. - - Two APIs - H5Pget_efile_prefix and H5Pset_efile_prefix - were - added so that users could specify the locations of external files. - - (DER - 2016/02/04, HDFFV-8740) - - - -Issues Addressed in this Release Since alpha0 -============================================= - - h5format_convert - - The h5format_convert tool did not downgrade the version of the - superblock. - - Fixed. The tool now will downgrade the version of the superblock. - - (EIP 2016/01/11) - - - Crashes with multiple threads: invalid pointers - - It was reported that alpha0 crashed when used with multiple - threads. The issue exists in the HDF5 Library versions 1.8 and - 1.9. The problem is related to a shared file pointer used in some - miscellaneous data structures. The thread-safe library exposed - paths in the library where a file pointer became invalid. - - The alpha1 release contains the fixes for the specific use case - as described in HDFFV-9643. We will keep working on identifying - and fixing other paths in the library with similar problems. - - (EIP - 2016/01/15, HDFFV-9643) - - - -Supported Platforms -=================== -The following platforms are supported and have been tested for this release. -They are built with the configure process unless specified otherwise. - - AIX 6.1 xlc/xlc_r 10.1.0.5 - (NASA G-ADA) xlC/xlC_r 10.1.0.5 - xlf90/xlf90_r 12.1.0.6 - - Linux 2.6.32-573.18.1.el6 GNU C (gcc), Fortran (gfortran), C++ (g++) - #1 SMP x86_64 GNU/Linux compilers: - (mayll/platypus) Version 4.4.7 20120313 (Red Hat 4.4.7-16) - Version 4.9.3, Version 5.2.0 - PGI C, Fortran, C++ for 64-bit target on - x86-64; - Version 15.7-0 - Intel(R) C (icc), C++ (icpc), Fortran (icc) - compilers: - Version 15.0.3.187 Build 20150407 - MPICH 3.1.4 compiled with GCC 4.9.3 - - Linux 2.6.32-504.8.1.el6.ppc64 gcc (GCC) 4.4.7 20120313 (Red Hat 4.4.7-11) - #1 SMP ppc64 GNU/Linux g++ (GCC) 4.4.7 20120313 (Red Hat 4.4.7-11) - (ostrich) GNU Fortran (GCC) 4.4.7 20120313 (Red Hat 4.4.7-11) - 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 15.0.3.187 Build 20150407 - 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 2012 w/ Intel Fortran 15 (cmake) - Visual Studio 2013 w/ Intel Fortran 15 (cmake) - Visual Studio 2015 w/ Intel Fortran 16 (cmake) - Cygwin(CYGWIN_NT-6.1 2.2.1(0.289/5/3) gcc(4.9.3) compiler and gfortran) - (cmake and autotools) - - Windows 7 x64 Visual Studio 2012 w/ Intel Fortran 15 (cmake) - Visual Studio 2013 w/ Intel Fortran 15 (cmake) - Visual Studio 2015 w/ Intel Fortran 16 (cmake) - - Windows 8.1 Visual Studio 2012 w/ Intel Fortran 15 (cmake) - Visual Studio 2013 w/ Intel Fortran 15 (cmake) - - Windows 8.1 x64 Visual Studio 2012 w/ Intel Fortran 15 (cmake) - Visual Studio 2013 w/ Intel Fortran 15 (cmake) - - Mac OS X Mt. Lion 10.8.5 Apple clang/clang++ version 5.1 from Xcode 5.1 - 64-bit gfortran GNU Fortran (GCC) 4.8.2 - (swallow/kite) Intel icc/icpc/ifort version 15.0.3 - - Mac OS X Mavericks 10.9.5 Apple clang/clang++ version 6.0 from Xcode 6.2.0 - 64-bit gfortran GNU Fortran (GCC) 4.9.2 - (wren/quail) Intel icc/icpc/ifort version 15.0.3 - - Mac OS X Yosemite 10.10.5 Apple clang/clang++ version 6.0 from Xcode 7.0.0 - 64-bit gfortran GNU Fortran (GCC) 4.9.2 - (osx1010dev/osx1010test) Intel icc/icpc/ifort version 15.0.3 - - Mac OS X El Capitan 10.11.3 Apple clang/clang++ version 7.0.2 from Xcode 7.0.2 - 64-bit gfortran GNU Fortran (GCC) 5.2.0 - (osx1010dev/osx1010test) Intel icc/icpc/ifort version 15.0.3 - - - -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 -SunOS 5.11 32-bit n y/y n y y y -SunOS 5.11 64-bit n y/y n y y y -Windows 7 y y/y n y y y -Windows 7 x64 y y/y n y y y -Windows 7 Cygwin n y/y n y y n -Windows 8.1 n y/y n y y y -Windows 8.1 x64 n 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 y -Mac OS X Yosemeti 10.10.5 64-bit n y/y n y y y -AIX 6.1 32- and 64-bit n y/n n y y y -CentOS 6.7 Linux 2.6.32 x86_64 GNU y y/y y y y y -CentOS 6.7 Linux 2.6.32 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 7.1 Linux 3.10.0 x86_64 GNU y y/y y y y y -CentOS 7.1 Linux 3.10.0 x86_64 Intel n y/y n y y y -Linux 2.6.32-431.11.2.el6.ppc64 n y/n n y y y - -Platform Shared Shared Shared Thread- - C libs F90 libs C++ libs safe -SunOS 5.11 32-bit y y y y -SunOS 5.11 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 8.1 y y y y -Windows 8.1 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 Yosemeti 10.10.5 64-bit y n y y -AIX 6.1 32- and 64-bit y n n y -CentOS 6.7 Linux 2.6.32 x86_64 GNU y y y y -CentOS 6.7 Linux 2.6.32 x86_64 Intel y y y y -CentOS 6.7 Linux 2.6.32 x86_64 PGI y y y y -CentOS 7.1 Linux 3.10.0 x86_64 GNU y y y y -CentOS 7.1 Linux 3.10.0 x86_64 Intel y y y y -Linux 2.6.32-431.11.2.el6.ppc64 y y y y - -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 2.6.18-431.11.2.el6 g95 (GCC 4.0.3 (g95 0.94!) - #1 SMP x86_64 GNU/Linux - (platypus) - - Windows 7 Visual Studio 2008 (cmake) - - Windows 7 x64 Visual Studio 2008 (cmake) - - Windows 7 x64 Visual Studio 2010 (cmake) with SWMR using GPFS - - Windows 10 Visual Studio 2013 w/ Intel Fortran 15 (cmake) - - Windows 10 x64 Visual Studio 2013 w/ Intel Fortran 15 (cmake) - - Debian7.5.0 3.2.0-4-amd64 #1 SMP Debian 3.2.51-1 x86_64 GNU/Linux - gcc (Debian 4.7.2-5) 4.7.2 - GNU Fortran (Debian 4.7.2-5) 4.7.2 - (cmake and autotools) - - Fedora20 3.15.3-200.fc20.x86_64 #1 SMP x86_64 x86_64 x86_64 GNU/Linux - gcc (GCC) 4.8.3 20140624 (Red Hat 4.8.3-1) - GNU Fortran (GCC) 4.8.3 20140624 (Red Hat 4.8.3-1) - (cmake and autotools) - - SUSE 13.1 3.11.10-17-desktop #1 SMP PREEMPT x86_64 x86_64 x86_64 GNU/Linux - gcc (SUSE Linux) 4.8.1 - GNU Fortran (SUSE Linux) 4.8.1 - (cmake and autotools) - - Ubuntu 14.04 3.13.0-35-generic #62-Ubuntu SMP x86_64 GNU/Linux - gcc (Ubuntu/Linaro 4.9.1-0ubuntu1) 4.9.1 - GNU Fortran (Ubuntu/Linaro 4.9.1-0ubuntu1) 4.9.1 - (cmake and autotools) - - hopper.nersc.gov PrgEnv-gnu/5.2.40 - gcc (GCC) 4.9.2 20141030 (Cray Inc.) - GNU Fortran (GCC) 4.9.2 20141030 (Cray Inc.) - g++ (GCC) 4.9.2 20141030 (Cray Inc.) - - - -Known Problems and Limitations -============================== -This section contains the list of known problems and limitations introduced -in this release of HDF5. - -Note: this list is not exhaustive of all known issues discovered in HDF5 -software to date. For a list of significant problems and known workarounds -identified in past releases, please refer to: - -https://www.hdfgroup.org/HDF5/release/known_problems/ - -The HDF Group also maintains a JIRA issue-tracking database which is used to -capture all known issues which are too numerous to reasonably list in this -document. The HDF Group is taking steps to make our JIRA issue database -open to the public, and this section will refer to that database in a future -release. In the meantime, please contact help@hdfgroup.org if you come across -an issue not listed here or at the link above, and we will provide any -information about known workarounds that we have or add it to our list of -known issues if it is a new issue. - - - The JUnit-interface test may fail on Solaris platforms. The result of - a test for verifying the content of the error stack to stdout is - in a different order on Solaris then other platforms. Use make -i option - to test beyond the java/test folder. - (ADB - 2016/03/22, HDFFV-9734) - - - The flush/refresh test occasionally fails on OS X platforms. This is - being investigated but no fix or workaround is available at this time. - (DER - 2016/03/22, HDFFV-9731) - - - The VDS/SWMR test will fail with a segmentation fault if the library - is built with --enable-using-memchecker. The is due to a VDS shutdown - procedure freeing a shared resource too early when the memory - checker changes are built. This problem does not arise when the - memory checker changes are not used since the internal library free - lists behave differently. The memory checker configure option should - normally only be used under special circumstances so this should not - affect most users. Users should be aware that the --enable-using-memchecker - + VDS combination may cause a segfault, however, so Valgrind et al. may - have to be used with an HDF5 library built without the feature if this - proves to be a problem. - (DER - 2016/03/21, HDFFV-9732) - - - SWMR feature limitations - The SWMR feature will only work if an HDF5 file under SWMR access resides - on a file system that obeys POSIX write() ordering semantics. Because of - this, SWMR will not work on network file systems such as NFS or SMB/Windows - file shares since those systems do not guarantee write odering. SWMR - regression tests are likely to fail if run on a network file system. SWMR - is currently not tested on Windows though it can be tested manually - (some of the SWMR test programs are built by CMake), and there are no - obvious reasons for it to not work on NTFS or GPFS. - (EIP - 2016/03/20, HDFFV-9733) - - - VDS feature limitation - Currently, the path to a VDS source file is interpreted as relative to the - directory where the executable program runs and not to the HDF5 file with - the VDS dataset unless a full path to the source file is specified during - the mapping. - (EIP - 2016/03/20, HDFFV-9724) - - - When building HDF5 with Java using CMake and specifying Debug for CMAKE_BUILD_TYPE, - there is a missing command argument for the tests of the examples. - - This error can be avoided by not building Java with Debug, HDF5_BUILD_JAVA:BOOL=OFF, - or not building Examples, HDF5_BUILD_EXAMPLES:BOOL=OFF. - (LRK - 2016/03/30, HDFFV-9743) - - - The H5Lexists API changed behavior in HDF5-1.10 when used with a file handle - and root group name ("/"): - - H5Lexists(fileid, "/") - - In HDF5-1.8 it returns false (0) and in HDF5-1.10 it returns true (1). - The documentation will be updated with information regarding this change. - (LRK - 2016/03/30, HDFFV-8746) - diff --git a/release_docs/HISTORY-1_12.txt b/release_docs/HISTORY-1_12.txt deleted file mode 100644 index 6d0c1e2..0000000 --- a/release_docs/HISTORY-1_12.txt +++ /dev/null @@ -1,628 +0,0 @@ -HDF5 History -============ - -This file contains development history of the HDF5 1.12 branch - -01. Release Information for hdf5-1.12.0 - -[Search on the string '%%%%' for section breaks of each release.] - -%%%%1.12.0%%%% - -HDF5 version 1.12.0 released on 2020-02-28 -================================================================================ - - -INTRODUCTION - -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 the -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/ - -More information about the new features can be found at: - - 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: - - help@hdfgroup.org - - -CONTENTS - -- New Features -- Support for new platforms and languages -- Bug Fixes since HDF5-1.12.0-alpha1 -- Major Bug Fixes since HDF5-1.10.0 -- Supported Platforms -- Tested Configuration Features Summary -- More Tested Platforms -- Known Problems -- CMake vs. Autotools installations - - -New Features -============ - - Configuration: - ------------- - - Added test script for file size compare - - If CMake minimum version is at least 3.14, the fileCompareTest.cmake - script will compare file sizes. - - (ADB - 2020/02/24, HDFFV-11036) - - - Update CMake minimum version to 3.12 - - Updated CMake minimum version to 3.12 and added version checks - for Windows features. - - (ADB - 2020/02/05, TRILABS-142) - - - Fixed CMake include properties for Fortran libraries - - Corrected the library properties for Fortran to use the - correct path for the Fortran module files. - - (ADB - 2020/02/04, HDFFV-11012) - - - Added common warnings files for gnu and intel - - Added warnings files to use one common set of flags - during configure for both autotools and CMake build - systems. The initial implementation only affects a - general set of flags for gnu and intel compilers. - - (ADB - 2020/01/17) - - - Added new options to CMake for control of testing - - Added CMake options (default ON); - HDF5_TEST_SERIAL AND/OR HDF5_TEST_PARALLEL - combined with: - HDF5_TEST_TOOLS - HDF5_TEST_EXAMPLES - HDF5_TEST_SWMR - HDF5_TEST_FORTRAN - HDF5_TEST_CPP - HDF5_TEST_JAVA - - (ADB - 2020/01/15, HDFFV-11001) - - - Added Clang sanitizers to CMake for analyzer support if compiler is clang. - - Added CMake code and files to execute the Clang sanitizers if - HDF5_ENABLE_SANITIZERS is enabled and the USE_SANITIZER option - is set to one of the following: - Address - Memory - MemoryWithOrigins - Undefined - Thread - Leak - 'Address;Undefined' - - (ADB - 2019/12/12, TRILAB-135) - - - Update CMake for VS2019 support - - CMake added support for VS2019 in version 3.15. Changes to the CMake - generator setting required changes to scripts. Also updated version - references in CMake files as necessary. - - (ADB - 2019/11/18, HDFFV-10962) - - - Library: - -------- - - Refactored public exposure of haddr_t type in favor of "object tokens" - - To better accommodate HDF5 VOL connectors where "object addresses in a file" - may not make much sense, the following changes were made to the library: - - * Introduced new H5O_token_t "object token" type, which represents a - unique and permanent identifier for referencing an HDF5 object within - a container; these "object tokens" are meant to replace object addresses. - Along with the new type, a new H5Oopen_by_token API call was introduced - to open an object by a token, similar to how object addresses were - previously used with H5Oopen_by_addr. - - * Introduced new H5Lget_info2, H5Lget_info_by_idx2, H5Literate2, H5Literate_by_name2, - H5Lvisit2 and H5Lvisit_by_name2 API calls, along with their associated H5L_info2_t - struct and H5L_iterate2_t callback function, which work with the newly-introduced - object tokens, instead of object addresses. The original functions have been - renamed to version 1 functions and are deprecated in favor of the new version 2 - functions. The H5L_info_t and H5L_iterate_t types have been renamed to version 1 - types and are now deprecated in favor of their version 2 counterparts. For each of - the functions and types, compatibility macros take place of the original symbols. - - * Introduced new H5Oget_info3, H5Oget_info_by_name3, H5Oget_info_by_idx3, - H5Ovisit3 and H5Ovisit_by_name3 API calls, along with their associated H5O_info2_t - struct and H5O_iterate2_t callback function, which work with the newly-introduced - object tokens, instead of object addresses. The version 2 functions are now - deprecated in favor of the version 3 functions. The H5O_info_t and H5O_iterate_t - types have been renamed to version 1 types and are now deprecated in favor of their - version 2 counterparts. For each, compatibility macros take place of the original - symbols. - - * Introduced new H5Oget_native_info, H5Oget_native_info_by_name and - H5Oget_native_info_by_idx API calls, along with their associated H5O_native_info_t - struct, which are used to retrieve the native HDF5 file format-specific information - about an object. This information (such as object header info and B-tree/heap info) - has been removed from the new H5O_info2_t struct so that the more generic - H5Oget_info(_by_name/_by_idx)3 routines will not try to retrieve it for non-native - VOL connectors. - - * Added new H5Otoken_cmp, H5Otoken_to_str and H5Otoken_from_str routines to compare - two object tokens, convert an object token into a nicely-readable string format and - to convert an object token string back into a real object token, respectively. - - (DER, QAK, JTH - 2020/01/16) - - - 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 - - - Add new public function H5Sselect_adjust. - - This function shifts a dataspace selection by a specified logical offset - within the dataspace extent. This can be useful for VOL developers to - implement chunked datasets. - - (NAF - 2019/11/18) - - - Add new public function H5Sselect_project_intersection. - - This function computes the intersection between two dataspace selections - and projects that intersection into a third selection. This can be useful - for VOL developers to implement chunked or virtual datasets. - - (NAF - 2019/11/13, ID-148) - - - Add new public function H5VLget_file_type. - - This function returns a datatype equivalent to the supplied datatype but - with the location set to be in the file. This datatype can then be used - with H5Tconvert to convert data between file and in-memory representation. - This funcition is intended for use only by VOL connector developers. - - (NAF - 2019/11/08, ID-127) - - - 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 files stored on Apache HDFS. - See https://portal.hdfgroup.org/display/HDF5/Virtual+File+Drivers+-+S3+and+HDFS - for information on enabling those drivers and using those APIs. - - Below are specific instructions for enabling 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 to the s3 url for the - s3 bucket containing the HDF5 files to be accessed. - - FORTRAN Library: - ---------------- - - Added new Fortran parameters: - - H5F_LIBVER_ERROR_F - H5F_LIBVER_NBOUNDS_F - H5F_LIBVER_V18_F - H5F_LIBVER_V110_F - H5F_LIBVER_V112_F - - - Added new Fortran API: h5pget_libver_bounds_f - - (MSB - 2020/02/11, HDFFV-11018) - - Java Library: - ---------------- - - Added ability to test java library with VOLs. - - Created new CMake script that combines the java and vol test scripts. - - (ADB - 2020/02/03, HDFFV-10996) - - - Tests fail for non-English locale. - - In the JUnit tests with a non-English locale, only the part before - the decimal comma is replaced by XXXX and this leads to a comparison - error. Changed the regex for the Time substitution. - - (ADB - 2020/01/09, HDFFV-10995) - - - Tools: - ------ - - h5diff was updated to use the new reference APIs. - - h5diff uses the new reference APIs to compare references. - Attribute references can also be compared. - - (ADB - 2019/12/19, HDFFV-10980) - - - h5dump and h5ls were updated to use the new reference APIs. - - The tools library now use the new reference APIs to inspect a - file. Also the DDL spec was updated to reflect the format - changes produced with the new APIs. The export API and support - functions in the JNI were updated to match. - - - 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. - - - h5repack was fixed to repack datasets with external storage - to other types of storage. - - -Support for new platforms, languages and compilers. -======================================= - - 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 - - -Bug Fixes since HDF5-1.12.0-alpha1 release -========================================== - Library - ------- - - Improved performance when creating a large number of small datasets by - retrieving default property values from the API context instead of doing - skip list searches. - - (CJH - 2019/12/10, HDFFV-10658) - - - Fixed user-created data access properties not existing in the property list - returned by H5Dget_access_plist. Thanks to Steven Varga for submitting a - reproducer and a patch. - - (CJH - 2019/12/09, HDFFV-10934) - - - Fixed an assertion failure in the parallel library when collectively - filling chunks. As it is required that chunks be written in - monotonically non-decreasing order of offset in the file, this assertion - was being triggered when the list of chunk file space allocations being - passed to the collective chunk filling routine was not sorted according - to this particular requirement. - - The addition of a sort of the out of order chunks trades a bit of - performance for the elimination of this assertion and of any complaints - from MPI implementations about the file offsets used being out of order. - - (JTH - 2019/10/07, HDFFV-10792) - - FORTRAN library: - ---------------- - - - Corrected INTERFACE INTENT(IN) to INTENT(OUT) for buf_size in h5fget_file_image_f. - - (MSB - 2020/2/18, HDFFV-11029) - - Java Library: - ---------------- - - Added ability to test java library with VOLs. - - Created new CMake script that combines the java and vol test scripts. - - (ADB - 2020/02/03, HDFFV-10996) - - - Tests fail for non-English locale. - - In the JUnit tests with a non-English locale, only the part before - the decimal comma is replaced by XXXX and this leads to a comparison - error. Changed the regex for the Time substitution. - - (ADB - 2020/01/09, HDFFV-10995) - - Tools: - ------ - - h5repack was fixed to repack the reference attributes properly. - The code line that checks if the update of reference inside a compound - datatype is misplaced outside the code block loop that carries out the - check. In consequence, the next attribute that is not the reference - type was repacked again as the reference type and caused the failure of - repacking. The fix is to move the corresponding code line to the correct - code block. - - (KY -2020/02/10, HDFFV-11014) - - - h5diff was updated to use the new reference APIs. - - h5diff uses the new reference APIs to compare references. - Attribute references can also be compared. - - (ADB - 2019/12/19, HDFFV-10980) - - - h5dump and h5ls were updated to use the new reference APIs. - - The tools library now use the new reference APIs to inspect a - file. Also the DDL spec was updated to reflect the format - changes produced with the new APIs. The export API and support - functions in the JNI were updated to match. - - (ADB - 2019/12/06, HDFFV-10876 and HDFFV-10877) - - -Major Bug Fixes since HDF5-1.10.0 release -========================================= - - - For major bug fixes please see HISTORY-1_10_0-1_12_0.txt file - - -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, 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 - - 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 - Sun C++ 5.12 SunOS_sparc - - Windows 7 x64 Visual Studio 2015 w/ Intel C, Fortran 2018 (cmake) - Visual Studio 2015 w/ MSMPI 10 (cmake) - - Windows 10 x64 Visual Studio 2015 w/ Intel Fortran 18 (cmake) - Visual Studio 2017 w/ Intel Fortran 19 (cmake) - Visual Studio 2019 w/ Intel Fortran 19 (cmake) - - macOS 10.13.6 High Sierra 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 - - macOS 10.14.6 Mohave 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 -===================================== - - 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 -SunOS 5.11 32-bit n y/y n y y y -SunOS 5.11 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 -macOS 10.13.6 64-bit n y/y n y y ? -macOS 10.14.6 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 -SunOS 5.11 32-bit y y y y -SunOS 5.11 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 -macOS 10.13.6 64-bit y n y y -macOS 10.14.6 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) - 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 - - Fedora30 5.3.11-200.fc30.x86_64 - #1 SMP x86_64 GNU/Linux GNU gcc (GCC) 9.2.1 20190827 (Red Hat 9.2.1 20190827) - GNU Fortran (GCC) 9.2.1 20190827 (Red Hat 9.2.1 20190827) - (cmake and autotools) - - Mac OS X El Capitan 10.11.6 Apple LLVM version 7.3.0 (clang/clang++-703.0.29) - 64-bit gfortran GNU Fortran (GCC) 5.2.0 - (osx1011dev/osx1011test) Intel icc/icpc/ifort version 16.0.2 - - macOS 10.12.6 Sierra Apple LLVM version 9.0.0 (clang/clang++-900.0.39.2) - 64-bit gfortran GNU Fortran (GCC) 7.4.0 - (kite) Intel icc/icpc/ifort version 17.0.8 - - -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, and in the HDF5 Jira database, available at - https://jira.hdfgroup.org/. Please register at https://www.hdfgroup.org to - create a free account for accessing the Jira database. 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/HISTORY-1_13.txt b/release_docs/HISTORY-1_14.txt index 73b7feb..f012f47 100644 --- a/release_docs/HISTORY-1_13.txt +++ b/release_docs/HISTORY-1_14.txt @@ -1,20 +1,15 @@ HDF5 History ============ -This file contains development history of the HDF5 1.13 releases from -the develop branch +This file contains development history of the HDF5 1.14 branch -04. Release Information for hdf5-1.13.3 -03. Release Information for hdf5-1.13.2 -02. Release Information for hdf5-1.13.1 -01. Release Information for hdf5-1.13.0 +01. Release Information for hdf5-1.14.0 [Search on the string '%%%%' for section breaks of each release.] +%%%%1.14.0%%%% -%%%%1.13.3%%%% - -HDF5 version 1.13.3 released on 2022-10-28 +HDF5 version 1.14.0 released on 2022-12-28 ================================================================================ @@ -40,7 +35,7 @@ The official HDF5 releases can be obtained from: Changes from Release to Release and New Features in the HDF5-1.13.x release series can be found at: - https://portal.hdfgroup.org/display/HDF5/HDF5+Application+Developer%27s+Guide + https://portal.hdfgroup.org/display/HDF5/Release+Specific+Information If you have any questions or comments, please send them to the HDF Help Desk: @@ -52,485 +47,75 @@ CONTENTS - New Features - Support for new platforms and languages -- Bug Fixes since HDF5-1.13.2 +- Bug Fixes since HDF5-1.12.0 - Platforms Tested - Known Problems - CMake vs. Autotools installations -New features and bug fixes previously added in 1.13.0 - 1.13.2 releases can be -found in release_docs/HISTORY-1_13.txt in the HDF5 source code. - New Features ============ Configuration: ------------- - - Add new CMake configuration variable HDF5_USE_GNU_DIRS - - HDF5_USE_GNU_DIRS (default OFF) selects the use of GNU Coding Standard install - directory variables by including the CMake module, GNUInstallDirs(see CMake - documentation for details). The HDF_DIR_PATHS macro in the HDFMacros.cmake file - sets various PATH variables for use during the build, test and install processes. - By default, the historical settings for these variables will be used. - - (ADB - 2022/10/21, GH-2175, GH-1716) - - - Update CMake minimum version to 3.18 - - Updated CMake minimum version from 3.12 to 3.18 and removed version checks - which were added for Windows features not yet available in version 3.12. Also - removed configure macros and code checks for old style code compile checks. - - (ADB - 2022/08/29, HDFFV-11329) - - - Library: - -------- - - Added multi dataset I/O feature - - Added H5Dread_multi, H5Dread_multi_async, H5Dwrite_multi, and - H5Dwrite_multi_async API routines to allow I/O on multiple datasets with a - single API call. Added H5Dread_multi_f and H5Dwrite_multi_f Fortran - wrappers. Updated VOL callbacks for dataset I/O to support multi dataset - I/O. - - (NAF - 2022/10/19) - - - Parallel Library: - ----------------- - - - - - Fortran Library: - ---------------- - - Added pointer based H5Dfill_f API - - Added Fortran H5Dfill_f, which is fully equivalent to the C API. It accepts pointers, - fill value datatype and datatype of dataspace elements. - - (MSB - 2022/10/10, HDFFV-10734.) - - C++ Library: - ------------ - - - - - Java Library: - ------------- - - - - - Tools: - ------ - - - - - High-Level APIs: - ---------------- - - - - - C Packet Table API: - ------------------- - - - + - Removal of MPE support - Internal header file: - --------------------- - - - - - Documentation: - -------------- - - Doxygen User Guide documentation is available when configured and generated. - The resulting documentation files will be in the share/html subdirectory - of the HDF5 install directory. - - (ADB - 2022/08/09) - - -Support for new platforms, languages and compilers -================================================== - - - - -Bug Fixes since HDF5-1.13.2 release -=================================== - Library - ------- - - Fixed an issue with variable length attributes - - Previously, if a variable length attribute was held open while its file - was opened through another handle, the same attribute was opened through - the second file handle, and the second file and attribute handles were - closed, attempting to write to the attribute through the first handle - would cause an error. - - (NAF - 2022/10/24) - - - Memory leak - - A memory leak was observed with variable-length fill value in - H5O_fill_convert() function in H5Ofill.c. The leak is - manifested by running valgrind on test/set_extent.c. - - Previously, fill->buf is used for datatype conversion - if it is large enough and the variable-length information - is therefore lost. A buffer is now allocated regardless - so that the element in fill->buf can later be reclaimed. - - (VC - 2022/10/10, HDFFV-10840) - - - Fixed an issue with hyperslab selections - - Previously, when combining hyperslab selections, it was possible for the - library to produce an incorrect combined selection. - - (NAF - 2022/09/25) - - - Fixed an issue with attribute type conversion with compound datatypes - - Previously, when performing type conversion for attribute I/O with a - compound datatype, the library would not fill the background buffer with - the contents of the destination, potentially causing data to be lost when - only writing to a subset of the compound fields. - - (NAF - 2022/08/22, GitHub #2016) - - - Java Library - ------------ - - Improve variable-length datatype handling in JNI. - - The existing JNI read-write functions could handle variable-length datatypes - that were simple variable-length datatype with an atomic sub-datatype. More - complex combinations could not be handled. Reworked the JNI read-write functions - to recursively inspect datatypes for variable-length sub-datatypes. - - (ADB - 2022/10/12, HDFFV-8701,10375) - - - Configuration - ------------- - - - - - Tools - ----- - - - - - Performance - ------------- - - - - - Fortran API - ----------- - - - - High-Level Library - ------------------ - - - - - Fortran High-Level APIs - ----------------------- - - - - - Documentation - ------------- - - - - - F90 APIs - -------- - - - - - C++ APIs - -------- - - - - - Testing - ------- - - + The ability to build with MPE instrumentation has been removed along with + the following configure options: + Autotools: + --with-mpe= -Platforms Tested -=================== - - Linux 5.16.14-200.fc35 GNU gcc (GCC) 11.2.1 20220127 (Red Hat 11.2.1-9) - #1 SMP x86_64 GNU/Linux GNU Fortran (GCC) 11.2.1 20220127 (Red Hat 11.2.1-9) - Fedora35 clang version 13.0.0 (Fedora 13.0.0-3.fc35) - (cmake and autotools) - - Linux 5.11.0-34-generic GNU gcc (GCC) 9.3.0-17ubuntu1 - #36-Ubuntu SMP x86_64 GNU/Linux GNU Fortran (GCC) 9.3.0-17ubuntu1 - Ubuntu 20.04 Ubuntu clang version 10.0.0-4 - (cmake and autotools) - - Linux 5.3.18-150300-cray_shasta_c cray-mpich/8.1.16 - #1 SMP x86_64 GNU/Linux Cray clang 14.0.0 - (crusher) GCC 11.2.0 - (cmake) - - Linux 4.14.0-115.35.1.1chaos openmpi 4.0.5 - #1 SMP aarch64 GNU/Linux GCC 9.2.0 (ARM-build-5) - (stria) GCC 7.2.0 (Spack GCC) - (cmake) - - Linux 4.14.0-115.35.1.3chaos spectrum-mpi/rolling-release - #1 SMP ppc64le GNU/Linux clang 12.0.1 - (vortex) GCC 8.3.1 - XL 16.1.1 - (cmake) - - Linux-4.14.0-115.21.2 spectrum-mpi/rolling-release - #1 SMP ppc64le GNU/Linux clang 12.0.1, 14.0.5 - (lassen) GCC 8.3.1 - XL 16.1.1.2, 2021,09.22, 2022.08.05 - (cmake) - - Linux-4.12.14-197.99-default cray-mpich/7.7.14 - #1 SMP x86_64 GNU/Linux cce 12.0.3 - (theta) GCC 11.2.0 - llvm 9.0 - Intel 19.1.2 - - Linux 3.10.0-1160.36.2.el7.ppc64 gcc (GCC) 4.8.5 20150623 (Red Hat 4.8.5-39) - #1 SMP ppc64be GNU/Linux g++ (GCC) 4.8.5 20150623 (Red Hat 4.8.5-39) - Power8 (echidna) GNU Fortran (GCC) 4.8.5 20150623 (Red Hat 4.8.5-39) - - Linux 3.10.0-1160.24.1.el7 GNU C (gcc), Fortran (gfortran), C++ (g++) - #1 SMP x86_64 GNU/Linux compilers: - Centos7 Version 4.8.5 20150623 (Red Hat 4.8.5-4) - (jelly/kituo/moohan) Version 4.9.3, Version 5.3.0, Version 6.3.0, - Version 7.2.0, Version 8.3.0, Version 9.1.0 - Intel(R) C (icc), C++ (icpc), Fortran (icc) - compilers: - Version 17.0.0.098 Build 20160721 - GNU C (gcc) and C++ (g++) 4.8.5 compilers - with NAG Fortran Compiler Release 6.1(Tozai) - Intel(R) C (icc) and C++ (icpc) 17.0.0.098 compilers - with NAG Fortran Compiler Release 6.1(Tozai) - MPICH 3.1.4 compiled with GCC 4.9.3 - MPICH 3.3 compiled with GCC 7.2.0 - OpenMPI 2.1.6 compiled with icc 18.0.1 - OpenMPI 3.1.3 and 4.0.0 compiled with GCC 7.2.0 - PGI C, Fortran, C++ for 64-bit target on - x86_64; - Version 19.10-0 - (autotools and cmake) - - Linux-3.10.0-1160.0.0.1chaos openmpi-4.1.2 - #1 SMP x86_64 GNU/Linux clang 6.0.0, 11.0.1 - (quartz) GCC 7.3.0, 8.1.0 - Intel 19.0.4, 2022.2, oneapi.2022.2 - - Linux-3.10.0-1160.71.1.1chaos openmpi/4.1 - #1 SMP x86_64 GNU/Linux GCC 7.2.0 - (skybridge) Intel/19.1 - (cmake) - - Linux-3.10.0-1160.66.1.1chaos openmpi/4.1 - #1 SMP x86_64 GNU/Linux GCC 7.2.0 - (attaway) Intel/19.1 - (cmake) - - Linux-3.10.0-1160.59.1.1chaos openmpi/4.1 - #1 SMP x86_64 GNU/Linux Intel/19.1 - (chama) (cmake) - - macOS Apple M1 11.6 Apple clang version 12.0.5 (clang-1205.0.22.11) - Darwin 20.6.0 arm64 gfortran GNU Fortran (Homebrew GCC 11.2.0) 11.1.0 - (macmini-m1) Intel icc/icpc/ifort version 2021.3.0 202106092021.3.0 20210609 - - macOS Big Sur 11.3.1 Apple clang version 12.0.5 (clang-1205.0.22.9) - Darwin 20.4.0 x86_64 gfortran GNU Fortran (Homebrew GCC 10.2.0_3) 10.2.0 - (bigsur-1) Intel icc/icpc/ifort version 2021.2.0 20210228 - - macOS High Sierra 10.13.6 Apple LLVM version 10.0.0 (clang-1000.10.44.4) - 64-bit gfortran GNU Fortran (GCC) 6.3.0 - (bear) Intel icc/icpc/ifort version 19.0.4.233 20190416 - - macOS Sierra 10.12.6 Apple LLVM version 9.0.0 (clang-900.39.2) - 64-bit gfortran GNU Fortran (GCC) 7.4.0 - (kite) Intel icc/icpc/ifort version 17.0.2 - - Mac OS X El Capitan 10.11.6 Apple clang version 7.3.0 from Xcode 7.3 - 64-bit gfortran GNU Fortran (GCC) 5.2.0 - (osx1011test) Intel icc/icpc/ifort version 16.0.2 - - - Linux 2.6.32-573.22.1.el6 GNU C (gcc), Fortran (gfortran), C++ (g++) - #1 SMP x86_64 GNU/Linux compilers: - Centos6 Version 4.4.7 20120313 - (platypus) Version 4.9.3, 5.3.0, 6.2.0 - MPICH 3.1.4 compiled with GCC 4.9.3 - PGI C, Fortran, C++ for 64-bit target on - x86_64; - Version 19.10-0 - - Windows 10 x64 Visual Studio 2015 w/ Intel C/C++/Fortran 18 (cmake) - Visual Studio 2017 w/ Intel C/C++/Fortran 19 (cmake) - Visual Studio 2019 w/ clang 12.0.0 - with MSVC-like command-line (C/C++ only - cmake) - Visual Studio 2019 w/ Intel C/C++/Fortran oneAPI 2021 (cmake) - Visual Studio 2019 w/ MSMPI 10.1 (C only - cmake) - - -Known Problems -============== - - ************************************************************ - * _ * - * (_) * - * __ ____ _ _ __ _ __ _ _ __ __ _ * - * \ \ /\ / / _` | '__| '_ \| | '_ \ / _` | * - * \ V V / (_| | | | | | | | | | | (_| | * - * \_/\_/ \__,_|_| |_| |_|_|_| |_|\__, | * - * __/ | * - * |___/ * - * * - * Please refrain from running any program (including * - * HDF5 tests) which uses the subfiling VFD on Perlmutter * - * at the National Energy Research Scientific Computing * - * Center, NERSC. * - * Doing so may cause a system disruption due to subfiling * - * crashing Lustre. The sytem's Lustre bug is expected * - * to be resolved by 2023. * - * * - ************************************************************ - - 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. - - CPP ptable test fails on both VS2017 and VS2019 with Intel compiler, JIRA - issue: HDFFV-10628. This test will pass with VS2015 with Intel compiler. - - The subsetting option in ph5diff currently will fail and should be avoided. - The subsetting option works correctly in serial h5diff. - - Several tests currently fail on certain platforms: - MPI_TEST-t_bigio fails with spectrum-mpi on ppc64le platforms. - - MPI_TEST-t_subfiling_vfd and MPI_TEST_EXAMPLES-ph5_subfiling fail with - cray-mpich on theta and with XL compilers on ppc64le platforms. - - MPI_TEST_testphdf5_tldsc fails with cray-mpich 7.7 on cori and theta. - - 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. - -The issues with the gif tool are: - HDFFV-10592 CVE-2018-17433 - HDFFV-10593 CVE-2018-17436 - HDFFV-11048 CVE-2020-10809 -These CVE issues have not yet been addressed and can be avoided by not building -the gif tool. Disable building the High-Level tools with these options: - autotools: --disable-hltools - cmake: HDF5_BUILD_HL_TOOLS=OFF - - -%%%%1.13.2%%%% - -HDF5 version 1.13.2 released on 2022-08-15 -================================================================================ - + CMake has never supported building with MPE support. -INTRODUCTION -============ + (DER - 2022/11/08) -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. + - Removal of dmalloc support -Note that documentation in the links below will be updated at the time of each -final release. + The ability to build with dmalloc support has been removed along with + the following configure options: -Links to HDF5 documentation can be found on The HDF5 web page: + Autotools: + --with-dmalloc= - https://portal.hdfgroup.org/display/HDF5/HDF5 + CMake: + HDF5_ENABLE_USING_DMALLOC -The official HDF5 releases can be obtained from: + (DER - 2022/11/08) + + - Removal of memory allocation sanity checks configure options - https://www.hdfgroup.org/downloads/hdf5/ + With the removal of the memory allocation sanity checks feature, the + following configure options are no longer necessary and have been + removed: -Changes from Release to Release and New Features in the HDF5-1.13.x release series -can be found at: + Autotools: + --enable-memory-alloc-sanity-check - https://portal.hdfgroup.org/display/HDF5/HDF5+Application+Developer%27s+Guide + CMake: + HDF5_MEMORY_ALLOC_SANITY_CHECK + HDF5_ENABLE_MEMORY_STATS -If you have any questions or comments, please send them to the HDF Help Desk: + (DER - 2022/11/03) - help@hdfgroup.org + - Add new CMake configuration variable HDF5_USE_GNU_DIRS + HDF5_USE_GNU_DIRS (default OFF) selects the use of GNU Coding Standard install + directory variables by including the CMake module, GNUInstallDirs(see CMake + documentation for details). The HDF_DIR_PATHS macro in the HDFMacros.cmake file + sets various PATH variables for use during the build, test and install processes. + By default, the historical settings for these variables will be used. -CONTENTS -======== + (ADB - 2022/10/21, GH-2175, GH-1716) -- New Features -- Support for new platforms and languages -- Bug Fixes since HDF5-1.13.1 -- Platforms Tested -- Known Problems -- CMake vs. Autotools installations + - Update CMake minimum version to 3.18 + Updated CMake minimum version from 3.12 to 3.18 and removed version checks + which were added for Windows features not yet available in version 3.12. Also + removed configure macros and code checks for old style code compile checks. -New Features -============ + (ADB - 2022/08/29, HDFFV-11329) - Configuration: - ------------- - Correct the usage of CMAKE_Fortran_MODULE_DIRECTORY and where to install Fortran mod files. @@ -566,526 +151,6 @@ New Features (JTH - 2022/03/01) - - Library: - -------- - - Onion VFD - - The onion VFD allows creating "versioned" HDF5 files. File open/close - operations after initial file creation will add changes to an external - "onion" file (.onion extension by default) instead of the original file. - Each written revision can be opened independently. - - To open a file with the onion VFD, use the H5Pset_fapl_onion() API call - (does not need to be used for the initial creation of the file). The - options for the H5FD_onion_fapl_info_t struct are described in H5FDonion.h. - - The H5FDonion_get_revision_count() API call can be used to query a file - to find out how many revisions have been created. - - (DER - 2022/08/02) - - - Subfiling VFD - - The HDF5 Subfiling VFD is a new MPI-based file driver that allows an - HDF5 application to distribute an HDF5 file across a collection of - "sub-files" in equal-sized data segment "stripes". I/O to the logical - HDF5 file is then directed to the appropriate "sub-file" according to - the Subfiling configuration and a system of I/O concentrators, which - are MPI ranks operating worker threads. - - By allowing a configurable stripe size, number of I/O concentrators and - method for selecting MPI ranks as I/O concentrators, the Subfiling VFD - aims to enable an HDF5 application to find a middle ground between the - single shared file and file-per-process approaches to parallel file I/O - for the particular machine the application is running on. In general, the - goal is to avoid some of the complexity of the file-per-process approach - while also minimizing the locking issues of the single shared file approach - on a parallel file system. - - Also included with the Subfiling VFD is a new h5fuse.sh script which - reads a Subfiling configuration file and then combines the various - sub-files back into a single HDF5 file. By default, the h5fuse.sh script - looks in the current directory for the Subfiling configuration file, - but can also be pointed to the configuration file with a command-line - option. - - The Subfiling VFD can be used by calling H5Pset_fapl_subfiling() on a - File Access Property List and using that FAPL for file operations. Note - that the Subfiling VFD currently has the following limitations: - - * Does not currently support HDF5 collective I/O, other than collective - metadata writes and reads as set by H5Pset_coll_metadata_write() and - H5Pset_all_coll_metadata_ops() - - * The Subfiling VFD should not currently be used with an HDF5 library - that has been built with thread-safety enabled. This can cause deadlocks - when failures occur due to interactions between the VFD's internal - threads and HDF5's global lock. - - (JTH - 2022/07/22) - - - Parallel Library: - ----------------- - - - - - Fortran Library: - ---------------- - - - - - C++ Library: - ------------ - - Added two new constructors to H5::H5File class - - Two new constructors were added to allow opening a file with non-default - access property list. - - - Java Library: - ------------- - - Added version of H5Rget_name to return the name as a Java string. - - Other functions that get_name process the get_size then get the name - within the JNI implementation. Now H5Rget_name has a H5Rget_name_string. - - (ADB - 2022/07/12) - - - Added reference support to H5A and H5D read write vlen JNI functions. - - Added the implementation to handle VL references as an Array of Lists - of byte arrays. - - The JNI wrappers translate the Array of Lists to/from the hvl_t vlen - structures. The wrappers use the specified datatype arguments for the - List type translation, it is expected that the Java type is correct. - - (ADB - 2022/07/11, HDFFV-11318) - - - H5A and H5D read write vlen JNI functions were incorrect. - - Corrected the vlen function implementations for the basic primitive types. - The VLStrings functions now correctly use the implementation that had been - the VL functions. (VLStrings functions did not have an implementation.) - The new VL functions implementation now expect an Array of Lists between - Java and the JNI wrapper. - - The JNI wrappers translate the Array of Lists to/from the hvl_t vlen - structures. The wrappers use the specified datatype arguments for the - List type translation, it is expected that the Java type is correct. - - (ADB - 2022/07/07, HDFFV-11310) - - - H5A and H5D read write JNI functions had flawed vlen datatype check. - - Adapted tools function for JNI utils file. This reduced multiple calls - to a single check and variable. The variable can then be used to call - the H5Treclaim function. Adjusted existing test and added new test. - - (ADB - 2022/06/22) - - - Tools: - ------ - - Building h5perf/h5perf_serial in "standalone mode" has been removed - - Building h5perf separately from the library was added circa 2008 - in HDF5 1.6.8. It's unclear what purpose this serves and the current - implementation is currently broken. The existing files require - H5private.h and the symbols we use to determine how the copied - platform-independence scheme should be used come from H5pubconf.h, - which may not match the compiler being used to build standalone h5perf. - - Due to the maintenance overhead and lack of a clear use case, support - for building h5perf and h5perf_serial separately from the HDF5 library - has been removed. - - (DER - 2022/07/15) - - - The perf tool has been removed - - The small `perf` tool didn't really do anything special and the name - conflicts with gnu's perf tool. - - (DER - 2022/07/15, GitHub #1787) - - - 1.10 References in containers were not displayed properly by h5dump. - - Ported 1.10 tools display function to provide ability to inspect and - display 1.10 reference data. - - (ADB - 2022/06/22) - - - High-Level APIs: - ---------------- - - - - - C Packet Table API: - ------------------- - - - - - Internal header file: - --------------------- - - All the #defines named H5FD_CTL__* were renamed to H5FD_CTL_*, i.e. the double underscore was reduced to a single underscore. - - - Documentation: - -------------- - - - - -Support for new platforms, languages and compilers -================================================== - - - - -Bug Fixes since HDF5-1.13.1 release -=================================== - Library - ------- - - The offset parameter in H5Dchunk_iter() is now scaled properly - - In earlier HDF5 1.13.x versions, the chunk offset was not scaled by the - chunk dimensions. This offset parameter in the callback now matches - that of H5Dget_chunk_info(). - - (@mkitti - 2022/08/06, GitHub #1419) - - - Converted an assertion on (possibly corrupt) file contents to a normal - error check - - Previously, the library contained an assertion check that a read superblock - doesn't contain a superblock extension message when the superblock - version < 2. When a corrupt HDF5 file is read, this assertion can be triggered - in debug builds of HDF5. In production builds, this situation could cause - either a library error or a crash, depending on the platform. - - (JTH - 2022/07/08, HDFFV-11316/HDFFV-11317) - - - Java Library - ------------ - - - - - Configuration - ------------- - - - - - Tools - ----- - - - - - Performance - ------------- - - - - - Fortran API - ----------- - - h5open_f and h5close_f fixes - * Fixed it so both h5open_f and h5close_f can be called multiple times. - * Fixed an issue with open objects remaining after h5close_f was called. - * Added additional tests. - (MSB, 2022/04/19, HDFFV-11306) - - - High-Level Library - ------------------ - - - - - Fortran High-Level APIs - ----------------------- - - - - - Documentation - ------------- - - - - - F90 APIs - -------- - - - - - C++ APIs - -------- - - - - - Testing - ------- - - - - -Platforms Tested -=================== - - Linux 5.16.14-200.fc35 GNU gcc (GCC) 11.2.1 20220127 (Red Hat 11.2.1-9) - #1 SMP x86_64 GNU/Linux GNU Fortran (GCC) 11.2.1 20220127 (Red Hat 11.2.1-9) - Fedora35 clang version 13.0.0 (Fedora 13.0.0-3.fc35) - (cmake and autotools) - - Linux 5.11.0-34-generic GNU gcc (GCC) 9.3.0-17ubuntu1 - #36-Ubuntu SMP x86_64 GNU/Linux GNU Fortran (GCC) 9.3.0-17ubuntu1 - Ubuntu 20.04 Ubuntu clang version 10.0.0-4 - (cmake and autotools) - - Linux 5.3.18-150300-cray_shasta_c cray-mpich/8.1.16 - #1 SMP x86_64 GNU/Linux Cray clang 14.0.0 - (crusher) GCC 11.2.0 - (cmake) - - Linux 5.3.18-24-cray_shasta_c cray-mpich/8.1.12 - #1 SMP x86_64 GNU/Linux Cray clang 13.0.0 - (spock) AMD clang 13.0.0 - GCC 8.2.0, 11.2.0 - (cmake) - - Linux 4.14.0-115.35.1.1chaos openmpi 4.0.5 - #1 SMP aarch64 GNU/Linux GCC 9.2.0 (ARM-build-5) - (stria) GCC 7.2.0 (Spack GCC) - (cmake) - - Linux 4.14.0-115.35.1.3chaos spectrum-mpi/rolling-release - #1 SMP ppc64le GNU/Linux clang 12.0.1 - (vortex) GCC 8.3.1 - XL 16.1.1 - (cmake) - - Linux-4.14.0-115.21.2 spectrum-mpi/rolling-release - #1 SMP ppc64le GNU/Linux clang 8.0.1, 11.0.1 - (lassen) GCC 7.3.1 - XL 16.1.1.2 - (cmake) - - Linux-4.12.14-150.75-default cray-mpich/7.7.10 - #1 SMP x86_64 GNU/Linux GCC 7.3.0, 8.2.0 - (cori) Intel (R) Version 19.0.3.199 - (cmake) - - Linux 3.10.0-1160.36.2.el7.ppc64 gcc (GCC) 4.8.5 20150623 (Red Hat 4.8.5-39) - #1 SMP ppc64be GNU/Linux g++ (GCC) 4.8.5 20150623 (Red Hat 4.8.5-39) - Power8 (echidna) GNU Fortran (GCC) 4.8.5 20150623 (Red Hat 4.8.5-39) - - Linux 3.10.0-1160.24.1.el7 GNU C (gcc), Fortran (gfortran), C++ (g++) - #1 SMP x86_64 GNU/Linux compilers: - Centos7 Version 4.8.5 20150623 (Red Hat 4.8.5-4) - (jelly/kituo/moohan) Version 4.9.3, Version 5.3.0, Version 6.3.0, - Version 7.2.0, Version 8.3.0, Version 9.1.0 - Intel(R) C (icc), C++ (icpc), Fortran (icc) - compilers: - Version 17.0.0.098 Build 20160721 - GNU C (gcc) and C++ (g++) 4.8.5 compilers - with NAG Fortran Compiler Release 6.1(Tozai) - Intel(R) C (icc) and C++ (icpc) 17.0.0.098 compilers - with NAG Fortran Compiler Release 6.1(Tozai) - MPICH 3.1.4 compiled with GCC 4.9.3 - MPICH 3.3 compiled with GCC 7.2.0 - OpenMPI 2.1.6 compiled with icc 18.0.1 - OpenMPI 3.1.3 and 4.0.0 compiled with GCC 7.2.0 - PGI C, Fortran, C++ for 64-bit target on - x86_64; - Version 19.10-0 - (autotools and cmake) - - Linux-3.10.0-1160.71.1.1chaos openmpi-4.0.0 - #1 SMP x86_64 GNU/Linux clang 6.0.0, 11.0.1 - (quartz) GCC 7.3.0, 8.1.0 - Intel 16.0.4, 18.0.2, 19.0.4 - (cmake) - - Linux-3.10.0-1160.71.1.1chaos openmpi/4.1 - #1 SMP x86_64 GNU/Linux GCC 7.2.0 - (skybridge) Intel/19.1 - (cmake) - - Linux-3.10.0-1160.66.1.1chaos openmpi/4.1 - #1 SMP x86_64 GNU/Linux GCC 7.2.0 - (attaway) Intel/19.1 - (cmake) - - Linux-3.10.0-1160.59.1.1chaos openmpi/4.1 - #1 SMP x86_64 GNU/Linux Intel/19.1 - (chama) (cmake) - - macOS Apple M1 11.6 Apple clang version 12.0.5 (clang-1205.0.22.11) - Darwin 20.6.0 arm64 gfortran GNU Fortran (Homebrew GCC 11.2.0) 11.1.0 - (macmini-m1) Intel icc/icpc/ifort version 2021.3.0 202106092021.3.0 20210609 - - macOS Big Sur 11.3.1 Apple clang version 12.0.5 (clang-1205.0.22.9) - Darwin 20.4.0 x86_64 gfortran GNU Fortran (Homebrew GCC 10.2.0_3) 10.2.0 - (bigsur-1) Intel icc/icpc/ifort version 2021.2.0 20210228 - - macOS High Sierra 10.13.6 Apple LLVM version 10.0.0 (clang-1000.10.44.4) - 64-bit gfortran GNU Fortran (GCC) 6.3.0 - (bear) Intel icc/icpc/ifort version 19.0.4.233 20190416 - - macOS Sierra 10.12.6 Apple LLVM version 9.0.0 (clang-900.39.2) - 64-bit gfortran GNU Fortran (GCC) 7.4.0 - (kite) Intel icc/icpc/ifort version 17.0.2 - - Mac OS X El Capitan 10.11.6 Apple clang version 7.3.0 from Xcode 7.3 - 64-bit gfortran GNU Fortran (GCC) 5.2.0 - (osx1011test) Intel icc/icpc/ifort version 16.0.2 - - - Linux 2.6.32-573.22.1.el6 GNU C (gcc), Fortran (gfortran), C++ (g++) - #1 SMP x86_64 GNU/Linux compilers: - Centos6 Version 4.4.7 20120313 - (platypus) Version 4.9.3, 5.3.0, 6.2.0 - MPICH 3.1.4 compiled with GCC 4.9.3 - PGI C, Fortran, C++ for 64-bit target on - x86_64; - Version 19.10-0 - - Windows 10 x64 Visual Studio 2015 w/ Intel C/C++/Fortran 18 (cmake) - Visual Studio 2017 w/ Intel C/C++/Fortran 19 (cmake) - Visual Studio 2019 w/ clang 12.0.0 - with MSVC-like command-line (C/C++ only - cmake) - Visual Studio 2019 w/ Intel C/C++/Fortran oneAPI 2021 (cmake) - Visual Studio 2019 w/ MSMPI 10.1 (C only - cmake) - - -Known Problems -============== - Setting a variable-length dataset fill value will leak the memory allocated - for the p field of the hvl_t struct. A fix is in progress for this. - HDFFV-10840 - - 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. - - CPP ptable test fails on both VS2017 and VS2019 with Intel compiler, JIRA - issue: HDFFV-10628. This test will pass with VS2015 with Intel compiler. - - The subsetting option in ph5diff currently will fail and should be avoided. - The subsetting option works correctly in serial h5diff. - - Several tests currently fail on certain platforms: - MPI_TEST-t_bigio fails with spectrum-mpi on ppc64le platforms. - - MPI_TEST-t_subfiling_vfd and MPI_TEST_EXAMPLES-ph5_subfiling fail with - cray-mpich on theta and with XL compilers on ppc64le platforms. - - MPI_TEST_testphdf5_tldsc fails with cray-mpich 7.7 on cori and theta. - - 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. - -The issues with the gif tool are: - HDFFV-10592 CVE-2018-17433 - HDFFV-10593 CVE-2018-17436 - HDFFV-11048 CVE-2020-10809 -These CVE issues have not yet been addressed and can be avoided by not building -the gif tool. Disable building the High-Level tools with these options: - autotools: --disable-hltools - cmake: HDF5_BUILD_HL_TOOLS=OFF - - -%%%%1.13.1%%%% - -HDF5 version 1.13.1 released on 2022-03-02 -================================================================================ - - -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 HDF5-1.13.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 HDF5-1.13.0 -- Platforms Tested -- Known Problems -- CMake vs. Autotools installations - - -New Features -============ - - Configuration: - ------------- - Reworked corrected path searched by CMake find_package command The install path for cmake find_package files had been changed to use @@ -1123,369 +188,6 @@ New Features (ADB - 2021/11/23) - - Library: - -------- - - Add a new public function, H5ESget_requests() - - This function allows the user to retrieve request pointers from an event - set. It is intended for use primarily by VOL plugin developers. - - (NAF - 2022/01/11) - - - Parallel Library: - ----------------- - - Several improvements to parallel compression feature, including: - - * Improved support for collective I/O (for both writes and reads) - - * Significant reduction of memory usage for the feature as a whole - - * Reduction of copying of application data buffers passed to H5Dwrite - - * Addition of support for incremental file space allocation for filtered - datasets created in parallel. Incremental file space allocation is the - default for these types of datasets (early file space allocation is - also still supported), while early file space allocation is still the - default (and only supported at allocation time) for unfiltered datasets - created in parallel. Incremental file space allocation should help with - parallel HDF5 applications that wish to use fill values on filtered - datasets, but would typically avoid doing so since dataset creation in - parallel would often take an excessive amount of time. Since these - datasets previously used early file space allocation, HDF5 would - allocate space for and write fill values to every chunk in the dataset - at creation time, leading to noticeable overhead. Instead, with - incremental file space allocation, allocation of file space for chunks - and writing of fill values to those chunks will be delayed until each - individual chunk is initially written to. - - * Addition of support for HDF5's "don't filter partial edge chunks" flag - (https://portal.hdfgroup.org/display/HDF5/H5P_SET_CHUNK_OPTS) - - * Addition of proper support for HDF5 fill values with the feature - - * Addition of 'H5_HAVE_PARALLEL_FILTERED_WRITES' macro to H5pubconf.h - so HDF5 applications can determine at compile-time whether the feature - is available - - * Addition of simple examples (ph5_filtered_writes.c and - ph5_filtered_writes_no_sel.c) under examples directory to demonstrate - usage of the feature - - * Improved coverage of regression testing for the feature - - (JTH - 2022/2/23) - - -Support for new platforms, languages and compilers -================================================== - - None - - -Bug Fixes since HDF5-1.13.0 release -=================================== - Library - ------- - - Fixed a metadata cache bug when resizing a pinned/protected cache entry - - When resizing a pinned/protected cache entry, the metadata - cache code previously would wait until after resizing the - entry to attempt to log the newly-dirtied entry. This - caused H5C_resize_entry to mark the entry as dirty and made - H5AC_resize_entry think that it didn't need to add the - newly-dirtied entry to the dirty entries skiplist. - - Thus, a subsequent H5AC__log_moved_entry would think it - needed to allocate a new entry for insertion into the dirty - entry skip list, since the entry didGn't exist on that list. - This caused an assertion failure, as the code to allocate a - new entry assumes that the entry is not dirty. - - (JRM - 2022/02/28) - - - Issue #1436 identified a problem with the H5_VERS_RELEASE check in the - H5check_version function. - - Investigating the original fix, #812, we discovered some inconsistencies - with a new block added to check H5_VERS_RELEASE for incompatibilities. - This new block was not using the new warning text dealing with the - H5_VERS_RELEASE check and would cause the warning to be duplicated. - - By removing the H5_VERS_RELEASE argument in the first check for - H5_VERS_MAJOR and H5_VERS_MINOR, the second check would only check - the H5_VERS_RELEASE for incompatible release versions. This adheres - to the statement that except for the develop branch, all release versions - in a major.minor maintenance branch should be compatible. The prerequisite - is that an application will not use any APIs not present in all release versions. - - (ADB - 2022/02/24, #1438) - - - Unified handling of collective metadata reads to correctly fix old bugs - - Due to MPI-related issues occurring in HDF5 from mismanagement of the - status of collective metadata reads, they were forced to be disabled - during chunked dataset raw data I/O in the HDF5 1.10.5 release. This - wouldn't generally have affected application performance because HDF5 - already disables collective metadata reads during chunk lookup, since - it is generally unlikely that the same chunks will be read by all MPI - ranks in the I/O operation. However, this was only a partial solution - that wasn't granular enough. - - This change now unifies the handling of the file-global flag and the - API context-level flag for collective metadata reads in order to - simplify querying of the true status of collective metadata reads. Thus, - collective metadata reads are once again enabled for chunked dataset - raw data I/O, but manually controlled at places where some processing - occurs on MPI rank 0 only and would cause issues when collective - metadata reads are enabled. - - (JTH - 2021/11/16, HDFFV-10501/HDFFV-10562) - - - Fixed several potential MPI deadlocks in library failure conditions - - In the parallel library, there were several places where MPI rank 0 - could end up skipping past collective MPI operations when some failure - occurs in rank 0-specific processing. This would lead to deadlocks - where rank 0 completes an operation while other ranks wait in the - collective operation. These places have been rewritten to have rank 0 - push an error and try to cleanup after the failure, then continue to - participate in the collective operation to the best of its ability. - - (JTH - 2021/11/09) - - -Platforms Tested -=================== - - Linux 5.13.14-200.fc34 GNU gcc (GCC) 11.2.1 2021078 (Red Hat 11.2.1-1) - #1 SMP x86_64 GNU/Linux GNU Fortran (GCC) 11.2.1 2021078 (Red Hat 11.2.1-1) - Fedora34 clang version 12.0.1 (Fedora 12.0.1-1.fc34) - (cmake and autotools) - - Linux 5.11.0-34-generic GNU gcc (GCC) 9.3.0-17ubuntu1 - #36-Ubuntu SMP x86_64 GNU/Linux GNU Fortran (GCC) 9.3.0-17ubuntu1 - Ubuntu 20.04 Ubuntu clang version 10.0.0-4 - (cmake and autotools) - - Linux 5.8.0-63-generic GNU gcc (GCC) 10.3.0-1ubuntu1 - #71-Ubuntu SMP x86_64 GNU/Linux GNU Fortran (GCC) 10.3.0-1ubuntu1 - Ubuntu20.10 Ubuntu clang version 11.0.0-2 - (cmake and autotools) - - Linux 5.3.18-22-default GNU gcc (SUSE Linux) 7.5.0 - #1 SMP x86_64 GNU/Linux GNU Fortran (SUSE Linux) 7.5.0 - SUSE15sp2 clang version 7.0.1 (tags/RELEASE_701/final 349238) - (cmake and autotools) - - Linux-4.14.0-115.21.2 spectrum-mpi/rolling-release - #1 SMP ppc64le GNU/Linux clang 8.0.1, 11.0.1 - (lassen) GCC 7.3.1 - XL 16.1.1.2 - (cmake) - - Linux-3.10.0-1160.49.1 openmpi-intel/4.1 - #1 SMP x86_64 GNU/Linux Intel(R) Version 18.0.5, 19.1.2 - (chama) (cmake) - - Linux-4.12.14-150.75-default cray-mpich/7.7.10 - #1 SMP x86_64 GNU/Linux GCC 7.3.0, 8.2.0 - (cori) Intel (R) Version 19.0.3.199 - (cmake) - - Linux-4.12.14-197.86-default cray-mpich/7.7.6 - # 1SMP x86_64 GNU/Linux GCC 7.3.0, 9.3.0, 10.2.0 - (mutrino) Intel (R) Version 17.0.4, 18.0.5, 19.1.3 - (cmake) - - Linux 3.10.0-1160.36.2.el7.ppc64 gcc (GCC) 4.8.5 20150623 (Red Hat 4.8.5-39) - #1 SMP ppc64be GNU/Linux g++ (GCC) 4.8.5 20150623 (Red Hat 4.8.5-39) - Power8 (echidna) GNU Fortran (GCC) 4.8.5 20150623 (Red Hat 4.8.5-39) - - Linux 3.10.0-1160.24.1.el7 GNU C (gcc), Fortran (gfortran), C++ (g++) - #1 SMP x86_64 GNU/Linux compilers: - Centos7 Version 4.8.5 20150623 (Red Hat 4.8.5-4) - (jelly/kituo/moohan) Version 4.9.3, Version 5.3.0, Version 6.3.0, - Version 7.2.0, Version 8.3.0, Version 9.1.0 - Intel(R) C (icc), C++ (icpc), Fortran (icc) - compilers: - Version 17.0.0.098 Build 20160721 - GNU C (gcc) and C++ (g++) 4.8.5 compilers - with NAG Fortran Compiler Release 6.1(Tozai) - Intel(R) C (icc) and C++ (icpc) 17.0.0.098 compilers - with NAG Fortran Compiler Release 6.1(Tozai) - MPICH 3.1.4 compiled with GCC 4.9.3 - MPICH 3.3 compiled with GCC 7.2.0 - OpenMPI 2.1.6 compiled with icc 18.0.1 - OpenMPI 3.1.3 and 4.0.0 compiled with GCC 7.2.0 - PGI C, Fortran, C++ for 64-bit target on - x86_64; - Version 19.10-0 - - Linux-3.10.0-1127.0.0.1chaos openmpi-4.0.0 - #1 SMP x86_64 GNU/Linux clang 6.0.0, 11.0.1 - (quartz) GCC 7.3.0, 8.1.0 - Intel 16.0.4, 18.0.2, 19.0.4 - - macOS Apple M1 11.6 Apple clang version 12.0.5 (clang-1205.0.22.11) - Darwin 20.6.0 arm64 gfortran GNU Fortran (Homebrew GCC 11.2.0) 11.1.0 - (macmini-m1) Intel icc/icpc/ifort version 2021.3.0 202106092021.3.0 20210609 - - macOS Big Sur 11.3.1 Apple clang version 12.0.5 (clang-1205.0.22.9) - Darwin 20.4.0 x86_64 gfortran GNU Fortran (Homebrew GCC 10.2.0_3) 10.2.0 - (bigsur-1) Intel icc/icpc/ifort version 2021.2.0 20210228 - - macOS High Sierra 10.13.6 Apple LLVM version 10.0.0 (clang-1000.10.44.4) - 64-bit gfortran GNU Fortran (GCC) 6.3.0 - (bear) Intel icc/icpc/ifort version 19.0.4.233 20190416 - - macOS Sierra 10.12.6 Apple LLVM version 9.0.0 (clang-900.39.2) - 64-bit gfortran GNU Fortran (GCC) 7.4.0 - (kite) Intel icc/icpc/ifort version 17.0.2 - - Mac OS X El Capitan 10.11.6 Apple clang version 7.3.0 from Xcode 7.3 - 64-bit gfortran GNU Fortran (GCC) 5.2.0 - (osx1011test) Intel icc/icpc/ifort version 16.0.2 - - - Linux 2.6.32-573.22.1.el6 GNU C (gcc), Fortran (gfortran), C++ (g++) - #1 SMP x86_64 GNU/Linux compilers: - Centos6 Version 4.4.7 20120313 - (platypus) Version 4.9.3, 5.3.0, 6.2.0 - MPICH 3.1.4 compiled with GCC 4.9.3 - PGI C, Fortran, C++ for 64-bit target on - x86_64; - Version 19.10-0 - - Windows 10 x64 Visual Studio 2015 w/ Intel C/C++/Fortran 18 (cmake) - Visual Studio 2017 w/ Intel C/C++/Fortran 19 (cmake) - Visual Studio 2019 w/ clang 12.0.0 - with MSVC-like command-line (C/C++ only - cmake) - Visual Studio 2019 w/ Intel Fortran 19 (cmake) - Visual Studio 2019 w/ MSMPI 10.1 (C only - cmake) - - -Known Problems -============== - Setting a variable-length dataset fill value will leak the memory allocated - for the p field of the hvl_t struct. A fix is in progress for this. - HDFFV-10840 - - 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. - - CPP ptable test fails on both VS2017 and VS2019 with Intel compiler, JIRA - issue: HDFFV-10628. This test will pass with VS2015 with Intel compiler. - - The subsetting option in ph5diff currently will fail and should be avoided. - The subsetting option works correctly in serial h5diff. - - 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. - -The issues with the gif tool are: - HDFFV-10592 CVE-2018-17433 - HDFFV-10593 CVE-2018-17436 - HDFFV-11048 CVE-2020-10809 -These CVE issues have not yet been addressed and can be avoided by not building -the gif tool. Disable building the High-Level tools with these options: - autotools: --disable-hltools - - -%%%%1.13.0%%%% - -HDF5 version 1.13.0 released on 2021-12-01 -================================================================================ - - -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 HDF5-1.13.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 -- New platforms, languages and compilers tested -- Bug Fixes since HDF5-1.12.0 -- Platforms Tested -- Known Problems -- CMake vs. Autotools installations - - -New Features -============ - - Configuration: - ------------- - Added new configure option to support building parallel tools. See Tools below (autotools - CMake): --enable-parallel-tools HDF5_BUILD_PARALLEL_TOOLS @@ -1517,20 +219,6 @@ New Features (DCY - 2021/09/29) - - Added new option to control the build of High-Level tools - that default ON/enabled. - - Add configure options (autotools - CMake): - --enable-hltools HDF5_BUILD_HL_TOOLS - - Disabling this option prevents building the gif tool which - contains the following CVEs: - HDFFV-10592 CVE-2018-17433 - HDFFV-10593 CVE-2018-17436 - HDFFV-11048 CVE-2020-10809 - - (ADB - 2021/09/16, HDFFV-11266) - - Adds C++ Autotools configuration file for Intel * Checks for icpc as the compiler @@ -1863,88 +551,143 @@ New Features (ADB - 2020/03/24, TRILAB-192) - - Added test script for file size compare - If CMake minimum version is at least 3.14, the fileCompareTest.cmake - script will compare file sizes. + Library: + -------- + - Overhauled the Virtual Object Layer (VOL) + + The virtual object layer (VOL) was added in HDF5 1.12.0 but the initial + implementation required API-breaking changes to better support optional + operations and pass-through VOL connectors. The original VOL API is + now considered deprecated and VOL users and connector authors should + target the 1.14 VOL API. + + The specific changes are too extensive to document in a release note, so + VOL users and connector authors should consult the updated VOL connector + author's guide and the 1.12-1.14 VOL migration guide. - (ADB - 2020/02/24, HDFFV-11036) + (DER - 2022/12/28) - - Update CMake minimum version to 3.12 + - H5VLquery_optional() signature change - Updated CMake minimum version to 3.12 and added version checks - for Windows features. + The last parameter of this API call has changed from a pointer to hbool_t + to a pointer to uint64_t. Due to the changes in how optional operations + are handled in the 1.14 VOL API, we cannot make the old API call work + with the new scheme, so there is no API compatibility macro for it. - (ADB - 2020/02/05, TRILABS-142) + (DER - 2022/12/28) - - Fixed CMake include properties for Fortran libraries + - H5I_free_t callback signature change - Corrected the library properties for Fortran to use the - correct path for the Fortran module files. + In order to support asynchronous operations and future IDs, the signature + of the H5I_free_t callback has been modified to take a second 'request' + parameter. Due to the nature of the internal library changes, no API + compatibility macro is available for this change. - (ADB - 2020/02/04, HDFFV-11012) + (DER - 2022/12/28) - - Added common warnings files for gnu and intel + - Fix for CVE-2019-8396 - Added warnings files to use one common set of flags - during configure for both autotools and CMake build - systems. The initial implementation only affects a - general set of flags for gnu and intel compilers. + Malformed HDF5 files may have truncated content which does not match + the expected size. When H5O__pline_decode() attempts to decode these it + may read past the end of the allocated space leading to heap overflows + as bounds checking is incomplete. - (ADB - 2020/01/17) + The fix ensures each element is within bounds before reading. - - Added new options to CMake for control of testing + (2022/11/09 - HDFFV-10712, CVE-2019-8396, GitHub #2209) - Added CMake options (default ON); - HDF5_TEST_SERIAL AND/OR HDF5_TEST_PARALLEL - combined with: - HDF5_TEST_TOOLS - HDF5_TEST_EXAMPLES - HDF5_TEST_SWMR - HDF5_TEST_FORTRAN - HDF5_TEST_CPP - HDF5_TEST_JAVA + - Removal of memory allocation sanity checks feature - (ADB - 2020/01/15, HDFFV-11001) + This feature added heap canaries and statistics tracking for internal + library memory operations. Unfortunately, the heap canaries caused + problems when library memory operations were mixed with standard C + library memory operations (such as in the filter pipeline, where + buffers may have to be reallocated). Since any platform with a C + compiler also usually has much more sophisticated memory sanity + checking tools than the HDF5 library provided (e.g., valgrind), we + have decided to to remove the feature entirely. - - Added Clang sanitizers to CMake for analyzer support if compiler is clang. + In addition to the configure changes described above, this also removes + the following from the public API: + H5get_alloc_stats() + H5_alloc_stats_t - Added CMake code and files to execute the Clang sanitizers if - HDF5_ENABLE_SANITIZERS is enabled and the USE_SANITIZER option - is set to one of the following: - Address - Memory - MemoryWithOrigins - Undefined - Thread - Leak - 'Address;Undefined' + (DER - 2022/11/03) + + - Added multi dataset I/O feature + + Added H5Dread_multi, H5Dread_multi_async, H5Dwrite_multi, and + H5Dwrite_multi_async API routines to allow I/O on multiple datasets with a + single API call. Added H5Dread_multi_f and H5Dwrite_multi_f Fortran + wrappers. Updated VOL callbacks for dataset I/O to support multi dataset + I/O. - (ADB - 2019/12/12, TRILAB-135) + (NAF - 2022/10/19) - - Update CMake for VS2019 support + - Onion VFD - CMake added support for VS2019 in version 3.15. Changes to the CMake - generator setting required changes to scripts. Also updated version - references in CMake files as necessary. + The onion VFD allows creating "versioned" HDF5 files. File open/close + operations after initial file creation will add changes to an external + "onion" file (.onion extension by default) instead of the original file. + Each written revision can be opened independently. - (ADB - 2019/11/18, HDFFV-10962) + To open a file with the onion VFD, use the H5Pset_fapl_onion() API call + (does not need to be used for the initial creation of the file). The + options for the H5FD_onion_fapl_info_t struct are described in H5FDonion.h. - - Update CMake options to match new autotools options + The H5FDonion_get_revision_count() API call can be used to query a file + to find out how many revisions have been created. - Add configure options (autotools - CMake): - enable-asserts HDF5_ENABLE_ASSERTS - enable-symbols HDF5_ENABLE_SYMBOLS - enable-profiling HDF5_ENABLE_PROFILING - enable-optimization HDF5_ENABLE_OPTIMIZATION - In addition NDEBUG is no longer forced defined and relies on the CMake - process. + (DER - 2022/08/02) - (ADB - 2019/10/07, HDFFV-100901, HDFFV-10637, TRILAB-97) + - Subfiling VFD + The HDF5 Subfiling VFD is a new MPI-based file driver that allows an + HDF5 application to distribute an HDF5 file across a collection of + "sub-files" in equal-sized data segment "stripes". I/O to the logical + HDF5 file is then directed to the appropriate "sub-file" according to + the Subfiling configuration and a system of I/O concentrators, which + are MPI ranks operating worker threads. + + By allowing a configurable stripe size, number of I/O concentrators and + method for selecting MPI ranks as I/O concentrators, the Subfiling VFD + aims to enable an HDF5 application to find a middle ground between the + single shared file and file-per-process approaches to parallel file I/O + for the particular machine the application is running on. In general, the + goal is to avoid some of the complexity of the file-per-process approach + while also minimizing the locking issues of the single shared file approach + on a parallel file system. + + Also included with the Subfiling VFD is a new h5fuse.sh script which + reads a Subfiling configuration file and then combines the various + sub-files back into a single HDF5 file. By default, the h5fuse.sh script + looks in the current directory for the Subfiling configuration file, + but can also be pointed to the configuration file with a command-line + option. + + The Subfiling VFD can be used by calling H5Pset_fapl_subfiling() on a + File Access Property List and using that FAPL for file operations. Note + that the Subfiling VFD currently has the following limitations: + + * Does not currently support HDF5 collective I/O, other than collective + metadata writes and reads as set by H5Pset_coll_metadata_write() and + H5Pset_all_coll_metadata_ops() + + * The Subfiling VFD should not currently be used with an HDF5 library + that has been built with thread-safety enabled. This can cause deadlocks + when failures occur due to interactions between the VFD's internal + threads and HDF5's global lock. + + (JTH - 2022/07/22) + + - Add a new public function, H5ESget_requests() + + This function allows the user to retrieve request pointers from an event + set. It is intended for use primarily by VOL plugin developers. + + (NAF - 2022/01/11) - Library: - -------- - Adds new file driver-level memory copy operation for "ctl" callback and updates compact dataset I/O routines to utilize it @@ -2217,83 +960,60 @@ New Features (JOS - 2020/03/13, TBD) - - Refactored public exposure of haddr_t type in favor of "object tokens" - - To better accommodate HDF5 VOL connectors where "object addresses in a file" - may not make much sense, the following changes were made to the library: - - * Introduced new H5O_token_t "object token" type, which represents a - unique and permanent identifier for referencing an HDF5 object within - a container; these "object tokens" are meant to replace object addresses. - Along with the new type, a new H5Oopen_by_token API call was introduced - to open an object by a token, similar to how object addresses were - previously used with H5Oopen_by_addr. - * Introduced new H5Lget_info2, H5Lget_info_by_idx2, H5Literate2, H5Literate_by_name2, - H5Lvisit2 and H5Lvisit_by_name2 API calls, along with their associated H5L_info2_t - struct and H5L_iterate2_t callback function, which work with the newly-introduced - object tokens, instead of object addresses. The original functions have been - renamed to version 1 functions and are deprecated in favor of the new version 2 - functions. The H5L_info_t and H5L_iterate_t types have been renamed to version 1 - types and are now deprecated in favor of their version 2 counterparts. For each of - the functions and types, compatibility macros take place of the original symbols. - - * Introduced new H5Oget_info3, H5Oget_info_by_name3, H5Oget_info_by_idx3, - H5Ovisit3 and H5Ovisit_by_name3 API calls, along with their associated H5O_info2_t - struct and H5O_iterate2_t callback function, which work with the newly-introduced - object tokens, instead of object addresses. The version 2 functions are now - deprecated in favor of the version 3 functions. The H5O_info_t and H5O_iterate_t - types have been renamed to version 1 types and are now deprecated in favor of their - version 2 counterparts. For each, compatibility macros take place of the original - symbols. - - * Introduced new H5Oget_native_info, H5Oget_native_info_by_name and - H5Oget_native_info_by_idx API calls, along with their associated H5O_native_info_t - struct, which are used to retrieve the native HDF5 file format-specific information - about an object. This information (such as object header info and B-tree/heap info) - has been removed from the new H5O_info2_t struct so that the more generic - H5Oget_info(_by_name/_by_idx)3 routines will not try to retrieve it for non-native - VOL connectors. + Parallel Library: + ----------------- + - Several improvements to parallel compression feature, including: - * Added new H5Otoken_cmp, H5Otoken_to_str and H5Otoken_from_str routines to compare - two object tokens, convert an object token into a nicely-readable string format and - to convert an object token string back into a real object token, respectively. + * Improved support for collective I/O (for both writes and reads) - (DER, QAK, JTH - 2020/01/16) + * Significant reduction of memory usage for the feature as a whole - - Add new public function H5Sselect_adjust. + * Reduction of copying of application data buffers passed to H5Dwrite - This function shifts a dataspace selection by a specified logical offset - within the dataspace extent. This can be useful for VOL developers to - implement chunked datasets. + * Addition of support for incremental file space allocation for filtered + datasets created in parallel. Incremental file space allocation is the + default for these types of datasets (early file space allocation is + also still supported), while early file space allocation is still the + default (and only supported at allocation time) for unfiltered datasets + created in parallel. Incremental file space allocation should help with + parallel HDF5 applications that wish to use fill values on filtered + datasets, but would typically avoid doing so since dataset creation in + parallel would often take an excessive amount of time. Since these + datasets previously used early file space allocation, HDF5 would + allocate space for and write fill values to every chunk in the dataset + at creation time, leading to noticeable overhead. Instead, with + incremental file space allocation, allocation of file space for chunks + and writing of fill values to those chunks will be delayed until each + individual chunk is initially written to. - (NAF - 2019/11/18) + * Addition of support for HDF5's "don't filter partial edge chunks" flag + (https://portal.hdfgroup.org/display/HDF5/H5P_SET_CHUNK_OPTS) - - Add new public function H5Sselect_project_intersection. + * Addition of proper support for HDF5 fill values with the feature - This function computes the intersection between two dataspace selections - and projects that intersection into a third selection. This can be useful - for VOL developers to implement chunked or virtual datasets. + * Addition of 'H5_HAVE_PARALLEL_FILTERED_WRITES' macro to H5pubconf.h + so HDF5 applications can determine at compile-time whether the feature + is available - (NAF - 2019/11/13, ID-148) + * Addition of simple examples (ph5_filtered_writes.c and + ph5_filtered_writes_no_sel.c) under examples directory to demonstrate + usage of the feature - - Add new public function H5VLget_file_type. + * Improved coverage of regression testing for the feature - This function returns a datatype equivalent to the supplied datatype but - with the location set to be in the file. This datatype can then be used - with H5Tconvert to convert data between file and in-memory representation. - This function is intended for use only by VOL connector developers. + (JTH - 2022/2/23) - (NAF - 2019/11/08, ID-127) + Fortran Library: + ---------------- + - Added pointer based H5Dfill_f API - Parallel Library: - ----------------- - - + Added Fortran H5Dfill_f, which is fully equivalent to the C API. It accepts pointers, + fill value datatype and datatype of dataspace elements. + (MSB - 2022/10/10, HDFFV-10734.) - Fortran Library: - ---------------- - H5Fget_name_f fixed to handle correctly trailing whitespaces and newly allocated buffers. @@ -2309,8 +1029,14 @@ New Features (DER - 2020/07/30, HDFFV-11092) + C++ Library: ------------ + - Added two new constructors to H5::H5File class + + Two new constructors were added to allow opening a file with non-default + access property list. + - Add wrappers for H5Pset/get_file_locking() API calls FileAccPropList::setFileLocking() @@ -2324,6 +1050,46 @@ New Features Java Library: ------------- + - Added version of H5Rget_name to return the name as a Java string. + + Other functions that get_name process the get_size then get the name + within the JNI implementation. Now H5Rget_name has a H5Rget_name_string. + + (ADB - 2022/07/12) + + - Added reference support to H5A and H5D read write vlen JNI functions. + + Added the implementation to handle VL references as an Array of Lists + of byte arrays. + + The JNI wrappers translate the Array of Lists to/from the hvl_t vlen + structures. The wrappers use the specified datatype arguments for the + List type translation, it is expected that the Java type is correct. + + (ADB - 2022/07/11, HDFFV-11318) + + - H5A and H5D read write vlen JNI functions were incorrect. + + Corrected the vlen function implementations for the basic primitive types. + The VLStrings functions now correctly use the implementation that had been + the VL functions. (VLStrings functions did not have an implementation.) + The new VL functions implementation now expect an Array of Lists between + Java and the JNI wrapper. + + The JNI wrappers translate the Array of Lists to/from the hvl_t vlen + structures. The wrappers use the specified datatype arguments for the + List type translation, it is expected that the Java type is correct. + + (ADB - 2022/07/07, HDFFV-11310) + + - H5A and H5D read write JNI functions had flawed vlen datatype check. + + Adapted tools function for JNI utils file. This reduced multiple calls + to a single check and variable. The variable can then be used to call + the H5Treclaim function. Adjusted existing test and added new test. + + (ADB - 2022/06/22) + - Replaced HDF5AtomException with HDF5IdException Since H5E_ATOM changed to H5E_ID in the C library, the Java exception @@ -2357,23 +1123,38 @@ New Features (DER - 2020/07/30, HDFFV-11092) - - Added ability to test java library with VOLs. - Created a new CMake script that combines the java and vol test scripts. + Tools: + ------ + - Building h5perf/h5perf_serial in "standalone mode" has been removed - (ADB - 2020/02/03, HDFFV-10996) + Building h5perf separately from the library was added circa 2008 + in HDF5 1.6.8. It's unclear what purpose this serves and the current + implementation is currently broken. The existing files require + H5private.h and the symbols we use to determine how the copied + platform-independence scheme should be used come from H5pubconf.h, + which may not match the compiler being used to build standalone h5perf. - - Tests fail for non-English locales. + Due to the maintenance overhead and lack of a clear use case, support + for building h5perf and h5perf_serial separately from the HDF5 library + has been removed. - In the JUnit tests with a non-English locale, only the part before - the decimal comma is replaced by XXXX and this leads to a comparison - error. Changed the regex for the Time substitution. + (DER - 2022/07/15) - (ADB - 2020/01/09, HDFFV-10995) + - The perf tool has been removed + The small `perf` tool didn't really do anything special and the name + conflicts with gnu's perf tool. + + (DER - 2022/07/15, GitHub #1787) + + - 1.10 References in containers were not displayed properly by h5dump. + + Ported 1.10 tools display function to provide ability to inspect and + display 1.10 reference data. + + (ADB - 2022/06/22) - Tools: - ------ - h5repack added an optional verbose value for reporting R/W timing. In addition to adding timing capture around the read/write calls in @@ -2458,22 +1239,6 @@ New Features (KY -2020/02/07, HDFFV-11014) - - h5diff was updated to use the new reference APIs. - - h5diff uses the new reference APIs to compare references. - Attribute references can also be compared. - - (ADB - 2019/12/19, HDFFV-10980) - - - h5dump and h5ls were updated to use the new reference APIs. - - The tools library now use the new reference APIs to inspect a - file. Also the DDL spec was updated to reflect the format - changes produced with the new APIs. The export API and support - functions in the JNI were updated to match. - - (ADB - 2019/12/06, HDFFV-10876 and HDFFV-10877) - High-Level APIs: ---------------- @@ -2485,36 +1250,282 @@ New Features (AF - 2021/09/08) + C Packet Table API: ------------------- - + Internal header file: --------------------- - - + - All the #defines named H5FD_CTL__* were renamed to H5FD_CTL_*, i.e. the double underscore was reduced to a single underscore. + Documentation: -------------- - - + - Doxygen User Guide documentation is available when configured and generated. + The resulting documentation files will be in the share/html subdirectory + of the HDF5 install directory. + (ADB - 2022/08/09) -New platforms, languages and compilers tested -============================================= - - Linux 5.13.14-200.fc34 #1 SMP x86_64 GNU/Linux Fedora34 - - Linux 5.11.0-34-generic #36-Ubuntu SMP x86_64 GNU/Linux Ubuntu 20.04 - - Linux 5.3.18-22-default #1 SMP x86_64 GNU/Linux SUSE15sp2 - - Linux-4.14.0-115.21.2 #1 SMP ppc64le GNU/Linux - - Linux-4.12.14-150.75-default #1 SMP x86_64 GNU/Linux - - macOS Apple M1 11.6 Darwin 20.6.0 arm64 - - macOS Big Sur 11.3.1 Darwin 20.4.0 x86_64 - - clang versions 11.0.1, 12.0.5 - - Visual Studio 2019 w/ clang 12.0.0 with MSVC-like command-line +Support for new platforms, languages and compilers +================================================== + - + Bug Fixes since HDF5-1.12.0 release =================================== Library ------- + - Seg fault on file close + + h5debug fails at file close with core dump on a file that has an + illegal file size in its cache image. In H5F_dest(), the library + performs all the closing operations for the file and keeps track of + the error encountered when reading the file cache image. + At the end of the routine, it frees the file's file structure and + returns error. Due to the error return, the file object is not removed + from the ID node table. This eventually causes assertion failure in + H5VL__native_file_close() when the library finally exits and tries to + access that file object in the table for closing. + + The closing routine, H5F_dest(), will not free the file structure if + there is error, keeping a valid file structure in the ID node table. + It will be freed later in H5VL__native_file_close() when the + library exits and terminates the file package. + + (VC - 2022/12/14, HDFFV-11052, CVE-2020-10812) + + - Fix CVE-2018-13867 / GHSA-j8jr-chrh-qfrf + + Validate location (offset) of the accumulated metadata when comparing. + + Initially, the accumulated metadata location is initialized to HADDR_UNDEF + - the highest available address. Bogus input files may provide a location + or size matching this value. Comparing this address against such bogus + values may provide false positives. Thus make sure, the value has been + initialized or fail the comparison early and let other parts of the + code deal with the bogus address/size. + Note: To avoid unnecessary checks, it is assumed that if the 'dirty' + member in the same structure is true the location is valid. + + (EFE - 2022/10/10 GH-2230) + + - Fix CVE-2018-16438 / GHSA-9xmm-cpf8-rgmx + + Make sure info block for external links has at least 3 bytes. + + According to the specification, the information block for external links + contains 1 byte of version/flag information and two 0 terminated strings + for the object linked to and the full path. + Although not very useful, the minimum string length for each (with + terminating 0) would be one byte. + Checking this helps to avoid SEGVs triggered by bogus files. + + (EFE - 2022/10/09 GH-2233) + + - CVE-2021-46244 / GHSA-vrxh-5gxg-rmhm + + Compound datatypes may not have members of size 0 + + A member size of 0 may lead to an FPE later on as reported in + CVE-2021-46244. To avoid this, check for this as soon as the + member is decoded. + + (EFE - 2022/10/05 GEH-2242) + + + - Fix CVE-2021-45830 / GHSA-5h2h-fjjr-x9m2 + + Make H5O__fsinfo_decode() more resilient to out-of-bound reads. + + When decoding a file space info message in H5O__fsinfo_decode() make + sure each element to be decoded is still within the message. Malformed + hdf5 files may have trunkated content which does not match the + expected size. Checking this will prevent attempting to decode + unrelated data and heap overflows. So far, only free space manager + address data was checked before decoding. + + (EFE - 2022/10/05 GH-2228) + + - Fix CVE-2021-46242 / GHSA-x9pw-hh7v-wjpf + + When evicting driver info block, NULL the corresponding entry. + + Since H5C_expunge_entry() called (from H5AC_expunge_entry()) sets the flag + H5C__FLUSH_INVALIDATE_FLAG, the driver info block will be freed. NULLing + the pointer in f->shared->drvinfo will prevent use-after-free when it is + used in other functions (like H5F__dest()) - as other places will check + whether the pointer is initialized before using its value. + + (EFE - 2022/09/29 GH-2254) + + - Fix CVE-2021-45833 / GHSA-x57p-jwp6-4v79 + + Report error if dimensions of chunked storage in data layout < 2 + + For Data Layout Messages version 1 & 2 the specification state + that the value stored in the data field is 1 greater than the + number of dimensions in the dataspace. For version 3 this is + not explicitly stated but the implementation suggests it to be + the case. + Thus the set value needs to be at least 2. For dimensionality + < 2 an out-of-bounds access occurs. + + (EFE - 2022/09/28 GH-2240) + + - Fix CVE-2018-14031 / GHSA-2xc7-724c-r36j + + Parent of enum datatype message must have the same size as the + enum datatype message itself. + Functions accessing the enumeration values use the size of the + enumeration datatype to determine the size of each element and + how much data to copy. + Thus the size of the enumeration and its parent need to match. + Check in H5O_dtype_decode_helper() to avoid unpleasant surprises + later. + + (EFE - 2022/09/28 GH-2236) + + - Fix CVE-2018-17439 / GHSA-vcxv-vp43-rch7 + + H5IMget_image_info(): Make sure to not exceed local array size + + Malformed hdf5 files may provide more dimensions than the array dim[] in + H5IMget_image_info() is able to hold. Check number of elements first by calling + H5Sget_simple_extent_dims() with NULL for both 'dims' and 'maxdims' arguments. + This will cause the function to return only the number of dimensions. + The fix addresses a stack overflow on write. + + (EFE - 2022/09/27 HDFFV-10589, GH-2226) + + - Fixed an issue with variable length attributes + + Previously, if a variable length attribute was held open while its file + was opened through another handle, the same attribute was opened through + the second file handle, and the second file and attribute handles were + closed, attempting to write to the attribute through the first handle + would cause an error. + + (NAF - 2022/10/24) + + - Memory leak + + A memory leak was observed with variable-length fill value in + H5O_fill_convert() function in H5Ofill.c. The leak is + manifested by running valgrind on test/set_extent.c. + + Previously, fill->buf is used for datatype conversion + if it is large enough and the variable-length information + is therefore lost. A buffer is now allocated regardless + so that the element in fill->buf can later be reclaimed. + + (VC - 2022/10/10, HDFFV-10840) + + - Fixed an issue with hyperslab selections + + Previously, when combining hyperslab selections, it was possible for the + library to produce an incorrect combined selection. + + (NAF - 2022/09/25) + + - Fixed an issue with attribute type conversion with compound datatypes + + Previously, when performing type conversion for attribute I/O with a + compound datatype, the library would not fill the background buffer with + the contents of the destination, potentially causing data to be lost when + only writing to a subset of the compound fields. + + (NAF - 2022/08/22, GitHub #2016) + + - The offset parameter in H5Dchunk_iter() is now scaled properly + + In earlier HDF5 1.13.x versions, the chunk offset was not scaled by the + chunk dimensions. This offset parameter in the callback now matches + that of H5Dget_chunk_info(). + + (@mkitti - 2022/08/06, GitHub #1419) + + - Converted an assertion on (possibly corrupt) file contents to a normal + error check + + Previously, the library contained an assertion check that a read superblock + doesn't contain a superblock extension message when the superblock + version < 2. When a corrupt HDF5 file is read, this assertion can be triggered + in debug builds of HDF5. In production builds, this situation could cause + either a library error or a crash, depending on the platform. + + (JTH - 2022/07/08, HDFFV-11316/HDFFV-11317) + + - Fixed a metadata cache bug when resizing a pinned/protected cache entry + + When resizing a pinned/protected cache entry, the metadata + cache code previously would wait until after resizing the + entry to attempt to log the newly-dirtied entry. This + caused H5C_resize_entry to mark the entry as dirty and made + H5AC_resize_entry think that it didn't need to add the + newly-dirtied entry to the dirty entries skiplist. + + Thus, a subsequent H5AC__log_moved_entry would think it + needed to allocate a new entry for insertion into the dirty + entry skip list, since the entry didGn't exist on that list. + This caused an assertion failure, as the code to allocate a + new entry assumes that the entry is not dirty. + + (JRM - 2022/02/28) + + - Issue #1436 identified a problem with the H5_VERS_RELEASE check in the + H5check_version function. + + Investigating the original fix, #812, we discovered some inconsistencies + with a new block added to check H5_VERS_RELEASE for incompatibilities. + This new block was not using the new warning text dealing with the + H5_VERS_RELEASE check and would cause the warning to be duplicated. + + By removing the H5_VERS_RELEASE argument in the first check for + H5_VERS_MAJOR and H5_VERS_MINOR, the second check would only check + the H5_VERS_RELEASE for incompatible release versions. This adheres + to the statement that except for the develop branch, all release versions + in a major.minor maintenance branch should be compatible. The prerequisite + is that an application will not use any APIs not present in all release versions. + + (ADB - 2022/02/24, #1438) + + - Unified handling of collective metadata reads to correctly fix old bugs + + Due to MPI-related issues occurring in HDF5 from mismanagement of the + status of collective metadata reads, they were forced to be disabled + during chunked dataset raw data I/O in the HDF5 1.10.5 release. This + wouldn't generally have affected application performance because HDF5 + already disables collective metadata reads during chunk lookup, since + it is generally unlikely that the same chunks will be read by all MPI + ranks in the I/O operation. However, this was only a partial solution + that wasn't granular enough. + + This change now unifies the handling of the file-global flag and the + API context-level flag for collective metadata reads in order to + simplify querying of the true status of collective metadata reads. Thus, + collective metadata reads are once again enabled for chunked dataset + raw data I/O, but manually controlled at places where some processing + occurs on MPI rank 0 only and would cause issues when collective + metadata reads are enabled. + + (JTH - 2021/11/16, HDFFV-10501/HDFFV-10562) + + - Fixed several potential MPI deadlocks in library failure conditions + + In the parallel library, there were several places where MPI rank 0 + could end up skipping past collective MPI operations when some failure + occurs in rank 0-specific processing. This would lead to deadlocks + where rank 0 completes an operation while other ranks wait in the + collective operation. These places have been rewritten to have rank 0 + push an error and try to cleanup after the failure, then continue to + participate in the collective operation to the best of its ability. + + (JTH - 2021/11/09) + - Fixed an H5Pget_filter_by_id1/2() assert w/ out of range filter IDs Both H5Pget_filter_by_id1 and 2 did not range check the filter ID, which @@ -2726,6 +1737,15 @@ Bug Fixes since HDF5-1.12.0 release Java Library ------------ + - Improve variable-length datatype handling in JNI. + + The existing JNI read-write functions could handle variable-length datatypes + that were simple variable-length datatype with an atomic sub-datatype. More + complex combinations could not be handled. Reworked the JNI read-write functions + to recursively inspect datatypes for variable-length sub-datatypes. + + (ADB - 2022/10/12, HDFFV-8701,10375) + - JNI utility function does not handle new references. The JNI utility function for converting reference data to string did @@ -2745,23 +1765,51 @@ Bug Fixes since HDF5-1.12.0 release (PGT,ADB - 2020/12/13, HDFFV-10865) - - Added ability to test java library with VOLs. - Created a new CMake script that combines the java and vol test scripts. + Configuration + ------------- + - Remove Javadoc generation + + The use of doxygen now supersedes the requirement to build javadocs. We do not + have the resources to continue to support two documentation methods and have + chosen doxygen as our standard. - (ADB - 2020/02/03, HDFFV-10996) + (ADB - 2022/12/19) - - Tests fail for non-English locales. + - Change the default for building the high-level GIF tools - In the JUnit tests with a non-English locale, only the part before - the decimal comma is replaced by XXXX and this leads to a comparison - error. Changed the regex for the Time substitution. + The gif2h5 and h52gif high-level tools are deprecated and will be removed + in a future release. The default build setting for them has been changed + from enabled to disabled. A user can enable the build of these tools if + needed. - (ADB - 2020/01/09, HDFFV-10995) + autotools: --enable-hlgiftools + cmake: HDF5_BUILD_HL_GIF_TOOLS=ON + Disabling the GIF tools eliminates the following CVEs: + + HDFFV-10592 CVE-2018-17433 + HDFFV-10593 CVE-2018-17436 + HDFFV-11048 CVE-2020-10809 + + (ADB - 2022/12/16) + + - Change the settings of the *pc files to use the correct format + + The pkg-config files generated by CMake uses incorrect syntax for the 'Requires' + settings. Changing the set to use 'lib-name = version' instead 'lib-name-version' + fixes the issue + + (ADB - 2022/12/06 HDFFV-11355) + + - Move MPI libraries link from PRIVATE to PUBLIC + + The install dependencies were not including the need for MPI libraries when + an application or library was built with the C library. Also updated the + CMake target link command to use the newer style MPI::MPI_C link variable. + + (ADB - 2022/10/27) - Configuration - ------------- - Corrected path searched by CMake find_package command The install path for cmake find_package files had been changed to use @@ -2873,6 +1921,13 @@ Bug Fixes since HDF5-1.12.0 release Tools ----- + - Fix h5repack to only print output when verbose option is selected + + When timing option was added to h5repack, the check for verbose was + incorrectly implemented. + + (ADB - 2022/12/02, GH #2270) + - Changed how h5dump and h5ls identify long double. Long double support is not consistent across platforms. Tools will always @@ -2931,33 +1986,6 @@ Bug Fixes since HDF5-1.12.0 release (ADB - 2020/07/20, HDFFV-1005) - - h5repack was fixed to repack the reference attributes properly. - - The code line that checks if the update of reference inside a compound - datatype is misplaced outside the code block loop that carries out the - check. In consequence, the next attribute that is not the reference - type was repacked again as the reference type and caused the failure of - repacking. The fix is to move the corresponding code line to the correct - code block. - - (KY -2020/02/10, HDFFV-11014) - - - h5diff was updated to use the new reference APIs. - - h5diff uses the new reference APIs to compare references. - Attribute references can also be compared. - - (ADB - 2019/12/19, HDFFV-10980) - - - h5dump and h5ls were updated to use the new reference APIs. - - The tools library now use the new reference APIs to inspect a - file. Also the DDL spec was updated to reflect the format - changes produced with the new APIs. The export API and support - functions in the JNI were updated to match. - - (ADB - 2019/12/06, HDFFV-10876 and HDFFV-10877) - Performance ------------- @@ -2966,9 +1994,11 @@ Bug Fixes since HDF5-1.12.0 release Fortran API ----------- - - Corrected INTERFACE INTENT(IN) to INTENT(OUT) for buf_size in h5fget_file_image_f. - - (MSB - 2020/02/18, HDFFV-11029) + - h5open_f and h5close_f fixes + * Fixed it so both h5open_f and h5close_f can be called multiple times. + * Fixed an issue with open objects remaining after h5close_f was called. + * Added additional tests. + (MSB, 2022/04/19, HDFFV-11306) High-Level Library @@ -3019,114 +2049,198 @@ Bug Fixes since HDF5-1.12.0 release Platforms Tested =================== - Linux 5.13.14-200.fc34 GNU gcc (GCC) 11.2.1 2021078 (Red Hat 11.2.1-1) - #1 SMP x86_64 GNU/Linux GNU Fortran (GCC) 11.2.1 2021078 (Red Hat 11.2.1-1) - Fedora34 clang version 12.0.1 (Fedora 12.0.1-1.fc34) - (cmake and autotools) - - Linux 5.11.0-34-generic GNU gcc (GCC) 9.3.0-17ubuntu1 - #36-Ubuntu SMP x86_64 GNU/Linux GNU Fortran (GCC) 9.3.0-17ubuntu1 - Ubuntu 20.04 Ubuntu clang version 10.0.0-4 - (cmake and autotools) - - Linux 5.8.0-63-generic GNU gcc (GCC) 10.3.0-1ubuntu1 - #71-Ubuntu SMP x86_64 GNU/Linux GNU Fortran (GCC) 10.3.0-1ubuntu1 - Ubuntu20.10 Ubuntu clang version 11.0.0-2 - (cmake and autotools) - - Linux 5.3.18-22-default GNU gcc (SUSE Linux) 7.5.0 - #1 SMP x86_64 GNU/Linux GNU Fortran (SUSE Linux) 7.5.0 - SUSE15sp2 clang version 7.0.1 (tags/RELEASE_701/final 349238) - (cmake and autotools) - - Linux-4.14.0-115.21.2 spectrum-mpi/rolling-release - #1 SMP ppc64le GNU/Linux clang 8.0.1, 11.0.1 - (lassen) GCC 7.3.1 - XL 16.1.1.2 - (cmake) - - Linux-4.12.14-150.75-default cray-mpich/7.7.10 - #1 SMP x86_64 GNU/Linux GCC 7.3.0, 8.2.0 - (cori) Intel (R) Version 19.0.3.199 - (cmake) - - Linux-4.12.14-197.86-default cray-mpich/7.7.6 - # 1SMP x86_64 GNU/Linux GCC 7.3.0, 9.3.0, 10.2.0 - (mutrino) Intel (R) Version 17.0.4, 18.0.5, 19.1.3 - (cmake) - - Linux 3.10.0-1160.36.2.el7.ppc64 gcc (GCC) 4.8.5 20150623 (Red Hat 4.8.5-39) - #1 SMP ppc64be GNU/Linux g++ (GCC) 4.8.5 20150623 (Red Hat 4.8.5-39) - Power8 (echidna) GNU Fortran (GCC) 4.8.5 20150623 (Red Hat 4.8.5-39) - - Linux 3.10.0-1160.24.1.el7 GNU C (gcc), Fortran (gfortran), C++ (g++) - #1 SMP x86_64 GNU/Linux compilers: + Linux 5.16.14-200.fc35 GNU gcc (GCC) 11.2.1 20220127 (Red Hat 11.2.1-9) + #1 SMP x86_64 GNU/Linux GNU Fortran (GCC) 11.2.1 20220127 (Red Hat 11.2.1-9) + Fedora35 clang version 13.0.0 (Fedora 13.0.0-3.fc35) + (cmake and autotools) + + Linux 5.15.0-1026-aws gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0 + #30-Ubuntu SMP x86_64 GNU/Linux GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0 + Ubuntu 22.04 Ubuntu clang version 14.0.0-1ubuntu1 + (cmake and autotools) + + Linux 5.13.0-1031-aws GNU gcc (GCC) 9.4.0-1ubuntu1 + #35-Ubuntu SMP x86_64 GNU/Linux GNU Fortran (GCC) 9.4.0-1ubuntu1 + Ubuntu 20.04 clang version 10.0.0-4ubuntu1 + (cmake and autotools) + + Linux 5.3.18-150300-cray_shasta_c cray-mpich/8.3.3 + #1 SMP x86_64 GNU/Linux Cray clang 14.0.2, 15.0.0 + (crusher) GCC 11.2.0, 12.1.0 + (cmake) + + Linux 4.18.0-348.7.1.el8_5 gcc (GCC) 8.5.0 20210514 (Red Hat 8.5.0-4) + #1 SMP x86_64 GNU/Linux GNU Fortran (GCC) 8.5.0 20210514 (Red Hat 8.5.0-4) + CentOS8 clang version 12.0.1 (Red Hat 12.0.1) + (cmake and autotools) + + Linux 4.14.0-115.35.1.1chaos openmpi 4.0.5 + #1 SMP aarch64 GNU/Linux GCC 9.3.0 (ARM-build-5) + (stria) GCC 7.2.0 (Spack GCC) + arm/20.1 + arm/22.1 + (cmake) + + Linux 4.14.0-115.35.1.3chaos spectrum-mpi/rolling-release + #1 SMP ppc64le GNU/Linux clang 12.0.1 + (vortex) GCC 8.3.1 + XL 16.1.1 + (cmake) + + Linux-4.14.0-115.21.2 spectrum-mpi/rolling-release + #1 SMP ppc64le GNU/Linux clang 12.0.1, 14.0.5 + (lassen) GCC 8.3.1 + XL 16.1.1.2, 2021,09.22, 2022.08.05 + (cmake) + + Linux-4.12.14-197.99-default cray-mpich/7.7.14 + #1 SMP x86_64 GNU/Linux cce 12.0.3 + (theta) GCC 11.2.0 + llvm 9.0 + Intel 19.1.2 + + Linux 3.10.0-1160.36.2.el7.ppc64 gcc (GCC) 4.8.5 20150623 (Red Hat 4.8.5-39) + #1 SMP ppc64be GNU/Linux g++ (GCC) 4.8.5 20150623 (Red Hat 4.8.5-39) + Power8 (echidna) GNU Fortran (GCC) 4.8.5 20150623 (Red Hat 4.8.5-39) + + Linux 3.10.0-1160.24.1.el7 GNU C (gcc), Fortran (gfortran), C++ (g++) + #1 SMP x86_64 GNU/Linux compilers: Centos7 Version 4.8.5 20150623 (Red Hat 4.8.5-4) (jelly/kituo/moohan) Version 4.9.3, Version 5.3.0, Version 6.3.0, Version 7.2.0, Version 8.3.0, Version 9.1.0 - Intel(R) C (icc), C++ (icpc), Fortran (icc) - compilers: + Intel(R) C (icc), C++ (icpc), Fortran (icc) + compilers: Version 17.0.0.098 Build 20160721 - GNU C (gcc) and C++ (g++) 4.8.5 compilers + GNU C (gcc) and C++ (g++) 4.8.5 compilers with NAG Fortran Compiler Release 6.1(Tozai) - Intel(R) C (icc) and C++ (icpc) 17.0.0.098 compilers + Intel(R) C (icc) and C++ (icpc) 17.0.0.098 compilers with NAG Fortran Compiler Release 6.1(Tozai) - MPICH 3.1.4 compiled with GCC 4.9.3 - MPICH 3.3 compiled with GCC 7.2.0 - OpenMPI 2.1.6 compiled with icc 18.0.1 - OpenMPI 3.1.3 and 4.0.0 compiled with GCC 7.2.0 - PGI C, Fortran, C++ for 64-bit target on - x86_64; + MPICH 3.1.4 compiled with GCC 4.9.3 + MPICH 3.3 compiled with GCC 7.2.0 + OpenMPI 2.1.6 compiled with icc 18.0.1 + OpenMPI 3.1.3 and 4.0.0 compiled with GCC 7.2.0 + PGI C, Fortran, C++ for 64-bit target on + x86_64; Version 19.10-0 + (autotools and cmake) - Linux-3.10.0-1127.0.0.1chaos openmpi-4.0.0 + Linux-3.10.0-1160.0.0.1chaos openmpi-4.1.2 #1 SMP x86_64 GNU/Linux clang 6.0.0, 11.0.1 (quartz) GCC 7.3.0, 8.1.0 - Intel 16.0.4, 18.0.2, 19.0.4 + Intel 19.0.4, 2022.2, oneapi.2022.2 + + Linux-3.10.0-1160.71.1.1chaos openmpi/4.1 + #1 SMP x86_64 GNU/Linux GCC 7.2.0 + (skybridge) Intel/19.1 + (cmake) + + Linux-3.10.0-1160.66.1.1chaos openmpi/4.1 + #1 SMP x86_64 GNU/Linux GCC 7.2.0 + (attaway) Intel/19.1 + (cmake) - macOS Apple M1 11.6 Apple clang version 12.0.5 (clang-1205.0.22.11) - Darwin 20.6.0 arm64 gfortran GNU Fortran (Homebrew GCC 11.2.0) 11.1.0 - (macmini-m1) Intel icc/icpc/ifort version 2021.3.0 202106092021.3.0 20210609 + Linux-3.10.0-1160.59.1.1chaos openmpi/4.1 + #1 SMP x86_64 GNU/Linux Intel/19.1 + (chama) (cmake) - macOS Big Sur 11.3.1 Apple clang version 12.0.5 (clang-1205.0.22.9) - Darwin 20.4.0 x86_64 gfortran GNU Fortran (Homebrew GCC 10.2.0_3) 10.2.0 - (bigsur-1) Intel icc/icpc/ifort version 2021.2.0 20210228 + macOS Apple M1 11.6 Apple clang version 12.0.5 (clang-1205.0.22.11) + Darwin 20.6.0 arm64 gfortran GNU Fortran (Homebrew GCC 11.2.0) 11.1.0 + (macmini-m1) Intel icc/icpc/ifort version 2021.3.0 202106092021.3.0 20210609 - macOS High Sierra 10.13.6 Apple LLVM version 10.0.0 (clang-1000.10.44.4) - 64-bit gfortran GNU Fortran (GCC) 6.3.0 - (bear) Intel icc/icpc/ifort version 19.0.4.233 20190416 + macOS Big Sur 11.3.1 Apple clang version 12.0.5 (clang-1205.0.22.9) + Darwin 20.4.0 x86_64 gfortran GNU Fortran (Homebrew GCC 10.2.0_3) 10.2.0 + (bigsur-1) Intel icc/icpc/ifort version 2021.2.0 20210228 - macOS Sierra 10.12.6 Apple LLVM version 9.0.0 (clang-900.39.2) - 64-bit gfortran GNU Fortran (GCC) 7.4.0 - (kite) Intel icc/icpc/ifort version 17.0.2 + macOS High Sierra 10.13.6 Apple LLVM version 10.0.0 (clang-1000.10.44.4) + 64-bit gfortran GNU Fortran (GCC) 6.3.0 + (bear) Intel icc/icpc/ifort version 19.0.4.233 20190416 - Mac OS X El Capitan 10.11.6 Apple clang version 7.3.0 from Xcode 7.3 - 64-bit gfortran GNU Fortran (GCC) 5.2.0 - (osx1011test) Intel icc/icpc/ifort version 16.0.2 + macOS Sierra 10.12.6 Apple LLVM version 9.0.0 (clang-900.39.2) + 64-bit gfortran GNU Fortran (GCC) 7.4.0 + (kite) Intel icc/icpc/ifort version 17.0.2 + Mac OS X El Capitan 10.11.6 Apple clang version 7.3.0 from Xcode 7.3 + 64-bit gfortran GNU Fortran (GCC) 5.2.0 + (osx1011test) Intel icc/icpc/ifort version 16.0.2 - Linux 2.6.32-573.22.1.el6 GNU C (gcc), Fortran (gfortran), C++ (g++) - #1 SMP x86_64 GNU/Linux compilers: + + Linux 2.6.32-573.22.1.el6 GNU C (gcc), Fortran (gfortran), C++ (g++) + #1 SMP x86_64 GNU/Linux compilers: Centos6 Version 4.4.7 20120313 (platypus) Version 4.9.3, 5.3.0, 6.2.0 - MPICH 3.1.4 compiled with GCC 4.9.3 - PGI C, Fortran, C++ for 64-bit target on - x86_64; + MPICH 3.1.4 compiled with GCC 4.9.3 + PGI C, Fortran, C++ for 64-bit target on + x86_64; Version 19.10-0 - Windows 10 x64 Visual Studio 2015 w/ Intel C/C++/Fortran 18 (cmake) - Visual Studio 2017 w/ Intel C/C++/Fortran 19 (cmake) - Visual Studio 2019 w/ clang 12.0.0 + Windows 10 x64 Visual Studio 2015 w/ Intel C/C++/Fortran 18 (cmake) + Visual Studio 2017 w/ Intel C/C++/Fortran 19 (cmake) + Visual Studio 2019 w/ clang 12.0.0 + with MSVC-like command-line (C/C++ only - cmake) + Visual Studio 2019 w/ Intel C/C++/Fortran oneAPI 2022 (cmake) + Visual Studio 2022 w/ clang 15.0.1 with MSVC-like command-line (C/C++ only - cmake) - Visual Studio 2019 w/ Intel Fortran 19 (cmake) - Visual Studio 2019 w/ MSMPI 10.1 (C only - cmake) + Visual Studio 2022 w/ Intel C/C++/Fortran oneAPI 2022 (cmake) + Visual Studio 2019 w/ MSMPI 10.1 (C only - cmake) Known Problems ============== - Setting a variable-length dataset fill value will leak the memory allocated - for the p field of the hvl_t struct. A fix is in progress for this. - HDFFV-10840 + + ************************************************************ + * _ * + * (_) * + * __ ____ _ _ __ _ __ _ _ __ __ _ * + * \ \ /\ / / _` | '__| '_ \| | '_ \ / _` | * + * \ V V / (_| | | | | | | | | | | (_| | * + * \_/\_/ \__,_|_| |_| |_|_|_| |_|\__, | * + * __/ | * + * |___/ * + * * + * Please refrain from running any program (including * + * HDF5 tests) which uses the subfiling VFD on Perlmutter * + * at the National Energy Research Scientific Computing * + * Center, NERSC. * + * Doing so may cause a system disruption due to subfiling * + * crashing Lustre. The system's Lustre bug is expected * + * to be resolved by 2023. * + * * + ************************************************************ + + There is a bug in OpenMPI 4.1.0-4.1.4 that can result in incorrect + results from MPI I/O requests unless one of the following parameters + is passed to mpirun: + + --mca io ^ompio + + --mca fbtl_posix_read_data_sieving 0 + + This bug has been fixed in later versions of OpenMPI. + + Further discussion can be found here: + + https://www.hdfgroup.org/2022/11/workarounds-for-openmpi-bug-exposed-by-make-check-in-hdf5-1-13-3/ + + When using the subfiling feature with OpenMPI it is often necessary to + increase the maximum number of threads: + + --mca common_pami_max_threads 4096 + + There is a bug in MPICH 4.0.0-4.0.3 where using device=ch4:ofi (the default) + can cause failures in the testphdf5 test program. Using ch4:ucx or ch3 + allows the test to pass. The bug appears to be fixed in the upcoming 4.1 + release. + + These MPI implementation bugs may also be present in implementations derived + from OpenMPI or MPICH. The workarounds listed above may need to be adjusted + to match the derived implementation, or in some cases, there may be no + workaround. + + The accum test fails on MacOS 12.6.2 (Monterey) with clang 14.0.0. The + reason for this failure and its impact are unknown. + + The onion test has failures on Windows when built using Intel OneAPI + 2022.3. The cause of these failures is under investigation. CMake files do not behave correctly with paths containing spaces. Do not use spaces in paths because the required escaping for handling spaces @@ -3144,6 +2258,14 @@ Known Problems The subsetting option in ph5diff currently will fail and should be avoided. The subsetting option works correctly in serial h5diff. + Several tests currently fail on certain platforms: + MPI_TEST-t_bigio fails with spectrum-mpi on ppc64le platforms. + + MPI_TEST-t_subfiling_vfd and MPI_TEST_EXAMPLES-ph5_subfiling fail with + cray-mpich on theta and with XL compilers on ppc64le platforms. + + MPI_TEST_testphdf5_tldsc fails with cray-mpich 7.7 on cori and theta. + 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. @@ -3187,8 +2309,7 @@ The issues with the gif tool are: HDFFV-10592 CVE-2018-17433 HDFFV-10593 CVE-2018-17436 HDFFV-11048 CVE-2020-10809 -These CVE issues have not yet been addressed and can be avoided by not building -the gif tool. Disable building the High-Level tools with these options: - autotools: --disable-hltools - cmake: HDF5_BUILD_HL_TOOLS=OFF - cmake: HDF5_BUILD_HL_TOOLS=OFF +These CVE issues have not yet been addressed and are avoided by not building +the gif tool by default. Enable building the High-Level tools with these options: + autotools: --enable-hltools + cmake: HDF5_BUILD_HL_TOOLS=ON diff --git a/release_docs/HISTORY-1_8.txt b/release_docs/HISTORY-1_8.txt deleted file mode 100644 index 461e0be..0000000 --- a/release_docs/HISTORY-1_8.txt +++ /dev/null @@ -1,14439 +0,0 @@ -HDF5 History -============ - -This file contains development history of HDF5 1.8 branch - -23. Release Information for hdf5-1.8.21 -22. Release Information for hdf5-1.8.20 -21. Release Information for hdf5-1.8.19 -20. Release Information for hdf5-1.8.18 -19. Release Information for hdf5-1.8.17 -18. Release Information for hdf5-1.8.16 -17. Release Information for hdf5-1.8.15 -16. Release Information for hdf5-1.8.14 -15. Release Information for hdf5-1.8.13 -14. Release Information for hdf5-1.8.12 -13. Release Information for hdf5-1.8.11 -12. Release Information for hdf5-1.8.10-patch1 -11. Release Information for hdf5-1.8.10 -10. Release Information for hdf5-1.8.9 -09. Release Information for hdf5-1.8.8 -08. Release Information for hdf5-1.8.7 -07. Release Information for hdf5-1.8.6 -06. Release Information for hdf5-1.8.5 -05. Release Information for hdf5-1.8.4 -04. Release Information for hdf5-1.8.3 -03. Release Information for hdf5-1.8.2 -02. Release Information for hdf5-1.8.1 -01. Release Information for hdf5-1.8.0 - -[Search on the string '%%%%' for section breaks of each release.] - -%%%%1.8.21%%%% - - -HDF5 version 1.8.21 released on 2018-06-04 -================================================================================ - -INTRODUCTION -============ - -This document describes the differences between HDF5-1.8.20 and -HDF5-1.8.21, and contains information on the platforms tested and -known problems in HDF5-1.8.21. -For more details, see the files HISTORY-1_0-1_8_0_rc3.txt -and HISTORY-1_8.txt in the release_docs/ directory of the HDF5 source. - -Links to the HDF5 1.8.21 source code, documentation, and additional materials -can be found on the HDF5 web page at: - - https://support.hdfgroup.org/HDF5/ - -The HDF5 1.8.21 release can be obtained from: - - https://support.hdfgroup.org/HDF5/release/obtain518.html - -User documentation for 1.8.21 can be accessed directly at this location: - - https://support.hdfgroup.org/HDF5/doc1.8/ - -New features in the HDF5-1.8.x release series, including brief general -descriptions of some new and modified APIs, are described in the "What's New -in 1.8.0?" document: - - https://support.hdfgroup.org/HDF5/doc/ADGuide/WhatsNew180.html - -All new and modified APIs are listed in detail in the "HDF5 Software Changes -from Release to Release" document, in the section "Release 1.8.21 (current -release) versus Release 1.8.20 - - https://support.hdfgroup.org/HDF5/doc1.8/ADGuide/Changes.html - -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, Languages, and Compilers -- Bug Fixes since HDF5-1.8.20 -- Supported Platforms -- Supported Configuration Features Summary -- More Tested Platforms -- Known Problems - - -New Features -============ - - Configuration - ------------- - - CMake - - Change minimum version to 3.10. - - This change removes the need to support a copy of the FindMPI.cmake module, - which has been removed, along with its subfolder in the config/cmake_ext_mod - location. - - (ADB - 2018/03/09) - - - CMake - - Add pkg-config file generation - - Added pkg-config file generation for the C, C++, HL, and HL C++ libraries. - In addition, builds on linux will create h5cXXX scripts that use the pkg-config - files. This is a limited implementation of a script like autotools h5cc. - - (ADB - 2018/03/08, HDFFV-4359) - - - CMake - - Refactor use of CMAKE_BUILD_TYPE for new variable, which understands - the type of generator in use. - - Added new configuration macros to use new HDF_BUILD_TYPE variable. This - variable is set correctly for the type of generator being used for the build. - - (ADB - 2018/01/08, HDFFV-10385, HDFFV-10296) - - C++ API - ------- - - The following C++ API wrappers have been added to class H5Location - + H5Lcreate_soft: - // Creates a soft link from link_name to target_name. - void link(const char *target_name, const char *link_name,...) - void link(const H5std_string& target_name,...) - - + H5Lcreate_hard: - // Creates a hard link from new_name to curr_name. - void link(const char *curr_name, const Group& new_loc,...) - void link(const H5std_string& curr_name, const Group& new_loc,...) - - // Creates a hard link from new_name to curr_name in the same location. - void link(const char *curr_name, const hid_t same_loc,...) - void link(const H5std_string& curr_name, const hid_t same_loc,...) - - Note: previous version CommonFG::link will be deprecated. - - + H5Lcopy: - // Copy an object from a group of file to another. - void copyLink(const char *src_name, const Group& dst,...) - void copyLink(const H5std_string& src_name, const Group& dst,...) - - // Copy an object from a group of file to the same location. - void copyLink(const char *src_name, const char *dst_name,...) - void copyLink(const H5std_string& src_name,...) - - + H5Lmove: - // Rename an object in a group or file to a new location. - void moveLink(const char* src_name, const Group& dst,...) - void moveLink(const H5std_string& src_name, const Group& dst,...) - - // Rename an object in a group or file to the same location. - void moveLink(const char* src_name, const char* dst_name,...) - void moveLink(const H5std_string& src_name,...) - - Note: previous version CommonFG::move will be deprecated. - - + H5Ldelete: - // Removes the specified link from this location. - void unlink(const char *link_name, - const LinkAccPropList& lapl = LinkAccPropList::DEFAULT) - void unlink(const H5std_string& link_name, - const LinkAccPropList& lapl = LinkAccPropList::DEFAULT) - - Note: An additional parameter is added to CommonFG::unlink and it - is moved to H5Location. - - (BMR - 2018/05/11 - HDFFV-10445) - - - New property list subclasses - - Property list subclasses StrCreatPropList, LinkCreatPropList, and - AttrCreatPropList are added for the C property list classes - H5P_STRING_CREATE, H5P_LINK_CREATE, and H5P_ATTRIBUTE_CREATE. - - (BMR - 2018/05/11 - HDFFV-10445) - - - Another argument, LinkCreatPropList& lcpl, is added to the following - functions for the use of link creation property list. - Group createGroup(const char* name, size_t size_hint = 0, - const LinkCreatPropList& lcpl = LinkCreatPropList::DEFAULT) - Group createGroup(const H5std_string& name, size_t size_hint = 0, - const LinkCreatPropList& lcpl = LinkCreatPropList::DEFAULT) - - (BMR - 2018/05/11 - HDFFV-10445) - - - -Support for New Platforms, Languages, and Compilers -=================================================== - - - Added support for Visual Studio 2017 w/ Intel Fortran 18 on Windows 10 x64. - - -Bug Fixes since HDF5-1.8.20 -=========================== - - - If an HDF5 file contains a filter pipeline message with a 'number of - filters' field that exceeds the maximum number of allowed filters, - the error handling code will attempt to dereference a NULL pointer. - - This issue was reported to The HDF Group as issue #CVE-2017-17505. - - 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. - - This problem arose because the error handling code assumed that - the 'number of filters' field implied that a dynamic array of that - size had already been created and that the cleanup code should - iterate over that array and clean up each element's resources. If - an error occurred before the array has been allocated, this will - not be true. - - This has been changed so that the number of filters is set to - zero on errors. Additionally, the filter array traversal in the - error handling code now requires that the filter array not be NULL. - - (DER - 2018/02/06, HDFFV-10354) - - - If an HDF5 file contains a filter pipeline message which contains - a 'number of filters' field that exceeds the actual number of - filters in the message, the HDF5 C library will read off the end of - the read buffer. - - This issue was reported to The HDF Group as issue #CVE-2017-17506. - - 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 problem was fixed by passing the buffer size with the buffer - and ensuring that the pointer cannot be incremented off the end - of the buffer. A mismatch between the number of filters declared - and the actual number of filters will now invoke normal HDF5 - error handling. - - (DER - 2018/02/26, HDFFV-10355) - - - 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) - - - If an HDF5 file contains a malformed compound type which contains - a member of size zero, a division by zero error will occur while - processing the type. - - This issue was reported to The HDF Group as issue #CVE-2017-17508. - - 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. - - Checking for zero before dividing fixes the problem. Instead of the - division by zero, the normal HDF5 error handling is invoked. - - (DER - 2018/02/26, HDFFV-10357) - - - If an HDF5 file contains a malformed symbol table node that declares - it contains more symbols than it actually contains, the library - can run off the end of the metadata cache buffer while processing - the symbol table node. - - This issue was reported to The HDF Group as issue #CVE-2017-17509. - - 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. - - Performing bounds checks on the buffer while processing fixes the - problem. Instead of the segmentation fault, the normal HDF5 error - handling is invoked. - - (DER - 2018/03/12, HDFFV-10358) - - - Configuration - ------------- - - Library - - 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) - - - CMake - - Update CMake commands configuration. - - A number of improvements were made to the CMake commands. Most - changes simplify usage or eliminate unused constructs. Also, - some changes support better cross-platform support. - - (ADB - 2018/02/01, HDFFV-10398) - - - CMake - - Correct usage of CMAKE_BUILD_TYPE variable. - - The use of the CMAKE_BUILD_TYPE is incorrect for multi-config - generators (Visual Studio and XCode) and is optional for single - config generators. Created a new macro to check - GLOBAL PROPERTY -> GENERATOR_IS_MULTI_CONFIG - Created two new HDF variable, HDF_BUILD_TYPE and HDF_CFG_BUILD_TYPE. - Defaults for these variables is "Release". - - (ADB - 2018/01/10, HDFFV-10385) - - - CMake - - Add replacement of fortran flags if using static CRT. - - Added TARGET_STATIC_CRT_FLAGS call to HDFUseFortran.cmake file in - config/cmake_ext_mod folder. - - (ADB - 2018/01/08, HDFFV-10334) - - - Library - ------- - - Utility function can not handle lowercase Windows drive letters - - Added call to toupper function for drive letter. - - (ADB - 2017/12/18, HDFFV-10307) - - - Tools - ----- - - h5repack - - h5repack changes the chunk parameters when a change of layout is not - specified and a filter is applied. - - HDFFV-10297, HDFFV-10319 reworked code for h5repack and h5diff code - in the tools library. The check for an existing layout was incorrectly - placed into an if block and not executed. The check was moved into - the normal path of the function. - - (ADB - 2018/02/21, HDFFV-10412) - - - h5dump - - the tools library will hide the error stack during file open. - - While this is preferable almost always, there are reasons to enable - display of the error stack when a tool will not open a file. Adding an - optional argument to the --enable-error-stack will provide this use case. - As an optional argument it will not affect the operation of the - --enable-error-stack. h5dump is the only tool to implement this change. - - (ADB - 2018/02/15, HDFFV-10384) - - - h5dump - - h5dump would output an indented blank line in the filters section. - - h5dump overused the h5tools_simple_prefix function, which is a - function intended to account for the data index (x,y,z) option. - Removed the function call for header information. - - (ADB - 2018/01/25, HDFFV-10396) - - - h5repack - - h5repack incorrectly searched internal object table for name. - - h5repack would search the table of objects for a name, if the - name did not match it tried to determine if the name without a - leading slash would match. The logic was flawed! The table - stored names(paths) without a leading slash and did a strstr - of the table path to the name. - The assumption was that if there was a difference of one then - it was a match, however "pressure" would match "/pressure" as - well as "/pressure1", "/pressure2", etc. Changed logic to remove - any leading slash and then do a full compare of the name. - - (ADB - 2018/01/18, HDFFV-10393) - - - h5repack - - h5repack failed to handle command line parameters for customer filters. - - User defined filter parameter conversions would fail when integers - were represented on the command line with character strings - larger than 9 characters. Increased local variable array for storing - the current command line parameter to prevent buffer overflows. - - (ADB - 2018/01/17, HDFFV-10392) - - - h5diff - - h5diff seg faulted if comparing VL strings against fixed strings. - - Reworked solution for HDFFV-8625 and HDFFV-8639. Implemented the check - for string objects of same type in the diff_can_type function by - adding an if(tclass1 == H5T_STRING) block. This "if block" moves the - same check that was added for attributes to this function, which is - used by all object types. This function handles complex type structures. - Also added a new test file in h5diffgentest for testing this issue - and removed the temporary files used in the test scripts. - - (ADB - 2018/01/04, HDFFV-8745) - - - C++ API - ------- - - Removal of memory leaks - - A private function was inadvertently called, causing memory leaks. This - is now fixed. - - (BMR - 2018/04/12 - User reported in email) - - - Changes in exception classes - - Some exception classes are reorganized to reflect the HDF5 object - hierarchy and allow customization. - DataSetIException -> LocationException -> Exception - DataTypeIException -> LocationException -> Exception - GroupIException -> LocationException -> Exception - AttributeIException -> LocationException -> Exception - FileIException -> GroupIException -> LocationException -> Exception - Member functions in H5Location and H5Object now throw specific exceptions - associated with the invoking objects. - - (BMR - 2018/05/11) - - - H5Location::closeObjId is made static - (BMR - 2018/05/11) - - - H5A wrappers in H5Location are removed as they have been in H5Object. - (BMR - 2018/05/11) - - -Supported Platforms -=================== -The following platforms are supported and have been tested for this release. -They are built with the configure process unless specified otherwise. - - Linux 2.6.32-573.22.1.el6 GNU C (gcc), Fortran (gfortran), C++ (g++) - #1 SMP x86_64 GNU/Linux compilers: - (platypus/mayll) Version 4.4.7 20120313 - Versions 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 20160721 - MPICH 3.1.4 compiled with GCC 4.9.3 - OpenMPI 2.0.1 compiled with GCC 4.9.3 - - Linux 2.6.32-573.18.1.el6 gcc (GCC) 4.4.7 20120313 (Red Hat 4.4.7-16) - #1 SMP ppc64 GNU/Linux g++ (GCC) 4.4.7 20120313 (Red Hat 4.4.7-16) - (ostrich) GNU Fortran (GCC) 4.4.7 20120313 (Red Hat 4.4.7-16) - 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/jelly Version 4.8.5 20150623 (Red Hat 4.8.5-4) - Versions 4.9.3, 5.3.0, 6.2.0 - 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 - NAG Fortran Compiler Release 6.1(Tozai) Build 6116 - - SunOS 5.11 32- and 64-bit Sun C 5.12 SunOS_sparc - (emu) Sun Fortran 95 8.6 SunOS_sparc - Sun C++ 5.12 SunOS_sparc - - Windows 7 Visual Studio 2015 w/ Intel Fortran 16 (cmake) - - Windows 7 x64 Visual Studio 2012 w/ Intel Fortran 15 (cmake) - Visual Studio 2013 w/ Intel Fortran 15 (cmake) - Visual Studio 2015 w/ Intel Fortran 16 (cmake) - Visual Studio 2015 w/ Intel C, Fortran 2017 (cmake) - Visual Studio 2015 w/ MSMPI 8 (cmake) - - Windows 10 Visual Studio 2015 w/ Intel Fortran 16 (cmake) - - Windows 10 x64 Visual Studio 2015 w/ Intel Fortran 16 (cmake) - Visual Studio 2017 w/ Intel Fortran 18 (cmake) - - Mac OS X Mavericks 10.9.5 Apple LLVM version 6.0 (clang-600.0.57) - 64-bit gfortran GNU Fortran (GCC) 4.9.2 - (wren/quail) Intel icc/icpc/ifort version 15.0.3 - - Mac OS X Yosemite 10.10.5 Apple LLVM version 6.1 (clang-602.0.53) - 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 LLVM version 7.3.0 (clang-703.0.29) - 64-bit gfortran GNU Fortran (GCC) 5.2.0 - (VM osx1011dev/osx1011test) Intel icc/icpc/ifort version 16.0.2 - - Mac OS Sierra 10.12.6 Apple LLVM version 8.1 (clang-802.0.42) - 64-bit gfortran GNU Fortran (GCC) 7.1.0 - (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 -SunOS 5.11 32-bit n y/y n y y y -SunOS 5.11 64-bit n y/y n y y y -Windows 7 y y/y n y y y -Windows 7 x64 y y/y n 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 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 -AIX 6.1 32- and 64-bit n y/n n y y y -CentOS 6.7 Linux 2.6.32 x86_64 GNU y y/y y y y y -CentOS 6.7 Linux 2.6.32 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 7.1 Linux 3.10.0 x86_64 GNU y y/y y y y y -CentOS 7.1 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/n n y y y - -Platform Shared Shared Shared Thread- - C libs F90 libs C++ libs safe -SunOS 5.11 32-bit y y y y -SunOS 5.11 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 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 -AIX 6.1 32- and 64-bit y n n y -CentOS 6.7 Linux 2.6.32 x86_64 GNU y y y y -CentOS 6.7 Linux 2.6.32 x86_64 Intel y y y y -CentOS 6.7 Linux 2.6.32 x86_64 PGI y y y y -CentOS 7.1 Linux 3.10.0 x86_64 GNU y y y y -CentOS 7.1 Linux 3.10.0 x86_64 Intel y y y y -Linux 2.6.32-573.18.1.el6.ppc64 y y y y - -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 g95 (GCC 4.0.3 (g95 0.94!) - #1 SMP x86_64 GNU/Linux - (mayll) - - Debian8.4.0 3.16.0-4-amd64 #1 SMP Debian 3.16.36-1 x86_64 GNU/Linux - gcc (Debian 4.9.2-10) 4.9.2 - GNU Fortran (Debian 4.9.2-10) 4.9.2 - (cmake and autotools) - - Fedora24 4.7.2-201.fc24.x86_64 #1 SMP x86_64 x86_64 x86_64 GNU/Linux - gcc (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) - - CentOS 7.2 3.10.0-327.28.2.el7.x86_64 #1 SMP x86_64 x86_64 x86_64 GNU/Linux - gcc (GCC) 4.8.5 20150623 (Red Hat 4.8.5-4) - GNU Fortran (GCC) 4.8.5 20150623 (Red Hat 4.8.5-4) - (cmake and autotools) - - Ubuntu 16.04 4.4.0-38-generic #62-Ubuntu SMP x86_64 GNU/Linux - gcc (Ubuntu 5.4.0-6ubuntu1~16.04.2) 5.4.0 - GNU Fortran (Ubuntu 5.4.0-6ubuntu1~16.04.2) 5.4.0 - (cmake and autotools) - - -Known Problems -============== - - The dynamically loaded plugin test libraries require undefined references - to HDF5 functions to be resolved at runtime in order to function properly. - With autotools on CYGWIN this results in build errors, and we have not - found a solution that satisfies both. Therefore the dynamically loaded - plugin tests have been disabled on CYGWIN. - - Mac OS X 10.13 added additional subdirectory structure in .libs for shared - libraries. Consequently "make check" will fail testing java and dynamically - loaded plugin test libraries attempting to copy files from the previous - locations in .libs directories. This will be addressed in the next release - when support for the Mac OS X 10.13 platform is added. - - 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. - - -%%%%1.8.20%%%% - - -HDF5 version 1.8.20 released on 2017-11-28 -================================================================================ - -INTRODUCTION -============ - -This document describes the differences between HDF5-1.8.19 and -HDF5-1.8.20, and contains information on the platforms tested and -known problems in HDF5-1.8.20. -For more details, see the files HISTORY-1_0-1_8_0_rc3.txt -and HISTORY-1_8.txt in the release_docs/ directory of the HDF5 source. - -Links to the HDF5 1.8.20 source code, documentation, and additional materials -can be found on the HDF5 web page at: - - https://support.hdfgroup.org/HDF5/ - -The HDF5 1.8.20 release can be obtained from: - - https://support.hdfgroup.org/HDF5/release/obtain518.html - -User documentation for 1.8.20 can be accessed directly at this location: - - https://support.hdfgroup.org/HDF5/doc1.8/ - -New features in the HDF5-1.8.x release series, including brief general -descriptions of some new and modified APIs, are described in the "What's New -in 1.8.0?" document: - - https://support.hdfgroup.org/HDF5/doc/ADGuide/WhatsNew180.html - -All new and modified APIs are listed in detail in the "HDF5 Software Changes -from Release to Release" document, in the section "Release 1.8.20 (current -release) versus Release 1.8.19 - - https://support.hdfgroup.org/HDF5/doc1.8/ADGuide/Changes.html - -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, Languages, and Compilers -- Bug Fixes since HDF5-1.8.20 -- Supported Platforms -- Supported Configuration Features Summary -- More Tested Platforms -- Known Problems - - -New Features -============ - - Tools - ----- - - h5diff - - h5diff has new option enable-error-stack. - - Updated h5diff with the --enable-error-stack argument, which - enables the display of the hdf5 error stack. This completes the - improvement to the main tools; h5copy, h5diff, h5dump, h5ls and - h5repack. - - (ADB - 2017/08/30, HDFFV-9774) - - - C++ API - ------- - - The following C++ API wrappers have been added to the C++ Library: - - // Creates a binary object description of this datatype. - void DataType::encode() - C API H5Tencode() - - // Returns the decoded type from the binary object description. - DataType::decode() - C API H5Tdecode() - ArrayType::decode() - C API H5Tdecode() - CompType::decode() - C API H5Tdecode() - DataType::decode() - C API H5Tdecode() - EnumType::decode() - C API H5Tdecode() - FloatType::decode() - C API H5Tdecode() - IntType::decode() - C API H5Tdecode() - StrType::decode() - C API H5Tdecode() - VarLenType::decode() - C API H5Tdecode() - - // Three overloaded functions to retrieve information about an object - H5Location::getObjectInfo() - H5Oget_info()/H5Oget_info_by_name() - - (BMR - 2017/10/17, HDFFV-10175) - - - New constructors to open existing datatypes added in ArrayType, - CompType, DataType, EnumType, FloatType, IntType, StrType, and - VarLenType. - - (BMR - 2017/10/17, HDFFV-10175) - - - A document is added to the HDF5 C++ API Reference Manual to show the - mapping from a C API to C++ wrappers. It can be found from the main - page of the C++ API Reference Manual. - - (BMR - 2017/10/17, HDFFV-10151) - - - High-Level APIs - --------------- - - H5DOread_chunk - - Users wanted to read compressed data directly from a file without any - processing by the HDF5 data transfer pipeline, just as they were able - to write it directly to a file with H5DOwrite_chunk. - - New API function, corresponding to existing function H5DOwrite_chunk. - H5DOread_chunk reads a raw data chunk directly from a chunked dataset - in the file into the application buffer, bypassing the library’s internal - data transfer pipeline, including filters. - - (VC - 2017/05/02, HDFFV-9934) - - -Support for New Platforms, Languages, and Compilers -=================================================== - - - Added NAG compiler - - -Bug Fixes since HDF5-1.8.19 -=========================== - - Configuration - ------------- - - cmake - - The hdf5 library used shared szip and zlib, which needlessly required - applications to link with the same szip and zlib libraries. - - Changed the target_link_libraries commands to use the static libs. - Removed improper link duplication of szip and zlib. - Adjusted the link dependencies and the link interface values of - the target_link_libraries commands. - - (ADB - 2017/11/14, HDFFV-10329) - - - cmake MPI - - CMake implementation for MPI was problematic and would create incorrect - MPI library references in the hdf5 libraries. - - Reworked the CMake MPI code to properly create CMake targets.Also merged - the latest CMake FindMPI.cmake changes to the local copy. This is necessary - until HDF changes the CMake minimum to 3.9 or greater. - - (ADB - 2017/11/02, HDFFV-10321) - - - - Fixed Fortran linker flags when using the NAG Fortran compiler (autotools). - - (HDFFV-10037, MSB, 2017/10/21) - - - cmake - - Too many commands for POST_BUILD step caused command line to be - too big on windows. - - Changed foreach of copy command to use a custom command with the - use of the HDFTEST_COPY_FILE macro. - - (ADB - 2017/07/12, HDFFV-10254) - - - Library - ------- - - filter plugin handling in H5PL.c and H5Z.c - - It was discovered that the dynamic loading process used by - filter plugins had issues with library dependencies. - - CMake build process changed to use LINK INTERFACE keywords, which - allowed HDF5 C library to make dependent libraries private. The - filter plugin libraries no longer require dependent libraries - (such as szip or zlib) to be available. - (ADB - 2017/11/16, HDFFV-10328) - - - Fix rare object header corruption bug - - In certain cases, such as when converting large attributes to dense - storage, an error could occur which would either fail an assertion or - cause file corruption. Fixed and added test. - - (NAF - 2017/11/14, HDFFV-10274) - - - H5Zfilter_avail in H5Z.c - - The public function checked for plugins, while the private - function did not. - - Modified H5Zfilter_avail and private function, H5Z_filter_avail. - Moved check for plugin from public to private function. Updated - H5P__set_filter due to change in H5Z_filter_avail. Updated tests. - - (ADB - 2017/10/10, HDFFV-10297, HDFFV-10319) - - - Fix H5Sencode bug when num points selected is >2^32 - - Modified to fail if the 32 bit limit is exceeded when encoding either - offsets or counts in the selection. - - (HDFFV-10323, VC, 2017/09/07) - - - Fix H5HL_offset_into() - - (1) Fix H5HL_offset_into() to return error when offset exceeds heap data - block size. - (2) Fix other places in the library that call this routine to detect - error routine. - - (HDFFV-10216, VC, 2017/09/05) - - - Tools - ----- - - h5repack - - h5repack failed to copy a dataset with existing filter. - - Reworked code for h5repack and h5diff code in tools library. Added - improved error handling, cleanup of resources and checks of calls. - Modified H5Zfilter_avail and private function, H5Z_filter_avail. - Moved check for plugin from public to private function. Updated - H5P__set_filter due to change in H5Z_filter_avail. Updated tests. - Note, h5repack output display has changed to clarify the individual - steps of the repack process. The output indicates if an operation - applies to all objects. Lines with notation and no information - have been removed. - - (ADB - 2017/10/10, HDFFV-10297, HDFFV-10319) - - - h5repack - - h5repack always set the User Defined filter flag to H5Z_FLAG_MANDATORY. - - Added another parameter to the 'UD=' option to set the flag by default - to '0' or H5Z_FLAG_MANDATORY, the other choice is '1' or H5Z_FLAG_OPTIONAL. - - (ADB - 2017/08/31, HDFFV-10269) - - - h5ls - - h5ls generated error on stack when it encountered a H5S_NULL - dataspace. - - Adding checks for H5S_NULL before calling H5Sis_simple (located - in the h5tools_dump_mem function) fixed the issue. - - (ADB - 2017/08/17, HDFFV-10188) - - - h5dump - - h5dump segfaulted on output of XML file. - - Function that escape'd strings used the full buffer length - instead of just the length of the replacement string in a - strncpy call. Using the correct length fixed the issue. - - (ADB - 2017/08/01, HDFFV-10256) - - - h5diff - - h5diff segfaulted on compare of a NULL variable length string. - - Improved h5diff compare of strings by adding a check for - NULL strings and setting the lengths to zero. - - (ADB - 2017/07/25, HDFFV-10246) - - - h5import - - h5import crashed trying to import data from a subset of a dataset. - - Improved h5import by adding the SUBSET keyword. h5import understands - to use the Count times the Block as the size of the dimensions. - Added INPUT_B_ORDER keyword to old-style configuration files. - The import from h5dump function expects the binary files to use native - types (FILE '-b' option) in the binary file. - - (ADB - 2017/06/15, HDFFV-10219) - - - C++ API - ------- - - Marked the following functions deprecated because they were moved to - class H5Object: - H5Location::createAttribute() - H5Location::openAttribute() - H5Location::attrExists() - H5Location::removeAttr() - H5Location::renameAttr() - H5Location::getNumAttrs() - - (BMR - 2017/10/17) - - -Supported Platforms -=================== -The following platforms are supported and have been tested for this release. -They are built with the configure process unless specified otherwise. - - Linux 2.6.32-573.22.1.el6 GNU C (gcc), Fortran (gfortran), C++ (g++) - #1 SMP x86_64 GNU/Linux compilers: - (platypus/mayll) Version 4.4.7 20120313 - Versions 4.9.3, 5.3.0, 6.2.0 - PGI C, Fortran, C++ for 64-bit target on - x86-64; - Version 16.10-0 - Intel(R) C (icc), C++ (icpc), Fortran (icc) - compilers: - Version 17.0.0.196 Build 20160721 - MPICH 3.1.4 compiled with GCC 4.9.3 - OpenMPI 2.0.1 compiled with GCC 4.9.3 - - Linux 2.6.32-573.18.1.el6 gcc (GCC) 4.4.7 20120313 (Red Hat 4.4.7-16) - #1 SMP ppc64 GNU/Linux g++ (GCC) 4.4.7 20120313 (Red Hat 4.4.7-16) - (ostrich) GNU Fortran (GCC) 4.4.7 20120313 (Red Hat 4.4.7-16) - 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/jelly Version 4.8.5 20150623 (Red Hat 4.8.5-4) - Versions 4.9.3, 5.3.0, 6.2.0 - 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 - NAG Fortran Compiler Release 6.1(Tozai) Build 6116 - - 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 2012 w/ Intel Fortran 15 (cmake) - Visual Studio 2013 w/ Intel Fortran 15 (cmake) - Visual Studio 2015 w/ Intel Fortran 16 (cmake) - - Windows 7 x64 Visual Studio 2012 w/ Intel Fortran 15 (cmake) - Visual Studio 2013 w/ Intel Fortran 15 (cmake) - Visual Studio 2015 w/ Intel Fortran 16 (cmake) - Visual Studio 2015 w/ Intel C, Fortran 2017 (cmake) - Visual Studio 2015 w/ MSMPI 8 (cmake) - Cygwin(CYGWIN_NT-6.1 2.8.0(0.309/5/3) - gcc and gfortran compilers (GCC 5.4.0) - (cmake and autotools) - - Windows 10 Visual Studio 2015 w/ Intel Fortran 16 (cmake) - Cygwin(CYGWIN_NT-6.1 2.8.0(0.309/5/3) - gcc and gfortran compilers (GCC 5.4.0) - (cmake and autotools) - - Windows 10 x64 Visual Studio 2015 w/ Intel Fortran 16 (cmake) - - Mac OS X Mavericks 10.9.5 Apple LLVM version 6.0 (clang-600.0.57) - 64-bit gfortran GNU Fortran (GCC) 4.9.2 - (wren/quail) Intel icc/icpc/ifort version 15.0.3 - - Mac OS X Yosemite 10.10.5 Apple LLVM version 6.1 (clang-602.0.53) - 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 LLVM version 7.3.0 (clang-703.0.29) - 64-bit gfortran GNU Fortran (GCC) 5.2.0 - (VM osx1011dev/osx1011test) Intel icc/icpc/ifort version 16.0.2 - - Mac OS Sierra 10.12.6 Apple LLVM version 8.1 (clang-802.0.42) - 64-bit gfortran GNU Fortran (GCC) 7.1.0 - (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 -SunOS 5.11 32-bit n y/y n y y y -SunOS 5.11 64-bit n y/y n y y y -Windows 7 y y/y n y y y -Windows 7 x64 y y/y n y y y -Windows 7 Cygwin n y/n n y y y -Windows 7 x64 Cygwin n y/n n y y y -Windows 10 y y/y n y y y -Windows 10 x64 y y/y n y y y -Mac OS X Mavericks 10.9.5 64-bit n y/y n y y y -Mac OS X Yosemite 10.10.5 64-bit n y/y n y y y -Mac OS X El Capitan 10.11.6 64-bit n y/y n y y y -Mac OS Sierra 10.12.6 64-bit n y/y n y y y -AIX 6.1 32- and 64-bit n y/n n y y y -CentOS 6.7 Linux 2.6.32 x86_64 GNU y y/y y y y y -CentOS 6.7 Linux 2.6.32 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 7.1 Linux 3.10.0 x86_64 GNU y y/y y y y y -CentOS 7.1 Linux 3.10.0 x86_64 Intel n y/y n y y y -Linux 2.6.32-431.11.2.el6.ppc64 n y/n n y y y - -Platform Shared Shared Shared Thread- - C libs F90 libs C++ libs safe -SunOS 5.11 32-bit y y y y -SunOS 5.11 64-bit y y y y -Windows 7 y y y y -Windows 7 x64 y y y y -Windows 7 Cygwin n n n y -Windows 7 x64 Cygwin n n n y -Windows 10 y y y y -Windows 10 x64 y y y y -Mac OS X Mavericks 10.9.5 64-bit y n y y -Mac OS X Yosemite 10.10.5 64-bit y n y y -Mac OS X El Capitan 10.11.6 64-bit y n y y -Mac OS Sierra 10.12.6 64-bit y n y y -AIX 6.1 32- and 64-bit y n n y -CentOS 6.7 Linux 2.6.32 x86_64 GNU y y y y -CentOS 6.7 Linux 2.6.32 x86_64 Intel y y y y -CentOS 6.7 Linux 2.6.32 x86_64 PGI y y y y -CentOS 7.1 Linux 3.10.0 x86_64 GNU y y y y -CentOS 7.1 Linux 3.10.0 x86_64 Intel y y y y -Linux 2.6.32-431.11.2.el6.ppc64 y y y y - -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 g95 (GCC 4.0.3 (g95 0.94!) - #1 SMP x86_64 GNU/Linux - (mayll) - - Debian8.4.0 3.16.0-4-amd64 #1 SMP Debian 3.16.36-1 x86_64 GNU/Linux - gcc (Debian 4.9.2-10) 4.9.2 - GNU Fortran (Debian 4.9.2-10) 4.9.2 - (cmake and autotools) - - Fedora24 4.7.2-201.fc24.x86_64 #1 SMP x86_64 x86_64 x86_64 GNU/Linux - gcc (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) - - CentOS 7.2 3.10.0-327.28.2.el7.x86_64 #1 SMP x86_64 x86_64 x86_64 GNU/Linux - gcc (GCC) 4.8.5 20150623 (Red Hat 4.8.5-4) - GNU Fortran (GCC) 4.8.5 20150623 (Red Hat 4.8.5-4) - (cmake and autotools) - - Ubuntu 16.04 4.4.0-38-generic #62-Ubuntu SMP x86_64 GNU/Linux - gcc (Ubuntu 5.4.0-6ubuntu1~16.04.2) 5.4.0 - GNU Fortran (Ubuntu 5.4.0-6ubuntu1~16.04.2) 5.4.0 - (cmake and autotools) - - -Known Problems -============== - - The dynamically loaded plugin test libraries require undefined references - to HDF5 functions to be resolved at runtime in order to function properly. - With autotools on CYGWIN this results in build errors, and we have not - found a solution that satisfies both. Therefore the dynamically loaded - plugin tests have been disabled on CYGWIN. - - Mac OS X 10.13 added additional subdirectory structure in .libs for shared - libraries. Consequently "make check" will fail testing java and dynamically - loaded plugin test libraries attempting to copy files from the previous - locations in .libs directories. This will be addressed in the next release - when support for the Mac OS X 10.13 platform is added. - - 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. - - -%%%%1.8.19%%%% - - -HDF5 version 1.8.19 released on 2017-06-15 -================================================================================ - -INTRODUCTION -============ - -This document describes the differences between HDF5-1.8.18 and -HDF5-1.8.19, and contains information on the platforms tested and -known problems in HDF5-1.8.19. -For more details, see the files HISTORY-1_0-1_8_0_rc3.txt -and HISTORY-1_8.txt in the release_docs/ directory of the HDF5 source. - -Links to the HDF5 1.8.19 source code, documentation, and additional materials -can be found on the HDF5 web page at: - - https://support.hdfgroup.org/HDF5/ - -The HDF5 1.8.19 release can be obtained from: - - https://support.hdfgroup.org/HDF5/release/obtain518.html - -User documentation for 1.8.19 can be accessed directly at this location: - - https://support.hdfgroup.org/HDF5/doc1.8/ - -New features in the HDF5-1.8.x release series, including brief general -descriptions of some new and modified APIs, are described in the "What's New -in 1.8.0?" document: - - https://support.hdfgroup.org/HDF5/doc/ADGuide/WhatsNew180.html - -All new and modified APIs are listed in detail in the "HDF5 Software Changes -from Release to Release" document, in the section "Release 1.8.19 (current -release) versus Release 1.8.18 - - https://support.hdfgroup.org/HDF5/doc1.8/ADGuide/Changes.html - -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, Languages, and Compilers -- Bug Fixes since HDF5-1.8.19 -- Supported Platforms -- Supported Configuration Features Summary -- More Tested Platforms -- Known Problems - - -New Features -============ - - Configuration - -------------- - - CMake in the Tools - - User-defined filters on Windows require that tools be built - with shared libraries. - - CMake command code added to build tools with - shared libraries as well as with static libraries. - - (ADB - 2017/02/07, HDFFV-10123) - - - Library - ------- - - H5PL package - - Users would like to be able to set the plugin path programmatically - instead of through the environment variable. - - H5PL package obtained new APIs for manipulating the entries of - the plugin path table. The new APIs are; - H5PLappend - Insert a plugin path at the end of the list. - H5PLprepend - Insert a plugin path at the beginning of the list. - H5PLreplace - Replace the path at the specified index. - H5PLinsert - Insert a plugin path at the specified index, moving - other paths after the index. - H5PLremove - Remove the plugin path at the specified index and - compacting the list. - H5PLget - Query the plugin path at the specified index. - H5PLsize - Query the size of the current list of plugin paths. - - (ADB - 2017/04/04, HDFFV-10143) - - - H5Dget_chunk_storage_size - - The storage size of a chunk in the file is needed to determine the size - of the buffer to be allocated for reading a chunk directly from a file. - - New API function gets the size in bytes currently allocated within a - file for a raw data chunk in a dataset. This function was added to get - the chunk size in support of the implementation of H5DOread_chunks, but - may also be useful for other purposes. - - (VC - 2017/05/02, HDFFV-9934) - - C++ API - ------- - - The following C++ API wrappers have been added to the C++ Library: - // Determines if a name exists. - H5Location::nameExists() - C API H5Lexists() - - // Checks if an ID is valid. - IdComponent::isValid() - C API H5Iis_valid() - - // Sets the number of soft or user-defined links that can be - // traversed before a failure occurs. - LinkAccPropList::setNumLinks() - C API H5Pset_nlinks() - - // Gets the number of soft or user-defined link traversals allowed - LinkAccPropList::getNumLinks() - C API H5Pget_nlinks() - - // Returns a copy of the creation property list of a datatype. - DataType::getCreatePlist() - C API H5Tget_create_plist() - - // Opens an object within a location, regardless its type. - H5Location::openObjId() - C API H5Oopen() - H5Location::openObjId() - C API H5Oopen() - - // Closes an object opened by openObjId(). - H5Location::closeObjId() - C API H5Oclose() - - // Gets general information about a file. - H5File::getFileInfo() - C API H5Fget_info() - - // Returns the header version of an HDF5 object. - H5Object::objVersion() - C API H5Oget_info() - - (BMR, 2017/05/13, HDFFV-10004, HDFFV-10156) - - - New class LinkAccPropList is added for link access property list - - (BMR, 2017/05/13, HDFFV-10156) - - High-Level APIs - --------------- - - H5DOread_chunk - - Users wanted to read compressed data directly from a file without any - processing by the HDF5 data transfer pipeline, just as they were able - to write it directly to a file with H5DOwrite_chunk. - - New API function, corresponding to existing function H5DOwrite_chunk. - H5DOread_chunk reads a raw data chunk directly from a chunked dataset - in the file into the application buffer, bypassing the library’s internal - data transfer pipeline, including filters. - - (VC - 2017/05/02, HDFFV-9934) - - -Support for New Platforms, Languages, and Compilers -=================================================== - - - Added OpenMPI 2.0.1 compiled with GCC 4.9.3 - - -Bug Fixes since HDF5-1.8.18 -=========================== - - Configuration - ------------- - - Support for Fortran shared libraries on OS X with autotools now - works. Cmake builds still disables Fortran shared libraries on OS X. - (MSB - 2017/04/30, HDFFV-2772) - - - Library - ------- - - bitfield datatypes - - bitfield datatypes did not fully support endianness of the data. - - Improved the endianness of bitfield datatypes by adding missing functional - code. This code used integer types as a template. - - (ADB - 2017/05/12, HDFFV-10186) - - - Newly created datasets with H5D_COMPACT layout failed to open after - several H5Dopen/H5Dclose cycles. - - The layout "dirty" flag for a compact dataset is now properly reset - before flushing the message. - - (VC - 2017/05/11, HDFFV-10051) - - Missing #ifdef __cplusplus macros were added to the generated H5Epubgen.h file. - - (DER - 2017/04/25, HDFFV-9638) - - - Tools - ----- - - h5repack - - h5repack did not maintain the creation order flag of the root - group. - - Improved h5repack by reading the creation order and applying the - flag to the new root group. Also added arguments to set the - order and index direction, which applies to the traversing of the - original file, on the command line. - - (ADB - 2017/05/26, HDFFV-8611) - - - h5diff - - h5diff failed to account for strpad type and null terminators - of char strings. Also, h5diff failed to account for string length - differences and would give a different result depending on file - order in the command line. - - Improved h5diff compare of strings and arrays by adding a check for - string lengths and if the strpad was null filled. - - (ADB - 2017/05/18, HDFFV-9055, HDFFV-10128) - - - h5diff - - h5diff help text about epsilon comparison was confusing. - - Changed h5diff help text to indicate that the 'a' refers to the - datapoint in file1 and 'b' refers to the datapoint value in file2. - - (ADB - 2017/05/16, HDFFV-9995) - - - h5diff - - h5diff did not report user-defined filter data differences correctly. - - Improved h5diff compare of user-defined filter data by reporting an - error if the user-defined filter plugin cannot be found. - - (ADB - 2017/01/18, HDFFV-9994) - C++ API - ------- - - The class hierarchy is revised to better reflect the HDF5 model. - Class H5File is now derived from class Group instead of H5Location. - Class Attribute is now derived from H5Location instead of IdComponent. - Wrappers of H5A APIs in H5Location are now duplicated in H5Object, - the original wrappers in H5Location will be deprecated in future - releases. - - (BMR - 2017/05/15, HDFFV-10156) - - - -Supported Platforms -=================== -The following platforms are supported and have been tested for this release. -They are built with the configure process unless specified otherwise. - - Linux 2.6.32-573.22.1.el6 GNU C (gcc), Fortran (gfortran), C++ (g++) - #1 SMP x86_64 GNU/Linux compilers: - (platypus/mayll) Version 4.4.7 20120313 - Versions 4.9.3, 5.2.0, 6.2.0 - PGI C, Fortran, C++ for 64-bit target on - x86-64; - Version 16.10-0 - 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 - OpenMPI 2.0.1 compiled with GCC 4.9.3 - - Linux 2.6.32-573.18.1.el6 gcc (GCC) 4.4.7 20120313 (Red Hat 4.4.7-16) - #1 SMP ppc64 GNU/Linux g++ (GCC) 4.4.7 20120313 (Red Hat 4.4.7-16) - (ostrich) GNU Fortran (GCC) 4.4.7 20120313 (Red Hat 4.4.7-16) - 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) - Versions 4.9.3, 5.3.0, 6.2.0 - 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 - - 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 2012 w/ Intel Fortran 15 (cmake) - Visual Studio 2013 w/ Intel Fortran 15 (cmake) - Visual Studio 2015 w/ Intel Fortran 16 (cmake) - - Windows 7 x64 Visual Studio 2012 w/ Intel Fortran 15 (cmake) - Visual Studio 2013 w/ Intel Fortran 15 (cmake) - Visual Studio 2015 w/ Intel Fortran 16 (cmake) - Visual Studio 2015 w/ Intel C, Fortran 2017 (cmake) - Visual Studio 2015 w/ MSMPI 8 (cmake) - Cygwin(CYGWIN_NT-6.1 2.8.0(0.309/5/3) - gcc and gfortran compilers (GCC 5.4.0) - (cmake and autotools) - - Windows 10 Visual Studio 2015 w/ Intel Fortran 16 (cmake) - Cygwin(CYGWIN_NT-6.1 2.8.0(0.309/5/3) - gcc and gfortran compilers (GCC 5.4.0) - (cmake and autotools) - - Windows 10 x64 Visual Studio 2015 w/ Intel Fortran 16 (cmake) - - Mac OS X Mt. Lion 10.8.5 Apple LLVM version 5.1 (clang-503.0.40) - 64-bit gfortran GNU Fortran (GCC) 4.8.2 - (swallow/kite) Intel icc/icpc/ifort version 15.0.3 - - Mac OS X Mavericks 10.9.5 Apple LLVM version 6.0 (clang-600.0.57) - 64-bit gfortran GNU Fortran (GCC) 4.9.2 - (wren/quail) Intel icc/icpc/ifort version 15.0.3 - - Mac OS X Yosemite 10.10.5 Apple LLVM version 6.1 (clang-602.0.53) - 64-bit gfortran GNU Fortran (GCC) 4.9.2 - (osx1010dev/osx1010test) Intel icc/icpc/ifort version 15.0.3 - - Mac OS X El Capitan 10.11.4 Apple LLVM version 7.3.0 (clang-703.0.29) - 64-bit gfortran GNU Fortran (GCC) 5.2.0 - (VM osx1011dev/osx1011test) Intel icc/icpc/ifort version 16.0.2 - - -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 -SunOS 5.11 32-bit n y/y n y y y -SunOS 5.11 64-bit n y/y n y y y -Windows 7 y y/y n y y y -Windows 7 x64 y y/y n 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 y -Mac OS X Yosemite 10.10.5 64-bit n y/y n y y y -AIX 6.1 32- and 64-bit n y/n n y y y -CentOS 6.7 Linux 2.6.32 x86_64 GNU y y/y y y y y -CentOS 6.7 Linux 2.6.32 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 7.1 Linux 3.10.0 x86_64 GNU y y/y y y y y -CentOS 7.1 Linux 3.10.0 x86_64 Intel n y/y n y y y -Linux 2.6.32-431.11.2.el6.ppc64 n y/n n y y y - -Platform Shared Shared Shared Thread- - C libs F90 libs C++ libs safe -SunOS 5.11 32-bit y y y y -SunOS 5.11 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 -AIX 6.1 32- and 64-bit y n n y -CentOS 6.7 Linux 2.6.32 x86_64 GNU y y y y -CentOS 6.7 Linux 2.6.32 x86_64 Intel y y y y -CentOS 6.7 Linux 2.6.32 x86_64 PGI y y y y -CentOS 7.1 Linux 3.10.0 x86_64 GNU y y y y -CentOS 7.1 Linux 3.10.0 x86_64 Intel y y y y -Linux 2.6.32-431.11.2.el6.ppc64 y y y y - -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 g95 (GCC 4.0.3 (g95 0.94!) - #1 SMP x86_64 GNU/Linux - (mayll) - - Debian8.4.0 3.16.0-4-amd64 #1 SMP Debian 3.16.36-1 x86_64 GNU/Linux - gcc (Debian 4.9.2-10) 4.9.2 - GNU Fortran (Debian 4.9.2-10) 4.9.2 - (cmake and autotools) - - Fedora24 4.7.2-201.fc24.x86_64 #1 SMP x86_64 x86_64 x86_64 GNU/Linux - gcc (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) - - CentOS 7.2 3.10.0-327.28.2.el7.x86_64 #1 SMP x86_64 x86_64 x86_64 GNU/Linux - gcc (GCC) 4.8.5 20150623 (Red Hat 4.8.5-4) - GNU Fortran (GCC) 4.8.5 20150623 (Red Hat 4.8.5-4) - (cmake and autotools) - - Ubuntu 16.04 4.4.0-38-generic #62-Ubuntu SMP x86_64 GNU/Linux - gcc (Ubuntu 5.4.0-6ubuntu1~16.04.2) 5.4.0 - GNU Fortran (Ubuntu 5.4.0-6ubuntu1~16.04.2) 5.4.0 - (cmake and autotools) - - -Known Problems -============== - - The dynamically loaded plugin test libraries require undefined references - to HDF5 functions to be resolved at runtime in order to function properly. - With autotools on CYGWIN this results in build errors, and we have not - found a solution that satisfies both. Therefore the dynamically loaded - plugin tests have been disabled on CYGWIN. - - 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. - - -%%%%1.8.18%%%% - - -HDF5 version 1.8.18 released on 2016-11-14 -================================================================================ - -INTRODUCTION -============ - -This document describes the differences between HDF5-1.8.17 and -HDF5-1.8.18, and contains information on the platforms tested and -known problems in HDF5-1.8.18. -For more details, see the files HISTORY-1_0-1_8_0_rc3.txt -and HISTORY-1_8.txt in the release_docs/ directory of the HDF5 source. - -Links to the HDF5 1.8.18 source code, documentation, and additional materials -can be found on the HDF5 web page at: - - https://support.hdfgroup.org/HDF5/ - -The HDF5 1.8.18 release can be obtained from: - - https://support.hdfgroup.org/HDF5/release/obtain518.html - -User documentation for 1.8.18 can be accessed directly at this location: - - https://support.hdfgroup.org/HDF5/doc1.8/ - -New features in the HDF5-1.8.x release series, including brief general -descriptions of some new and modified APIs, are described in the "What's New -in 1.8.0?" document: - - https://support.hdfgroup.org/HDF5/doc/ADGuide/WhatsNew180.html - -All new and modified APIs are listed in detail in the "HDF5 Software Changes -from Release to Release" document, in the section "Release 1.8.18 (current -release) versus Release 1.8.17 - - https://support.hdfgroup.org/HDF5/doc1.8/ADGuide/Changes.html - -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, Languages, and Compilers -- Bug Fixes since HDF5-1.8.17 -- Supported Platforms -- Supported Configuration Features Summary -- More Tested Platforms -- Known Problems - - -New Features -============ - - Configuration - ------------- - - - CMake: Added NAMESPACE hdf5:: to package configuration files to allow - projects using installed HDF5 binaries built with CMake to link with - them without specifying the HDF5 library location via IMPORTED_LOCATION. - - (ADB, 2016/10/17, HDFFV-10003) - - - - CMake: Changed the CTEST_BUILD_CONFIGURATION option to - CTEST_CONFIGURATION_TYPE as recommended by the CMake documentation. - - (ADB, 2016/10/17, HDFFV-9971) - - - CMake: Added support for GIT - - (ADB, 2016/07/12) - - - Library - ------- - - None - - - Parallel Library - ---------------- - - None - - - Tools - ----- - - None - - - High-Level APIs - --------------- - - None - - - Fortran API - ----------- - - None - - - C++ API - ------- - - None - - -Support for New Platforms, Languages, and Compilers -=================================================== - - - -Bug Fixes since HDF5-1.8.17 -=========================== - - Configuration - ------------- - - - Fixed a problem preventing HDF5 to be built on 32-bit CYGWIN by - condensing cygwin configuration files into a single file and - removing outdated compiler settings. - - (ABD, 2016/07/12, HDFFV-9946) - - - - CMake: Fixed a command length overflow error by converting custom - commands inside CMakeTest.cmake files into regular dependencies and - targets. - - (ABD, 2016/07/12, HDFFV-9939) - - - - CMake: Fixed a timeout error that would occasionally occur when running - the virtual file driver tests simultaneously due to test directory and file - name collisions. - - (ABD, 2016/09/19, HDFFV-9431) - - - Library - ------- - - - Fixed a memory leak that would occur when the library allocated memory - for an external file prefix (H5Pset_efile_prefix) and failed to free it. - - (DER, 2016/04/29) - - - - Fixed an error that would occur when calling H5Adelete on an attribute - which is attached to an externally linked object in the target file and - whose datatype is a committed datatype in the main file. - - (VC, 2016-07-04, HDFFV-9940) - - - - Fixed a problem where a plugin compiled into a DLL in the default plugin - directory could not be found by the HDF5 library at runtime on Windows - when the HDF5_PLUGIN_PATH environment variable was not set. - - (ABD, 2016/08/01, HDFFV-9706) - - - - Fixed an issue where H5Pset_alignment could result in misaligned blocks - with some input combinations, causing an assertion failure in debug mode. - - (NAF, 2016/08/11, HDFFV-9948) - - - - A number of issues were fixed when reading/writing from/to corrupted - files to ensure that the library fails gracefully in these cases: - - * Writing to a corrupted file that has an object message which is - incorrectly marked as shareable on disk results in a buffer overflow / - invalid write instead of a clean error message. - - * Decoding data from a corrupted file with a dataset encoded with the - H5Z_NBIT decoding can result in a code execution vulnerability under - the context of the application using the HDF5 library. - - * When decoding an array datatype from a corrupted file, the HDF5 library - fails to return an error in production if the number of dimensions - decoded is greater than the maximum rank. - - * When decoding an "old style" array datatype from a corrupted file, the - HDF5 library fails to return an error in production if the number of - dimensions decoded is greater than the maximum rank. - - (NAF, 2016/10/06, HDFFV-9950, HDFFV-9951, HDFFV-9992, HDFFV-9993) - - - - Fixed an error that would occur when copying an object with an attribute - which is a compound datatype consisting of a variable length string. - - (VC, 2016-10-17, HDFFV-7991) - - - Parallel Library - ---------------- - - - Fixed a bug that could occur when allocating a chunked dataset in parallel - with an alignment set and an alignment threshold greater than the chunk - size but less than or equal to the raw data aggregator size. - - (NAF, 2016/08/11, HDFFV-9969) - - - Performance - ------------- - - None - - - Tools - ----- - - - Fixed an error in the compiler wrapper scripts (h5cc, h5fc, et al.) - in which they would erroneously drop the file argument specified via - the -o flag when the -o flag was specified before the -c flag on the - command line, resulting in a failure to compile. - - (LRK, 2016/06/08, HDFFV-9938, HDFFV-9530) - - - - h5repack User Defined (UD) filter parameters were not parsed correctly. - - The UD filter parameters were not being parsed correctly. Reworked coding - section to parse the correct values and verify number of parameters. - - (ADB, 2016/10/19, HDFFV-9996, HDFFV-9974, HDFFV-9515, HDFFV-9039) - - - Fortran API - ----------- - - - Fortran library fails to compile and fails tests with NAG compiler. - - * Removed the non-standard assumption that KIND=SIZEOF, in the HDF5 - configure programs. - * Removed Fortran 66 character/integer conversions from tests. - * Removed the use of C_SIZEOF in the test programs - * Changed to using STORAGE_SIZE in the test programs if available. Otherwise, - uses C_SIZEOF or SIZEOF. - - (MSB, 2016/9/22, HDFFV-9973) - - - - Fortran segfaults for F03 tests with NAG compiler - - * Removed INTENT(OUT) from 'fillvalue' in F2003 interface - for H5Pget_fill_value_f. - - (MSB, 2016/9/22, HDFFV-9980) - - - C++ API - ------- - - - The macro H5_NO_NAMESPACE is deprecated from the HDF5 C++ API library. - In future releases, the macros H5_NO_STD and OLD_HEADER_FILENAME may - also be removed. - - (BMR, 2016/10/27, HDFFV-9532) - - - High-Level APIs: - --------------- - - - The high-level API Packet Table (PT) did not write data correctly when - the datatype is a compound type that has string type as one of the - members. This problem started in 1.8.15, after the fix of HDFFV-9042 - was applied, which caused the Packet Table to use native type to access - the data. It should be up to the application to specify whether the - buffer to be read into memory in the machine’s native architecture. - Thus, the PT is fixed to not use native type but to make a copy of the - user's provided datatype during creation or the packet table's datatype - during opening. If an application wishes to use native type to read the - data, then the application will request that. However, the Packet Table - doesn't provide a way to specify memory datatype in this release. This - feature will be available in future releases, HDFFV-10023. - - (BMR, 2016/10/27, HDFFV-9758) - - - Fortran High-Level APIs: - ------------------------ - - None - - - Testing - ------- - - None - - -Supported Platforms -=================== -The following platforms are supported and have been tested for this release. -They are built with the configure process unless specified otherwise. - - Linux 2.6.32-573.22.1.el6 GNU C (gcc), Fortran (gfortran), C++ (g++) - #1 SMP x86_64 GNU/Linux compilers: - (platypus/mayll) Version 4.4.7 20120313 - Versions 4.8.4, 4.9.3, 5.2.0 - PGI C, Fortran, C++ for 64-bit target on - x86-64; - Version 15.7-0 - Intel(R) C (icc), C++ (icpc), Fortran (icc) - compilers: - Version 15.0.3.187 Build 20150407 - MPICH 3.1.4 compiled with GCC 4.9.3 - - Linux 2.6.32-573.18.1.el6 gcc (GCC) 4.4.7 20120313 (Red Hat 4.4.7-16) - #1 SMP ppc64 GNU/Linux g++ (GCC) 4.4.7 20120313 (Red Hat 4.4.7-16) - (ostrich) GNU Fortran (GCC) 4.4.7 20120313 (Red Hat 4.4.7-16) - 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) - Versions 4.9.3, 5.2.0 - Intel(R) C (icc), C++ (icpc), Fortran (icc) - compilers: - Version 15.0.3.187 Build 20150407 - 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 2012 w/ Intel Fortran 15 (cmake) - Visual Studio 2013 w/ Intel Fortran 15 (cmake) - Visual Studio 2015 w/ Intel Fortran 16 (cmake) - Cygwin(CYGWIN_NT-6.1 2.2.1(0.289/5/3) gcc(4.9.3) compiler and gfortran) - (cmake and autotools) - - Windows 7 x64 Visual Studio 2012 w/ Intel Fortran 15 (cmake) - Visual Studio 2013 w/ Intel Fortran 15 (cmake) - Visual Studio 2015 w/ Intel Fortran 16 (cmake) - - Windows 10 Visual Studio 2015 w/ Intel Fortran 16 (cmake) - - Windows 10 x64 Visual Studio 2015 w/ Intel Fortran 16 (cmake) - - Mac OS X Mt. Lion 10.8.5 Apple LLVM version 5.1 (clang-503.0.40) - 64-bit gfortran GNU Fortran (GCC) 4.8.2 - (swallow/kite) Intel icc/icpc/ifort version 15.0.3 - - Mac OS X Mavericks 10.9.5 Apple LLVM version 6.0 (clang-600.0.57) - 64-bit gfortran GNU Fortran (GCC) 4.9.2 - (wren/quail) Intel icc/icpc/ifort version 15.0.3 - - Mac OS X Yosemite 10.10.5 Apple LLVM version 6.1 (clang-602.0.53) - 64-bit gfortran GNU Fortran (GCC) 4.9.2 - (osx1010dev/osx1010test) Intel icc/icpc/ifort version 15.0.3 - - Mac OS X El Capitan 10.11.4 Apple LLVM version 7.3.0 (clang-703.0.29) - 64-bit gfortran GNU Fortran (GCC) 5.2.0 - (VM osx1011dev/osx1011test) Intel icc/icpc/ifort version 16.0.2 - - -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 -SunOS 5.11 32-bit n y/y n y y y -SunOS 5.11 64-bit n y/y n y y y -Windows 7 y y/y n y y y -Windows 7 x64 y y/y n y y y -Windows 7 Cygwin n y/y n y y n -Windows 10 n y/y n y y y -Windows 10 x64 n 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 y -Mac OS X Yosemite 10.10.5 64-bit n y/y n y y y -AIX 6.1 32- and 64-bit n y/n n y y y -CentOS 6.7 Linux 2.6.32 x86_64 GNU y y/y y y y y -CentOS 6.7 Linux 2.6.32 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 7.1 Linux 3.10.0 x86_64 GNU y y/y y y y y -CentOS 7.1 Linux 3.10.0 x86_64 Intel n y/y n y y y -Linux 2.6.32-431.11.2.el6.ppc64 n y/n n y y y - -Platform Shared Shared Shared Thread- - C libs F90 libs C++ libs safe -SunOS 5.11 32-bit y y y y -SunOS 5.11 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 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 -AIX 6.1 32- and 64-bit y n n y -CentOS 6.7 Linux 2.6.32 x86_64 GNU y y y y -CentOS 6.7 Linux 2.6.32 x86_64 Intel y y y y -CentOS 6.7 Linux 2.6.32 x86_64 PGI y y y y -CentOS 7.1 Linux 3.10.0 x86_64 GNU y y y y -CentOS 7.1 Linux 3.10.0 x86_64 Intel y y y y -Linux 2.6.32-431.11.2.el6.ppc64 y y y y - -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 g95 (GCC 4.0.3 (g95 0.94!) - #1 SMP x86_64 GNU/Linux - (platypus) - - Debian8.4.0 3.16.0-4-amd64 #1 SMP Debian 3.16.36-1 x86_64 GNU/Linux - gcc (Debian 4.9.2-10) 4.9.2 - GNU Fortran (Debian 4.9.2-10) 4.9.2 - (cmake and autotools) - - Fedora24 4.7.2-201.fc24.x86_64 #1 SMP x86_64 x86_64 x86_64 GNU/Linux - gcc (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) - - CentOS 7.2 3.10.0-327.28.2.el7.x86_64 #1 SMP x86_64 x86_64 x86_64 GNU/Linux - gcc (GCC) 4.8.5 20150623 (Red Hat 4.8.5-4) - GNU Fortran (GCC) 4.8.5 20150623 (Red Hat 4.8.5-4) - (cmake and autotools) - - Ubuntu 16.04 4.4.0-38-generic #62-Ubuntu SMP x86_64 GNU/Linux - gcc (Ubuntu 5.4.0-6ubuntu1~16.04.2) 5.4.0 - GNU Fortran (Ubuntu 5.4.0-6ubuntu1~16.04.2) 5.4.0 - (cmake and autotools) - - -Known Problems -============== -* On windows platforms in debug configurations, the VFD flush1 tests will fail - with the split and multi VFD drivers. These tests will display a modal debug - dialog which must be answered or wait for the test timeout to expire. - (ADB - 2014/06/23 - HDFFV-8851) - -* CLANG compiler with the options -fcatch-undefined-behavior and -ftrapv - catches some undefined behavior in the alignment algorithm of the macro DETECT_I - in H5detect.c (Issue 8147). Since the algorithm is trying to detect the alignment - of integers, ideally the flag -fcatch-undefined-behavior shouldn't to be used for - H5detect.c. In the future, we can separate flags for H5detect.c from the rest of - the library. (SLU - 2013/10/16) - -* Make provided by Solaris fails in "make check". Solaris users should use - gmake to build and install the HDF5 software. (AKC - 2013/10/08 - HDFFV-8534) - -* The C++ and FORTRAN bindings are not currently working on FreeBSD with the - native release 8.2 compilers (4.2.1), but are working with gcc 4.6 from the - ports (and probably gcc releases after that). - (QAK - 2012/10/19) - -* The following h5dump test case fails in BG/P machines (and potentially other - machines that use a command script to launch executables): - - h5dump --no-compact-subset -d "AHFINDERDIRECT::ah_centroid_t[0] it=0 tl=0" - tno-subset.h5 - - This is due to the embedded spaces in the dataset name being interpreted - by the command script launcher as meta-characters, thus passing three - arguments to h5dump's -d flag. The command passes if run by hand, just - not via the test script. - (AKC - 2012/05/03) - -* The STDIO VFD does not work on some architectures, possibly due to 32/64 - bit or large file issues. The basic STDIO VFD test is known to fail on - 64-bit SunOS 5.10 on SPARC when built with -m64 and 32-bit OS X/Darwin - 10.7.0. The STDIO VFD test has been disabled while we investigate and - a fix should appear in a future release. - (DER - 2011/10/14 - HDFFV-8235) - -* h5diff can report inconsistent results when comparing datasets of enum type - that contain invalid values. This is due to how enum types are handled in - the library and will be addressed in a future release. - (DER - 2011/10/14 - HDFFV-7527) - -* The links test can fail under the stdio VFD due to some issues with external - links. This will be investigated and fixed in a future release. - (DER - 2011/10/14 - HDFFV-7768) - -* After the shared library support was fixed for some bugs, it was discovered - that "make prefix=XXX install" no longer works for shared libraries. It - still works correctly for static libraries. Therefore, if you want to - install the HDF5 shared libraries in a location such as /usr/local/hdf5, - you need to specify the location via the --prefix option during configure - time. E.g, ./configure --prefix=/usr/local/hdf5 ... - (AKC - 2011/05/07 - HDFFV-7583) - -* The parallel test, t_shapesame, in testpar/, may run for a long time and may - be terminated by the alarm signal. If that happens, one can increase the - alarm seconds (default is 1200 seconds = 20 minutes) by setting the - environment variable, $HDF5_ALARM_SECONDS, to a larger value such as 3600 - (60 minutes). Note that the t_shapesame test may fail in some systems - (see the "While working on the 1.8.6 release..." problem below). If - it does, it will waste more time if $HDF5_ALARM_SECONDS is set - to a larger value. - (AKC - 2011/05/07) - -* Shared Fortran libraries are not quite working on AIX. While they are - generated when --enable-shared is specified, the fortran and hl/fortran - tests fail. the issue. HL and C++ shared libraries should now be - working as intended, however. - (MAM - 2011/04/20) - -* While working on the 1.8.6 release of HDF5, a bug was discovered that can - occur when reading from a dataset in parallel shortly after it has been - written to collectively. The issue was exposed by a new test in the parallel - HDF5 test suite, but had existed before that. We believe the problem lies with - certain MPI implementations and/or file systems. - - We have provided a pure MPI test program, as well as a standalone HDF5 - program, that can be used to determine if this is an issue on your system. - They should be run across multiple nodes with a varying number of processes. - These programs can be found at: - http://www.hdfgroup.org/ftp/HDF5/examples/known_problems/ - (NAF - 2011/01/19) - -* All the VFL drivers aren't backward compatible. In H5FDpublic.h, the - structure H5FD_class_t changed in 1.8. There is new parameter added to - get_eoa and set_eoa callback functions. A new callback function - get_type_map was added in. The public function H5FDrealloc was taken - out in 1.8. The problem only happens when users define their own driver - for 1.6 and try to plug in 1.8 library. Because there's only one user - complaining about it, we (Elena, Quincey, and I) decided to leave it as - it is (see bug report #1279). Quincey will make a plan for 1.10. - (SLU - 2010/02/02) - -* The --enable-static-exec configure flag will only statically link libraries - if the static version of that library is present. If only the shared version - of a library exists (i.e., most system libraries on Solaris, AIX, and Mac, - for example, only have shared versions), the flag should still result in a - successful compilation, but note that the installed executables will not be - fully static. Thus, the only guarantee on these systems is that the - executable is statically linked with just the HDF5 library. - (MAM - 2009/11/04) - -* A dataset created or rewritten with a v1.6.3 library or after cannot be read - with the v1.6.2 library or before when the Fletcher32 EDC filter is enabled. - There was a bug in the calculation of the Fletcher32 checksum in the - library before v1.6.3; the checksum value was not consistent between big- - endian and little-endian systems. This bug was fixed in Release 1.6.3. - However, after fixing the bug, the checksum value was no longer the same as - before on little-endian system. Library releases after 1.6.4 can still read - datasets created or rewritten with an HDF5 library of v1.6.2 or before. - (SLU - 2005/06/30) - - -%%%%1.8.17%%%% - - -HDF5 version 1.8.17 released on 2016-05-10 -================================================================================ - -INTRODUCTION -============ - -This document describes the differences between HDF5-1.8.16 and -HDF5-1.8.17-*, and contains information on the platforms tested and -known problems in HDF5-1.8.17-*. -For more details, see the files HISTORY-1_0-1_8_0_rc3.txt -and HISTORY-1_8.txt in the release_docs/ directory of the HDF5 source. - -Links to the HDF5 1.8.17 source code, documentation, and additional materials -can be found on the HDF5 web page at: - - http://www.hdfgroup.org/products/hdf5/ - -The HDF5 1.8.17 release can be obtained from: - - http://www.hdfgroup.org/HDF5/release/obtain5.html - -User documentation for 1.8.17 can be accessed directly at this location: - - http://www.hdfgroup.org/HDF5/doc/ - -New features in the HDF5-1.8.x release series, including brief general -descriptions of some new and modified APIs, are described in the "What's New -in 1.8.0?" document: - - http://www.hdfgroup.org/HDF5/doc/ADGuide/WhatsNew180.html - -All new and modified APIs are listed in detail in the "HDF5 Software Changes -from Release to Release" document, in the section "Release 1.8.17 (current -release) versus Release 1.8.16 - - http://www.hdfgroup.org/HDF5/doc/ADGuide/Changes.html - -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, Languages, and Compilers -- Bug Fixes since HDF5-1.8.16 -- Supported Platforms -- Supported Configuration Features Summary -- More Tested Platforms -- Known Problems - - - -New Features -============ - - Configuration - ------------- - - Cmakehdf5: Added Ability to Run Multiple Make Commands - - Added option --njobs to specify up to how many jobs to launch during - build (cmake) and testing (ctest). - - (AKC - 2015/12/13, HDFFV-9612) - - - Cmakehdf5: Added Szip Support and Verbose Option - - Added --with-szlib to support the Szip library; and - --enable/disable-verbose to display all CMake process output. - - (AKC - 2015/11/16, HDFFV-8932 and DAILYTEST-195) - - - CMake minimum is now 3.1.0. (ADB - 2015/11/14) - - - Large File System (LFS) Support has Changed in the Autotools - - We assume that fseeko and ftello exist. - - The *64 I/O functions and types are no longer explicitly used. - We now rely on a mapping provided by _FILE_OFFSET_BITS (or its - equivalent). - - _LARGEFILE(64)_SOURCE is no longer exposed via AM_CPPFLAGS. - - (DER - 2016/03/29, HDFFV-9626 and HDFFV-9541) - - - - Library - ------- - - New API Calls for Searching for External Dataset Storage - - API calls that determine the search path for dataset external - storage were added. H5Pset/get_efile_prefix() API calls were added - to the library. These functions give control over the search path - for dataset external storage that has been configured with - H5Pset_external(). - - Additionally, the HDF5_EXTFILE_PREFIX environment variable can be - used to control the search path. - - (DER - 2016/04/20, HDFFV-8740) - - - - Parallel Library - ---------------- - - None - - - - Tools - ----- - - None - - - - High-Level APIs - --------------- - - C Packet Table API - ------------------ - - Replacement of a Public Function with H5PTcreate - - The existing function H5PTcreate_fl limits applications so they - can use the deflate compression only. The public function - H5PTcreate has been added to replace H5PTcreate_fl. H5PTcreate - takes a property list identifier to provide flexibility on - creation properties. This also removes the following warning: - "deprecated conversion from string constant to "char*" - [-Wwrite-strings]". - - (BMR - 2016/04/25, HDFFV-9708, HDFFV-8615) - - - New Public Functions: H5PTget_dataset and H5PTget_type - - Two accessor functions have been added. H5PTget_dataset returns - the identifier of the dataset associated with the packet table, - and H5PTget_type returns the identifier of the datatype used by - the packet table. - - (BMR - 2016/04/25, HDFFV-8623 patch 3) - - - Regarding #ifdef VLPT_REMOVED - - The #ifdef VLPT_REMOVED blocks have been removed from the packet - table (PT) library source except for the following functions: - + H5PTis_varlen() has been made available again - + H5PTfree_vlen_readbuff() is now H5PTfree_vlen_buff() - - (BMR - 2016/04/25, HDFFV-442) - - C++ Packet Table API - -------------------- - - New Constructor in FL_PacketTable - - An overloaded constructor has been added to FL_PacketTable and - takes a property list identifier to provide flexibility on - creation properties such as compression. - - FL_PacketTable(hid_t fileID, const char* name, hid_t dtypeID, - hsize_t chunkSize = 0, hid_t plistID = H5P_DEFAULT) - - (BMR - 2016/04/25, HDFFV-8623 patch 5) - - - New Member Functions in PacketTable - - Two accessor wrappers were added to class PacketTable. - - PacketTable::GetDataset() returns the identifier of the dataset - associated with the packet table, and PacketTable::GetDatatype() - returns the identifier of the datatype that the packet table uses. - - (BMR - 2016/04/25, HDFFV-8623 patch 4) - - - New Member Functions with "char*" as an Argument - - Overloaded functions were added to provide the "const char*" - argument; the existing version will be deprecated in future - releases. This also removes the following warning: - "deprecated conversion from string constant to "char*" - [-Wwrite-strings]". - - (BMR - 2016/04/25, HDFFV-8623 patch 1, HDFFV-8615) - - - Regarding #ifdef VLPT_REMOVED - - The #ifdef VLPT_REMOVED blocks have been removed from the packet - table library source code except for the following functions: - + VL_PacketTable::IsVariableLength() was moved to PacketTable - + VL_PacketTable::FreeReadBuff() is now PacketTable::FreeBuff() - - (BMR - 2016/04/25, HDFFV-442) - - - - Fortran API - ----------- - - None - - - - C++ API - ------- - - New Member Function in DSetCreatPropList - - DSetCreatPropList::setNbit() was added to setup N-bit compression for - a dataset. - - (BMR - 2016/04/25, HDFFV-8623 patch 7) - - - New Overloaded "const" Member Functions in ArrayType - - The two following functions were added: - ArrayType::getArrayNDims() const - ArrayType::getArrayDims() const - to provide const version, and the non-const version was marked - deprecated. In-memory array information, ArrayType::rank and - ArrayType::dimensions, were removed. This is an implementation - detail and should not affect applications. - - (BMR, 2016/04/25, HDFFV-9725) - - - New member function added - - The assignment operator ArrayType::operator= is added because ArrayType - has pointer data members. - - (BMR, 2016/03/07, HDFFV-9562) - - -Support for New Platforms, Languages, and Compilers -=================================================== - - Mac OS X El Capitan 10.11.4 with compilers Apple clang/clang++ - version 7.3.0 from Xcode 7.3, gfortran GNU Fortran (GCC) 5.2.0 - and Intel icc/icpc/ifort version 16.0.2 - - - -Bug Fixes since HDF5-1.8.16 -=========================== - - Configuration - ------------- - - Updated Linux Language Level Flags to Match the Autotools. Removed - Linux-specific Flags from OS X. - - An addition to the flags simply being out of sync with the Autotools, - the Linux flags were used on OS X builds which led to symbols not being - found. Although this was non-fatal and compilation continued (implicit - definitions were used by the compiler and the symbols resolved at link - time), a large number of warnings were raised. - - Linux changes: - - * CHANGED: _POSIX_C_SOURCE (from 199605 to 200112L) - * ADDED: _GNU_SOURCE - * REMOVED: _BSD_SOURCE - * REMOVED: _DEFAULT_SOURCE - - (DER - 2015/12/08, HDFFV-9627) - - - The --enable-clear-file-buffers configure Option was Non-functional - so the Feature was Always Enabled (its default value). - - Regardless of the configure flag, the setting was always enabled when - the Autotools were used to configure HDF5. This was due to the "no" - option being processed after the "*" option in configure.ac so "*" - matched first. CMake was unaffected. - - The option now works correctly. - - NOTE that builders are always advised to leave this option enabled. - When disabled, buffers that are written to disk may contain the - memory's previous contents, which may include secure information. - The performance overhead of the feature (a single memset call per - allocation) is minimal. - - (DER - 2016/02/03, HDFFV-9676) - - - Added a patch to remove '"'s from arguments for MPI compilers that - were causing errors compiling H5lib_settings.c with SGI MPT. - - (LRK - 2016/04/20, HDFFV-9439) - - Library - ------- - - Fixed shared file pointer problem which caused a crash when running a - program provided by a user. - - (VC - 2016/04/01, HDFFV-9469) - - - Fixed some format string warnings that prevent compiling with - -Werror=format-security on gcc. - - These only appeared in error messages and would not cause problems - under normal operation. - - (DER - 2016/01/13, HDFFV-9640) - - - Fixed a library segmentation fault when accessing a corrupted - file provided by a user. - - (MSC - 2016/02/19, HDFFV-9670) - - - - Parallel Library - ---------------- - - None - - - - Performance - ------------- - - None - - - - Tools - ----- - - h5dump: Sub-setting Fixed for Dimensions Greater than Two - - When a dataset has more than two dimensions, sub-setting would - incorrectly calculate the data that needed to be displayed. - Added in block and stride calculations that account for dimensions - greater than two. NOTE: lines that have line breaks inserted - because of display length calculations may have index info that - is incorrect until the next dimension break. - - (ADB - 2016/03/07, HDFFV-9698) - - - h5dump: Issue with Argument Segmentation Fault - - When an argument with an optional value was at the end of the command - line with a value, h5dump would crash. Reworked check for remaining - arguments. - - (ADB - 2016/03/07, HDFFV-9570, HDFFV-9684) - - - h5dump: Issue with Default Fill Value - - Added all default cases of fill value to the display of fill value. - - (ADB -, 2016/03/07, HDFFV-9241) - - - h5dump: Clarified Help - - Clarified usage of -O F option in h5dump utility help. - - (ADB - 2016/03/07, HDFFV-9066) - - - h5dump: Issue with Double Free Fault - - Added a check for filename not null before calling free(). - - (ADB - 2016/01/27, HDFFV-9639) - - - VS2015 Release Changed how Timezone was Handled - - Created a function, HDget_timezone, in H5system.c. Replaced - timezone variable usage with function call. - - (ADB - 2015/11/02, HDFFV-9550) - - - - Fortran API - ----------- - - None - - - - C++ API - ------- - - Removal of Obsolete Methods - - The overloaded methods which had parameters that should be const - but were not have been removed. - - (BMR - 2016/01/13, HDFFV-9789) - - - - High-Level APIs: - --------------- - - Fixed Memory Leak in Packet Table API - - Applied user's patch to fix memory leak in the creation of a - packet table. - - (BMR - 2016/04/25, HDFFV-9700) - - - - Fortran High-Level APIs: - ------------------------ - - None - - - - Testing - ------- - - None - - - -Supported Platforms -=================== -The following platforms are supported and have been tested for this release. -They are built with the configure process unless specified otherwise. - - AIX 6.1 xlc/xlc_r 10.1.0.5 - (NASA G-ADA) xlC/xlC_r 10.1.0.5 - xlf90/xlf90_r 12.1.0.6 - - Linux 2.6.32-573.22.1.el6 GNU C (gcc), Fortran (gfortran), C++ (g++) - #1 SMP x86_64 GNU/Linux compilers: - (platypus) Version 4.4.7 20120313 - Version 4.9.3, Version 5.2.0 - PGI C, Fortran, C++ for 64-bit target on - x86-64; - Version 15.7-0 - Intel(R) C (icc), C++ (icpc), Fortran (icc) - compilers: - Version 15.0.3.187 Build 20150407 - MPICH 3.1.4 compiled with GCC 4.9.3 - - Linux 2.6.32-504.8.1.el6.ppc64 gcc (GCC) 4.4.7 20120313 (Red Hat 4.4.7-16) - #1 SMP ppc64 GNU/Linux g++ (GCC) 4.4.7 20120313 (Red Hat 4.4.7-16) - (ostrich) GNU Fortran (GCC) 4.4.7 20120313 (Red Hat 4.4.7-16) - IBM XL C/C++ V13.1 - IBM XL Fortran V15.1 - - Linux 3.10.0-229.14.1.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 5.2.0 - Intel(R) C (icc), C++ (icpc), Fortran (icc) - compilers: - Version 15.0.3.187 Build 20150407 - 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 2012 w/ Intel Fortran 15 (cmake) - Visual Studio 2013 w/ Intel Fortran 15 (cmake) - Visual Studio 2015 (cmake) - Cygwin(CYGWIN_NT-6.1 2.2.1(0.289/5/3) gcc(4.9.3) compiler and gfortran) - (cmake and autotools) - - Windows 7 x64 Visual Studio 2012 w/ Intel Fortran 15 (cmake) - Visual Studio 2013 w/ Intel Fortran 15 (cmake) - Visual Studio 2015 (cmake) - - Windows 8.1 Visual Studio 2012 w/ Intel Fortran 15 (cmake) - Visual Studio 2013 w/ Intel Fortran 15 (cmake) - - Windows 8.1 x64 Visual Studio 2012 w/ Intel Fortran 15 (cmake) - Visual Studio 2013 w/ Intel Fortran 15 (cmake) - - Mac OS X Mt. Lion 10.8.5 Apple clang/clang++ version 5.1 from Xcode 5.1 - 64-bit gfortran GNU Fortran (GCC) 4.8.2 - (swallow/kite) Intel icc/icpc/ifort version 15.0.3 - - Mac OS X Mavericks 10.9.5 Apple clang/clang++ version 6.0 from Xcode 6.2 - 64-bit gfortran GNU Fortran (GCC) 4.9.2 - (wren/quail) Intel icc/icpc/ifort version 15.0.3 - - 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 10.11.4 Apple clang/clang++ version 7.3.0 from Xcode 7.3 - 64-bit gfortran GNU Fortran (GCC) 5.2.0 - (osx1011dev/ox1011test) Intel icc/icpc/ifort version 16.0.2 - - -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 -SunOS 5.11 32-bit n y/y n y y y -SunOS 5.11 64-bit n y/y n y y y -Windows 7 y y/y n y y y -Windows 7 x64 y y/y n y y y -Windows 7 Cygwin n y/y n y y n -Windows 8.1 n y/y n y y y -Windows 8.1 x64 n 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 y -Mac OS X Yosemeti 10.10.5 64-bit n y/y n y y y -AIX 6.1 32- and 64-bit n y/n n y y y -CentOS 6.7 Linux 2.6.32 x86_64 GNU y y/y y y y y -CentOS 6.7 Linux 2.6.32 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 7.1 Linux 3.10.0 x86_64 GNU y y/y y y y y -CentOS 7.1 Linux 3.10.0 x86_64 Intel n y/y n y y y -Linux 2.6.32-431.11.2.el6.ppc64 n y/n n y y y - -Platform Shared Shared Shared Thread- - C libs F90 libs C++ libs safe -SunOS 5.11 32-bit y y y y -SunOS 5.11 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 8.1 y y y y -Windows 8.1 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 Yosemeti 10.10.5 64-bit y n y y -AIX 6.1 32- and 64-bit y n n y -CentOS 6.7 Linux 2.6.32 x86_64 GNU y y y y -CentOS 6.7 Linux 2.6.32 x86_64 Intel y y y y -CentOS 6.7 Linux 2.6.32 x86_64 PGI y y y y -CentOS 7.1 Linux 3.10.0 x86_64 GNU y y y y -CentOS 7.1 Linux 3.10.0 x86_64 Intel y y y y -Linux 2.6.32-431.11.2.el6.ppc64 y y y y - -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 2.6.18-431.11.2.el6 g95 (GCC 4.0.3 (g95 0.94!) - #1 SMP x86_64 GNU/Linux - (platypus) - - Windows 7 Visual Studio 2008 (cmake) - - Windows 7 x64 Visual Studio 2008 (cmake) - - Windows 10 Visual Studio 2013 w/ Intel Fortran 15 (cmake) - - Windows 10 x64 Visual Studio 2013 w/ Intel Fortran 15 (cmake) - - Debian7.5.0 3.2.0-4-amd64 #1 SMP Debian 3.2.51-1 x86_64 GNU/Linux - gcc (Debian 4.7.2-5) 4.7.2 - GNU Fortran (Debian 4.7.2-5) 4.7.2 - (cmake and autotools) - - Fedora20 3.15.3-200.fc20.x86_64 #1 SMP x86_64 x86_64 x86_64 GNU/Linux - gcc (GCC) 4.8.3 20140624 (Red Hat 4.8.3-1) - GNU Fortran (GCC) 4.8.3 20140624 (Red Hat 4.8.3-1) - (cmake and autotools) - - SUSE 13.1 3.11.10-17-desktop #1 SMP PREEMPT x86_64 x86_64 x86_64 GNU/Linux - gcc (SUSE Linux) 4.8.1 - GNU Fortran (SUSE Linux) 4.8.1 - (cmake and autotools) - - Ubuntu 14.04 3.13.0-35-generic #62-Ubuntu SMP x86_64 GNU/Linux - gcc (Ubuntu/Linaro 4.9.1-0ubuntu1) 4.9.1 - GNU Fortran (Ubuntu/Linaro 4.9.1-0ubuntu1) 4.9.1 - (cmake and autotools) - - hopper.nersc.gov PrgEnv-gnu/5.2.40 - gcc (GCC) 4.9.2 20141030 (Cray Inc.) - GNU Fortran (GCC) 4.9.2 20141030 (Cray Inc.) - g++ (GCC) 4.9.2 20141030 (Cray Inc.) - - -Known Problems -============== -* On windows platforms in debug configurations, the VFD flush1 tests will fail - with the split and multi VFD drivers. These tests will display a modal debug - dialog which must be answered or wait for the test timeout to expire. - (ADB - 2014/06/23 - HDFFV-8851) - -* CLANG compiler with the options -fcatch-undefined-behavior and -ftrapv - catches some undefined behavior in the alignment algorithm of the macro DETECT_I - in H5detect.c (Issue 8147). Since the algorithm is trying to detect the alignment - of integers, ideally the flag -fcatch-undefined-behavior shouldn't to be used for - H5detect.c. In the future, we can separate flags for H5detect.c from the rest of - the library. (SLU - 2013/10/16) - -* Make provided by Solaris fails in "make check". Solaris users should use - gmake to build and install the HDF5 software. (AKC - 2013/10/08 - HDFFV-8534) - -* The C++ and FORTRAN bindings are not currently working on FreeBSD with the - native release 8.2 compilers (4.2.1), but are working with gcc 4.6 from the - ports (and probably gcc releases after that). - (QAK - 2012/10/19) - -* The following h5dump test case fails in BG/P machines (and potentially other - machines that use a command script to launch executables): - - h5dump --no-compact-subset -d "AHFINDERDIRECT::ah_centroid_t[0] it=0 tl=0" - tno-subset.h5 - - This is due to the embedded spaces in the dataset name being interpreted - by the command script launcher as meta-characters, thus passing three - arguments to h5dump's -d flag. The command passes if run by hand, just - not via the test script. - (AKC - 2012/05/03) - -* The STDIO VFD does not work on some architectures, possibly due to 32/64 - bit or large file issues. The basic STDIO VFD test is known to fail on - 64-bit SunOS 5.10 on SPARC when built with -m64 and 32-bit OS X/Darwin - 10.7.0. The STDIO VFD test has been disabled while we investigate and - a fix should appear in a future release. - (DER - 2011/10/14 - HDFFV-8235) - -* h5diff can report inconsistent results when comparing datasets of enum type - that contain invalid values. This is due to how enum types are handled in - the library and will be addressed in a future release. - (DER - 2011/10/14 - HDFFV-7527) - -* The links test can fail under the stdio VFD due to some issues with external - links. This will be investigated and fixed in a future release. - (DER - 2011/10/14 - HDFFV-7768) - -* After the shared library support was fixed for some bugs, it was discovered - that "make prefix=XXX install" no longer works for shared libraries. It - still works correctly for static libraries. Therefore, if you want to - install the HDF5 shared libraries in a location such as /usr/local/hdf5, - you need to specify the location via the --prefix option during configure - time. E.g, ./configure --prefix=/usr/local/hdf5 ... - (AKC - 2011/05/07 - HDFFV-7583) - -* The parallel test, t_shapesame, in testpar/, may run for a long time and may - be terminated by the alarm signal. If that happens, one can increase the - alarm seconds (default is 1200 seconds = 20 minutes) by setting the - environment variable, $HDF5_ALARM_SECONDS, to a larger value such as 3600 - (60 minutes). Note that the t_shapesame test may fail in some systems - (see the "While working on the 1.8.6 release..." problem below). If - it does, it will waste more time if $HDF5_ALARM_SECONDS is set - to a larger value. - (AKC - 2011/05/07) - -* Shared Fortran libraries are not quite working on AIX. While they are - generated when --enable-shared is specified, the fortran and hl/fortran - tests fail. the issue. HL and C++ shared libraries should now be - working as intended, however. - (MAM - 2011/04/20) - -* While working on the 1.8.6 release of HDF5, a bug was discovered that can - occur when reading from a dataset in parallel shortly after it has been - written to collectively. The issue was exposed by a new test in the parallel - HDF5 test suite, but had existed before that. We believe the problem lies with - certain MPI implementations and/or file systems. - - We have provided a pure MPI test program, as well as a standalone HDF5 - program, that can be used to determine if this is an issue on your system. - They should be run across multiple nodes with a varying number of processes. - These programs can be found at: - http://www.hdfgroup.org/ftp/HDF5/examples/known_problems/ - (NAF - 2011/01/19) - -* All the VFL drivers aren't backward compatible. In H5FDpublic.h, the - structure H5FD_class_t changed in 1.8. There is new parameter added to - get_eoa and set_eoa callback functions. A new callback function - get_type_map was added in. The public function H5FDrealloc was taken - out in 1.8. The problem only happens when users define their own driver - for 1.6 and try to plug in 1.8 library. Because there's only one user - complaining about it, we (Elena, Quincey, and I) decided to leave it as - it is (see bug report #1279). Quincey will make a plan for 1.10. - (SLU - 2010/02/02) - -* The --enable-static-exec configure flag will only statically link libraries - if the static version of that library is present. If only the shared version - of a library exists (i.e., most system libraries on Solaris, AIX, and Mac, - for example, only have shared versions), the flag should still result in a - successful compilation, but note that the installed executables will not be - fully static. Thus, the only guarantee on these systems is that the - executable is statically linked with just the HDF5 library. - (MAM - 2009/11/04) - -* A dataset created or rewritten with a v1.6.3 library or after cannot be read - with the v1.6.2 library or before when the Fletcher32 EDC filter is enabled. - There was a bug in the calculation of the Fletcher32 checksum in the - library before v1.6.3; the checksum value was not consistent between big- - endian and little-endian systems. This bug was fixed in Release 1.6.3. - However, after fixing the bug, the checksum value was no longer the same as - before on little-endian system. Library releases after 1.6.4 can still read - datasets created or rewritten with an HDF5 library of v1.6.2 or before. - (SLU - 2005/06/30) - - -%%%%1.8.16%%%% - - -HDF5 version 1.8.16 released on 2015-11-10 -================================================================================ - -INTRODUCTION -============ - -This document describes the differences between HDF5-1.8.15 and -HDF5-1.8.16, and contains information on the platforms tested and -known problems in HDF5-1.8.16. -For more details, see the files HISTORY-1_0-1_8_0_rc3.txt -and HISTORY-1_8.txt in the release_docs/ directory of the HDF5 source. - -Links to the HDF5 1.8.16 source code, documentation, and additional materials -can be found on the HDF5 web page at: - - http://www.hdfgroup.org/products/hdf5/ - -The HDF5 1.8.16 release can be obtained from: - - http://www.hdfgroup.org/HDF5/release/obtain5.html - -User documentation for 1.8.16 can be accessed directly at this location: - - http://www.hdfgroup.org/HDF5/doc/ - -New features in the HDF5-1.8.x release series, including brief general -descriptions of some new and modified APIs, are described in the "What's New -in 1.8.0?" document: - - http://www.hdfgroup.org/HDF5/doc/ADGuide/WhatsNew180.html - -All new and modified APIs are listed in detail in the "HDF5 Software Changes -from Release to Release" document, in the section "Release 1.8.16 (current -release) versus Release 1.8.15": - - http://www.hdfgroup.org/HDF5/doc/ADGuide/Changes.html - -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, Languages, and Compilers -- Bug Fixes since HDF5-1.8.15 -- Supported Platforms -- Supported Configuration Features Summary -- More Tested Platforms -- Known Problems - -New Features -============ - - Configuration and Build - ------------- - - The thread-safety + high-level library combination has been marked - as "unsupported" in the Autotools - - The global lock used by the thread-safety feature has never been - raised to the high-level library level, making it possible that - the library state could change if a context switch were to occur in - a high-level library call. Because of this, the combination of - thread-safety and high-level library is officially unsupported by - The HDF Group. - - In the past, although this combination has never been supported, this - was not enforced by the build systems. These changes will cause an - Autotools configure step to fail if --enable-threadsafe and - --enable-hl are combined unless additional options are specified. - Since the high-level library is built by default, this means that - these extra configuration options will need to be used any time - --enable-threadsafe is selected. - - To build with --enable-threadsafe, either: - - 1) Use --disable-hl to disable the high-level library (recommended) - - 2) Use --enable-unsupported to build the high-level library with - the thread-safety feature. - - (DER - 2015/09/10 HDFFV-8719) - - - Using CMake now builds both static and shared libraries. - - The CMake files have been updated to build both static and shared - libraries, with tools only built statically. The packaging of the - libraries and tools will include cmake-config files that allows - projects to choose either shared or static (default) libraries - to be found with the find_package command using the COMPONENTS - keyword and a list of components. The imported libraries will - include any interface specific settings and dependent libraries. - - The default setting for BUILD_SHARED_LIBS has changed from OFF - to ON, which builds both static and shared libraries. The static - libraries are always built because of tools requirements. - - (ADB - 2015/08/24 HDFFV-5881) - - - Inline functions now correctly annotated with Autotools builds. - - The method used to detect the appropriate inline markup scheme was - nonfunctional in Autotools builds. The Autotools have been modified - to correctly detect the compiler's inline markup symbol and apply it - to the source. Note that only a very small number of internal - functions are marked inline so this was not a very big change or - likely to significantly affect performance. - - As a part of this change, the H5_inline symbol no longer appears in - H5pubconf.h. - - (DER - 2015/08/13 HDFFV-9119, HDFFV-9421) - - - Removed obsolete/unmaintained files from config/ - - Several files were removed from the config directory. These files - represent old operating systems, were no longer necessary, and/or - were no longer maintained. configure.ac was updated to reflect the - removed files. - - Removed: - - craynv - dec-flags - hpux11.23 - ia64-linux-gnu - nec-superux14.1 - sv1-cray - x86_64-redstorm-linux-gnu - powerpc-ibm-aix5.x - - As a part of this work, a few lines that deal with locating the - sys/fpu.h header on SGI machines and some OSF/1 configure lines - were also removed. The Solaris config was also renamed to not have - a version number since the version number was ignored by configure - as it applies to all Solaris versions. - - (DER - 2015/09/04 HDFFV-9116) - - - Removed the FP_TO_INTEGER_OVERFLOW_WORKS macro/defines from the library - - This was for working around bugs in the Cray X1 compiler, which is no - longer supported. - - (DER - 2015/09/09 HDFFV-9191) - - - Removed the H5_SW_ULONG_TO_FP_BOTTOM_BIT_WORKS and - H5_FP_TO_ULLONG_BOTTOM_BIT_WORKS symbols and associated code. - - H5_SW_ULONG_TO_FP_BOTTOM_BIT_WORKS was a work-around on old 64-bit - SGI and Solaris systems. - - H5_FP_TO_ULLONG_BOTTOM_BIT_WORKS was a work-around for old PGI - compilers on Linux. - - Neither of these were used in any current library code and only appeared - in the dt_arith test. - - (DER - 2015/09/09 HDFFV-9187) - - - Removed CONVERT_DENORMAL_FLOAT symbol and associated code from the - library. - - This was only set in configure files for Cray and NEC computers. These - config files no longer exist so there is no effect on currently - supported platforms. - - (DER - 2015/09/09 HDFFV-9188) - - - Removed _BSD_SOURCE and _DEFAULT_SOURCE from configure.ac - - These are old BSD-compatibility symbols that are no longer needed by - the library. - - (DER - 2015/09/10 HDFFV-9079) - - - Removed HW_FP_TO_LLONG_NOT_WORKS symbol and associated code from the - library. - - This was part of a work-around for the VS.NET 2003 compiler, which is - no longer supported. - - (DER - 2015/09/10 HDFFV-9189) - - - Removed the BAD_LOG2_CODE_GENERATED symbol and associated code from the - library. - - This was an IRIX work-around. - - (DER - 2015/09/11 HDFFV-9195) - - - Decoupled shared object version numbers for wrapper libraries from the - shared object version number for the HDF5 library. These will be - maintained on an individual basis according to the interface changes - specific to these wrapper libraries. - - For HDF5 1.8.16 the shared object version numbers were changed from - 10.0.1 to 10.1.0 for the HDF5 library due to added APIs. For the C++ - wrapper library they were changed from 10.0.1 to 11.0.0 due to changes - in existing APIs. For all other wrapper libraries the versions were - changed from 10.0.1 to 10.0.2 because while the APIs had no changes - there have been changes in code that did not result in changes to their - interfaces. - - (LRK - 2015/10/28) - - Library - ------- - - - H5F_ACC_DEBUG flag for H5Fopen/create: functionality removed - - The symbol was used to emit some extra debugging information - for HDF Group developers in the multi VFD. The underlying - functionality has been removed due to disuse. The symbol - remains defined since it was visible in H5Fpublic.h but it - has been set to zero and has no effect anywhere in the library. - - (DER - 2015-05-02, HDFFV-1074) - - - New public API call: H5is_library_threadsafe() - - This API call indicates if the library was built with thread- - safety enabled. - - (DER - 2015-09-01, HDFFV-9496) - - Parallel Library - ---------------- - - None - - Tools - ----- - - None - - High-Level APIs - --------------- - - None - - Fortran API - ----------- - - None - - - C++ API - ------- - - Class H5::ObjCreatPropList is added for the object creation property - list class. - - Class H5::ObjCreatPropList is derived from H5::PropList and is a - baseclass of H5::DSetCreatPropList. Additional property list classes - will be derived from H5::ObjCreatPropList when they are added to the - library in future releases. - - (BMR, 2015/10/13, Part of HDFFV-9169) - - - New Wrappers for C Functions H5P[s/g]et_attr_phase_change and - H5P[s/g]et_attr_creation_order. - - Wrappers were added to class H5::ObjCreatPropList for the C Functions - H5Pset_attr_phase_change: H5::ObjCreatPropList::setAttrPhaseChange - H5Pget_attr_phase_change: H5::ObjCreatPropList::getAttrPhaseChange - H5Pset_attr_creation_order: H5::ObjCreatPropList::setAttrCrtOrder - H5Pget_attr_creation_order: H5::ObjCreatPropList::getAttrCrtOrder - - (BMR, 2015/10/13, Part of HDFFV-9167 and HDFFV-9169) - - -Support for New Platforms, Languages, and Compilers -=================================================== - - Added VS2015 with Intel Fortran 16 to supported Windows 7 platforms - - -Bug Fixes since HDF5-1.8.15 -=========================== - - Configuration - ------------- - - - CMake test for long long printf format improved - - The CMake configuration test for determining the printf format string - for printing a long long integer was fixed. The test would crash - when executed with VS2015. - - (ADB - 2015-10-21 HDFFV-9488) - - Library - ------- - - VS2015 removed global variable timezone - - The usage of the global variable timezone was modified for VS2015 by - adding an alias to Windows builds. - - (ADB - 2015-10-23 HDFFV-9550) - - - Fix potential error in H5Iclear_type - - If the ID type's close callback could close another ID of the same type, - H5Iclear_type could occasionally run into problems due to the inner - workings of the skip list package. This could potentially cause an - error on library shutdown without calling H5Iclear_type directly. This - issue has been fixed. - - (NAF - 2015-08-12) - - - Fix uninitialized memory in dataspace selection code - - When creating a dataspace with H5Screate and setting the extent with - H5Sextent_copy, the selection offset was not initialized, potentially - causing invalid I/O. There may be other cases where this happened. - Modified the library to always initialize the offset. - - (NAF - 2015-09-08) - - - Truncate file in H5Fflush() if EOA != EOF to avoid file - corruption in certain scenarios - - In the following scenario, the resulting HDF5 file would be - incorrectly corrupted because the truncate operation - was at some point wrongly moved out of the flush operation: - - Create a new file with a single dataset. - - Write parts of the dataset (make sure that some values at - the end of the dataset are not initialized). - - Flush the file. - - Crash the program. - - Try to open the file with h5dump or h5debug, but the - resulting file is corrupted. - - (MSC - 2015-06-15 HDFFV-9418) - - - Parallel Library - ---------------- - - - (XYZ - YYYY/MM/DD HDFFV-####) - - Performance - ------------- - - None - - Tools - ----- - - VS2015 changed the default format for printing of exponents - - VS2015 default format for exponents changed with the elimination - of the leading '0'. CMake now tests for the VS2015 compiler and - adjusts which reference files are used by tests. - - (ADB - 2015-10-23 HDFFV-9550) - - - Fixed h5repack with user-defined filters - - h5repack would throw a buffer overrun exception on Windows when - parsing a user-defined filter ID of 5 digits. A local variable in - the parse routine was not of sufficient size. - - (ADB - 2015/09/01 HDFFV-9515) - - Fortran API - ------------ - - None - - - C++ API - ------ - - Removed memory leaks - - The static global constant objects were changed to constant references - referencing dynamically allocated objects. This ensures that the clean-up - process in the C++ library occurs before the termination of the C library - and prevents memory leaks because the previous global constants were not - properly deleted before the C library termination. - - (BMR, 2015/10/13, HDFFV-9529) - - - Fixed the problem about identifiers being closed prematurely. - - The C++ library needs to increment the ID's reference counter when it is - duplicated in the form of C++ objects, but not when the ID is obtained - from a C function. With this approach, both problems, prematurely - closing ID's and memory leaks due to ID's not being closed, should be - eliminated. - - (BMR, 2015/10/15, HDFFV-7947) - - - High-Level APIs: - ------ - - None - - - Fortran High-Level APIs: - ------------------------ - - None - - - Testing - ------- - - None - - -Supported Platforms -=================== -The following platforms are supported and have been tested for this release. -They are built with the configure process unless specified otherwise. - - AIX 6.1 xlc/xlc_r 10.1.0.5 - (NASA G-ADA) xlC/xlC_r 10.1.0.5 - xlf90/xlf90_r 12.1.0.6 - - Linux 2.6.32-573.3.1.el6 GNU C (gcc), Fortran (gfortran), C++ (g++) - #1 SMP x86_64 GNU/Linux compilers: - (platypus) Version 4.4.7 20120313 - Version 4.8.4, Version 5.2.0 - PGI C, Fortran, C++ for 64-bit target on - x86-64; - Version 15.7-0 - Intel(R) C (icc), C++ (icpc), Fortran (icc) - compilers: - Version 15.0.3.187 Build 20150407 - MPICH 3.1.4 compiled with GCC 4.9.3 - - Linux 2.6.32-504.8.1.el6.ppc64 gcc (GCC) 4.4.7 20120313 (Red Hat 4.4.7-11) - #1 SMP ppc64 GNU/Linux g++ (GCC) 4.4.7 20120313 (Red Hat 4.4.7-11) - (ostrich) GNU Fortran (GCC) 4.4.7 20120313 (Red Hat 4.4.7-11) - IBM XL C/C++ V13.1 - IBM XL Fortran V15.1 - - Linux 3.10.0-229.14.1.el7 GNU C (gcc), Fortran (gfortran), C++ (g++) - #1 SMP x86_64 GNU/Linux compilers: - (kituo/moohan) Version 4.8.3 20140911 (Red Hat 4.8.3-9) - Version 5.2.0 - Intel(R) C (icc), C++ (icpc), Fortran (icc) - compilers: - Version 15.0.3.187 Build 20150407 - 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 2012 w/ Intel Fortran 15 (cmake) - Visual Studio 2013 w/ Intel Fortran 15 (cmake) - Visual Studio 2015 w/ Intel Fortran 16 (cmake) - Cygwin(CYGWIN_NT-6.1 2.2.1(0.289/5/3) gcc(4.9.3) compiler and gfortran) - (cmake and autotools) - - Windows 7 x64 Visual Studio 2012 w/ Intel Fortran 15 (cmake) - Visual Studio 2013 w/ Intel Fortran 15 (cmake) - Visual Studio 2015 w/ Intel Fortran 16 (cmake) - - Windows 8.1 Visual Studio 2012 w/ Intel Fortran 15 (cmake) - Visual Studio 2013 w/ Intel Fortran 15 (cmake) - - Windows 8.1 x64 Visual Studio 2012 w/ Intel Fortran 15 (cmake) - Visual Studio 2013 w/ Intel Fortran 15 (cmake) - - Mac OS X Mt. Lion 10.8.5 Apple clang/clang++ version 5.1 from Xcode 5.1 - 64-bit gfortran GNU Fortran (GCC) 4.8.2 - (swallow/kite) Intel icc/icpc/ifort version 15.0.3 - - Mac OS X Mavericks 10.9.5 Apple clang/clang++ version 6.0 from Xcode 6.2.0 - 64-bit gfortran GNU Fortran (GCC) 4.9.2 - (wren/quail) Intel icc/icpc/ifort version 15.0.3 - - Mac OS X Yosemite 10.10.5 Apple clang/clang++ version 6.0 from Xcode 7.0.0 - 64-bit gfortran GNU Fortran (GCC) 4.9.2 - (osx1010dev/osx1010test) Intel icc/icpc/ifort version 15.0.3 - -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 -SunOS 5.11 32-bit n y/y n y y y -SunOS 5.11 64-bit n y/y n y y y -Windows 7 y y/y n y y y -Windows 7 x64 y y/y n y y y -Windows 7 Cygwin n y/y n y y n -Windows 8.1 n y/y n y y y -Windows 8.1 x64 n 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 y -Mac OS X Yosemeti 10.10.5 64-bit n y/y n y y y -AIX 6.1 32- and 64-bit n y/n n y y y -CentOS 6.7 Linux 2.6.32 x86_64 GNU y y/y y y y y -CentOS 6.7 Linux 2.6.32 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 7.1 Linux 3.10.0 x86_64 GNU y y/y y y y y -CentOS 7.1 Linux 3.10.0 x86_64 Intel n y/y n y y y -Linux 2.6.32-431.11.2.el6.ppc64 n y/n n y y y - -Platform Shared Shared Shared Thread- - C libs F90 libs C++ libs safe -SunOS 5.11 32-bit y y y y -SunOS 5.11 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 8.1 y y y y -Windows 8.1 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 Yosemeti 10.10.5 64-bit y n y y -AIX 6.1 32- and 64-bit y n n y -CentOS 6.7 Linux 2.6.32 x86_64 GNU y y y y -CentOS 6.7 Linux 2.6.32 x86_64 Intel y y y y -CentOS 6.7 Linux 2.6.32 x86_64 PGI y y y y -CentOS 7.1 Linux 3.10.0 x86_64 GNU y y y y -CentOS 7.1 Linux 3.10.0 x86_64 Intel y y y y -Linux 2.6.32-431.11.2.el6.ppc64 y y y y - -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 2.6.18-431.11.2.el6 g95 (GCC 4.0.3 (g95 0.94!) - #1 SMP x86_64 GNU/Linux - (platypus) - - Mac OS X El Capitan 10.11 Apple clang/clang++ version 7.0.0 from Xcode 7.0.1 - 64-bit gfortran GNU Fortran (GCC) 5.2.0 - (VM) - - Windows 7 Visual Studio 2008 (cmake) - - Windows 7 x64 Visual Studio 2008 (cmake) - - Windows 10 Visual Studio 2013 w/ Intel Fortran 15 (cmake) - - Windows 10 x64 Visual Studio 2013 w/ Intel Fortran 15 (cmake) - - Debian7.5.0 3.2.0-4-amd64 #1 SMP Debian 3.2.51-1 x86_64 GNU/Linux - gcc (Debian 4.7.2-5) 4.7.2 - GNU Fortran (Debian 4.7.2-5) 4.7.2 - (cmake and autotools) - - Fedora20 3.15.3-200.fc20.x86_64 #1 SMP x86_64 x86_64 x86_64 GNU/Linux - gcc (GCC) 4.8.3 20140624 (Red Hat 4.8.3-1) - GNU Fortran (GCC) 4.8.3 20140624 (Red Hat 4.8.3-1) - (cmake and autotools) - - SUSE 13.1 3.11.10-17-desktop #1 SMP PREEMPT x86_64 x86_64 x86_64 GNU/Linux - gcc (SUSE Linux) 4.8.1 - GNU Fortran (SUSE Linux) 4.8.1 - (cmake and autotools) - - Ubuntu 14.04 3.13.0-35-generic #62-Ubuntu SMP x86_64 GNU/Linux - gcc (Ubuntu/Linaro 4.9.1-0ubuntu1) 4.9.1 - GNU Fortran (Ubuntu/Linaro 4.9.1-0ubuntu1) 4.9.1 - (cmake and autotools) - - hopper.nersc.gov PrgEnv-gnu/5.2.40 - gcc (GCC) 4.9.2 20141030 (Cray Inc.) - GNU Fortran (GCC) 4.9.2 20141030 (Cray Inc.) - g++ (GCC) 4.9.2 20141030 (Cray Inc.) - - -Known Problems -============== -* On Windows platforms in debug configurations, the VFD flush1 tests will fail - with the split and multi VFD drivers. These tests will display a modal debug - dialog which must be answered or wait for the test timeout to expire. - (ADB - 2014/06/23 - HDFFV-8851) - -* CLANG compiler with the options -fcatch-undefined-behavior and -ftrapv - catches some undefined behavior in the alignment algorithm of the macro DETECT_I - in H5detect.c (Issue 8147). Since the algorithm is trying to detect the alignment - of integers, ideally the flag -fcatch-undefined-behavior shouldn't to be used for - H5detect.c. In the future, we can separate flags for H5detect.c from the rest of - the library. (SLU - 2013/10/16) - -* Make provided by Solaris fails in "make check". Solaris users should use - gmake to build and install the HDF5 software. (AKC - 2013/10/08 - HDFFV-8534) - -* The C++ and FORTRAN bindings are not currently working on FreeBSD with the - native release 8.2 compilers (4.2.1), but are working with gcc 4.6 from the - ports (and probably gcc releases after that). - (QAK - 2012/10/19) - -* The following h5dump test case fails in BG/P machines (and potentially other - machines that use a command script to launch executables): - - h5dump --no-compact-subset -d "AHFINDERDIRECT::ah_centroid_t[0] it=0 tl=0" - tno-subset.h5 - - This is due to the embedded spaces in the dataset name being interpreted - by the command script launcher as meta-characters, thus passing three - arguments to h5dump's -d flag. The command passes if run by hand, just - not via the test script. - (AKC - 2012/05/03) - -* The STDIO VFD does not work on some architectures, possibly due to 32/64 - bit or large file issues. The basic STDIO VFD test is known to fail on - 64-bit SunOS 5.10 on SPARC when built with -m64 and 32-bit OS X/Darwin - 10.7.0. The STDIO VFD test has been disabled while we investigate and - a fix should appear in a future release. - (DER - 2011/10/14 - HDFFV-8235) - -* h5diff can report inconsistent results when comparing datasets of enum type - that contain invalid values. This is due to how enum types are handled in - the library and will be addressed in a future release. - (DER - 2011/10/14 - HDFFV-7527) - -* The links test can fail under the stdio VFD due to some issues with external - links. This will be investigated and fixed in a future release. - (DER - 2011/10/14 - HDFFV-7768) - -* After the shared library support was fixed for some bugs, it was discovered - that "make prefix=XXX install" no longer works for shared libraries. It - still works correctly for static libraries. Therefore, if you want to - install the HDF5 shared libraries in a location such as /usr/local/hdf5, - you need to specify the location via the --prefix option during configure - time. E.g, ./configure --prefix=/usr/local/hdf5 ... - (AKC - 2011/05/07 - HDFFV-7583) - -* The parallel test, t_shapesame, in testpar/, may run for a long time and may - be terminated by the alarm signal. If that happens, one can increase the - alarm seconds (default is 1200 seconds = 20 minutes) by setting the - environment variable, $HDF5_ALARM_SECONDS, to a larger value such as 3600 - (60 minutes). Note that the t_shapesame test may fail in some systems - (see the "While working on the 1.8.6 release..." problem below). If - it does, it will waste more time if $HDF5_ALARM_SECONDS is set - to a larger value. - (AKC - 2011/05/07) - -* Shared Fortran libraries are not quite working on AIX. While they are - generated when --enable-shared is specified, the Fortran and HL/Fortran - tests fail. HL and C++ shared libraries should now be working as intended, - however. - (MAM - 2011/04/20) - -* While working on the 1.8.6 release of HDF5, a bug was discovered that can - occur when reading from a dataset in parallel shortly after it has been - written to collectively. The issue was exposed by a new test in the parallel - HDF5 test suite, but had existed before that. We believe the problem lies with - certain MPI implementations and/or file systems. - - We have provided a pure MPI test program, as well as a standalone HDF5 - program, that can be used to determine if this is an issue on your system. - They should be run across multiple nodes with a varying number of processes. - These programs can be found at: - http://www.hdfgroup.org/ftp/HDF5/examples/known_problems/ - (NAF - 2011/01/19) - -* All of the VFL drivers aren't backward compatible. In H5FDpublic.h, the - structure H5FD_class_t changed in 1.8. There is new parameter added to - get_eoa and set_eoa callback functions. A new callback function - get_type_map was added in. The public function H5FDrealloc was taken - out in 1.8. The problem only happens when users define their own driver - for 1.6 and try to plug in 1.8 library. Because there's only one user - complaining about it, we (Elena, Quincey, and I) decided to leave it as - it is (see bug report #1279). Quincey will make a plan for 1.10. - (SLU - 2010/02/02) - -* The --enable-static-exec configure flag will only statically link libraries - if the static version of that library is present. If only the shared version - of a library exists (i.e., most system libraries on Solaris, AIX, and Mac, - for example, only have shared versions), the flag should still result in a - successful compilation, but note that the installed executables will not be - fully static. Thus, the only guarantee on these systems is that the - executable is statically linked with just the HDF5 library. - (MAM - 2009/11/04) - -* A dataset created or rewritten with a v1.6.3 library or after cannot be read - with the v1.6.2 library or before when the Fletcher32 EDC filter is enabled. - There was a bug in the calculation of the Fletcher32 checksum in the - library before v1.6.3; the checksum value was not consistent between big- - endian and little-endian systems. This bug was fixed in Release 1.6.3. - However, after fixing the bug, the checksum value was no longer the same as - before on little-endian systems. Library releases after 1.6.4 can still read - datasets created or rewritten with an HDF5 library of v1.6.2 or before. - (SLU - 2005/06/30) - - -%%%%1.8.15%%%% - - -HDF5 version 1.8.15 released on 2015-05-04 -================================================================================ - -INTRODUCTION -============ - -This document describes the differences between HDF5-1.8.14 and -HDF5-1.8.15, and contains information on the platforms tested and -known problems in HDF5-1.8.15. - -Links to the HDF5 source code, documentation, and additional materials -can be found on the HDF5 web page at: - - http://www.hdfgroup.org/products/hdf5/ - -The HDF5 release can be obtained from: - - http://www.hdfgroup.org/HDF5/release/obtain5.html - -User documentation for HDF5 can be accessed directly at this location: - - http://www.hdfgroup.org/HDF5/doc/ - -All new and modified APIs are listed in detail in the "HDF5 Software Changes -from Release to Release" document at this location: - - http://www.hdfgroup.org/HDF5/doc/ADGuide/Changes.html - -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, Languages, and Compilers -- Bug Fixes since HDF5-1.8.14 -- Supported Platforms -- Supported Configuration Features Summary -- More Tested Platforms -- Known Problems - - -New Features -============ - - Configuration - ------------- - - CMake - - Improvements made to the CMake build system. - - The default options were changed to align with the Autotools configure - defaults. CMake configure files now support components when packaged - with CPack. Windows CPack supports WiX packaging, and will look for - WiX and NSIS in the standard locations. - - The CMake minimum has been changed to 3.1. - - (ADB - 2015/04/01 HDFFV-8074, 8968, 9006) - - - cmakehdf5 for Cmake building. - Added configure options to support the building of Fortran or CXX API, - to enable/disable testings. Use "cmakehdf5 --help" for details. - (AKC - 2014/12/09 HDFFV-8932) - - - Building Shared and Parallel Made Explicit - - When --enable-parallel is specified, configure used to disable - shared by default. - - Removed the restriction for building shared when parallel is - enabled. --disable-shared has to be used explicitly if user - wishes to disable shared libraries. - - (MSC - 2015/02/19 HDFFV-9069) - - - Inferring Parallel Compilers - - configure was trying to infer if a compiler is a parallel - compiler with MPI support and enable parallel even if the user - did not explicitly enable parallel. This should not happen. - - Disabled inferring parallel compilers to enable parallel HDF5 - build. --enable-parallel has to be used explicitly to build - parallel HDF5 regardless of the compiler type being used. - - (MSC - 2015/02/19 HDFFV-9068) - - - Large File Support Configuration Option - - Removed the option to enable or disable large file support. It will - always be enabled. - - (MSC - 2015/02/19 HDFFV-9097) - - - Removed Configuration Feature - - When configure detected that the CodeWarrior compiler was being used it - would define a symbol that caused a test in test/tfile.c to be skipped - due to a broken CodeWarrior open() command. - - Since this only masks the problem instead of fixing it and we don't - support CodeWarrior anyway, this functionality was removed. - - (DER - 2015/02/21, HDFFV-9080) - - - VMS Build/Test Files Have Been Removed - - HDF5 no longer supports VMS, and the files were getting out of date. - Since we have no access to a VMS machine, there is no way for us to - maintain them. - - A Subversion tag was created at: - - https://svn.hdfgroup.uiuc.edu/tags/vms_last_support_1_8 - - immediately before removing the files. - - (DER - 2015-02-26, HDFFV-9147) - - - Removal of --with-default-vfd configure Option - - In theory, this option was intended to allow setting a default - VFD that would be used by the library. In practice, the feature - only accepted the POSIX (SEC2) VFD (already the default) and - the stdio VFD (a demo VFD not intended for production use). The - inability to pass key VFD parameters at configure time limits the - full implementation of this feature, so it was retired. - - (DER - 2015-02-26, HDFFV-9081) - - - Direct VFD configure Behavior - - The configure options for Linux now allow the Direct VFD to build - without passing additional compiler options/defines like _GNU_SOURCE. - Passing --enable-direct-vfd is now all that is needed to enable - the feature. - - The Direct VFD is now disabled by default since it is intended for - specialized audiences. It was previously enabled by default, but the - configure script did not set correct POSIX levels, etc. making this - a moot point. - - Note that the Direct VFD can only be configured on Linux when - the O_DIRECT flag to open()/create() and posix_memalign() function - are available. This is unchanged from previous behavior. - - (DER - 2015-02-26, HDFFV-9057, 7567, 9088, 7566) - - - _POSIX_C_SOURCE, _GNU_SOURCE, and _BSD_SOURCE No Longer Exported - to h5cc and Other Compiler Wrappers - - The _POSIX_C_SOURCE, _GNU_SOURCE, and _BSD_SOURCE definitions are - not required for using API functions and may conflict with user - code requirements. - - (DER - 2015-03-08, HDFFV-9152) - - - Removed the --enable-filters Option from configure - - This option allowed the user to disable selected internal filters, - presumably to make the library smaller. It has been removed since - it saved little space (the internal filters are small with respect - to the overall library size) and was not generally extendible to - the library at large due to the large number of #ifdefs that would - be required. - - Note that this features applied to internal filters such as shuffle - and n-bit and not external filters like gzip or Szip. Those are still - enabled or disabled via their own configure options. - - (DER - 2015-03-08, HDFFV-9086) - - - Removed Obsolete Time Functionality from configure and the C Library - - The library contained some residual functionality from obsolete - time zone handling code. This has been removed, and the configure - checks for the time functions have been cleaned up. - - * Lumped all the time functionality together in configure.ac. - This was previously more spread out due to Solaris issues - with the ordering of certain checks. - - * Removed processing that handles __tm_gmtoff members of struct - tm. (libc-4) - - * Removed BSDgettimeofday(). (IRIX 5.3) - - * Removed timezone struct handling in gettimeofday() (considered - harmful). - - Note that the HDF5 Library stores timestamps in a platform-independent - manner, so old files can still be read. This only affects converting - system time to HDF5 timestamps. - - The library currently uses the tm_gmtoff member of the tm struct - (preferred, if available) or the timezone global variable to - construct HDF5 timestamps. - - (DER - 2015-03-09, HDFFV-9083 and 9085) - - - Added -D_DEFAULT_SOURCE to CPPFLAGS on Linux Systems - - This is the replacement for -D_BSD_SOURCE in versions of glibc since 2.19. - Since both are defined, it should work for all versions of glibc. Defining - both suppresses the warning about defining _BSD_SOURCE. - - (NAF - 2015-04-02, HDFFV-9079) - - Library - ------- - - Added Memory Allocation Functions that Use the Library's Allocator - - HDF5 filters may need to allocate or resize the buffer that is passed - to them from the library. If the filter has been compiled separately - from the library, it and the library may use different memory - allocation libraries for the (re)allocation and free calls. This can - cause heap corruption and crashes. This is particularly a problem on - Windows since each C run-time library is implemented as a separate - shared library, but can also show up on POSIX systems when debug or - high-performance allocation libraries are in use. - - Two new functions (H5allocate_memory() and H5resize_memory()) were - added to the HDF5 C library. These functions have the same semantics as - malloc/calloc and realloc, respectively. Their primary purpose is to - allow filter authors to allocate or resize memory using the same - memory allocation library as the HDF5 library. Filter authors are - highly encouraged to use these new functions in place of malloc, - calloc, and realloc. They should also use the H5free_memory() call when - freeing memory. - - Note that the filters provided with the library (zlib, szip, etc.) do - not experience the problems that these new functions are intended to - fix. This work only applies to third-party filters that are compiled - separately from the library. - - (DER - 2015-04-01, HDFFV-9100) - - - H5Pset_istore_k and H5Pset_sym_k - - These two functions didn't check the value of the input parameter "ik". - When 2*ik exceeded 2 bytes of storage, data was lost in the file; - for example, some chunks would be overwritten. - - Added validation of "ik" to not exceed the max v1 btree entries (2 bytes) - to these two routines. - - (VC - 2015-03-24, HDFFV-9173) - - - Added Functions to Control the Value of H5PL_no_plugin_g without - Using an Environment Variable - - Sometimes it is necessary for an application to disable the use of - dynamically loaded plugin libraries without requiring the library to - be built with plugin support disabled or to set an environment - variable to disable plugin support globally. - - Two new functions (H5PLset_loading_state() and H5PLget_loading_state()) - were added to the HDF5 C Library. These functions require a parameter - that indicates which type of dynamically loaded plugin is enabled or - disabled. - - (ADB - 2015-03-17, HDFFV-8520) - - Parallel Library - ---------------- - - MPI_Finalize and HDF5 Library Shutdown - - Calling HDF5 routines after MPI_Finalize has been closed should - not be done, since those routines might call MPI functions that - would not be possible to do after finalizing the MPI library. - - Attached an attribute destroy callback to MPI_COMM_SELF that - shuts down the HDF5 library when MPI_COMM_SELF is destroyed, - in other words, on MPI_Finalize. This should fix several issues - that users see when they forget to close HDF5 objects before - calling MPI_Finalize(). - - (MSC - 2015/02/25, HDFFV-883) - - Tools - ----- - - None - - High-Level APIs - --------------- - - None - - Fortran API - ----------- - - Added Global Variables - - These new global variables are equivalent to the C definitions - without the '_F': - - H5G_UDLINK_F - H5G_SAME_LOC_F - H5O_TYPE_UNKNOWN_F - H5O_TYPE_GROUP_F - H5O_TYPE_DATASET_F - H5O_NAMED_DATATYPE_F - H5O_TYPE_NTYPES_F - - (MSB - 2015/02/03, HDFFV-9040) - - - C++ API - ------- - - New Wrappers for C Functions H5P[s/g]et_libver_bounds - - Wrappers were added to class H5::FileAccPropList for the - C Functions H5Pget_libver_bounds and H5Pset_libver_bounds. - - (BMR, 2015/04/06, Part of HDFFV-9167) - - - New Wrappers to Get the Object Header's Version - - The following wrappers are added to class H5::CommonFG - Returns the object header version of an object in a file or group, - given the object's name. - - unsigned childObjVersion(const char* objname) const; - unsigned childObjVersion(const H5std_string& objname) const; - - (BMR, 2015/04/06) - - - New DataType Constructor - - Added a DataType constructor that takes a PredType object, and this - constructor will invoke H5Tcopy to generate another datatype id - from a predefined datatype. - - (BMR, 2015/04/06) - - -Support for New Platforms, Languages, and Compilers -=================================================== - - Support for Linux 3.10.0-123.20.1.el7 added (LK - 2015/04/01) - - Support for Mac OS X Yosemite 10.10 added (AKC - 2015/03/04, HDFFV-9007) - - Support for AIX 6.1 added and AIX 5.3 is retired. (AKC - 2015/01/09) - -Bug Fixes since HDF5-1.8.14 -=========================== - - Configuration - ------------- - - Make uninstall generated "test: argument expected". - The error is due to $EXAMPLETOPDIR is used without setting a value first. - - Fixed by assign it with the proper value. - - (AKC - 2015/04/29, HDFFV-9298) - - - Windows Installer Incorrect Display of PATH Environment Variable - - In the Windows installer, the dialog box where the user can elect to - add the product's bin path to the %PATH% environment variable displayed - an incorrect path. This path was missing the C:\Program Files part - and used the POSIX file separator '/' before the bin (<path>/bin, - instead of <path>\bin). - - The dialog box text was changed to simply say that the product's bin - path would be added instead of explicitly displaying the path. - This is in line with most installers. The reason for not fixing the - displayed path instead is that it is difficult to pass the correct - path from CPack to the NSIS installer for display. - - Note that this was never a code issue - it was just a display - problem. The installer always did the right thing when updating the - environment variable. - - (DER - 2014/11/14, HDFFV-9016) - - Library - ------- - - Incorrect Usage of List in CMake COMPILE_DEFINITIONS set_property - - The CMake command set_property with COMPILE_DEFINITIONS property - needs a quoted semi-colon separated list of values. CMake will - transform the list to a series of -D{value} for the compile. - - (ADB - 2014/12/09, HDFV-9041) - - - Fixed Compile Errors on Windows w/ Visual Studio and CMake When - UNICODE is Defined - - The HDF5 Library could not be built on Windows with Visual Studio when - UNICODE was defined. This was due to the incorrect use of the TEXT() - macro and some Win32 API functions that take TCHAR parameters. The faulty - code was a part of the filter plugin functionality. This was a - compile-time error that only affected users who build HDF5 from source - and define UNICODE, usually when HDF5 is being built as a part of a - larger product. There were no run-time effects. - - These errors caused no problems when UNICODE was not defined. HDF5 is - normally not built with UNICODE defined and the binaries were - unaffected. - - The fix was to remove the TEXT() macro and explicitly use the - 'A' form of the Win32 API calls, which expect char strings instead of - wchar_t strings. - - Note that HDF5 currently does not support Unicode file paths on Windows. - - (DER - 2015/02/22, HDFFV-8927) - - - Addition of Error Tracing Functionality to Several C API Calls - - A bug in a text processing script caused API calls that return a - pointer to not receive error tracing macros/functionality. - - The bug has been corrected and error tracing functionality has been - added to the affected API calls. These functions will now correctly - print trace information when library errors are encountered. - - (DER - 2015/02/26, HDFFV-9141) - - - H5Rdereference Now Checks for HADDR_UNDEF or Uninitialized References - - When passed HADDR_UNDEF or uninitialized references, the previous - behavior of H5Rdereference was to continue to process the reference - as a valid address. - - H5Rdereference was changed to return immediately (with an error - message) if the references are HADDR_UNDEF or uninitialized. - - (MSB - 2015/3/10, HDFFV-7959) - - - Fixed Bugs in H5Sextent_copy - - H5Sextent_copy would not free the previous extent, resulting in a memory - leak. Also, H5Sextent_copy would not update the number of elements - selected if the selection was "all", causing various problems. These - issues have been fixed. - - (NAF - 2015/04/02) - - - Parallel Library - ---------------- - - Fixed a Potential Memory Error - - Fixed a potential memory error when performing parallel I/O on a - dataset with a single chunk, and at least one process has nothing - to do. - - (NAF - 2015/02/16) - - - Parallel Test Problem Fixed - - Fixed problem with parallel tests where they failed beyond a - certain number of ranks. All tests should work for any arbitrary - number of ranks. - - (MSC - 2014/11/06, HDFFV-1027,8962,8963) - - - MPE Support - - Enabling MPE was causing HDF5 build to fail. Support for it was - dropped at some point in time. - - Fixed problem with enabling MPE. Users should use the community - maintained MPE on github (http://git.mpich.org/mpe.git/). - - (MSC - 2015/02/20, HDFFV-9135) - - Performance - ------------- - - None - - Tools - ----- - - h5repack crashed on enumerated 8-bit type. - - Previous version 1.8.14 introduced an error that caused the reading - of enumerated 8-bit type nested in compound type to fail. - - Fixed library code responsible for reading the particular type. - (AKC - 2015.03/31, HDFFV-8667) - - - h52gif crashed non-8bit images. - - h52gif crashed if instructed to convert images other than 8bit images. - - h52gif could handle only 8bit images. Added code to detect non-8bit - images and flag them as failure. Update tool document page to reflect - the limit. - (AKC - 2015/03/31, HDFFV-8957) - - - perform/benchpar.c retired. - - benchpar.c has not been built for a long time and its original purpose - is not needed any more. - (AKC - 2014/12/19, HDFFV-8156) - - - Source perform/ directory moved to tools/perform. - The perform directory is moved to tools/perform for easier maintenance. - (AKC - 2014/12/17, HDFFV-9046) - - Fortran API - ------------ - - Fortran Fails with --enable-fortran2003 and Intel 15.x Compilers - - Added BIND(C) to the offending APIs. - - The Fortran Library (--enable-fortran2003) now works using Intel 15.x - without the need for any additional compilers flags. - - (MSB - 2015/1/26, HDFFV-9049) - - - h5tenum_insert_f Does Not Work with Default 8 Byte Integers - (xlf compiler) - - In the Fortran 90 API, 'value' is no longer cast into the C int type. - Therefore, if h5tenum_insert_f is passed an 8 byte integer (via -i8) - then 'value' is written as the same type as the default Fortran - integer type (which can be 8 bytes). - - A new Fortran 2003 API was added which is more in line with the C - API and users are strongly encouraged to use the Fortran 2003 API - instead of the Fortran 90 API. - - SUBROUTINE h5tenum_insert_f(type_id, name, value, hdferr) - INTEGER(HID_T) , INTENT(IN) :: type_id - CHARACTER(LEN=*), INTENT(IN) :: name - TYPE(C_PTR) , INTENT(IN) :: value - INTEGER, INTENT(OUT) :: hdferr - - (MSB - 2015/2/19, HDFFV-8908) - - - Some Fortran APIs Never Returned the Error State - - Some Fortran APIs never returned the error state: they - would always return a positive number. The APIs include - the following: - - h5fget_file_image_f - h5lget_name_by_idx_f - h5oget_comment_by_name_f - - They were corrected to return a negative number as described in - the Reference Manual if an error occurred. - - (MSB - 2015/3/19, HDF5-239) - - - Fixed h5pget_class_f - - h5pget_class_f never correlated the class identifier to the property - list class name as indicated in the HDF5 Reference Manual; it instead - returned a property list class identifier as an INTEGER. The INTEGER - needed to be of type INTEGER(HID_T) to be correct. - - The h5pget_class_f API was changed to return an INTEGER(HID_T) - property list class identifier instead of an INTEGER. This mimics the - intended behavior of the C API. - - (MSB - 2015/3/16, HDFFV5-9162) - - C++ API - ------ - - Combined Two H5File::getObjCount Overloaded Methods - - The following two methods - - ssize_t getObjCount(unsigned types) const; - ssize_t getObjCount() const; - - were combined into one: - - ssize_t getObjCount(unsigned types = H5F_OBJ_ALL) const; - - (BMR - 2015/04/06) - - - Many Warnings Were Removed - - Many warnings such as conversion, unused variables, missing base - class initialization, and initializing base classes in wrong order - were removed. - - (BMR, 2015/04/06) - - - Functionality Deprecation - - The following two constructors of classes AbstractDs, IdComponent, - H5Location, and H5Object are no longer appropriate after the data member - "id" had been moved from IdComponent to the sub-classes in previous - releases. - - <Classname>(const hid_t h5_id); - <Classname>(const <Classname>& original); - - The copy constructors were no-op and removed in 1.8.15. The other - constructors will be removed from 1.10 release, and then from 1.8.17 - if their removal does not cause any problems. - - (BMR, 2015-04-06) - - - High-Level APIs: - ------ - - Suppress Warnings from Flex/Bison-generated Code - - Warning suppression #pragmas, etc. have been added to H5LTparse.c and - H5LTanalyze.c. We have no control over this code since it's created by - a generator. - - (DER - 2015/03/08 - HDFFV-9149) - - - Changed hdf5_hl.h to Include the HDF5 Main Library "hdf5.h" - - User's no longer need to include both hdf5_hl.h and hdf5.h - - (MSB - 2015/2/14, HDFFV-8685) - - - - H5PTcreate_fl Does Not Convert to Memory Datatype - - H5PTcreate_fl now converts to the table's native memory datatype - to fix the problem of handling BE and LE packet tables. - - (MSB - 2015/2/26 - HDFFV-9042) - - - Fix for H5LT Attribute Functions - - H5LT attribute functions fail to create attributes whose name - is a substring of an existing attribute. - - H5LT attribute functions can now create attributes whose name - is a substring of an existing attribute. - - (MSB - 2015/2/24, HDFFV-9132) - - - Fortran High-Level APIs: - ------------------------ - - - Internal Library Fix for Missing Argument Declaration - - In Interface block for h5tbmake_table_c, "max_char_size_field_names" - is listed as an input, but in the argument definitions it is - "INTEGER :: max_char_size". This caused no known problems with the - Fortran HL API. - - Fixed missing argument definition. - - (MSB - 2015/2/18, HDFFV-8559) - - - Testing - ------- - - None - - -Supported Platforms -=================== -The following platforms are supported and have been tested for this release. -They are built with the configure process unless specified otherwise. - - AIX 6.1 xlc/xlc_r 10.1.0.5 - (NASA G-ADA) xlC/xlC_r 10.1.0.5 - xlf90/xlf90_r 12.1.0.6 - - Linux 2.6.18-308.13.1.el5PAE GNU C (gcc), Fortran (gfortran), C++ (g++) - #1 SMP i686 i686 i386 compilers for 32-bit applications; - (jam) Version 4.1.2 20080704 (Red Hat 4.1.2-55) - Version 4.8.4, 4.9.2 - PGI C, Fortran, C++ Compilers for 32-bit - applications; - Version 14.10-0 - Intel(R) C, C++, Fortran Compiler for 32-bit - applications; - Version 15.0.1.133 (Build 20141023) - - Linux 2.6.18-371.6.1.el5 GNU C (gcc), Fortran (gfortran), C++ (g++) - #1 SMP x86_64 GNU/Linux compilers for 64-bit applications; - (koala) Version 4.1.2 20080704 (Red Hat 4.1.2-55) - Version 4.8.4, 4.9.2 - Intel(R) C, C++, Fortran Compilers for - applications running on Intel(R) 64; - Version 15.0.1.133 Build 20141023 - - Linux 2.6.32-431.11.2.el6 GNU C (gcc), Fortran (gfortran), C++ (g++) - #1 SMP x86_64 GNU/Linux compilers: - (platypus) Version 4.4.7 20120313 - Version 4.8.2, Version 4.9.2 - PGI C, Fortran, C++ for 64-bit target on - x86-64; - Version 14.10-0 - Intel(R) C (icc), C++ (icpc), Fortran (icc) - compilers: - Version 15.0.1.133 Build 20141023 - - Linux 3.10.0-123.20.1.el7 GNU C (gcc), Fortran (gfortran), C++ (g++) - #1 SMP x86_64 GNU/Linux compilers: - (moohan) Version 4.8.2 20140120 (Red Hat 4.8.2-16) - Intel(R) C Intel(R) 64 Compiler XE for - applications running on Intel(R) 64, - Version 15.0.1.133 Build 20141023 - - Linux 2.6.32-431.29.2.el6.ppc64 gcc (GCC) 4.4.7 20120313 (Red Hat 4.4.7-4) - #1 SMP ppc64 GNU/Linux g++ (GCC) 4.4.7 20120313 (Red Hat 4.4.7-4) - (ostrich) GNU Fortran (GCC) 4.4.7 20120313 (Red Hat 4.4.7-4) - IBM XL C/C++ V13.1 - IBM XL Fortran V15.1 - - 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 2008 (cmake) - Visual Studio 2010 w/ Intel Fortran 14 (cmake) - Visual Studio 2012 w/ Intel Fortran 15 (cmake) - Visual Studio 2013 w/ Intel Fortran 15 (cmake) - Cygwin(CYGWIN_NT-6.1 1.7.34(0.285/5/3) gcc(4.9.2) compiler and gfortran) - (cmake and autotools) - - Windows 7 x64 Visual Studio 2008 (cmake) - Visual Studio 2010 w/ Intel Fortran 14 (cmake) - Visual Studio 2012 w/ Intel Fortran 15 (cmake) - Visual Studio 2013 w/ Intel Fortran 15 (cmake) - - Windows 8.1 Visual Studio 2012 w/ Intel Fortran 15 (cmake) - Visual Studio 2013 w/ Intel Fortran 15 (cmake) - - Windows 8.1 x64 Visual Studio 2012 w/ Intel Fortran 15 (cmake) - Visual Studio 2013 w/ Intel Fortran 15 (cmake) - - Mac OS X Mt. Lion 10.8.5 Apple clang/clang++ version 5.1 from Xcode 5.1 - 64-bit gfortran GNU Fortran (GCC) 4.8.2 - (swallow/kite) Intel icc/icpc/ifort version 14.0.2 - - Mac OS X Mavericks 10.9.5 Apple clang/clang++ version 6.0 from Xcode 6.1.1 - 64-bit gfortran GNU Fortran (GCC) 4.8.2 - (wren/quail) Intel icc/icpc/ifort version 14.0.2 - - Mac OS X Yosemite 10.10.2 Apple clang/clang++ version 6.0 from Xcode 6.1.1 - 64-bit gfortran GNU Fortran (GCC) 4.9.2 - (osx1010dev/osx1010test) Intel icc/icpc/ifort version 15.0.1 - - -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 -SunOS 5.11 32-bit n y/y n y y y -SunOS 5.11 64-bit n y/y n y y y -Windows 7 y y/y n y y y -Windows 7 x64 y y/y n y y y -Windows 7 Cygwin n y/y n y y n -Windows 8.1 n y/y n y y y -Windows 8.1 x64 n 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 y -Mac OS X Yosemeti 10.10.2 64-bit n y/y n y y y -AIX 6.1 32- and 64-bit n y/n n y y y -CentOS 5.9 Linux 2.6.18-308 i686 GNU y y/y y y y y -CentOS 5.9 Linux 2.6.18-308 i686 Intel n y/y n y y y -CentOS 5.9 Linux 2.6.18-308 i686 PGI n y/y n y y y -CentOS 5.9 Linux 2.6.18 x86_64 GNU n y/y n y y y -CentOS 5.9 Linux 2.6.18 x86_64 Intel n y/y n y y y -CentOS 6.4 Linux 2.6.32 x86_64 GNU y y/y y y y y -CentOS 6.4 Linux 2.6.32 x86_64 Intel n y/y n y y y -CentOS 6.4 Linux 2.6.32 x86_64 PGI n y/y n y y y -CentOS 7.0 Linux 3.10.0 x86_64 GNU y y/y y y y y -CentOS 7.0 Linux 3.10.0 x86_64 Intel n y/y n y y y -Linux 2.6.32-431.11.2.el6.ppc64 n y/n n y y y - -Platform Shared Shared Shared Thread- - C libs F90 libs C++ libs safe -SunOS 5.11 32-bit y y y y -SunOS 5.11 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 8.1 y y y y -Windows 8.1 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 Yosemeti 10.10.2 64-bit y n y y -AIX 6.1 32- and 64-bit y n n y -CentOS 5.9 Linux 2.6.18-308 i686 GNU y y y y -CentOS 5.9 Linux 2.6.18-308 i686 Intel y y y n -CentOS 5.9 Linux 2.6.18-308 i686 PGI y y y n -CentOS 5.9 Linux 2.6.18 x86_64 GNU y y y y -CentOS 5.9 Linux 2.6.18 x86_64 Intel y y y n -CentOS 6.4 Linux 2.6.32 x86_64 GNU y y y n -CentOS 6.4 Linux 2.6.32 x86_64 Intel y y y n -CentOS 6.4 Linux 2.6.32 x86_64 PGI y y y n -CentOS 7.0 Linux 3.10.0 x86_64 GNU y y y n -CentOS 7.0 Linux 3.10.0 x86_64 Intel y y y n -Linux 2.6.32-431.11.2.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 2.6.18-308.13.1.el5PAE MPICH mpich 3.1.3 compiled with - #1 SMP i686 i686 i386 gcc 4.9.2 and gfortran 4.9.2 - (jam) g95 (GCC 4.0.3 (g95 0.94!) - - Linux 2.6.18-431.11.2.el6 MPICH mpich 3.1.3 compiled with - #1 SMP x86_64 GNU/Linux gcc 4.9.2 and gfortran 4.9.2 - (platypus) g95 (GCC 4.0.3 (g95 0.94!) - - FreeBSD 8.2-STABLE i386 gcc 4.5.4 [FreeBSD] 20110526 - (loyalty) gcc 4.6.1 20110527 - g++ 4.6.1 20110527 - gfortran 4.6.1 20110527 - - FreeBSD 8.2-STABLE amd64 gcc 4.5.4 [FreeBSD] 20110526 - (freedom) gcc 4.6.1 20110527 - g++ 4.6.1 20110527 - gfortran 4.6.1 20110527 - - Debian7.5.0 3.2.0-4-amd64 #1 SMP Debian 3.2.51-1 x86_64 GNU/Linux - gcc (Debian 4.7.2-5) 4.7.2 - GNU Fortran (Debian 4.7.2-5) 4.7.2 - (cmake and autotools) - - Fedora20 3.15.3-200.fc20.x86_64 #1 SMP x86_64 x86_64 x86_64 GNU/Linux - gcc (GCC) 4.8.3 20140624 (Red Hat 4.8.3-1) - GNU Fortran (GCC) 4.8.3 20140624 (Red Hat 4.8.3-1) - (cmake and autotools) - - SUSE 13.1 3.11.10-17-desktop #1 SMP PREEMPT x86_64 x86_64 x86_64 GNU/Linux - gcc (SUSE Linux) 4.8.1 - GNU Fortran (SUSE Linux) 4.8.1 - (cmake and autotools) - - Ubuntu 14.04 3.13.0-35-generic #62-Ubuntu SMP x86_64 GNU/Linux - gcc (Ubuntu/Linaro 4.9.1-0ubuntu1) 4.9.1 - GNU Fortran (Ubuntu/Linaro 4.9.1-0ubuntu1) 4.9.1 - (cmake and autotools) - - hopper.nersc.gov PrgEnv-gnu/5.2.40 - gcc (GCC) 4.9.2 20141030 (Cray Inc.) - GNU Fortran (GCC) 4.9.2 20141030 (Cray Inc.) - g++ (GCC) 4.9.2 20141030 (Cray Inc.) - - -Known Problems -============== -* On Windows platforms in debug configurations, the VFD flush1 tests will fail - with the split and multi VFD drivers. These tests will display a modal debug - dialog which must be answered or wait for the test timeout to expire. - (ADB - 2014/06/23 - HDFFV-8851) - -* CLANG compiler with the options -fcatch-undefined-behavior and -ftrapv - catches some undefined behavior in the alignment algorithm of the macro DETECT_I - in H5detect.c (Issue 8147). Since the algorithm is trying to detect the alignment - of integers, ideally the flag -fcatch-undefined-behavior shouldn't to be used for - H5detect.c. In the future, we can separate flags for H5detect.c from the rest of - the library. (SLU - 2013/10/16) - -* Make provided by Solaris fails in "make check". Solaris users should use - gmake to build and install the HDF5 software. (AKC - 2013/10/08 - HDFFV-8534) - -* The C++ and FORTRAN bindings are not currently working on FreeBSD with the - native release 8.2 compilers (4.2.1), but are working with gcc 4.6 from the - ports (and probably gcc releases after that). - (QAK - 2012/10/19) - -* The following h5dump test case fails in BG/P machines (and potentially other - machines that use a command script to launch executables): - - h5dump --no-compact-subset -d "AHFINDERDIRECT::ah_centroid_t[0] it=0 tl=0" - tno-subset.h5 - - This is due to the embedded spaces in the dataset name being interpreted - by the command script launcher as meta-characters, thus passing three - arguments to h5dump's -d flag. The command passes if run by hand, just - not via the test script. - (AKC - 2012/05/03) - -* The STDIO VFD does not work on some architectures, possibly due to 32/64 - bit or large file issues. The basic STDIO VFD test is known to fail on - 64-bit SunOS 5.10 on SPARC when built with -m64 and 32-bit OS X/Darwin - 10.7.0. The STDIO VFD test has been disabled while we investigate and - a fix should appear in a future release. - (DER - 2011/10/14 - HDFFV-8235) - -* h5diff can report inconsistent results when comparing datasets of enum type - that contain invalid values. This is due to how enum types are handled in - the library and will be addressed in a future release. - (DER - 2011/10/14 - HDFFV-7527) - -* The links test can fail under the stdio VFD due to some issues with external - links. This will be investigated and fixed in a future release. - (DER - 2011/10/14 - HDFFV-7768) - -* After the shared library support was fixed for some bugs, it was discovered - that "make prefix=XXX install" no longer works for shared libraries. It - still works correctly for static libraries. Therefore, if you want to - install the HDF5 shared libraries in a location such as /usr/local/hdf5, - you need to specify the location via the --prefix option during configure - time. E.g, ./configure --prefix=/usr/local/hdf5 ... - (AKC - 2011/05/07 - HDFFV-7583) - -* The parallel test, t_shapesame, in testpar/, may run for a long time and may - be terminated by the alarm signal. If that happens, one can increase the - alarm seconds (default is 1200 seconds = 20 minutes) by setting the - environment variable, $HDF5_ALARM_SECONDS, to a larger value such as 3600 - (60 minutes). Note that the t_shapesame test may fail in some systems - (see the "While working on the 1.8.6 release..." problem below). If - it does, it will waste more time if $HDF5_ALARM_SECONDS is set - to a larger value. - (AKC - 2011/05/07) - -* Shared Fortran libraries are not quite working on AIX. While they are - generated when --enable-shared is specified, the fortran and hl/fortran - tests fail. the issue. HL and C++ shared libraries should now be - working as intended, however. - (MAM - 2011/04/20) - -* While working on the 1.8.6 release of HDF5, a bug was discovered that can - occur when reading from a dataset in parallel shortly after it has been - written to collectively. The issue was exposed by a new test in the parallel - HDF5 test suite, but had existed before that. We believe the problem lies with - certain MPI implementations and/or file systems. - - We have provided a pure MPI test program, as well as a standalone HDF5 - program, that can be used to determine if this is an issue on your system. - They should be run across multiple nodes with a varying number of processes. - These programs can be found at: - http://www.hdfgroup.org/ftp/HDF5/examples/known_problems/ - (NAF - 2011/01/19) - -* All the VFL drivers aren't backward compatible. In H5FDpublic.h, the - structure H5FD_class_t changed in 1.8. There is new parameter added to - get_eoa and set_eoa callback functions. A new callback function - get_type_map was added in. The public function H5FDrealloc was taken - out in 1.8. The problem only happens when users define their own driver - for 1.6 and try to plug in 1.8 library. Because there's only one user - complaining about it, we (Elena, Quincey, and I) decided to leave it as - it is (see bug report #1279). Quincey will make a plan for 1.10. - (SLU - 2010/02/02) - -* The --enable-static-exec configure flag will only statically link libraries - if the static version of that library is present. If only the shared version - of a library exists (i.e., most system libraries on Solaris, AIX, and Mac, - for example, only have shared versions), the flag should still result in a - successful compilation, but note that the installed executables will not be - fully static. Thus, the only guarantee on these systems is that the - executable is statically linked with just the HDF5 library. - (MAM - 2009/11/04) - -* A dataset created or rewritten with a v1.6.3 library or after cannot be read - with the v1.6.2 library or before when the Fletcher32 EDC filter is enabled. - There was a bug in the calculation of the Fletcher32 checksum in the - library before v1.6.3; the checksum value was not consistent between big- - endian and little-endian systems. This bug was fixed in Release 1.6.3. - However, after fixing the bug, the checksum value was no longer the same as - before on little-endian system. Library releases after 1.6.4 can still read - datasets created or rewritten with an HDF5 library of v1.6.2 or before. - (SLU - 2005/06/30) - - -%%%%1.8.14%%%% - - -HDF5 version 1.8.14 released on 2014-11-12 -================================================================================ - -INTRODUCTION -============ - -This document describes the differences between HDF5-1.8.13 and -HDF5-1.8.14, and contains information on the platforms tested and -known problems in HDF5-1.8.14. - -All new and modified APIs are listed in the "HDF5 Software Changes -from Release to Release" document along with details about previous -releases at: - - http://www.hdfgroup.org/HDF5/doc/ADGuide/Changes.html - -Links to the HDF5 1.8.14 source code, documentation, and additional materials -can be found on the HDF5 web page at: - - http://www.hdfgroup.org/products/hdf5/ - -The HDF5 1.8.14 release can be obtained from: - - http://www.hdfgroup.org/HDF5/release/obtain5.html - -User documentation for 1.8.14 can be accessed directly at this location: - - http://www.hdfgroup.org/HDF5/doc/ - -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, Languages, and Compilers -- Bug Fixes since HDF5-1.8.13 -- Supported Platforms -- Supported Configuration Features Summary -- More Tested Platforms -- Known Problems - - -New Features -============ - - Configuration - ------------- - - bin/cmakehdf5 configures, builds and installs C, C++, Fortran and High - level API's. (It used to build the C API only). - (AKC 2014/10/17 HDFFV-8932). - - Library - ------- - - None - - Parallel Library - ---------------- - - Chunk Fill Writes Changed to Collective - - Slow performance in chunk fill writes. Chunk fills - in the past were written independently by rank 0 one block - at a time. - - Optimized the chunk fill write algorithm so that all - chunk fill values will be written collectively in a single MPI-IO - call. This should show a great performance improvement when - creating chunked datasets in parallel when the chunk dimensions - are fairly small. - - (MSC - 2014/08/22, HDFFV-8878) - - Tools - ----- - - None - - High-level APIs - --------------- - - None - - Fortran API - ----------- - - None - - C++ API - ------- - - Initialization of Object IDs - - The data member "id" in classes that represent HDF5 objects were - initialized to 0, which caused problem for some users. - - Replaced 0 with H5I_INVALID_HID to initialize these "id"s. For the - PropList class, H5P_DEFAULT is used instead of H5I_INVALID_HID. - - (BMR - 2014/09/30, HDFFV-4259) - - - -Support for New Platforms, Languages, and Compilers -=================================================== - - None - -Bug Fixes since HDF5-1.8.13 -=========================== - - Configuration - ------------- - - CMake and SVN URLs - - The SVN URLs will be different when the HDF Group domain name changes. - - Removed the SVN URL references in the cacheinit.cmake and release_docs files. - - (ADB - 2014/10/27, HDFFV-8953) - - - CMake Packaging - - A Fortran module was not generated if the compiler was not F2003 - compliant. - - Removed the module name from the package list of Fortran modules because - that module was never generated. This was only an issue for Fortran - compilers that are not F2003 compatible. - - (ADB - 2014/10/16, HDFFV-8932) - - - Shared Library Interface Version Number (soname) - - In order to increase the maintainability of HDF5, an architectural - change was made which required the renaming of several public symbols in - H5Ppublic.h. - - The shared library interface version number ("soname") has been increased - on account of these changes. For a full list of the changed symbols, see - the interface compatibility report, which is available as a link off of - the 'HDF5 Software Changes from Release to Release' document: - - http://www.hdfgroup.org/HDF5/doc/ADGuide/Changes.html - - (AKC - 2014/10/03, HDFFV-8937) - - - Configure Settings for Mac OSX Need Defaults for PROD_XXX, DEBUG_XXX, - and PROFILE_XXX - - The configure setting files for Mac OSX (config/apple) did not - have the default settings of PROD_XXX, DEBUG_XXX, PROFILE_XXX. - - Added the default settings. Mac platforms now builds library with - "-O3" optimization when the default clang compiler is used. - - (AKC - 2014/10/01, HDFFV-8933) - - - CMake ConfigureChecks - - Two include files were missing from two C tests. - - Propagated the configure test changes to H5_LDOUBLE_TO_INTEGER_WORKS_TEST - and H5_ULLONG_TO_LDOUBLE_PRECISION_TEST to ConfigureChecks.cmake (added - stdlib.h and string.h in the HDFTests.c file). - - (ADB - 2014/09/02 HDFFV-8845) - - - CMake Parallel Test Missing - - The source file was removed in the previous release but the parallel - test t_posix_compliant was not. - - Removed the t_posix_compliant parallel test from the library. - - (ADB - 2014/8/14 HDFFV-8880) - - - Autotools Reconfigure. Bison. Flex. - - The Bison and Flex files were out of date. - - Bison was upgraded to 2.7, and Flex was upgraded to 2.5.37. The - bin/reconfigure script now will execute Bison and Flex and update - the hl/src files. - - (ADB - 2014/06/16 HDFFV-8709) - - - Autotools Reconfigure. m4. - - The m4 macro processor was out of date. - - Reconfigured Autotools with m4 upgraded to 1.4.17. - - (ADB - 2014/06/12 HDFFV-8743) - - - Autotools: Modified configure to add an entry at the beginning of AM_LDFLAGS - for the hdf5 install directory. Without this entry the relink commands - invoked by "make install" to create libraries dependent on libhdf5.so added - a dependency on the first libhdf5.so found in any directory in AM_LDFLAGS - regardless of its version. (LRK - 2014/10/17 HDFFV-8944) - - - Changed Autotools Build Behavior. Fortran High-level Library. - - The Fortran high-level (HL) library did not compile if the default - size of a REAL is DOUBLE PRECISION; the build would fail during - compilation. - - Configure now checks to see if REAL is DOUBLE PRECISION, Fortran is - enabled, and HL library is enabled. If this is true, then configure - will stop with an error message. - - (MSB - 2014/8/11, HDFFV-8883/HDFFV-889) - - - - Library - ------- - - Fixed Identifier Management Code - - Opening an object returns an identifier; closing the object should - free up the identifier. A problem was found where the identifiers - were not being freed up correctly. - - Fixed the problem so that identifiers that have been used can be - used again after their object has been closed. - - (QAK - 2014/10/16, HDFFV-8930) - - - Removal of DllMain() from Static Windows Builds - - A DllMain() function was added in HDF5 1.8.13 in order to handle - win32 thread cleanup. The preprocessor #ifdefs around the DllMain - function allowed it to be compiled when the static library is built, - which is incorrect behavior that can cause linkage problems in - clients. - - The fix was to change the preprocessor #ifdefs to exclude compiling - DllMain() in static builds. Our DllMain function is now only - compiled when the shared, thread-safe library is built on Windows. - - (DER - 2014/06/13, HDFFV-8837) - - - Enforce Constraint on page_size Parameter in H5Pset_core_write_tracking() - - The reference manual states that the page_size parameter cannot be - zero. - - This change checks the page_size parameter to see it is zero and - returns an error code if it is. - - (DER - 2014/08/11, HDFFV-8891) - - - H5Ldelete_by_idx() fails on non-existent group name. - (MSC - 2014/07/31, HDFFV-8888) - - - H5Ldelete_by_idx() Seg Fault on Non-existent Group Name - - If a non-existent group name was used by H5Ldelete_by_idx(), a - segmentation fault would result. - - Bug was fixed. - - (MSC - 2014/07/31, HDFFV-8888) - - - Bug in Test When Building Parallel HDF5 on PVFS2 - - There was a bug in a test when building Parallel HDF5 on PVFS2. - - The build now uses MPI_File_get_size() instead of stat(). - - (MSC - 2014/07/14, HDFFV-8856) - - - MPI-IO Driver Tried to Allocate Space for Zero-length Dataset - - MPI-IO driver tried to allocate space for zero-length dataset - and asserts. - - Fixed driver and added a regression test. - - (MSC - 2014/07/03, HDFFV-8761) - - - Parallel Library - ---------------- - - None - - Performance - ------------- - - None - - Tools - ----- - - None - - Fortran API - ------- - - SIZEOF Replaced by C_SIZEOF and STORAGE_SIZE. - - The intrinsic function SIZEOF is non-standard and should be replaced with a - standard intrinsic function. - - If the F2008 intrinsic C_SIZEOF and STORAGE_SIZE are available, then they will - be used instead of the non-standard SIZEOF intrinsic, even when the SIZEOF - function is available. - - (MSB - 2014/6/16, HDFFV-8653) - - - Non-functional API: h5pget_fill_value_f - - The Fortran wrapper h5pget_fill_value_f was calling the wrong C API. - - The correct C API, H5Pget_fill_value, is now called by the Fortran - wrapper. - - (MSB - 2014/9/25, HDFFV-8879) - - - Interoperability with C HDF5: H5Literate and h5literate_f - - h5literate_f assumes the return value for the callback function to - be of type int (or int_f in C). However, in the C wrapper the return - value of H5Literate is type herr_t, and this could cause - interoperability issues. - - The callback function should be declared INTEGER(C_INT) for - portability. The tests were updated accordingly. - - (MSB - 2014/9/26, HDFFV-8909) - - - Interoperability with C HDF5: Constant INTEGER Parameters with the - H5FD Interface - - Wrong type cast of constant Fortran INTEGER parameters was used. - - The following parameter constant types were changed from INTEGER to - INTEGER(HID_T) to match the C types: H5FD_CORE, H5FD_FAMILY, H5FD_LOG, - H5FD_MPIO, H5FD_MULTI, H5FD_SEC2, and H5FD_STDIO. - - Other internal 'int' types where changed to 'hid_t'; these are - transparent to the user. - - (MSB - 2014/7/18, HDFFV-8748) - - C++ API - ------ - - Memory Leaks - - There were several potential memory leaks in the library due to - dynamically allocated strings not being freed when failure occurs. - - Applied user's patches to remove these potential memory leaks. - - (BMR - 2014/09/30, HDFFV-8928) - - - Disallow H5F_ACC_CREAT - - H5F_ACC_CREAT was included in the C++ API but the C library does not - allow it at this time. - - Removed this flag from the functions in H5File class. - - (BMR - 2014/09/29, HDFFV-8852) - - - Missing Flags in Documentation: H5F_ACC_RDONLY and H5F_ACC_RDWR - - The H5F_ACC_RDONLY and H5F_ACC_RDWR flags were missing from the - documentation of the H5File constructors. - - These two flags are now included in the documentation for opening - files. - - (BMR - 2014/09/29, HDFFV-8852) - - High-level APIs: - ------ - - Seg Faults in H5TBread_field_name and H5TBread_field_name_f - - When H5TBread_field_name or H5TBread_field_name_f were used to read a - field and if the name of the field was wrong, a segmentation fault - would result. - - Both C and Fortran APIs were fixed so they no longer seg fault if - the name of the field is wrong, and both APIs return a negative - value if the name of the field is wrong. - - (MSB - 2014/09/29, HDFFV-8912) - - - Possible Buffer Overflow in High-level (HL) APIs - - Multiple HL APIs (H5DSis_scale is one example) had issues: - (1) The datatype from the file was re-used as the memory datatype, - and - (2) No effort was made to ensure that strings were actually - null-terminated. - - All of the HL routines now check for NULL pointers, for null-terminated - strings, and to see if string buffers are short enough not to overflow - the buffer. The minimum length of the buffers is now used in strncmp - to avoid overflow. - - (MSB - 2014/9/29, HDFFV-8670) - - - Behavior Change of H5LTdtype_to_text - - If a user buffer was passed in to H5LTdtype_to_text along with the - length, then the function would not truncate at the end of the - buffer, but would exceed the end of the user buffer. - - H5LTdtype_to_text was changed to truncate the string if the user - buffer is too small. - - (MSB - 2014/9/29, HDFFV-8855) - - Fortran High-level APIs: - ------ - - See entry for HDFFV-8912 above. - - Testing - ------- - - A subtest in parallel h5diff (ph5diff) testing was bypassed for the - local Linux 32 machine due to unknown issue in the previous version of - Mpich. The failure no long exists in the current Mpich. Therefore the - bypass is removed. (AKC - 2014/11/03 HDFFV-8954) - - - Fixed incorrect exit code values (was -1) in testframe which is commonly - used by several test programs. (AKC - 2014/07/22 HDFFV-8881) - - - Fixed Incorrect Exit Code Values in Testframe - The testframe which is commonly used by several test programs - had some incorrect exit code values. Fixed the incorrect exit code - values. (AKC - 2014/07/22, HDFFV-8881) - -Supported Platforms -=================== -The following platforms are supported and have been tested for this release. -They are built with the configure process unless specified otherwise. - - AIX 5.3 xlc 10.1.0.5 - (NASA G-ADA) xlC 10.1.0.5 - xlf90 12.1.0.6 - - Linux 2.6.18-308.13.1.el5PAE GNU C (gcc), Fortran (gfortran), C++ (g++) - #1 SMP i686 i686 i386 compilers for 32-bit applications; - (jam) Version 4.1.2 20080704 (Red Hat 4.1.2-54) - Version 4.8.2 - PGI C, Fortran, C++ Compilers for 32-bit - applications; - Version 13.7-0 - Intel(R) C, C++, Fortran Compiler for 32-bit - applications; - Version 14.0.2 (Build 20140120) - - Linux 2.6.18-371.6.1.el5 GNU C (gcc), Fortran (gfortran), C++ (g++) - #1 SMP x86_64 GNU/Linux compilers for 64-bit applications; - (koala) Version 4.1.2 20080704 (Red Hat 4.1.2-54) - Version 4.8.2 - Intel(R) C, C++, Fortran Compilers for - applications running on Intel(R) 64; - Version 14.0.2 (Build 20140120) - - Linux 2.6.32-431.11.2.el6 GNU C (gcc), Fortran (gfortran), C++ (g++) - #1 SMP x86_64 GNU/Linux compilers: - (platypus) Version 4.4.7 20120313 - Version 4.8.2 - PGI C, Fortran, C++ for 64-bit target on - x86-64; - Version 13.7-0 - Intel(R) C (icc), C++ (icpc), Fortran (icc) - compilers: - Version 14.0.2 (Build 20140120) - - Linux 2.6.32-431.29.2.el6.ppc64 gcc (GCC) 4.4.7 20120313 (Red Hat 4.4.7-4) - #1 SMP ppc64 GNU/Linux g++ (GCC) 4.4.7 20120313 (Red Hat 4.4.7-4) - (ostrich) GNU Fortran (GCC) 4.4.7 20120313 (Red Hat 4.4.7-4) - IBM XL C/C++ V13.1 - IBM XL Fortran V15.1 - - 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 2008 (cmake) - Visual Studio 2010 w/ Intel Fortran 14 (cmake) - Visual Studio 2012 w/ Intel Fortran 14 (cmake) - Visual Studio 2013 w/ Intel Fortran 14 (cmake) - Cygwin(CYGWIN_NT-6.1 1.7.32(0.274/5/3) gcc(4.8.3) compiler and gfortran) - (cmake and autotools) - - Windows 7 x64 Visual Studio 2008 (cmake) - Visual Studio 2010 w/ Intel Fortran 14 (cmake) - Visual Studio 2012 w/ Intel Fortran 14 (cmake) - Visual Studio 2013 w/ Intel Fortran 14 (cmake) - - Windows 8.1 Visual Studio 2012 w/ Intel Fortran 14 (cmake) - Visual Studio 2013 w/ Intel Fortran 14 (cmake) - - Windows 8.1 x64 Visual Studio 2012 w/ Intel Fortran 14 (cmake) - Visual Studio 2013 w/ Intel Fortran 14 (cmake) - - Mac OS X Lion 10.7.5 Apple clang/clang++ version 3.0 from Xcode 4.6.1 - 64-bit gfortran GNU Fortran (GCC) 4.8.2 - (duck) Intel icc/icpc/ifort version 13.0.3 - - Mac OS X Mt. Lion 10.8.5 Apple clang/clang++ version 5.1 from Xcode 5.1 - 64-bit gfortran GNU Fortran (GCC) 4.8.2 - (swallow/kite) Intel icc/icpc/ifort version 14.0.2 - - Mac OS X Mavericks 10.9.5 Apple clang/clang++ version 6.0 from Xcode 6.0.1 - 64-bit gfortran GNU Fortran (GCC) 4.8.2 - (wren) Intel icc/icpc/ifort version 14.0.2 - - -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/y n y y y -Windows 7 y y/y n y y y -Windows 7 x64 y y/y n y y y -Windows 7 Cygwin n y/y n y y n -Windows 8.1 n y/y n y y y -Windows 8.1 x64 n y/y n y y y -Mac OS X Lion 10.7.5 64-bit n 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 ? -AIX 5.3 32- and 64-bit n y/n n y y y -CentOS 5.9 Linux 2.6.18-308 i686 GNU y y/y y y y y -CentOS 5.9 Linux 2.6.18-308 i686 Intel n y/y n y y y -CentOS 5.9 Linux 2.6.18-308 i686 PGI n y/y n y y y -CentOS 5.9 Linux 2.6.18 x86_64 GNU n y/y n y y y -CentOS 5.9 Linux 2.6.18 x86_64 Intel n y/y n y y y -CentOS 6.4 Linux 2.6.32 x86_64 GNU y y/y y y y y -CentOS 6.4 Linux 2.6.32 x86_64 Intel n y/y n y y y -CentOS 6.4 Linux 2.6.32 x86_64 PGI n y/y n y y y -Linux 2.6.32-431.11.2.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 8.1 y y y y -Windows 8.1 x64 y y y y -Mac OS X Lion 10.7.5 64-bit y n 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 -AIX 5.3 32- and 64-bit y n n y -CentOS 5.9 Linux 2.6.18-308 i686 GNU y y y y -CentOS 5.9 Linux 2.6.18-308 i686 Intel y y y n -CentOS 5.9 Linux 2.6.18-308 i686 PGI y y y n -CentOS 5.9 Linux 2.6.18 x86_64 GNU y y y y -CentOS 5.9 Linux 2.6.18 x86_64 Intel y y y n -CentOS 6.4 Linux 2.6.32 x86_64 GNU y y y n -CentOS 6.4 Linux 2.6.32 x86_64 Intel y y y n -CentOS 6.4 Linux 2.6.32 x86_64 PGI y y y n -Linux 2.6.32-431.11.2.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 2.6.18-308.13.1.el5PAE MPICH mpich 3.1.2 compiled with - #1 SMP i686 i686 i386 gcc 4.9.1 and gfortran 4.9.1 - (jam) g95 (GCC 4.0.3 (g95 0.94!) - - Linux 2.6.18-431.11.2.el6 MPICH mpich 3.1.2 compiled with - #1 SMP x86_64 GNU/Linux gcc 4.9.1 and gfortran 4.9.1 - (platypus) g95 (GCC 4.0.3 (g95 0.94!) - - FreeBSD 8.2-STABLE i386 gcc 4.5.4 [FreeBSD] 20110526 - (loyalty) gcc 4.6.1 20110527 - g++ 4.6.1 20110527 - gfortran 4.6.1 20110527 - - FreeBSD 8.2-STABLE amd64 gcc 4.5.4 [FreeBSD] 20110526 - (freedom) gcc 4.6.1 20110527 - g++ 4.6.1 20110527 - gfortran 4.6.1 20110527 - - Debian7.5.0 3.2.0-4-amd64 #1 SMP Debian 3.2.51-1 x86_64 GNU/Linux - gcc (Debian 4.7.2-5) 4.7.2 - GNU Fortran (Debian 4.7.2-5) 4.7.2 - (cmake and autotools) - - Fedora20 3.15.3-200.fc20.x86_64 #1 SMP x86_64 x86_64 x86_64 GNU/Linux - gcc (GCC) 4.8.3 20140624 (Red Hat 4.8.3-1) - GNU Fortran (GCC) 4.8.3 20140624 (Red Hat 4.8.3-1) - (cmake and autotools) - - SUSE 13.1 3.11.10-17-desktop #1 SMP PREEMPT x86_64 x86_64 x86_64 GNU/Linux - gcc (SUSE Linux) 4.8.1 - GNU Fortran (SUSE Linux) 4.8.1 - (cmake and autotools) - - Ubuntu 14.04 3.13.0-35-generic #62-Ubuntu SMP x86_64 GNU/Linux - gcc (Ubuntu/Linaro 4.9.1-0ubuntu1) 4.9.1 - GNU Fortran (Ubuntu/Linaro 4.9.1-0ubuntu1) 4.9.1 - (cmake and autotools) - - Cray Linux Environment (CLE) PrgEnv-pgi/4.2.34 - hopper.nersc.gov pgcc 13.6-0 64-bit target on x86-64 Linux -tp istanbul - pgf90 13.6-0 64-bit target on x86-64 Linux -tp istanbul - pgCC 13.6-0 64-bit target on x86-64 Linux -tp istanbul - - -Known Problems -============== -* On cygwin platforms the feature to load dynamic filter libraries only looks - for libraries with the a so extension. Support for cygwin cygxxx.dll libraries - is planned for the next release. - (ADB - 2014/11/04 - HDFFV-8736) - -* On windows platforms in debug configurations, the VFD flush1 tests will fail - with the split and multi VFD drivers. These tests will display a modal debug - dialog which must be answered or wait for the test timeout to expire. - The flush1 and flush2 tests will be skipped under debug for this release. - (ADB - 2014/06/23 - HDFFV-8851) - -* CLANG compiler with the options -fcatch-undefined-behavior and -ftrapv - catches some undefined behavior in the alignment algorithm of the macro DETECT_I - in H5detect.c (Issue 8147). Since the algorithm is trying to detect the alignment - of integers, ideally the flag -fcatch-undefined-behavior shouldn't to be used for - H5detect.c. In the future, we can separate flags for H5detect.c from the rest of - the library. (SLU - 2013/10/16) - -* Make provided by Solaris fails in "make check". Solaris users should use - gmake to build and install the HDF5 software. (AKC - 2013/10/08 - HDFFV-8534) - -* The h5dump and h5diff utilities occasionally produce different output - between Linux and Windows systems. This is caused by lower-level library - routines that fail to write fill values to the user's buffer when reading - unallocated chunks from datasets that have a fill value set to - H5D_FILL_VALUE_DEFAULT. Due to platform differences the return of - spurious data values has only been encountered on Windows 32-bit systems. - (Issue HDFFV-8247; JP - 2013/03/27) - -* The C++ and FORTRAN bindings are not currently working on FreeBSD with the - native release 8.2 compilers (4.2.1), but are working with gcc 4.6 from the - ports (and probably gcc releases after that). - (QAK - 2012/10/19) - -* The STDIO VFD does not work on some architectures, possibly due to 32/64 - bit or large file issues. The basic STDIO VFD test is known to fail on - 64-bit SunOS 5.10 on SPARC when built with -m64 and 32-bit OS X/Darwin - 10.7.0. The STDIO VFD test has been disabled while we investigate and - a fix should appear in a future release. - (DER - 2011/10/14 - HDFFV-8235) - -* h5diff can report inconsistent results when comparing datasets of enum type - that contain invalid values. This is due to how enum types are handled in - the library and will be addressed in a future release. - (DER - 2011/10/14 - HDFFV-7527) - -* The links test can fail under the stdio VFD due to some issues with external - links. This will be investigated and fixed in a future release. - (DER - 2011/10/14 - HDFFV-7768) - -* After the shared library support was fixed for some bugs, it was discovered - that "make prefix=XXX install" no longer works for shared libraries. It - still works correctly for static libraries. Therefore, if you want to - install the HDF5 shared libraries in a location such as /usr/local/hdf5, - you need to specify the location via the --prefix option during configure - time. E.g, ./configure --prefix=/usr/local/hdf5 ... - (AKC - 2011/05/07 - HDFFV-7583) - -* The parallel test, t_shapesame, in testpar/, may run for a long time and may - be terminated by the alarm signal. If that happens, one can increase the - alarm seconds (default is 1200 seconds = 20 minutes) by setting the - environment variable, $HDF5_ALARM_SECONDS, to a larger value such as 3600 - (60 minutes). Note that the t_shapesame test may fail in some systems - (see the "While working on the 1.8.6 release..." problem below). If - it does, it will waste more time if $HDF5_ALARM_SECONDS is set - to a larger value. - (AKC - 2011/05/07) - -* Shared Fortran libraries are not quite working on AIX. While they are - generated when --enable-shared is specified, the fortran and hl/fortran - tests fail. We are looking into the issue. HL and C++ shared libraries - should now be working as intended, however. - (MAM - 2011/04/20) - -* The --with-mpe configure option does not work with Mpich2. - (AKC - 2011/03/10) - -* While working on the 1.8.6 release of HDF5, a bug was discovered that can - occur when reading from a dataset in parallel shortly after it has been - written to collectively. The issue was exposed by a new test in the parallel - HDF5 test suite, but had existed before that. We believe the problem lies with - certain MPI implementations and/or file systems. - - We have provided a pure MPI test program, as well as a standalone HDF5 - program, that can be used to determine if this is an issue on your system. - They should be run across multiple nodes with a varying number of processes. - These programs can be found at: - http://www.hdfgroup.org/ftp/HDF5/examples/known_problems/ - (NAF - 2011/01/19) - -* All the VFL drivers aren't backward compatible. In H5FDpublic.h, the - structure H5FD_class_t changed in 1.8. There is new parameter added to - get_eoa and set_eoa callback functions. A new callback function - get_type_map was added in. The public function H5FDrealloc was taken - out in 1.8. The problem only happens when users define their own driver - for 1.6 and try to plug in 1.8 library. Because there's only one user - complaining about it, we (Elena, Quincey, and I) decided to leave it as - it is (see bug report #1279). Quincey will make a plan for 1.10. - (SLU - 2010/02/02) - -* The --enable-static-exec configure flag will only statically link libraries - if the static version of that library is present. If only the shared version - of a library exists (i.e., most system libraries on Solaris, AIX, and Mac, - for example, only have shared versions), the flag should still result in a - successful compilation, but note that the installed executables will not be - fully static. Thus, the only guarantee on these systems is that the - executable is statically linked with just the HDF5 library. - (MAM - 2009/11/04) - -* Parallel tests failed with 16 processes with data inconsistency at testphdf5 - / dataset_readAll. Parallel tests also failed with 32 and 64 processes with - collective abort of all ranks at t_posix_compliant / allwrite_allread_blocks - with MPI IO. - (CMC - 2009/04/28) - -* A dataset created or rewritten with a v1.6.3 library or after cannot be read - with the v1.6.2 library or before when the Fletcher32 EDC filter is enabled. - There was a bug in the calculation of the Fletcher32 checksum in the - library before v1.6.3; the checksum value was not consistent between big- - endian and little-endian systems. This bug was fixed in Release 1.6.3. - However, after fixing the bug, the checksum value was no longer the same as - before on little-endian system. Library releases after 1.6.4 can still read - datasets created or rewritten with an HDF5 library of v1.6.2 or before. - (SLU - 2005/06/30) - - -%%%%1.8.13%%%% - - -HDF5 version 1.8.13 released on 2014-05-05 -================================================================================ - -INTRODUCTION -============ - -This document describes the differences between HDF5-1.8.12 and -HDF5-1.8.13, and contains information on the platforms tested and -known problems in HDF5-1.8.13. -For more details, see the files HISTORY-1_0-1_8_0_rc3.txt -and HISTORY-1_8.txt in the release_docs/ directory of the HDF5 source. - -Links to the HDF5 1.8.13 source code, documentation, and additional materials -can be found on the HDF5 web page at: - - http://www.hdfgroup.org/products/hdf5/ - -The HDF5 1.8.13 release can be obtained from: - - http://www.hdfgroup.org/HDF5/release/obtain5.html - -User documentation for 1.8.13 can be accessed directly at this location: - - http://www.hdfgroup.org/HDF5/doc/ - -New features in the HDF5-1.8.x release series, including brief general -descriptions of some new and modified APIs, are described in the "What's New -in 1.8.0?" document: - - http://www.hdfgroup.org/HDF5/doc/ADGuide/WhatsNew180.html - -All new and modified APIs are listed in detail in the "HDF5 Software Changes -from Release to Release" document, in the section "Release 1.8.13 (current -release) versus Release 1.8.12": - - http://www.hdfgroup.org/HDF5/doc/ADGuide/Changes.html - -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, Languages, and Compilers -- Bug Fixes since HDF5-1.8.12 -- Supported Platforms -- Supported Configuration Features Summary -- More Tested Platforms -- Known Problems - - -New Features -============ - - Configuration - ------------- - - Autotools: Automake updated to 1.14.1 (ADB - 2014/04/08) - - - CMake: Moved minimum CMake version to 2.8.11 which enables better library - include processing. (ADB - 2014/03/26) - - - When configuring a thread-safe HDF5 Library it is no longer necessary - to specify --enable-threadsafe with --with-pthreads if the Pthreads - library is in a standard location. (DER - 2014/04/11 HDFFV-8693) - - Library - ------- - - Added an H5free_memory API call. This should be used to free memory - that has been allocated by HDF5 API calls. H5Tget_member_name and - H5Pget_class_name are two examples. The main motivation for this call - is Windows, where it is common for application code and the HDF5 Library - to be using different C run-time libraries (CRT). Using the new call - ensures that the same CRT handles both the allocation and free. This - new function can also be useful in any case where the library uses a - different memory manager than the application, such as when a debug - memory manager is in use or when the HDF5 Library is wrapped for use - in a managed language like Python or Java. Fixes HDFFV-7710, 8519, - and 8851. (DER - 2014/04/11) - - - The Core VFD (aka Memory VFD) can now be configured to track dirty - regions in the file and only write out the changed regions on - flush/close. Additionally, a "page aggregation" size can be set that - will aggregate small writes into larger writes. For example, setting - a 1 MiB page aggregation size will logically partition the the - in-memory file into 1 MiB pages that will be written out in their - entirety if even a single byte is dirtied. The feature is controlled - via the new H5Pset/get_core_write_tracking() API call. A new - "core_paged" target has been added to the check-vfd target in - test/Makefile.am that exercises the feature over all HDF5 VFD-aware - tests. (DER - 2014/04/12) - - Parallel Library - ---------------- - - Removed MPI-POSIX VFD, as it wasn't helping anyone and was just - generating support questions. Application developers performing - parallel I/O should always use the MPI-IO VFD. - (QAK - 2014/03/28 HDFFV-8659) - - - Improved parallel I/O support to allow collective I/O on point - selections. (QAK - 2014/03/15) - - Tools - ----- - - None - - High-Level APIs - --------------- - - None - - Fortran API - ----------- - - Wrappers h5pset_file_image_f and h5pget_file_image_f were added to the - library. (MSB - 2014/1/2014) - - C++ API - ------- - - The following new features are added: - + Wrappers to class H5Object to get an object's name (HDFFV-8548). - ssize_t getObjName(char *obj_name, size_t buf_size = 0) - ssize_t getObjName(H5std_string& obj_name, size_t len = 0) - H5std_string getObjName() - + Wrappers to class H5CommonFG to get a child object's type from a - group or file (HDFFV-8367). - H5O_type_t childObjType(const H5std_string& objname) - H5O_type_t childObjType(const char* objname) - H5O_type_t childObjType(hsize_t index, - H5_index_t index_type=H5_INDEX_NAME, - H5_iter_order_t order=H5_ITER_INC, const char* objname=".") - + Wrappers to class DSetMemXferPropList for setting/getting a transform - property list (HDFFV-7907). - DSetMemXferPropList(const char* expression); - void setDataTransform(const char* expression) - void setDataTransform(const H5std_string& expression) - ssize_t getDataTransform(char* exp, size_t buf_size=0) - H5std_string getDataTransform() - + Wrapper to CompType for setting size to compound datatype (HDFFV-8642). - void setSize(size_t size) - + Overloaded functions to provide prototypes that declare constant - arguments const (HDFFV-3384). These include: - DataSet::fillMemBuf - DataSet::getVlenBufSize - DataSpace::extentCopy - DataType::commit - FileAccPropList::setSplit - H5File::getVFDHandle - + Additional overload to class H5Location to get a comment as a char* - ssize_t getComment(const char* name, size_t buf_size, char* comment) - + Additional overloads to class Attribute to get an attribute's name for - convenience: - ssize_t getName(char* attr_name, size_t buf_size=0) - ssize_t getName(H5std_string& attr_name, size_t buf_size=0) - (BMR, 2014/04/15) - + A static wrapper to Exception for printing the error stack without an - instance of Exception - static void printErrorStack(FILE* stream = stderr, - hid_t err_stack = H5E_DEFAULT); - (BMR, 2014/04/25) - - -Support for New Platforms, Languages, and Compilers -=================================================== - Mac OS X 10.6 Snow Leopard is not supported by Apple any more. In view of - the added support of Mac OS X 10.9, Mac OS X 10.6 is retired from HDF5 - supported platforms. (AKC - 2014/03/14 HDFFV-8704) - - Mac OS X 10.9 Mavericks is supported. (AKC - 2014/03/04 HDFFV-8694) - - -Bug Fixes since HDF5-1.8.12 -=========================== - - Configuration - ------------- - - CMake: When CMake commands are executed individually on the command line - and the external filters are being built, the CMAKE_BUILD_TYPE define - must be set to the same value as the configuration - (-DCMAKE_BUILD_TYPE:STRING=Release if using -C Release). This is needed - by the the szip and zlib filter build commands. (ADB - HDFFV-8695) - - - CMake: Removed use of the XLATE_UTILITY program. - (ADB - 2014/03/28 HDFFV-8640) - - - CMake: Added missing quotes in setting the CMAKE_EXE_LINKER_FLAGS for the - MPI option. (ADB - 2014/02/27 HDFFV-8674) - - - CMake: Configuration of the HDF5 C++ or Fortran libraries with the - thread-safety feature. - - C++ and/or Fortran + thread-safe is enforced as a non-supported - configuration. This matches the autotools. (DER - 2014/04/11) - - - CMake: Configuration of static HDF5 C library with the thread-safety - feature. - - Static + thread-safe + Win32 threads is not a supported configuration - due to the inability to automatically clean up thread-local storage. - This is expected to be fixed in a future release. In the meantime, a - work-around that uses internal functionality may allow the combination - to be used without resource leaks. Contact the help desk for more - information. (DER - 2014/04/11) - - - Autotools: Several changes were done to configure and installcheck. - - An export of LD_LIBRARY_PATH=<szip library location> was - removed from configure; make installcheck was revised to run - scripts installed in share/hdf5_examples to use the installed h5cc, etc. - to compile and run example source files also installed there. - - Make installcheck will now fail when a shared szip or other external lib - file cannot be found in the same manner that executables compiled and - linked with h5cc will fail to run when those lib files cannot be found - after install. Make installcheck should pass after setting - LD_LIBRARY_PATH to the szip location. (LRK - 2014/04/16) - - Library - ------- - - A Gnu Make directive (.NOTPARALLEL) is added to fortran/test/Makefile. - - AIX native make does not support this directive and would fail if - parallel make (e.g. make -j4) is used to build the library. AIX users - either do not use parallel make or install Gnu Make to build the library. - (AKC 2014/04/08 HDFFV-8738) - - - H5R.c: H5Rget_name gave an assertion failure if the "name" parameter - was NULL. - - Fixed H5Rget_name to return the size of the buffer needed to read a - name of the referenced object in this case. The size doesn't include - the NULL terminator. H5Rget_name returns negative on failure. - (MSB - 2014/01/22 HDFFV-8620) - - - H5Z.c: H5Zfilter_avail didn't check if a filter was available as a - dynamically loaded filter. The error manifested itself in the h5repack - tool when removing user-defined dynamically loaded filter. - - Added a code to find the filter among the dynamically loaded filters - after the function fails to find it among the registered filters. - (ADB - 2014/03/03 HDFFV-8629) - - - Memory leak: a memory leak was observed in conjunction to the - H5TS_errstk_key_g thread-local variable allocated in the H5E_get_stack - function in H5E.c. - - The shared HDF5 thread-safe library now no longer leaks thread-local - storage resources on Windows with Win32 threads. Currently, there is - no solution for this problem when HDF5 is statically built. We - disabled the build of the static HDF5 thread-safe library with - Win32 threads. (DER - 2014/04/11 HDFFV-8518) - - - H5Dio.c: Improved handling of NULL pointers to H5Dread/H5Dwrite - calls. Credit to Jason Newton (nevion@gmail.com) for the original patch. - - H5Dwrite/read failed when a NULL pointer was passed for a data buffer - and 0 elements were selected. Fixed. (QAK - 2014/04/16 HDFFV-8705) - - - Deprecated API (1_6 API): Improved handling of closing the library and - re-accessing it with a deprecated routine. - - When a program used a deprecated API (for example, H5Gcreate1), - closed the library, and reopened it again to access a group, dataset, - datatype, dataspace, attribute, or property list, HDF5 failed to - provide an identifier for the object. Fixed. - (NAF, QAK - 2014/04/16 HDFFV-8232) - - Parallel Library - ---------------- - - Fixed a missing H5F_Provisional module in HDF5mpio.f90 - (MSB - 2014/2/7 HDFFV-8651) - - Performance - ------------- - - None - - Tools - ----- - - The h5diff tool would report that a datafile compared with an exact - copy of the same datafile had differences. This was due to the issue - below of reading un-written chunks. This problem is also fixed. - (AKC - 2014/05/01 HDFFV-8637) - - - The h5dump and h5diff utilities occasionally produced different output - between Linux and Windows systems. This has been fixed. - - This happened to datasets that used chunked storage, with default fill - values, and some of the chunks had not been written. - When the dataset was read, the library failed to write the default fill - values to parts of the use buffer that were associated with the unwritten - chunks. (JP - 2014/05/01 HDFFV-8247) - - - The compress option is retired from bin/release. - (AKC - 2014/04/25 HDFFV-8755) - - - bin/release has a new option "zip" that produces a release zip file for - the Windows platform. (AKC - 2014/04/24 HDFFV-8433) - - - h5diff: Several failures relating to handling of strings attributes - are fixed. - - The tool crashed or gave an error message when one of the strings had - fixed size type and another variable-length size type. h5diff now flags such - strings as "not comparable". We plan to enhance the tool to handle - strings of the different types in the future releases. - (AKC - 2014/04/18 HDFFV-8625, 8639, 8745) - - - h5repack: h5repack would not remove user-defined filters. - Fixed by modifying h5repack to check if the filter is registered or - can be dynamically loaded. (ADB - 2014/03/03 HDFFV-8629) - - F90 API - ------- - - H5D_CHUNK_CACHE_NSLOTS_DFLT_F and H5D_CHUNK_CACHE_NBYTES_DFLT_F were - changed from the default KIND for INTEGER to INTEGER of KIND size_t. - (MSB - 2014/3/31 HDFFV-8689) - - C++ API - ------ - - Added throw() to all exception destructors. Credit to Jason Newton - (nevion@gmail.com) for the patch. (BMR - 2014/4/15 HDFFV-8623) - - Changed the default value for H5Location::getComment from 256 to 0 - to conform to C function and because it makes more sense. - (BMR - 2014/4/15) - - High-Level APIs: - ------ - - None - - Fortran High-Level APIs: - ------ - - None - - Testing - ------- - - testhdf5 now exits with EXIT_SUCCESS(0) if no errors, else - EXIT_FAILURE(1). (AKC - 2014/01/27 HDFFV-8572) - - - The big test now pays attention to the HDF5_DRIVER environment variable. - Previously, it would run all tests with the family, stdio, and sec2 - virtual file drivers (VFDs) for each VFD in the check-vfd make target, - regardless of the variable setting. It now checks the variable and - either runs the appropriate VFD-specific tests or skips as needed. - This saves much testing time. Fixes HDFFV-8554. (DER - 2014/04/11) - -Supported Platforms -=================== -The following platforms are supported and have been tested for this release. -They are built with the configure process unless specified otherwise. - - AIX 5.3 xlc 10.1.0.5 - (NASA G-ADA) xlC 10.1.0.5 - xlf90 12.1.0.6 - gmake v3.82 - - Linux 2.6.18-308.13.1.el5PAE GNU C (gcc), Fortran (gfortran), C++ (g++) - #1 SMP i686 i686 i386 compilers for 32-bit applications; - (jam) Version 4.1.2 20080704 (Red Hat 4.1.2-54) - Version 4.8.2 - PGI C, Fortran, C++ Compilers for 32-bit - applications; - Version 13.7-0 - Intel(R) C, C++, Fortran Compiler for 32-bit - applications; - Version 14.0.2 (Build 20140120) - - Linux 2.6.18-371.6.1.el5 GNU C (gcc), Fortran (gfortran), C++ (g++) - #1 SMP x86_64 GNU/Linux compilers for 64-bit applications; - (koala) Version 4.1.2 20080704 (Red Hat 4.1.2-54) - Version 4.8.2 - PGI C, Fortran, C++ for 64-bit target on - x86-64; - Version 13.7-0 - Intel(R) C, C++, Fortran Compilers for - applications running on Intel(R) 64; - Version 14.0.2 (Build 20140120) - - Linux 2.6.32-431.11.2.el6 GNU C (gcc), Fortran (gfortran), C++ (g++) - #1 SMP x86_64 GNU/Linux compilers: - (platypus) Version 4.4.7 20120313 - Version 4.8.2 - PGI C, Fortran, C++ for 64-bit target on - x86-64; - Version 13.7-0 - Intel(R) C (icc), C++ (icpc), Fortran (icc) - compilers: - Version 14.0.2 (Build 20140120) - - Linux 2.6.32-431.11.2.el6.ppc64 gcc (GCC) 4.4.7 20120313 (Red Hat 4.4.7-3) - #1 SMP ppc64 GNU/Linux g++ (GCC) 4.4.7 20120313 (Red Hat 4.4.7-3) - (ostrich) GNU Fortran (GCC) 4.4.7 20120313 (Red Hat 4.4.7-3) - IBM XL C/C++ V11.1 - IBM XL Fortran V13.1 - - 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 2008 w/ Intel Fortran 14 (cmake) - Visual Studio 2010 w/ Intel Fortran 14 (cmake) - Visual Studio 2012 w/ Intel Fortran 14 (cmake) - Cygwin(CYGWIN_NT-6.1 1.7.28(0.271/5/3) gcc(4.8.2) compiler and gfortran) - (cmake and autotools) - - Windows 7 x64 Visual Studio 2008 w/ Intel Fortran 14 (cmake) - Visual Studio 2010 w/ Intel Fortran 14 (cmake) - Visual Studio 2012 w/ Intel Fortran 14 (cmake) - - Windows 8.1 Visual Studio 2012 w/ Intel Fortran 14 (cmake) - - Windows 8.1 x64 Visual Studio 2012 w/ Intel Fortran 14 (cmake) - - Mac OS X Lion 10.7.3 Apple clang/clang++ version 3.0 from Xcode 4.6.1 - 64-bit gfortran GNU Fortran (GCC) 4.6.2 - (duck) Intel icc/icpc/ifort version 13.0.3 - - Mac OS X Mt. Lion 10.8.5 Apple clang/clang++ version 5.0 from Xcode 5.0.2 - 64-bit gfortran GNU Fortran (GCC) 4.8.2 - (swallow/kite) Intel icc/icpc/ifort version 14.0.2 - - Mac OS X Mavericks 10.9.2 Apple clang/clang++ version 5.1 from Xcode 5.1 - 64-bit gfortran GNU Fortran (GCC) 4.8.2 - (wren/quail) Intel icc/icpc/ifort version 14.0.2 - - -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/y n y y y -Windows 7 y y/y n y y y -Windows 7 x64 y y/y n y y y -Windows 7 Cygwin n y/y n y y y -Windows 8.1 n y/y n y y y -Windows 8.1 x64 n y/y n y y y -Mac OS X Lion 10.7.3 64-bit n y/y n y y y -Mac OS X Mountain Lion 10.8.1 64-bit n y/y n y y y -Mac OS X Mavericks 10.9.1 64-bit n y/y n y y y -AIX 5.3 32- and 64-bit n y/n n y y y -CentOS 5.9 Linux 2.6.18-308 i686 GNU y y/y y y y y -CentOS 5.9 Linux 2.6.18-308 i686 Intel n y/y n y y y -CentOS 5.9 Linux 2.6.18-308 i686 PGI n y/y n y y y -CentOS 5.9 Linux 2.6.18 x86_64 GNU n y/y n y y y -CentOS 5.9 Linux 2.6.18 x86_64 Intel n y/y n y y y -CentOS 6.4 Linux 2.6.32 x86_64 GNU y y/y y y y y -CentOS 6.4 Linux 2.6.32 x86_64 Intel n y/y n y y y -CentOS 6.4 Linux 2.6.32 x86_64 PGI n y/y n y y y -Linux 2.6.32-431.11.2.el6.ppc64 n y/n n y y y -OpenVMS IA64 V8.4 n y/n n y y n - -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 8.1 y y y y -Windows 8.1 x64 y y y y -Mac OS X Lion 10.7.3 64-bit y n y y -Mac OS X Mountain Lion 10.8.1 64-bit y n y y -Mac OS X Mavericks 10.9.1 64-bit y n y y -AIX 5.3 32- and 64-bit y n n y -CentOS 5.9 Linux 2.6.18-308 i686 GNU y y y y -CentOS 5.9 Linux 2.6.18-308 i686 Intel y y y n -CentOS 5.9 Linux 2.6.18-308 i686 PGI y y y n -CentOS 5.9 Linux 2.6.18 x86_64 GNU y y y y -CentOS 5.9 Linux 2.6.18 x86_64 Intel y y y n -CentOS 6.4 Linux 2.6.32 x86_64 GNU y y y n -CentOS 6.4 Linux 2.6.32 x86_64 Intel y y y n -CentOS 6.4 Linux 2.6.32 x86_64 PGI y y y n -Linux 2.6.32-431.11.2.el6.ppc64 y y y n -OpenVMS IA64 V8.4 n n n 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 2.6.18-308.13.1.el5PAE MPICH mpich 3.1 compiled with - #1 SMP i686 i686 i386 gcc 4.8.2 and gfortran 4.8.2 - (jam) g95 (GCC 4.0.3 (g95 0.94!) - - Linux 2.6.18-431.11.2.el6 MPICH mpich 3.1 compiled with - #1 SMP x86_64 GNU/Linux gcc 4.8.2 and gfortran 4.8.2 - (platypus) g95 (GCC 4.0.3 (g95 0.94!) - - FreeBSD 8.2-STABLE i386 gcc 4.5.4 [FreeBSD] 20110526 - (loyalty) gcc 4.6.1 20110527 - g++ 4.6.1 20110527 - gfortran 4.6.1 20110527 - - FreeBSD 8.2-STABLE amd64 gcc 4.5.4 [FreeBSD] 20110526 - (freedom) gcc 4.6.1 20110527 - g++ 4.6.1 20110527 - gfortran 4.6.1 20110527 - - Debian7.1.0 3.2.0-4-amd64 #1 SMP Debian 3.2.51-1 x86_64 GNU/Linux - gcc (Debian 4.7.2-5) 4.7.2 - GNU Fortran (Debian 4.7.2-5) 4.7.2 - (cmake and autotools) - - Fedora20 3.11.10-301.fc20.x86_64 #1 SMP x86_64 x86_64 x86_64 GNU/Linux - gcc (GCC) 4.8.2 20131212 (Red Hat 4.8.2-7) - GNU Fortran (GCC) 4.8.2 20130603 (Red Hat 4.8.2-7) - (cmake and autotools) - - SUSE 13.1 3.11.6-4-desktop #1 SMP PREEMPT x86_64 x86_64 x86_64 GNU/Linux - gcc (SUSE Linux) 4.8.1 - GNU Fortran (SUSE Linux) 4.8.1 - (cmake and autotools) - - Ubuntu 13.10 3.11.0-13-generic #20-Ubuntu SMP x86_64 GNU/Linux - gcc (Ubuntu/Linaro 4.8.1-10ubuntu8) 4.8.1 - GNU Fortran (Ubuntu/Linaro 4.8.1-10ubuntu8) 4.8.1 - (cmake and autotools) - - Cray Linux Environment (CLE) PrgEnv-pgi/4.0.46 - hopper.nersc.gov pgcc 12.5-0 64-bit target on x86-64 Linux -tp shanghai - pgf90 12.5-0 64-bit target on x86-64 Linux -tp shanghai - pgCC 12.5-0 64-bit target on x86-64 Linux -tp shanghai - - -Known Problems -============== -* When reading or writing a dataset (H5Dread/H5Dwrite) with a large selection - size (e.g., 2GB ~= 500 million of 4 bytes integers or floating point - numbers), some I/O systems may not be able to process it correctly. - We advise users to find out system limits before using large selections. If - I/O size limits exist, application should use HDF5 partial I/O capabilities - (e.g., H5Sselect_hyperslab(...)) to divide large requests into smaller sizes. - In this case we also advise users not to use chunk storage sizes larger that - 2GB since the HDF5 library performs I/O on the entire chunk. We will work - on the HDF5 library to divide large data requests to smaller I/O requests. - (AKC 2014/05/02 HDFFV-8479) - -* Due to an Intel compiler bug introduced in version 14.0.1, the HDF5 FORTRAN - wrappers do not work with configure option --enable-fortran2003. - However, the option --enable-fortran works with Intel 14.0.1. The compiler - bug was fixed in Intel version 14.0.2 and resolved the issue. - (MSB - 2014/4/15) - -* Due to a PGI compiler bug introduced in versions before 13.3 and versions - after 14.2, the FORTRAN test 'Testing get file image' will fail. - (MSB - 2014/4/15) - -* On CYGWIN, when building the library dynamically, testing will fail on - dynamically loaded filters. The test process will build dynamic filter - libraries with the *.dll.a extension, and the HDF5 Library will be looking - for *.so libraries. Entered as issue HDFFV-8736. (ADB - 2014/04/14) - -* A Gnu Make directive (.NOTPARALLEL) is added to fortran/test/Makefile. - AIX native make does not support this directive and would fail if - parallel make (e.g. make -j4) is used to build the library. AIX users - either do not use parallel make or install Gnu Make to build the library. - (AKC 2014/04/08 HDFFV-8738) - -* CLANG compiler with the options -fcatch-undefined-behavior and -ftrapv - catches some undefined behavior in the alignment algorithm of the macro - DETECT_I in H5detect.c. Since the algorithm is trying to detect the alignment - of integers, ideally the flag -fcatch-undefined-behavior should not to be - used for H5detect.c. In the future, we can separate flags for H5detect.c - from the rest of the library. (SLU - 2013/10/16 HDFFV-8147) - -* Make provided by Solaris fails in "make check". Solaris users should use - gmake to build and install the HDF5 software. (AKC - 2013/10/08 - HDFFV-8534) - -* On OpenVMS, two soft conversion functions (H5T__conv_i_f and H5T__conv_f_i) - have bugs. They convert data between floating-point numbers and integers. - But the library's default is hard conversion. The user should avoid - explicitly enabling soft conversion between floating-point numbers and - integers. (Issue VMS-8; SLU - 2013/09/19) - -* On OpenVMS, ZLIB 1.2.8 library doesn't work properly. ZLIB 1.2.5 works - fine. So please use ZLIB 1.2.5 to build HDF5 library. (Issue VMS-5; - SLU 2013/09/19) - -* When building using the Cray compilers on Cray machines, HDF5 - configure mistakenly thinks the compiler is an intel compiler and - sets the -std=c99 flag which breaks configure on Cray. To build HDF5 - properly on a Cray machine, please consult with the instructions in - INSTALL_parallel for building on Hopper. - (MSC - 2013/04/26 - HDFFV-8429) - -* The 5.9 C++ compiler on Sun failed to compile a C++ test ttypes.cpp. It - complains with this message: - "/home/hdf5/src/H5Vprivate.h", line 130: Error: __func__ is not defined. - - The reason is that __func__ is a predefined identifier in C99 standard. The - HDF5 C library uses it in H5private.h. The test ttypes.cpp includes - H5private.h (H5Tpkg.h<-H5Fprivate.h<-H5Vprivate.h<-H5private.h). Sun's 5.9 - C++ compiler doesn't support __func__, thus fails to compile the C++ test. - But Sun's 5.11 C++ compiler does. To check whether your Sun C++ compiler - knows this identifier, try to compile the following simple C++ program: - #include<stdio.h> - - int main(void) - { - printf("%s\n", __func__); - return 0; - } - (SLU - 2012/11/5) - -* The C++ and FORTRAN bindings are not currently working on FreeBSD with the - native release 8.2 compilers (4.2.1), but are working with gcc 4.6 from the - ports (and probably gcc releases after that). - (QAK - 2012/10/19) - -* The following h5dump test case fails in BG/P machines (and potentially other - machines that use a command script to launch executables): - - h5dump --no-compact-subset -d "AHFINDERDIRECT::ah_centroid_t[0] it=0 tl=0" - tno-subset.h5 - - This is due to the embedded spaces in the dataset name being interpreted - by the command script launcher as meta-characters, thus passing three - arguments to h5dump's -d flag. The command passes if run by hand, just - not via the test script. - (AKC - 2012/05/03) - -* On hopper, the build failed when RUNSERIAL and RUNPARALLEL are set - to aprun -np X, because the H5lib_settings.c file was not generated - properly. Not setting those environment variables works, because - configure was able to automatically detect that it's a Cray system - and used the proper launch commands when necessary. - (MSC - 2012/04/18) - -* The data conversion test dt_arith.c fails in "long double" to integer - conversion on Ubuntu 11.10 (3.0.0.13 kernel) with GCC 4.6.1 if the library - is built with optimization -O3 or -O2. The older GCC (4.5) or newer kernel - (3.2.2 on Fedora) doesn't have the problem. Users should lower the - optimization level (-O1 or -O0) by defining CFLAGS in the command line of - "configure" like: - - CFLAGS=-O1 ./configure - - This will overwrite the library's default optimization level. - (SLU - 2012/02/07 - HDFFV-7829) - This issue is no longer present on Ubuntu 12.10 (3.5.0 kernel) with - gcc 4.7.2. - -* The STDIO VFD does not work on some architectures, possibly due to 32/64 - bit or large file issues. The basic STDIO VFD test is known to fail on - 64-bit SunOS 5.10 on SPARC when built with -m64 and 32-bit OS X/Darwin - 10.7.0. The STDIO VFD test has been disabled while we investigate and - a fix should appear in a future release. - (DER - 2011/10/14 - HDFFV-8235) - -* h5diff can report inconsistent results when comparing datasets of enum type - that contain invalid values. This is due to how enum types are handled in - the library and will be addressed in a future release. - (DER - 2011/10/14 - HDFFV-7527) - -* The links test can fail under the stdio VFD due to some issues with external - links. This will be investigated and fixed in a future release. - (DER - 2011/10/14 - HDFFV-7768) - -* After the shared library support was fixed for some bugs, it was discovered - that "make prefix=XXX install" no longer works for shared libraries. It - still works correctly for static libraries. Therefore, if you want to - install the HDF5 shared libraries in a location such as /usr/local/hdf5, - you need to specify the location via the --prefix option during configure - time. E.g, ./configure --prefix=/usr/local/hdf5 ... - (AKC - 2011/05/07 - HDFFV-7583) - -* The parallel test, t_shapesame, in testpar/, may run for a long time and may - be terminated by the alarm signal. If that happens, one can increase the - alarm seconds (default is 1200 seconds = 20 minutes) by setting the - environment variable, $HDF5_ALARM_SECONDS, to a larger value such as 3600 - (60 minutes). Note that the t_shapesame test may fail in some systems - (see the "While working on the 1.8.6 release..." problem below). If - it does, it will waste more time if $HDF5_ALARM_SECONDS is set - to a larger value. - (AKC - 2011/05/07) - -* The C++ and FORTRAN bindings are not currently working on FreeBSD. - (QAK - 2011/04/26) - -* Shared Fortran libraries are not quite working on AIX. While they are - generated when --enable-shared is specified, the fortran and hl/fortran - tests fail. We are looking into the issue. HL and C++ shared libraries - should now be working as intended, however. - (MAM - 2011/04/20) - -* The --with-mpe configure option does not work with Mpich2. - (AKC - 2011/03/10) - -* While working on the 1.8.6 release of HDF5, a bug was discovered that can - occur when reading from a dataset in parallel shortly after it has been - written to collectively. The issue was exposed by a new test in the parallel - HDF5 test suite, but had existed before that. We believe the problem lies with - certain MPI implementations and/or file systems. - - We have provided a pure MPI test program, as well as a standalone HDF5 - program, that can be used to determine if this is an issue on your system. - They should be run across multiple nodes with a varying number of processes. - These programs can be found at: - http://www.hdfgroup.org/ftp/HDF5/examples/known_problems/ - (NAF - 2011/01/19) - -* All the VFL drivers aren't backward compatible. In H5FDpublic.h, the - structure H5FD_class_t changed in 1.8. There is new parameter added to - get_eoa and set_eoa callback functions. A new callback function - get_type_map was added in. The public function H5FDrealloc was taken - out in 1.8. The problem only happens when users define their own driver - for 1.6 and try to plug in 1.8 library. Because there's only one user - complaining about it, we (Elena, Quincey, and I) decided to leave it as - it is (see bug report #1279). Quincey will make a plan for 1.10. - (SLU - 2010/02/02) - -* The --enable-static-exec configure flag will only statically link libraries - if the static version of that library is present. If only the shared version - of a library exists (i.e., most system libraries on Solaris, AIX, and Mac, - for example, only have shared versions), the flag should still result in a - successful compilation, but note that the installed executables will not be - fully static. Thus, the only guarantee on these systems is that the - executable is statically linked with just the HDF5 library. - (MAM - 2009/11/04) - -* Parallel tests failed with 16 processes with data inconsistency at testphdf5 - / dataset_readAll. Parallel tests also failed with 32 and 64 processes with - collective abort of all ranks at t_posix_compliant / allwrite_allread_blocks - with MPI IO. - (CMC - 2009/04/28) - -* On an Intel 64 Linux cluster (RH 4, Linux 2.6.9) with Intel 10.0 compilers, - use -mp -O1 compilation flags to build the libraries. A higher level of - optimization causes failures in several HDF5 library tests. - -* A dataset created or rewritten with a v1.6.3 library or after cannot be read - with the v1.6.2 library or before when the Fletcher32 EDC filter is enabled. - There was a bug in the calculation of the Fletcher32 checksum in the - library before v1.6.3; the checksum value was not consistent between big- - endian and little-endian systems. This bug was fixed in Release 1.6.3. - However, after fixing the bug, the checksum value was no longer the same as - before on little-endian system. Library releases after 1.6.4 can still read - datasets created or rewritten with an HDF5 library of v1.6.2 or before. - (SLU - 2005/06/30) - - -%%%%1.8.12%%%% - - -HDF5 version 1.8.12 released on 2013-11-04 -================================================================================ - -INTRODUCTION -============ - -This document describes the differences between HDF5-1.8.11 and -HDF5-1.8.12, and contains information on the platforms tested and -known problems in HDF5-1.8.12. -For more details, see the files HISTORY-1_0-1_8_0_rc3.txt -and HISTORY-1_8.txt in the release_docs/ directory of the HDF5 source. - -Links to the HDF5 1.8.12 source code, documentation, and additional materials -can be found on the HDF5 web page at: - - http://www.hdfgroup.org/products/hdf5/ - -The HDF5 1.8.12 release can be obtained from: - - http://www.hdfgroup.org/HDF5/release/obtain5.html - -User documentation for 1.8.12 can be accessed directly at this location: - - http://www.hdfgroup.org/HDF5/doc/ - -New features in the HDF5-1.8.x release series, including brief general -descriptions of some new and modified APIs, are described in the "What's New -in 1.8.0?" document: - - http://www.hdfgroup.org/HDF5/doc/ADGuide/WhatsNew180.html - -All new and modified APIs are listed in detail in the "HDF5 Software Changes -from Release to Release" document, in the section "Release 1.8.12 (current -release) versus Release 1.8.11": - - http://www.hdfgroup.org/HDF5/doc/ADGuide/Changes.html - -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, Languages, and Compilers -- Bug Fixes since HDF5-1.8.11 -- Supported Platforms -- Supported Configuration Features Summary -- More Tested Platforms -- Known Problems - - -New Features -============ - - Configuration - ------------- - - Added a configuration option to change the default plugin path. - The configure option is --with-default-plugindir=location. - The cmake option is -DH5_DEFAULT_PLUGINDIR:PATH=location. - HDFFV-8513. (ADB 2013/09/04) - - Renamed FFLAGS to FCFLAGS in configure. (ADB 2013/08/13) - - CMake can now package a compressed examples file, the default for - Windows binaries from HDF Group. (ADB - 2013/07/22) - - Library - ------- - - None - - Parallel Library - ---------------- - - None - - Tools - ----- - - h5repack: Added the ability to use plugin filters to read and write - files. The option uses the filter number. HDFFV-8345 - (ADB - 2013/09/04). - - h5dump: Added the option -N --any_path, which searches the file for - paths that match the search path. HDFFV-7989 (ADB - 2013/08/12). - - h5dump: Added the optional arg 0 to -A, which excludes attributes - from display. HDFFV-8134 (ADB - 2013/08/01). - - High-Level APIs - --------------- - - None - - Fortran API - ----------- - - None - - C++ API - ------- - - Added tutorial examples to C++/examples. They can be installed by - "make install-examples" and, in the installed directory, they can be - executed by running the script file run-c++-ex.sh. (BMR - 2013/09/28) - - A new class, H5::H5Location, is added to represent the location concept - in the C library. It is a base class to H5::H5File and H5::H5Ojbect, - whose member functions are moved into H5::H5Location. H5::H5File can - now inherent those functions. As a result, an H5::H5File object can have - an attribute. (BMR - 2013/09/27) - - Added wrappers for H5Rget_obj_type2 to retrieve the type of the object - that an object reference points to. (BMR - 2013/09/27) - H5O_type_t H5Location::getRefObjType(void *ref, H5R_type_t ref_type) - - Added wrappers for H5Aexist to check whether an attribute exists given - a name. (BMR - 2013/09/27) - bool H5::H5Location::attrExists(const char* name) - bool H5::H5Location::attrExists(const H5std_string& name) - - Added a number of overloaded functions for convenience. (BMR - 2013/09/27) - - -Support for New Platforms, Languages, and Compilers -=================================================== - - None - -Bug Fixes since HDF5-1.8.11 -=========================== - - Configuration - ------------- - - Modified H5detect.c to scan floating point types for padding bits before - analyzing the type further. This should fix problems with gcc 4.8. - (NAF - 2013/09/19 - HDFFV-8523/HDFFV-8500) - - HDF5 rpaths are no longer encoded in the library files when configured - with --disable-sharedlib-rpath. (LRK-2013-09-23 - HDFFV-8276) - - Library - ------- - - Added const qualifier to source buffer parameters in H5Dgather and - H5D_scatter_func_t (H5Dscatter callback). (NAF - 2013/7/09) - - - CMake now creates *.so.{lt_version} files with the same version as - configure. (ADB - 2013/06/05 HDFFV-8437) - - Parallel Library - ---------------- - - None - - Performance - ------------- - - None - - Tools - ----- - - h5dump: Added the option -N --any_path, which searches the file for - paths that match the search path. HDFFV-7989 (ADB - 2013/08/12). - - h5dump: Added the optional arg 0 to -A, which excludes attributes - from display. HDFFV-8134 (ADB - 2013/08/01). - - h5dump correctly exports subsetted data to a file, using the --output - option. (ADB - 2013/06/07 HDFFV-8447) - - h5cc and other compile scripts now default to linking shared libraries - when HDF5 is configured with the --disable-static option. - (LRK - 2013-09-23 - HDFFV-8141) - - F90 API - ------- - - None - - C++ API - ------ - - None - - High-Level APIs: - ------ - - None - - Fortran High-Level APIs: - ------ - - None - - Testing - ------- - - test/big sometimes failed with the message of "file selection+offset not - within extent". This has been fixed. (AKC - 2013/09/28 HDFFV-8271). - - tools/h5diff/testh5diff.sh is run in every "make check", even after it - has passed in the previous run. It should not run again if there are no - code changes. Fixed. (AKC - 2013/07/19 HDFFV-8392) - -Supported Platforms -=================== -The following platforms are supported and have been tested for this release. -They are built with the configure process unless specified otherwise. - - AIX 5.3 xlc 10.1.0.5 - (NASA G-ADA) xlC 10.1.0.5 - xlf90 12.1.0.6 - - Linux 2.6.18-308.13.1.el5PAE GNU C (gcc), Fortran (gfortran), C++ (g++) - #1 SMP i686 i686 i386 compilers for 32-bit applications; - (jam) Version 4.1.2 20080704 (Red Hat 4.1.2-54) - Version 4.8.1 - PGI C, Fortran, C++ Compilers for 32-bit - applications; - Version 13.7-0 - Intel(R) C, C++, Fortran Compiler for 32-bit - applications; - Version 13.1.3 (Build 20130607) - - Linux 2.6.18-308.16.1.el5 GNU C (gcc), Fortran (gfortran), C++ (g++) - #1 SMP x86_64 GNU/Linux compilers for 64-bit applications; - (koala) Version 4.1.2 20080704 (Red Hat 4.1.2-54) - Version 4.8.1 - PGI C, Fortran, C++ for 64-bit target on - x86-64; - Version 13.7-0 - Intel(R) C, C++, Fortran Compilers for - applications running on Intel(R) 64; - Version 13.1.3 (Build 20130607) - - Linux 2.6.32-358.18.1.el6 GNU C (gcc), Fortran (gfortran), C++ (g++) - #1 SMP x86_64 GNU/Linux compilers: - (platypus) Version 4.4.7 20120313 - Version 4.8.1 - PGI C, Fortran, C++ for 64-bit target on - x86-64; - Version 13.7-0 - Intel(R) C (icc), C++ (icpc), Fortran (icc) - compilers: - Version 13.1.3 (Build 20130607) - - Linux 2.6.32-358.18.1.el6.ppc64 gcc (GCC) 4.4.7 20120313 (Red Hat 4.4.7-3) - #1 SMP ppc64 GNU/Linux g++ (GCC) 4.4.7 20120313 (Red Hat 4.4.7-3) - (ostrich) GNU Fortran (GCC) 4.4.7 20120313 (Red Hat 4.4.7-3) - IBM XL C/C++ V11.1 - IBM XL Fortran V13.1 - - 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 2008 w/ Intel Fortran 11 (cmake) - Visual Studio 2010 w/ Intel Fortran 12 (cmake) - Visual Studio 2012 w/ Intel Fortran 13 (cmake) - Cygwin(CYGWIN_NT-6.1 1.7.15(0.260/5/3) gcc(4.5.3) compiler and gfortran) - (cmake and autotools) - - Windows 7 x64 Visual Studio 2008 w/ Intel Fortran 11 (cmake) - Visual Studio 2010 w/ Intel Fortran 12 (cmake) - Visual Studio 2012 w/ Intel Fortran 13 (cmake) - - Windows 8.1 Visual Studio 2012 w/ Intel Fortran 13 (cmake) - - Windows 8.1 x64 Visual Studio 2012 w/ Intel Fortran 13 (cmake) - - Mac OS X Snow Leopard 10.6.8 gcc i686-apple-darwin11-llvm-gcc-4.2 (GCC) 4.2.1 from Xcode 3.2.6 - Darwin Kernel Version 10.8.0 g++ i686-apple-darwin11-llvm-g++-4.2 (GCC) 4.2.1 from Xcode 3.2.6 - 64-bit gfortran GNU Fortran (GCC) 4.6.2 - (fred) Intel C (icc), Fortran (ifort), C++ (icpc) - 12.1 Build 20120928 - - Mac OS X Lion 10.7.3 Apple clang/clang++ version 3.0 from Xcode 4.6.1 - 64-bit gfortran GNU Fortran (GCC) 4.6.2 - (duck) Intel icc/icpc/ifort version 13.0.3 - - Mac OS X Mountain Lion 10.8.1 Apple clang/clang++ version 4.2 from Xcode 4.6.1 - 64-bit gfortran GNU Fortran (GCC) 4.6.2 - (wren) Intel icc/icpc/ifort version 13.0.3 - - OpenVMS IA64 V8.4 HP C V7.3-018 - HP Fortran V8.2-104939-50H96 - HP C++ V7.4-004 - -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/y n y y y -Windows 7 y y/y n y y y -Windows 7 x64 y y/y n y y y -Windows 7 Cygwin n y/n n y y y -Windows 8.1 n y/y n y y y -Windows 8.1 x64 n y/y n y y y -Mac OS X Snow Leopard 10.6.8 64-bit n y/y n y y y -Mac OS X Lion 10.7.3 64-bit n y/y n y y y -Mac OS X Mountain Lion 10.8.1 64-bit n y/y n y y y -AIX 5.3 32- and 64-bit n y/n n y y y -CentOS 5.9 Linux 2.6.18-308 i686 GNU y y/y y y y y -CentOS 5.9 Linux 2.6.18-308 i686 Intel n y/y n y y y -CentOS 5.9 Linux 2.6.18-308 i686 PGI n y/y n y y y -CentOS 5.9 Linux 2.6.18 x86_64 GNU y y/y y y y y -CentOS 5.9 Linux 2.6.18 x86_64 Intel n y/y n y y y -CentOS 5.9 Linux 2.6.18 x86_64 PGI n y/y n y y y -CentOS 6.4 Linux 2.6.32 x86_64 GNU n y/y n y y y -CentOS 6.4 Linux 2.6.32 x86_64 Intel n y/y n y y y -Linux 2.6.32-358.2.1.el6.ppc64 n y/n n y y y -OpenVMS IA64 V8.4 n y/n n y y n - -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 8.1 y y y y -Windows 8.1 x64 y y y y -Mac OS X Snow Leopard 10.6.8 64-bit y n y n -Mac OS X Lion 10.7.3 64-bit y n y y -Mac OS X Mountain Lion 10.8.1 64-bit y n y y -AIX 5.3 32- and 64-bit y n n y -CentOS 5.9 Linux 2.6.18-308 i686 GNU y y y y -CentOS 5.9 Linux 2.6.18-308 i686 Intel y y y n -CentOS 5.9 Linux 2.6.18-308 i686 PGI y y y n -CentOS 5.9 Linux 2.6.18 x86_64 GNU y y y y -CentOS 5.9 Linux 2.6.18 x86_64 Intel y y y n -CentOS 5.9 Linux 2.6.18 x86_64 PGI y y y n -CentOS 6.4 Linux 2.6.32 x86_64 GNU y y y n -CentOS 6.4 Linux 2.6.32 x86_64 Intel y y y n -Linux 2.6.32-358.2.1.el6.ppc64 y y y n -OpenVMS IA64 V8.4 n n n 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 2.6.18-308.13.1.el5PAE MPICH mpich2-1.4.1p1 compiled with - #1 SMP i686 i686 i386 gcc 4.1.2 and gfortran 4.1.2 - (jam) g95 (GCC 4.0.3 (g95 0.94!) - - Linux 2.6.18-308.16.1.el5 MPICH mpich2-1.4.1p1 compiled with - #1 SMP x86_64 GNU/Linux gcc 4.1.2 and gfortran 4.1.2 - (koala) g95 (GCC 4.0.3 (g95 0.94!) - - FreeBSD 8.2-STABLE i386 gcc 4.5.4 [FreeBSD] 20110526 - (loyalty) gcc 4.6.1 20110527 - g++ 4.6.1 20110527 - gfortran 4.6.1 20110527 - - FreeBSD 8.2-STABLE amd64 gcc 4.5.4 [FreeBSD] 20110526 - (freedom) gcc 4.6.1 20110527 - g++ 4.6.1 20110527 - gfortran 4.6.1 20110527 - - Debian7.1.0 3.2.0-4-amd64 #1 SMP Debian 3.2.46-1 x86_64 GNU/Linux - gcc (Debian 4.7.2-5) 4.7.2 - GNU Fortran (Debian 4.7.2-5) 4.7.2 - (cmake and autotools) - - Fedora19 3.11.1-200.fc19.x86_64 #1 SMP x86_64 x86_64 x86_64 GNU/Linux - gcc (GCC) 4.8.1 20130603 (Red Hat 4.8.1-1) - GNU Fortran (GCC) 4.8.1 20130603 (Red Hat 4.8.1-1) - (cmake and autotools) - - SUSE 12.3 3.7.10-1.16-desktop #1 SMP PREEMPT x86_64 x86_64 x86_64 GNU/Linux - gcc (SUSE Linux) 4.7.2 - GNU Fortran (SUSE Linux) 4.7.2 - (cmake and autotools) - - Ubuntu 13.04 3.8.0-30-generic #44-Ubuntu SMP x86_64 GNU/Linux - gcc (Ubuntu/Linaro 4.7.3-1ubuntu1) 4.7.3 - GNU Fortran (Ubuntu/Linaro 4.7.3-1ubuntu1) 4.7.3 - (cmake and autotools) - - Cray Linux Environment (CLE) PrgEnv-pgi/4.0.46 - hopper.nersc.gov pgcc 12.5-0 64-bit target on x86-64 Linux -tp shanghai - pgf90 12.5-0 64-bit target on x86-64 Linux -tp shanghai - pgCC 12.5-0 64-bit target on x86-64 Linux -tp shanghai - - -Known Problems -============== -* Several HDF5 command-line tools and tests leave behind generated files - that are not cleaned up with "make clean" or "make distclean" when software - is built in place. The issue will be addressed in the 1.8.13 release. We - recommend to use build directory to compile and test HDF5 as described - in the INSTALL file, section 4.2. - -* Source directory names with spaces in them will cause failures in configure - or make on Mac (HDFFV-8152), Linux, and probably all other platforms. If a - configure command with a space is run from a build directory, it will exit - with an error message: "checking whether build environment is sane... - configure: error: unsafe srcdir value: '/scr/lrknox/hdf5 v1.8.12'". If - configure is run inside or below the directory with the space in the name, - libtool will get the directory path from the system, put the part of the - path before the space in the libdir variable in .../src/libhdf5.la, and - then fail to find the nonexistent directory. This is a known libtool issue - and the suggested workaround is to rename the directory without spaces. - (LRK - 2013/10/22) - -* CLANG compiler with the options -fcatch-undefined-behavior and -ftrapv - catches some undefined behavior in the alignment algorithm of the macro - DETECT_I in H5detect.c (HDFFV-8147). This issue will be addressed in the - next release. (SLU - 2013/10/16) - -* Running make check for the tools can fail in the tools tests if make was not - run prior. The tests for the tools use other tools in the tests, therefore - all the tools should be built before testing the tools. (ADB - 2013/10/09) - -* Make provided by Solaris fails in "make check". Solaris users should use - gmake to build and install HDF5 software. (AKC - 2013/10/08 - HDFFV-8534) - -* On OpenVMS, two soft conversion functions (H5T__conv_i_f and H5T__conv_f_i) - have bugs. They convert data between floating-point numbers and integers. - But the library's default is hard conversion. The user should avoid - explicitly enabling soft conversion between floating-point numbers and - integers. (Issue VMS-8; SLU - 2013/09/19) - -* On OpenVMS, ZLIB 1.2.8 library doesn't work properly. ZLIB 1.2.5 works - fine. So please use ZLIB 1.2.5 to build HDF5 library. (Issue VMS-5; - SLU 2013/09/19) - -* When building using the Cray compilers on Cray machines, HDF5 - configure mistakenly thinks the compiler is an intel compiler and - sets the -std=c99 flag which breaks configure on Cray. To build HDF5 - properly on a Cray machine, please consult with the instructions in - INSTALL_parallel for building on Hopper. - (MSC - 2013/04/26 - HDFFV-8429) - -* The h5dump and h5diff utilities occasionally produce different output - between Linux and Windows systems. This is caused by lower-level library - routines that fail to write fill values to the user's buffer when reading - unallocated chunks from datasets that have a fill value set to - H5D_FILL_VALUE_DEFAULT. Due to platform differences the return of - spurious data values has only been encountered on Windows 32-bit systems. - (Issue HDFFV-8247; JP - 2013/03/27) - -* The 5.9 C++ compiler on Sun failed to compile a C++ test ttypes.cpp. It - complains with this message: - "/home/hdf5/src/H5Vprivate.h", line 130: Error: __func__ is not defined. - - The reason is that __func__ is a predefined identifier in C99 standard. The - HDF5 C library uses it in H5private.h. The test ttypes.cpp includes - H5private.h (H5Tpkg.h<-H5Fprivate.h<-H5Vprivate.h<-H5private.h). Sun's 5.9 - C++ compiler doesn't support __func__, thus fails to compile the C++ test. - But Sun's 5.11 C++ compiler does. To check whether your Sun C++ compiler - knows this identifier, try to compile the following simple C++ program: - #include<stdio.h> - - int main(void) - { - printf("%s\n", __func__); - return 0; - } - (SLU - 2012/11/5) - -* The C++ and FORTRAN bindings are not currently working on FreeBSD with the - native release 8.2 compilers (4.2.1), but are working with gcc 4.6 from the - ports (and probably gcc releases after that). - (QAK - 2012/10/19) - -* The following h5dump test case fails in BG/P machines (and potentially other - machines that use a command script to launch executables): - - h5dump --no-compact-subset -d "AHFINDERDIRECT::ah_centroid_t[0] it=0 tl=0" - tno-subset.h5 - - This is due to the embedded spaces in the dataset name being interpreted - by the command script launcher as meta-characters, thus passing three - arguments to h5dump's -d flag. The command passes if run by hand, just - not via the test script. - (AKC - 2012/05/03) - -* On hopper, the build failed when RUNSERIAL and RUNPARALLEL are set - to aprun -np X, because the H5lib_settings.c file was not generated - properly. Not setting those environment variables works, because - configure was able to automatically detect that it is a Cray system - and used the proper launch commands when necessary. - (MSC - 2012/04/18) - -* The data conversion test dt_arith.c fails in "long double" to integer - conversion on Ubuntu 11.10 (3.0.0.13 kernel) with GCC 4.6.1 if the library - is built with optimization -O3 or -O2. The older GCC (4.5) or newer kernel - (3.2.2 on Fedora) do not have the problem. Users should lower the - optimization level (-O1 or -O0) by defining CFLAGS in the command line of - "configure" like: - - CFLAGS=-O1 ./configure - - This will overwrite the library's default optimization level. - (SLU - 2012/02/07 - HDFFV-7829) - This issue is no longer present on Ubuntu 12.10 (3.5.0 kernel) with - gcc 4.7.2. - -* The STDIO VFD does not work on some architectures, possibly due to 32/64 - bit or large file issues. The basic STDIO VFD test is known to fail on - 64-bit SunOS 5.10 on SPARC when built with -m64 and 32-bit OS X/Darwin - 10.7.0. The STDIO VFD test has been disabled while we investigate and - a fix should appear in a future release. - (DER - 2011/10/14 - HDFFV-8235) - -* h5diff can report inconsistent results when comparing datasets of enum type - that contain invalid values. This is due to how enum types are handled in - the library and will be addressed in a future release. - (DER - 2011/10/14 - HDFFV-7527) - -* The links test can fail under the stdio VFD due to some issues with external - links. This will be investigated and fixed in a future release. - (DER - 2011/10/14 - HDFFV-7768) - -* After the shared library support was fixed for some bugs, it was discovered - that "make prefix=XXX install" no longer works for shared libraries. It - still works correctly for static libraries. Therefore, if you want to - install the HDF5 shared libraries in a location such as /usr/local/hdf5, - you need to specify the location via the --prefix option during configure - time. E.g, ./configure --prefix=/usr/local/hdf5 ... - (AKC - 2011/05/07 - HDFFV-7583) - -* The parallel test, t_shapesame, in testpar/, may run for a long time and may - be terminated by the alarm signal. If that happens, one can increase the - alarm seconds (default is 1200 seconds = 20 minutes) by setting the - environment variable, $HDF5_ALARM_SECONDS, to a larger value such as 3600 - (60 minutes). Note that the t_shapesame test may fail in some systems - (see the "While working on the 1.8.6 release..." problem below). If - it does, it will waste more time if $HDF5_ALARM_SECONDS is set - to a larger value. - (AKC - 2011/05/07) - -* The C++ and FORTRAN bindings are not currently working on FreeBSD. - (QAK - 2011/04/26) - -* Shared Fortran libraries are not quite working on AIX. While they are - generated when --enable-shared is specified, the fortran and hl/fortran - tests fail. We are looking into the issue. HL and C++ shared libraries - should now be working as intended, however. - (MAM - 2011/04/20) - -* The --with-mpe configure option does not work with Mpich2. - (AKC - 2011/03/10) - -* While working on the 1.8.6 release of HDF5, a bug was discovered that can - occur when reading from a dataset in parallel shortly after it has been - written to collectively. The issue was exposed by a new test in the parallel - HDF5 test suite, but had existed before that. We believe the problem lies with - certain MPI implementations and/or file systems. - - We have provided a pure MPI test program, as well as a standalone HDF5 - program, that can be used to determine if this is an issue on your system. - They should be run across multiple nodes with a varying number of processes. - These programs can be found at: - http://www.hdfgroup.org/ftp/HDF5/examples/known_problems/ - (NAF - 2011/01/19) - -* All the VFL drivers aren't backward compatible. In H5FDpublic.h, the - structure H5FD_class_t changed in 1.8. There is new parameter added to - get_eoa and set_eoa callback functions. A new callback function - get_type_map was added in. The public function H5FDrealloc was taken - out in 1.8. The problem only happens when users define their own driver - for 1.6 and try to plug in 1.8 library. Because there's only one user - complaining about it, we (Elena, Quincey, and I) decided to leave it as - it is (see bug report #1279). Quincey will make a plan for 1.10. - (SLU - 2010/02/02) - -* The --enable-static-exec configure flag will only statically link libraries - if the static version of that library is present. If only the shared version - of a library exists (i.e., most system libraries on Solaris, AIX, and Mac, - for example, only have shared versions), the flag should still result in a - successful compilation, but note that the installed executables will not be - fully static. Thus, the only guarantee on these systems is that the - executable is statically linked with just the HDF5 library. - (MAM - 2009/11/04) - -* Parallel tests failed with 16 processes with data inconsistency at testphdf5 - / dataset_readAll. Parallel tests also failed with 32 and 64 processes with - collective abort of all ranks at t_posix_compliant / allwrite_allread_blocks - with MPI IO. - (CMC - 2009/04/28) - -* On an Intel 64 Linux cluster (RH 4, Linux 2.6.9) with Intel 10.0 compilers, - use -mp -O1 compilation flags to build the libraries. A higher level of - optimization causes failures in several HDF5 library tests. - -* A dataset created or rewritten with a v1.6.3 library or after cannot be read - with the v1.6.2 library or before when the Fletcher32 EDC filter is enabled. - There was a bug in the calculation of the Fletcher32 checksum in the - library before v1.6.3; the checksum value was not consistent between big- - endian and little-endian systems. This bug was fixed in Release 1.6.3. - However, after fixing the bug, the checksum value was no longer the same as - before on little-endian system. Library releases after 1.6.4 can still read - datasets created or rewritten with an HDF5 library of v1.6.2 or before. - (SLU - 2005/06/30) - - -%%%%1.8.11%%%% - - -HDF5 version 1.8.11 released on 2013-05-08 -================================================================================ - -INTRODUCTION -============ - -This document describes the differences between HDF5-1.8.10 and -HDF5-1.8.11-*, and contains information on the platforms tested and -known problems in HDF5-1.8.11-*. -For more details, see the files HISTORY-1_0-1_8_0_rc3.txt -and HISTORY-1_8.txt in the release_docs/ directory of the HDF5 source. - -Links to the HDF5 1.8.11 source code, documentation, and additional materials -can be found on the HDF5 web page at: - - http://www.hdfgroup.org/products/hdf5/ - -The HDF5 1.8.11 release can be obtained from: - - http://www.hdfgroup.org/HDF5/release/obtain5.html - -User documentation for 1.8.11 can be accessed directly at this location: - - http://www.hdfgroup.org/HDF5/doc/ - -New features in the HDF5-1.8.x release series, including brief general -descriptions of some new and modified APIs, are described in the "What's New -in 1.8.0?" document: - - http://www.hdfgroup.org/HDF5/doc/ADGuide/WhatsNew180.html - -All new and modified APIs are listed in detail in the "HDF5 Software Changes -from Release to Release" document, in the section "Release 1.8.11 (current -release) versus Release 1.8.10": - - http://www.hdfgroup.org/HDF5/doc/ADGuide/Changes.html - -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, Languages, and Compilers -- Bug Fixes since HDF5-1.8.10 -- Supported Platforms -- Supported Configuration Features Summary -- More Tested Platforms -- Known Problems - - -New Features -============ - - Configuration - ------------- - - Libtool version number is changed to 8.0.0 because there are API - changes. See below for details. (AKC - 2013/05/07 HDFFV-8435) - - Mac OS X 10.7 (Lion) and 10.8 (Mountain Lion) uses clang/clang++ as the - default C and C++ compilers. (AKC - 2013/04/19 HDFFV-8245) - - CMake minimum is now 2.8.10. (ADB 2013/1/14) - - A new tool, cmakehdf5, which is a build command script similar to - buildhdf5 is added and is available in the bin directory. - (AKC - 2013/01/16 HDFFV-8336) - - Library - ------- - - The library can load filter libraries dynamically during runtime. Users - can set the search path through environment variable HDF5_PLUGIN_PATH - and call H5Pset_filter to enable a dynamic filter. (SLU - 2013/04/08) - - Added new API functions H5Dscatter and H5Dgather to scatter data to and - and gather data from a selection within a memory buffer. - (NAF - 2013/02/05) - - The library now supports the data conversion from enumeration to numeric - (integer and floating-point number) datatypes. See Issue HDFFV-8221. - (SLU - 2012/10/23) - - Parallel Library - ---------------- - - None - - Tools - ----- - - h5dump: added new option -O or -ddl to output the ddl text to a file. This - is a complement to the -o or --output option, which redirects the data to - a file. HDFFV-8229 (ADB - 2013/2/25) - - High-Level APIs - --------------- - - A new API function, H5DOwrite_chunk. This function writes a data chunk - directly into a file, bypassing hyperslab selection, data conversion, - and the filter pipeline. The user must be careful with the function and - clearly understand the I/O process of the library. (SLU - 2013/2/11) - - Fortran API - ----------- - - New API functions added (MSB - 2013/3/23): - - h5odecr_refcount_f, h5oexists_by_name_f, h5oget_comment_f, - h5oget_comment_by_name_f, h5oincr_refcount_f, h5oopen_by_idx_f, - h5oset_comment_f, h5oset_comment_by_name_f, h5oset_comment_by_name_f - - F2003: h5oget_info_f, h5oget_info_by_idx_f, h5ovisit_by_name_f - - - C++ API - ------- - - None - - -Support for New Platforms, Languages, and Compilers -=================================================== - - SunOS 5.11 (emu) 32-bit and 64-bit with Sun C/C++ 5.12 compiler and - Sun Fortran 95 8.6 compiler. - - Visual Studio 2012 w/ Intel Fortran 13 on Windows 7 - - g95 released new version recently and is tested in this release. - -Bug Fixes since HDF5-1.8.10 -========================== - - Configuration - ------------- - - Fixed Thread-safe configure failure for the AIX platform. - (AKC - 2013/04/19 HDFFV-8390) - - Configure will check the result of header searches before searching for - the library. - Fixes HDFFV-8257 (ADB 2013/03/04) - - HDF does not support building SHARED Fortran libraries on OSX. Added - CMake code to check for this condition. - Fixes HDFFV-8227 (ADB 2013/03/04) - - CMake builds on Windows will no longer use legacy naming for libraries. - The "dll" tag will no longer be added to the name of *.lib and *.dll. - The option HDF_LEGACY_NAMING is now OFF by default. - Fixes HDFFV-8292 (ADB 2013/01/30) - - Library - ------- - - The library now behaves correctly when performing large I/O operations - on Mac OS-X. Previously, single I/O operations > 2 GB would fail - since the Darwin read/write calls cannot handle the number of bytes - that their parameter types imply. - Fixes HDFFV-7975 and HDFFV-8240 (DER 2013/01/07) - - Fixed a bug in the core VFD that causes failures when opening files - > 2 GB. - Fixes HDFFV-8124 and HDFFV-8158 (DER 2013/01/07) - - Fixed a bug where uninitialized memory was read during variable-length - type conversion. This caused segfaults in netCDF. Fixes HDFFV-8159. - (DER 2013/03/30) - - Removed the H5Pset/get_dxpl_multi functions from the library. The - intended functionality for them was never fully implemented, and they - have always been fundamentally broken. NOTE: This does not affect - setting the multi VFD or any expected VFD functionality. Multi VFD - usage remains unchanged. - Fixes HDFFV-8296. (DER 2013/03/30) - - Parallel Library - ---------------- - - None - - Performance - ------------- - - None - - Tools - ----- - - h5redeploy is changed to do this by default: - Installation directories: - prefix architecture-independent files. - exec_prefix architecture-dependent files, default is <prefix>. - libdir libraries, default is <exec_prefix>/lib. - includedir header files, default is <prefix/include>. - This allows users to just change the first line of prefix=<...> and the - effect will change libdir and includedir too. (AKC 2013/04/05 HDFFV-8358) - - h5repack: Fixed failure to convert the layout of a small chunked - dataset (size < 1K) to contiguous layout. HDFFV-8214 (JKM 2013/03/26) - - h5dump: Fixed displaying compression ratio for unknown or user-defined - filters. HDFFV-8344 (XCAO 2013/03/19) - - h5dump: Changed UNKNOWN_FILTER to USER_DEFINED_FILTER for user defined - filter. HDFFV-8346 (XCAO 2013/03/19) - - h5diff: Fixed to return the correct exit code 1 when the program - detects a unique extra attribute. Prior to this fix, h5diff returned - exit code 0 indicating the two files are identical. - HDFFV-7643 (JKM 2013/02/15) - - h5dump: Fixed writing nulls to a binary file when exporting a dataset - with compound string datatype. HDFFV-8169 (ADB 2013/1/31) - - The following h5stat test case failed in BG/P machines (and potentially - other machines that display extra output if an MPI task returns with a - non-zero code.) - Testing h5stat notexist.h5 - The test script was fixed to ignore the extra output. HDFFV-8233 - (AKC - 2012/11/30) - - h5diff: Improved speed when comparing HDF5 files with lots of - attributes. Much slower performance was identified with release versions - from 1.8.7 to 1.8.10 compared to 1.8.6. (JKM 2012/10/19) - - F90 API - ------- - - The integer type of the 'offset' argument in h5pset_external_f and - h5pget_external_f was changed to INTEGER(KIND=OFF_T) to support 8-byte - integers, matching the C type definition of off_t. (MSB - 2013/3/23) - - h5fc updated to recognize .f95, .f03 and .f08 file extensions. - - C++ API - ------ - - The C++ wrappers DSetMemXferPropList::setMulti/getMulti were removed - because the C functions H5Pset/get_dxpl_multi functions are removed - from the library. Fixes HDFFV-8296 by DER. (BMR 2013/03/30) - - An exception thrown by an internal function was not propagating to the - test program during stack unwinding, so it couldn't be caught by the - test, and the program terminated "without an active exception." It - seemed that the problem happened when c_str() was used to generate - an equivalent const char* from a std::string and the resulting string - was passed to the internal function. As a work-around, we added a - try/catch around the the call to the internal function and when the - exception is caught there, it is re-thrown. Fixes HDFFV-8067. - (BMR 2013/03/30) - - High-Level APIs: - ------ - - Fixed a problem with H5DSget_scale_name including the NULL terminator - in the size calculation returned by the function. The API was changed - to NOT include the NULL terminator in the size of name returned - (MSB- 2013/2/10) - - Fortran High-Level APIs: - ------ - - None - - Testing - ------- - - In some Mac systems, testlibinfo.sh failed with this error: - Check file ../src/.libs/libhdf5.7.dylib - strings: object: ../src/.libs/libhdf5.7.dylib malformed object \ - (unknown load command 15) - The strings command of Mac systems inspects library files, and older - versions of strings may not know newer library formats, resulting - in errors. Fixed by sending the library file as stdin to the strings - command to avoid this problem. (AKC - 2013/03/08 HDFFV-8305) - - Fixed a typo in the ERROR macro in test/testhdf5.h. It segmentation - faulted when used before. (AKC - 2013/02/12 HDFFV-8267) - -Supported Platforms -=================== -The following platforms are supported and have been tested for this release. -They are built with the configure process unless specified otherwise. - - AIX 5.3 xlc 10.1.0.5 - (NASA G-ADA) xlC 10.1.0.5 - xlf90 12.1.0.6 - - Linux 2.6.18-308.13.1.el5PAE GNU C (gcc), Fortran (gfortran), C++ (g++) - #1 SMP i686 i686 i386 compilers for 32-bit applications; - (jam) Version 4.1.2 20080704 (Red Hat 4.1.2-54) - Version 4.6.3 - PGI C, Fortran, C++ Compilers for 32-bit - applications; - Version 11.9-0 - Version 12.5-0 - Intel(R) C, C++, Fortran Compiler for 32-bit - applications; - Version 12.1 (Build 20110811) - Version 12.1 (Build 20120212) - - Linux 2.6.18-308.16.1.el5 GNU C (gcc), Fortran (gfortran), C++ (g++) - #1 SMP x86_64 GNU/Linux compilers for 64-bit applications; - (koala) Version 4.1.2 20080704 (Red Hat 4.1.2-52) - Version 4.6.3 - PGI C, Fortran, C++ for 64-bit target on - x86-64; - Version 11.9-0 - Version 12.5-0 - Intel(R) C, C++, Fortran Compilers for - applications running on Intel(R) 64; - Version 12.1 (Build 20110811) - Version 12.1 (Build 20120212) - - Linux 2.6.32-358.2.1.el6 GNU C (gcc), Fortran (gfortran), C++ (g++) - #1 SMP x86_64 GNU/Linux compilers: - (platypus) Version 4.4.7 20120313 - Intel(R) C (icc), C++ (icpc), Fortran (icc) - compilers: - Version 12.1 20120212 - - Linux 2.6.32-358.2.1.el6.ppc64 gcc (GCC) 4.4.7 20120313 (Red Hat 4.4.7-3) - #1 SMP ppc64 GNU/Linux g++ (GCC) 4.4.7 20120313 (Red Hat 4.4.7-3) - (ostrich) GNU Fortran (GCC) 4.4.7 20120313 (Red Hat 4.4.7-3) - IBM XL C/C++ V11.1 - IBM XL Fortran V13.1 - - 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 2008 w/ Intel Fortran 11 (cmake) - Visual Studio 2010 w/ Intel Fortran 12 (cmake) - Visual Studio 2012 w/ Intel Fortran 13 (cmake) - Cygwin(CYGWIN_NT-6.1 1.7.15(0.260/5/3) gcc(4.5.3) compiler and gfortran) - (cmake and autotools) - - Windows 7 x64 Visual Studio 2008 w/ Intel Fortran 11 (cmake) - Visual Studio 2010 w/ Intel Fortran 12 (cmake) - Visual Studio 2012 w/ Intel Fortran 13 (cmake) - Cygwin(CYGWIN_NT-6.1 1.7.15(0.260/5/3) gcc(4.5.3) compiler and gfortran) - (cmake and autotools) - - Mac OS X Snow Leopard 10.6.8 gcc i686-apple-darwin11-llvm-gcc-4.2 (GCC) 4.2.1 from Xcode 3.2.6 - Darwin Kernel Version 10.8.0 g++ i686-apple-darwin11-llvm-g++-4.2 (GCC) 4.2.1 from Xcode 3.2.6 - 64-bit gfortran GNU Fortran (GCC) 4.6.2 - (fred) Intel C (icc), Fortran (ifort), C++ (icpc) - 12.1 Build 20120928 - - Mac OS X Lion 10.7.3 Apple clang/clang++ version 3.0 from Xcode 4.6.1 - 64-bit gfortran GNU Fortran (GCC) 4.6.2 - (duck) Intel icc/icpc/ifort version 13.0 - - Mac OS X Mountain Lion 10.8.1 Apple clang/clang++ version 4.2 from Xcode 4.6.1 - 64-bit gfortran GNU Fortran (GCC) 4.6.2 - (wren) Intel icc/icpc/ifort version 13.0.1.119 - - -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 n y y y -Windows 7 Cygwin n y/n n y y y -Windows 7 x64 Cygwin n y/n n y y y -Mac OS X Snow Leopard 10.6.8 64-bit n y/y n y y y -Mac OS X Lion 10.7.3 64-bit n y/y n y y y -Mac OS X Mountain Lion 10.8.1 64-bit n y/y n y y y -AIX 5.3 32- and 64-bit n y/n n y y y -CentOS 5.9 Linux 2.6.18-308 i686 GNU y y/y y y y y -CentOS 5.9 Linux 2.6.18-308 i686 Intel n y/y n y y y -CentOS 5.9 Linux 2.6.18-308 i686 PGI n y/y n y y y -CentOS 5.9 Linux 2.6.18 x86_64 GNU y y/y y y y y -CentOS 5.9 Linux 2.6.18 x86_64 Intel n y/y n y y y -CentOS 5.9 Linux 2.6.18 x86_64 PGI n y/y n y y y -CentOS 6.4 Linux 2.6.32 x86_64 GNU n y/n n y y y -CentOS 6.4 Linux 2.6.32 x86_64 Intel n y/y n y y y -Linux 2.6.32-358.2.1.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 -Mac OS X Snow Leopard 10.6.8 64-bit y n y n -Mac OS X Lion 10.7.3 64-bit y n y y -Mac OS X Mountain Lion 10.8.1 64-bit y n y y -AIX 5.3 32- and 64-bit y n n y -CentOS 5.9 Linux 2.6.18-308 i686 GNU y y y y -CentOS 5.9 Linux 2.6.18-308 i686 Intel y y y n -CentOS 5.9 Linux 2.6.18-308 i686 PGI y y y n -CentOS 5.9 Linux 2.6.18 x86_64 GNU y y y y -CentOS 5.9 Linux 2.6.18 x86_64 Intel y y y n -CentOS 5.9 Linux 2.6.18 x86_64 PGI y y y n -CentOS 6.4 Linux 2.6.32 x86_64 GNU y y y n -CentOS 6.4 Linux 2.6.32 x86_64 Intel y y y n -Linux 2.6.32-358.2.1.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 2.6.18-308.13.1.el5PAE MPICH mpich2-1.4.1p1 compiled with - #1 SMP i686 i686 i386 gcc 4.1.2 and gfortran 4.1.2 - (jam) g95 (GCC 4.0.3 (g95 0.94!) - - Linux 2.6.18-308.16.1.el5 MPICH mpich2-1.4.1p1 compiled with - #1 SMP x86_64 GNU/Linux gcc 4.1.2 and gfortran 4.1.2 - (koala) g95 (GCC 4.0.3 (g95 0.94!) - - FreeBSD 8.2-STABLE i386 gcc 4.2.1 [FreeBSD] 20070719 - (loyalty) gcc 4.6.1 20110422 - g++ 4.6.1 20110422 - gfortran 4.6.1 20110422 - - FreeBSD 8.2-STABLE amd64 gcc 4.2.1 [FreeBSD] 20070719 - (freedom) gcc 4.6.1 20110422 - g++ 4.6.1 20110422 - gfortran 4.6.1 20110422 - - Debian6.0.7 2.6.32-5-amd64 #1 SMP x86_64 GNU/Linux - gcc (Debian 4.4.5-8) 4.4.5 - GNU Fortran (Debian 4.4.5-8) 4.4.5 - (cmake and autotools) - - Fedora18 3.7.9-205.fc18.x86_64 #1 SMP x86_64 x86_64 x86_64 GNU/Linux - gcc (GCC) 4.7.2 20121109 (Red Hat 4.7.2-8) - GNU Fortran (GCC) 4.7.2 20120507 (Red Hat 4.7.2-8) - (cmake and autotools) - - SUSE 12.3 3.7.10-1.1-desktop #1 SMP PREEMPT x86_64 x86_64 x86_64 GNU/Linux - gcc (SUSE Linux) 4.7.2 - GNU Fortran (SUSE Linux) 4.7.2 - (cmake and autotools) - - Ubuntu 12.10 3.5.0-25-generic #39-Ubuntu SMP x86_64 GNU/Linux - gcc (Ubuntu/Linaro 4.7.2-2ubuntu1) 4.7.2 - GNU Fortran (Ubuntu/Linaro 4.7.2-2ubuntu1) 4.7.2 - (cmake and autotools) - - Cray Linux Environment (CLE) PrgEnv-pgi/4.0.46 - hopper.nersc.gov pgcc 12.5-0 64-bit target on x86-64 Linux -tp shanghai - pgf90 12.5-0 64-bit target on x86-64 Linux -tp shanghai - pgCC 12.5-0 64-bit target on x86-64 Linux -tp shanghai - - -Known Problems -============== - -* When building using the Cray compilers on Cray machines, HDF5 - configure mistakenly thinks the compiler is an intel compiler and - sets the -std=c99 flag which breaks configure on Cray. To build HDF5 - properly on a Cray machine, please consult with the instructions in - INSTALL_parallel for building on Hopper. - (MSC - 2013/04/26 - HDFFV-8429) - -* The h5dump and h5diff utilities occasionally produce different output - between Linux and Windows systems. This is caused by lower-level library - routines that fail to write fill values to the user's buffer when reading - unallocated chunks from datasets that have a fill value set to - H5D_FILL_VALUE_DEFAULT. Due to platform differences the return of - spurious data values has only been encountered on Windows 32-bit systems. - (Issue HDFFV-8247; JP - 2013/03/27) - -* The 5.9 C++ compiler on Sun failed to compile a C++ test ttypes.cpp. It - complains with this message: - "/home/hdf5/src/H5Vprivate.h", line 130: Error: __func__ is not defined. - - The reason is that __func__ is a predefined identifier in C99 standard. The - HDF5 C library uses it in H5private.h. The test ttypes.cpp includes - H5private.h (H5Tpkg.h<-H5Fprivate.h<-H5Vprivate.h<-H5private.h). Sun's 5.9 - C++ compiler doesn't support __func__, thus fails to compile the C++ test. - But Sun's 5.11 C++ compiler does. To check whether your Sun C++ compiler - knows this identifier, try to compile the following simple C++ program: - #include<stdio.h> - - int main(void) - { - printf("%s\n", __func__); - return 0; - } - (SLU - 2012/11/5) - -* The C++ and FORTRAN bindings are not currently working on FreeBSD with the - native release 8.2 compilers (4.2.1), but are working with gcc 4.6 from the - ports (and probably gcc releases after that). - (QAK - 2012/10/19) - -* The following h5dump test case fails in BG/P machines (and potentially other - machines that use a command script to launch executables): - - h5dump --no-compact-subset -d "AHFINDERDIRECT::ah_centroid_t[0] it=0 tl=0" - tno-subset.h5 - - This is due to the embedded spaces in the dataset name being interpreted - by the command script launcher as meta-characters, thus passing three - arguments to h5dump's -d flag. The command passes if run by hand, just - not via the test script. - (AKC - 2012/05/03) - -* On hopper, the build failed when RUNSERIAL and RUNPARALLEL are set - to aprun -np X, because the H5lib_settings.c file was not generated - properly. Not setting those environment variables works, because - configure was able to automatically detect that it's a Cray system - and used the proper launch commands when necessary. - (MSC - 2012/04/18) - -* The data conversion test dt_arith.c fails in "long double" to integer - conversion on Ubuntu 11.10 (3.0.0.13 kernel) with GCC 4.6.1 if the library - is built with optimization -O3 or -O2. The older GCC (4.5) or newer kernel - (3.2.2 on Fedora) doesn't have the problem. Users should lower the - optimization level (-O1 or -O0) by defining CFLAGS in the command line of - "configure" like: - - CFLAGS=-O1 ./configure - - This will overwrite the library's default optimization level. - (SLU - 2012/02/07 - HDFFV-7829) - This issue is no longer present on Ubuntu 12.10 (3.5.0 kernel) with - gcc 4.7.2. - -* The STDIO VFD does not work on some architectures, possibly due to 32/64 - bit or large file issues. The basic STDIO VFD test is known to fail on - 64-bit SunOS 5.10 on SPARC when built with -m64 and 32-bit OS X/Darwin - 10.7.0. The STDIO VFD test has been disabled while we investigate and - a fix should appear in a future release. - (DER - 2011/10/14 - HDFFV-8235) - -* h5diff can report inconsistent results when comparing datasets of enum type - that contain invalid values. This is due to how enum types are handled in - the library and will be addressed in a future release. - (DER - 2011/10/14 - HDFFV-7527) - -* The links test can fail under the stdio VFD due to some issues with external - links. This will be investigated and fixed in a future release. - (DER - 2011/10/14 - HDFFV-7768) - -* After the shared library support was fixed for some bugs, it was discovered - that "make prefix=XXX install" no longer works for shared libraries. It - still works correctly for static libraries. Therefore, if you want to - install the HDF5 shared libraries in a location such as /usr/local/hdf5, - you need to specify the location via the --prefix option during configure - time. E.g, ./configure --prefix=/usr/local/hdf5 ... - (AKC - 2011/05/07 - HDFFV-7583) - -* The parallel test, t_shapesame, in testpar/, may run for a long time and may - be terminated by the alarm signal. If that happens, one can increase the - alarm seconds (default is 1200 seconds = 20 minutes) by setting the - environment variable, $HDF5_ALARM_SECONDS, to a larger value such as 3600 - (60 minutes). Note that the t_shapesame test may fail in some systems - (see the "While working on the 1.8.6 release..." problem below). If - it does, it will waste more time if $HDF5_ALARM_SECONDS is set - to a larger value. - (AKC - 2011/05/07) - -* The C++ and FORTRAN bindings are not currently working on FreeBSD. - (QAK - 2011/04/26) - -* Shared Fortran libraries are not quite working on AIX. While they are - generated when --enable-shared is specified, the fortran and hl/fortran - tests fail. We are looking into the issue. HL and C++ shared libraries - should now be working as intended, however. - (MAM - 2011/04/20) - -* The --with-mpe configure option does not work with Mpich2. - (AKC - 2011/03/10) - -* While working on the 1.8.6 release of HDF5, a bug was discovered that can - occur when reading from a dataset in parallel shortly after it has been - written to collectively. The issue was exposed by a new test in the parallel - HDF5 test suite, but had existed before that. We believe the problem lies with - certain MPI implementations and/or file systems. - - We have provided a pure MPI test program, as well as a standalone HDF5 - program, that can be used to determine if this is an issue on your system. - They should be run across multiple nodes with a varying number of processes. - These programs can be found at: - http://www.hdfgroup.org/ftp/HDF5/examples/known_problems/ - (NAF - 2011/01/19) - -* The library's test dt_arith.c showed a compiler's rounding problem on - Cygwin when converting from unsigned long long to long double. The - library's own conversion works fine. We defined a macro for Cygwin to - skip this test until we can solve the problem. - (SLU - 2010/05/05 - HDFFV-1264) - -* All the VFL drivers aren't backward compatible. In H5FDpublic.h, the - structure H5FD_class_t changed in 1.8. There is new parameter added to - get_eoa and set_eoa callback functions. A new callback function - get_type_map was added in. The public function H5FDrealloc was taken - out in 1.8. The problem only happens when users define their own driver - for 1.6 and try to plug in 1.8 library. Because there's only one user - complaining about it, we (Elena, Quincey, and I) decided to leave it as - it is (see bug report #1279). Quincey will make a plan for 1.10. - (SLU - 2010/02/02) - -* The --enable-static-exec configure flag will only statically link libraries - if the static version of that library is present. If only the shared version - of a library exists (i.e., most system libraries on Solaris, AIX, and Mac, - for example, only have shared versions), the flag should still result in a - successful compilation, but note that the installed executables will not be - fully static. Thus, the only guarantee on these systems is that the - executable is statically linked with just the HDF5 library. - (MAM - 2009/11/04) - -* Parallel tests failed with 16 processes with data inconsistency at testphdf5 - / dataset_readAll. Parallel tests also failed with 32 and 64 processes with - collective abort of all ranks at t_posix_compliant / allwrite_allread_blocks - with MPI IO. - (CMC - 2009/04/28) - -* On an Intel 64 Linux cluster (RH 4, Linux 2.6.9) with Intel 10.0 compilers, - use -mp -O1 compilation flags to build the libraries. A higher level of - optimization causes failures in several HDF5 library tests. - -* A dataset created or rewritten with a v1.6.3 library or after cannot be read - with the v1.6.2 library or before when the Fletcher32 EDC filter is enabled. - There was a bug in the calculation of the Fletcher32 checksum in the - library before v1.6.3; the checksum value was not consistent between big- - endian and little-endian systems. This bug was fixed in Release 1.6.3. - However, after fixing the bug, the checksum value was no longer the same as - before on little-endian system. Library releases after 1.6.4 can still read - datasets created or rewritten with an HDF5 library of v1.6.2 or before. - (SLU - 2005/06/30) - - -%%%%1.8.10-patch1%%%% - - -HDF5 version 1.8.10-patch1 released on 2013-01-22 -================================================================================ - -INTRODUCTION -============ - -This document describes the differences between HDF5-1.8.9 and -HDF5 1.8.10, and contains information on the platforms tested and -known problems in HDF5-1.8.10. -For more details, see the files HISTORY-1_0-1_8_0_rc3.txt -and HISTORY-1_8.txt in the release_docs/ directory of the HDF5 source. - -Links to the HDF5 1.8.10 source code, documentation, and additional materials -can be found on the HDF5 web page at: - - http://www.hdfgroup.org/products/hdf5/ - -The HDF5 1.8.10 release can be obtained from: - - http://www.hdfgroup.org/HDF5/release/obtain5.html - -User documentation for 1.8.10 can be accessed directly at this location: - - http://www.hdfgroup.org/HDF5/doc/ - -New features in the HDF5-1.8.x release series, including brief general -descriptions of some new and modified APIs, are described in the "What's New -in 1.8.0?" document: - - http://www.hdfgroup.org/HDF5/doc/ADGuide/WhatsNew180.html - -All new and modified APIs are listed in detail in the "HDF5 Software Changes -from Release to Release" document, in the section "Release 1.8.10 (current -release) versus Release 1.8.9": - - http://www.hdfgroup.org/HDF5/doc/ADGuide/Changes.html - -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, Languages, and Compilers -- Bug Fixes since HDF5-1.8.10 -- Bug Fixes since HDF5-1.8.9 -- Supported Platforms -- Supported Configuration Features Summary -- More Tested Platforms -- Known Problems - - -New Features -============ - - Configuration - ------------- - - A new tool, cmakehdf5, which is a build command script similar to - buildhdf5 is added and is available in the bin directory. - (AKC - 2013/01/21) - - Library - ------- - - Updated to latest autotools and changed all hard *.sh scripts to - configure managed *.sh.in files. Removed overloading of autotools - TESTS variable by examples and tests. Renamed configure.in to - configure.ac. (ADB - 2012/08/23 - HDFFV-8129) - - The data sieve buffer size was set for all the datasets in the file. It - could waste memory if any dataset size is smaller than the sieve buffer - size. Now the library picks the smaller one between the dataset size - and the sieve buffer size from the file access property. See Issue 7934. - (SLU - 2012/4/11) - - Parallel Library - ---------------- - - Added the H5Pget_mpio_no_collective_cause() function that retrieves - reasons why the collective I/O was broken during read/write IO access. - (JKM - 2012/08/30 HDFFV-8143) - - - Added H5Pget_mpio_actual_io_mode_f (MSB - 2012/09/27) - - Tools - ----- - - h5import: Changed to allow the use of h5dump output as input files to - h5import. h5dump must include the "-p" option to print the properties; - configuration file is captured output of h5dump. The restrictions are - that only one dataset with a simple datatype (integer, floating-point, - or string) can be processed. Integers and floating-point imports from - h5dump must use the "binary" option for the data file. The string version - uses the h5dump "-y --width=1" options to disable the indexing printouts, - print single columns, and obviously NOT use the "binary" option. - (ADB - 2012/07/19 HDFFV-721) - - High-Level APIs - --------------- - - None - - Fortran API - ----------- - - Fixed a typo in return value of the nh5dread_f_c function (was 1 - instead of 0 on success); fixed the return value to make it consistent - with other Fortran functions; cleaned debug statements from the code. - (EIP - 2012/06/23) - - C++ API - ------- - - None - - -Support for New Platforms, Languages, and Compilers -=================================================== - - None - -Bug Fixes since HDF5-1.8.10 -=========================== - Library - ------- - - The library now behaves correctly when performing large I/O operations on - Mac OS-X. Previously, single I/O operations > 2 GB would fail since the - Darwin read/write calls cannot handle the number of bytes that their - parameter types imply. - Fixes HDFFV-7975 and HDFFV-8240 (DER - 07 JAN 2013) - - Fixed a bug in the core VFD that cause failures when opening files > 2 GB. - Fixes HDFFV-8124 and HDFFV-8158 (DER - 07 JAN 2013) - - Tools - ----- - - The following h5stat test case failed in BG/P machines (and potentially - other machines that display extra output if an MPI task returns with a - non-zero code.) - Testing h5stat notexist.h5 - The test script was fixed to ignore the extra output. - HDFFV-8233 (AKC - 2012/12/17) - - h5diff: Fixed slowness when comparing HDF5 files with many attributes. - Much slower performance was identified with later release version - (from 1.8.7 to 1.8.10) compared to 1.8.6. The issue was introduced - from fixing an attribute related bug for 1.8.7 release in the past. - HDFFV-8145 (JKM 2012/12/13) - - Testing - ------- - - None - -Bug Fixes since HDF5-1.8.9 -========================== - - Configuration - ------------- - - Fixed configure --enable-production to not use -O optimization for Lion - and Mountain Lion systems when gcc (i686-apple-darwin11-llvm-gcc-4.2 - (GCC) 4.2.1) is used. Somehow the -O optimization will cause some of - the hard conversion code in test/dt_arith.c to fail. HDFFV-8017. - (AKC - 2012/10/10) - - Fixed AIX Fortran compiler flags to use appropriate settings for - debugging, profiling, and optimization situations. HDFFV-8069. - (AKC 2012/09/27) - - Library - ------- - - Fixed a memory leak exposed when inserting/removing a property - from a property list several times. HDFFV-8022. (MSC 2012/05/18) - - The file_image test will fail in the "initial file image and callbacks in - the core VFD" sub-test if the source directory is read-only as the test - fails to create its test files in the build directory. This has been - fixed. HDFFV-8009 (AKC - 2012/07/06) - - - Parallel Library - ---------------- - - The MPI-POSIX VFD was updated to include the POSIX and Windows - correctness features added that had already been added to the other VFDs. - HDFFV-8058/7845. (DER 2012/09/17) - - Performance - ------------- - - Removed program perform/benchpar from the enable-build-all list. The - program will be retired or moved to another location. HDFFV-8156 - (AKC 2012/10/01) - - Retired program perform/mpi-perf. Its purpose has been incorporated - into h5perf. (AKC 2012/09/21) - - Tools - ----- - - h5repack: "h5repack -f NONE file1.h5 out.h5" command failed if - source file contains chunked dataset and a chunk dim is bigger than - the dataset dim. Another issue is that the command changed max dims - if chunk dim is smaller than the dataset dim. These issue occurred - when dataset size is smaller than 64k (compact size limit) Fixed both. - HDFFV-8012 (JKM 2012/09/24) - - h5diff: Fixed the counter in verbose mode (-v, -r) so that it will no - longer add together the differences between datasets and the differences - between attributes of those datasets. This change makes the output of - verbose mode consistent for datasets, groups, and committed datatypes. - HDFFV-5919 (JKM 2012/09/10) - - h5diff: Fixed the incorrect result when comparing attribute data - values and the data type has the same class but different sizes. - HDFFV-7942 (JKM 2012/08/15) - - h5dump: Replaced single element fwrite with block writes. - HDFFV-1208 (ADB 2012/08/13) - - h5diff: Fixed test failure for "make check" due to failure of - copying test files when performed in HDF5 source tree. Also applied - to other tools. HDFFV-8107 (JKM 2012/08/01) - - ph5diff: Fixed intermittent hang issue on a certain operation in - parallel mode. It was detected by daily test for comparing - non-comparable objects, but it could have occurred in other - operations depending on machine condition. HDFFV-8003 (JKM 2012/08/01) - - h5diff: Fixed the function COPY_TESTFILES_TO_TESTDIR() of testh5diff.sh - to better report when there is an error in the file copying. - HDFFV-8105 (AKC 2012/07/22) - - h5dump: Fixed the sort by name display to maintain correct parent/child - relationships between ascending/descending order. - HDFFV-8095 (ADB 2012/07/12) - - h5dump: Fixed the display by creation order when using option -n - (print contents). - HDFFV-5942 (ADB 2012/07/09) - - h5dump: Changed to allow H5T_CSET_UTF8 to be displayed in h5dump output. - Used technique similar to what was done in h5ls (matches library - options). - HDFFV-7999 (ADB 2012/05/23) - - h5diff: Fixed the tool so that it will not check and display the status - of dangling links without setting the --follow-symlinks option. This - also improved performance when comparing lots of external links without - the --follow-symlinks option. - HDFFV-7998 (JKM 2012/04/26) - - F90 API - ------- - - - Fixed a typo in return value of the nh5dread_f_c function (was 1 - instead of 0 on success); fixed the return value to make it consistent - with other Fortran functions; cleaned debug statements from the code. - (EIP - 2012/06/23) - - - Fixed a problem writing/reading control characters to a dataset; writing - a string containing alerts, backspace, carriage_return, form_feed, - horizontal_tab, vertical_tab, or new_line is now tested and working. - (MSB - 2012/09/01) - - - Corrected the integer type of H5S_UNLIMITED_F to HSIZE_T (MSB - 2012/09/01) - - - Corrected the number of continuation lines in the src files - to be less than 32 lines for F95 compliance. (MSB - 2012/10/01) - - C++ API - ------ - - None - - High-Level APIs: - ------ - - - Fixed problem with H5TBdelete_record destroying all data following the - deletion of a row. (MSB- 2012/7/26) - - - Fixed H5LTget_attribute_string not closing an object identifier when an - error occurs. (MSB- 2012/7/21) - - - Corrected the return type of H5TBAget_fill from herr_t to htri_t to - reflect that a return value of 1 indicates that a fill value is - present, 0 indicates a fill value is not present, and <0 indicates an - error. - - Fortran High-Level APIs: - ------ - - None - -Supported Platforms -=================== - AIX 5.3 xlc 10.1.0.5 - (NASA G-ADA) xlC 10.1.0.5 - xlf90 12.1.0.6 - - Linux 2.6.18-308.13.1.el5PAE GNU C (gcc), Fortran (gfortran), C++ (g++) - #1 SMP i686 i686 i386 compilers for 32-bit applications; - (jam) Version 4.1.2 20080704 (Red Hat 4.1.2-52) - Version 4.6.3 - PGI C, Fortran, C++ Compilers for 32-bit - applications; - Version 11.9-0 - Intel(R) C, C++, Fortran Compiler for 32-bit - applications; - Version 12.1 - MPICH mpich2-1.4.1p1 compiled with - gcc 4.1.2 and gfortran 4.1.2 - - Linux 2.6.18-308.16.1.el5 GNU C (gcc), Fortran (gfortran), C++ (g++) - #1 SMP x86_64 GNU/Linux compilers for 32-bit applications; - (koala) Version 4.1.2 20080704 (Red Hat 4.1.2-52) - Version 4.6.3 - PGI C, Fortran, C++ for 64-bit target on - x86-64; - Version 11.9-0 - Version 12.5-0 - Intel(R) C, C++, Fortran Compilers for - applications running on Intel(R) 64; - Version 12.1 (Build 20110811) - Version 12.1 (Build 20120212) - MPICH mpich2-1.4.1p1 compiled with - gcc 4.1.2 and gfortran 4.1.2 - - Linux 2.6.32-220.7.1.el6.ppc64 gcc (GCC) 4.4.6 20110731 (Red Hat 4.4.6-3) - #1 SMP ppc64 GNU/Linux g++ (GCC) 4.4.6 20110731 - (ostrich) GNU Fortran (GCC) 4.4.6 20110731 (Red Hat 4.4.6-3) - - Linux 2.6.32-220.23.1.1chaos Intel C, C++, Fortran Compilers - ch5.x86_64 GNU/Linux Version 12.1.5.339 - (LLNL Aztec) - - IBM Blue Gene/P XL C for Blue Gene/P, bgxlc V9.0 - (LLNL uDawn) XL C++ for Blue Gene/P, bgxlC V9.0 - XL Fortran for Blue Gene/P, bgxlf90 V11.1 - - SunOS 5.10 32- and 64-bit Sun C 5.9 Sun OS_sparc Patch 124867-16 - (linew) Sun Fortran 95 8.3 Sun OS_sparc Patch 127000-13 - Sun C++ 5.9 Sun OS_sparc Patch 124863-26 - Sun C 5.11 SunOS_sparc - Sun Fortran 95 8.5 SunOS_sparc - Sun C++ 5.11 SunOS_sparc - - Windows XP Visual Studio 2008 w/ Intel Fortran 10.1 (project files) - - Windows XP x64 Visual Studio 2008 w/ Intel Fortran 10.1 (project files) - - Windows 7 Visual Studio 2008 w/ Intel Fortran 11.1 (cmake) - Visual Studio 2010 w/ Intel Fortran 12 (cmake) - Cygwin(CYGWIN_NT-6.1 1.7.15(0.260/5/3) gcc(4.5.3) compiler and gfortran) - (cmake and autotools) - - Windows 7 x64 Visual Studio 2008 w/ Intel Fortran 11.1 (cmake) - Visual Studio 2010 w/ Intel Fortran 12 (cmake) - Cygwin(CYGWIN_NT-6.1 1.7.15(0.260/5/3) gcc(4.5.3) compiler and gfortran) - (cmake and autotools) - - Mac OS X Snow Leopard 10.6.8 gcc i686-apple-darwin11-llvm-gcc-4.2 (GCC) 4.2.1 from Xcode 3.2.6 - Darwin Kernel Version 10.8.0 g++ i686-apple-darwin11-llvm-g++-4.2 (GCC) 4.2.1 from Xcode 3.2.6 - (fred) gfortran GNU Fortran (GCC) 4.6.2 - Intel C (icc), Fortran (ifort), C++ (icpc) - 12.1.0.038 Build 20110811 - - Mac OS X Snow Leopard 10.6.8 gcc i686-apple-darwin11-llvm-gcc-4.2 (GCC) 4.2.1 from Xcode 3.2.6 - Darwin Kernel Version 10.8.0 g++ i686-apple-darwin11-llvm-g++-4.2 (GCC) 4.2.1 from Xcode 3.2.6 - Intel 32-bit gfortran GNU Fortran (GCC) 4.6.1 - (tejeda) Intel C (icc), Fortran (ifort), C++ (icpc) - 12.1.0.038 Build 20110811 - - Mac OS X Lion 10.7.3 gcc i686-apple-darwin11-llvm-gcc-4.2 (GCC) 4.2.1 from Xcode 4.2.1 - 32- and 64-bit g++ i686-apple-darwin11-llvm-g++-4.2 (GCC) 4.2.1 from Xcode 4.2.1 - (duck) gfortran GNU Fortran (GCC) 4.6.2 - - Mac OS X Mountain Lion 10.8.1 cc Apple clang version 4.0 from Xcode 4.5.1 - (owl) c++ Apple clang version 4.0 from Xcode 4.5.1 - gcc i686-apple-darwin11-llvm-gcc-4.2 (GCC) 4.2.1 from Xcode 4.5.1 - g++ i686-apple-darwin11-llvm-g++-4.2 (GCC) 4.2.1 from Xcode 4.5.1 - gfortran GNU Fortran (GCC) 4.6.2 - - -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 -Solaris2.10 32-bit n y/y n y y y -Solaris2.10 64-bit n y/n n y y y -Windows 7 y y/n n y y y -Windows 7 x64 y y/n n y y y -Mac OS X Snow Leopard 10.6.8 32-bit n y/y n y y n -Mac OS X Snow Leopard 10.6.8 64-bit n y/y n y y y -Mac OS X Lion 10.7.3 32-bit n y/y n y y n -Mac OS X Lion 10.7.3 64-bit n y/y n y y y -Mac OS X Mountain Lion 10.8.1 64-bit n y/n n y y n -AIX 5.3 32- and 64-bit y y/n y y y y -CentOS 5.5 Linux 2.6.18-308 i686 GNU y y/y y y y y -CentOS 5.5 Linux 2.6.18-308 i686 Intel n y/y n y y y -CentOS 5.5 Linux 2.6.18-308 i686 PGI n y/y n y y y -CentOS 5.5 Linux 2.6.18 x86_64 GNU y y/y y y y y -CentOS 5.5 Linux 2.6.18 x86_64 Intel n y/y n y y y -CentOS 5.5 Linux 2.6.18 x86_64 PGI n y/y n y y y -Linux 2.6.32-220.7.1.el6.ppc64 n y/n n y y y - - -Platform Shared Shared Shared Thread- - C libs F90 libs C++ libs safe -Solaris2.10 32-bit y y y y -Solaris2.10 64-bit n n n n -Windows 7 y y y y -Windows 7 x64 y y y y -Mac OS X Snow Leopard 10.6.8 32-bit y n y n -Mac OS X Snow Leopard 10.6.8 64-bit y n y n -Mac OS X Lion 10.7.3 32-bit y n y y -Mac OS X Lion 10.7.3 64-bit y n y y -Mac OS X Mountain Lion 10.8.1 64-bit y n y y -AIX 5.3 32- and 64-bit n n n y -CentOS 5.5 Linux 2.6.18-308 i686 GNU y y y y -CentOS 5.5 Linux 2.6.18-308 i686 Intel y y y n -CentOS 5.5 Linux 2.6.18-308 i686 PGI y y y n -CentOS 5.5 Linux 2.6.18 x86_64 GNU y y y y -CentOS 5.5 Linux 2.6.18 x86_64 Intel y y y n -CentOS 5.5 Linux 2.6.18 x86_64 PGI y y y n -Linux 2.6.32-220.7.1.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. - - FreeBSD 8.2-STABLE i386 gcc 4.2.1 [FreeBSD] 20070719 - (loyalty) gcc 4.6.1 20110422 - g++ 4.6.1 20110422 - gfortran 4.6.1 20110422 - - FreeBSD 8.2-STABLE amd64 gcc 4.2.1 [FreeBSD] 20070719 - (freedom) gcc 4.6.1 20110422 - g++ 4.6.1 20110422 - gfortran 4.6.1 20110422 - - Debian6.0.3 2.6.32-5-686 #1 SMP i686 GNU/Linux - gcc (Debian 4.4.5-8) 4.4.5 - GNU Fortran (Debian 4.4.5-8) 4.4.5 - (cmake and autotools) - - Debian6.0.3 2.6.32-5-amd64 #1 SMP x86_64 GNU/Linux - gcc (Debian 4.4.5-8) 4.4.5 - GNU Fortran (Debian 4.4.5-8) 4.4.5 - (cmake and autotools) - - Fedora17 3.5.2-1.fc17.i6866 #1 SMP i686 i686 i386 GNU/Linux - gcc (GCC) 4.7.0 20120507 (Red Hat 4.7.0-5) - GNU Fortran (GCC) 4.7.0 20120507 (Red Hat 4.7.0-5) - (cmake and autotools) - - Fedora17 3.5.2-1.fc17.x86_64 #1 SMP x86_64 x86_64 x86_64 GNU/Linux - gcc (GCC) 4.7.0 20120507 (Red Hat 4.7.0-5) - GNU Fortran (GCC) 4.7.0 20120507 (Red Hat 4.7.0-5) - (cmake and autotools) - - SUSE 12.2 3.4.6-2.10-desktop #1 SMP PREEMPT i686 i686 i386 GNU/Linux - gcc (SUSE Linux) 4.7.1 - GNU Fortran (SUSE Linux) 4.7.1 - (cmake and autotools) - - SUSE 12.2 3.4.6-2.10-desktop #1 SMP PREEMPT x86_64 x86_64 x86_64 GNU/Linux - gcc (SUSE Linux) 4.7.1 - GNU Fortran (SUSE Linux) 4.7.1 - (cmake and autotools) - - Ubuntu 12.04 3.2.0-29-generic #46-Ubuntu SMP i686 GNU/Linux - gcc (Ubuntu/Linaro 4.6.3-1ubuntu5) 4.6.3 - GNU Fortran (Ubuntu/Linaro 4.6.3-1ubuntu5) 4.6.3 - (cmake and autotools) - - Ubuntu 12.04 3.2.0-29-generic #46-Ubuntu SMP x86_64 GNU/Linux - gcc (Ubuntu/Linaro 4.6.3-1ubuntu5) 4.6.3 - GNU Fortran (Ubuntu/Linaro 4.6.3-1ubuntu5) 4.6.3 - (cmake and autotools) - (Use optimization level -O1) - - Cray Linux Environment (CLE) PrgEnv-pgi/4.0.46 - hopper.nersc.gov pgcc 12.5-0 64-bit target on x86-64 Linux -tp shanghai - pgf90 12.5-0 64-bit target on x86-64 Linux -tp shanghai - pgCC 12.5-0 64-bit target on x86-64 Linux -tp shanghai - - -Known Problems -============== -* The C++ and FORTRAN bindings are not currently working on FreeBSD with the - native release 8.2 compilers (4.2.1), but are working with gcc 4.6 from the - ports (and probably gcc releases after that). - (QAK - 2012/10/19) - -* The following h5dump test case fails in BG/P machines (and potentially other - machines that use a command script to launch executables): - - h5dump --no-compact-subset -d "AHFINDERDIRECT::ah_centroid_t[0] it=0 tl=0" - tno-subset.h5 - - This is due to the embedded spaces in the dataset name being interpreted - by the command script launcher as meta-characters, thus passing three - arguments to h5dump's -d flag. The command passes if run by hand, just - not via the test script. - (AKC - 2012/05/03) - -* On hopper, the build failed when RUNSERIAL and RUNPARALLEL are set - to aprun -np X, because the H5lib_settings.c file was not generated - properly. Not setting those environment variables works, because - configure was able to automatically detect that it's a Cray system - and used the proper launch commands when necessary. - (MSC - 2012/04/18) - -* The data conversion test dt_arith.c fails in "long double" to integer - conversion on Ubuntu 11.10 (3.0.0.13 kernel) with GCC 4.6.1 if the library - is built with optimization -O3 or -O2. The older GCC (4.5) or newer kernel - (3.2.2 on Fedora) doesn't have the problem. Users should lower the - optimization level (-O1 or -O0) by defining CFLAGS in the command line of - "configure" like: - - CFLAGS=-O1 ./configure - - This will overwrite the library's default optimization level. - (SLU - 2012/02/07 - HDFFV-7829) - -* The STDIO VFD does not work on some architectures, possibly due to 32/64 - bit or large file issues. The basic STDIO VFD test is known to fail on - 64-bit SunOS 5.10 on SPARC when built with -m64 and 32-bit OS X/Darwin - 10.7.0. The STDIO VFD test has been disabled while we investigate and - a fix should appear in a future release. - (DER - 2011/10/14 - HDFFV-8235) - -* h5diff can report inconsistent results when comparing datasets of enum type - that contain invalid values. This is due to how enum types are handled in - the library and will be addressed in a future release. - (DER - 2011/10/14 - HDFFV-7527) - -* The links test can fail under the stdio VFD due to some issues with external - links. This will be investigated and fixed in a future release. - (DER - 2011/10/14 - HDFFV-7768) - -* After the shared library support was fixed for some bugs, it was discovered - that "make prefix=XXX install" no longer works for shared libraries. It - still works correctly for static libraries. Therefore, if you want to - install the HDF5 shared libraries in a location such as /usr/local/hdf5, - you need to specify the location via the --prefix option during configure - time. E.g, ./configure --prefix=/usr/local/hdf5 ... - (AKC - 2011/05/07 - HDFFV-7583) - -* The parallel test, t_shapesame, in testpar/, may run for a long time and may - be terminated by the alarm signal. If that happens, one can increase the - alarm seconds (default is 1200 seconds = 20 minutes) by setting the - environment variable, $HDF5_ALARM_SECONDS, to a larger value such as 3600 - (60 minutes). Note that the t_shapesame test may fail in some systems - (see the "While working on the 1.8.6 release..." problem below). If - it does, it will waste more time if $HDF5_ALARM_SECONDS is set - to a larger value. - (AKC - 2011/05/07) - -* The C++ and FORTRAN bindings are not currently working on FreeBSD. - (QAK - 2011/04/26) - -* Shared Fortran libraries are not quite working on AIX. While they are - generated when --enable-shared is specified, the fortran and hl/fortran - tests fail. We are looking into the issue. HL and C++ shared libraries - should now be working as intended, however. - (MAM - 2011/04/20) - -* The --with-mpe configure option does not work with Mpich2. - (AKC - 2011/03/10) - -* While working on the 1.8.6 release of HDF5, a bug was discovered that can - occur when reading from a dataset in parallel shortly after it has been - written to collectively. The issue was exposed by a new test in the parallel - HDF5 test suite, but had existed before that. We believe the problem lies with - certain MPI implementations and/or file systems. - - We have provided a pure MPI test program, as well as a standalone HDF5 - program, that can be used to determine if this is an issue on your system. - They should be run across multiple nodes with a varying number of processes. - These programs can be found at: - http://www.hdfgroup.org/ftp/HDF5/examples/known_problems/ - (NAF - 2011/01/19) - -* The library's test dt_arith.c showed a compiler's rounding problem on - Cygwin when converting from unsigned long long to long double. The - library's own conversion works fine. We defined a macro for Cygwin to - skip this test until we can solve the problem. - (SLU - 2010/05/05 - HDFFV-1264) - -* All the VFL drivers aren't backward compatible. In H5FDpublic.h, the - structure H5FD_class_t changed in 1.8. There is new parameter added to - get_eoa and set_eoa callback functions. A new callback function - get_type_map was added in. The public function H5FDrealloc was taken - out in 1.8. The problem only happens when users define their own driver - for 1.6 and try to plug in 1.8 library. Because there's only one user - complaining about it, we (Elena, Quincey, and I) decided to leave it as - it is (see bug report #1279). Quincey will make a plan for 1.10. - (SLU - 2010/02/02) - -* The --enable-static-exec configure flag will only statically link libraries - if the static version of that library is present. If only the shared version - of a library exists (i.e., most system libraries on Solaris, AIX, and Mac, - for example, only have shared versions), the flag should still result in a - successful compilation, but note that the installed executables will not be - fully static. Thus, the only guarantee on these systems is that the - executable is statically linked with just the HDF5 library. - (MAM - 2009/11/04) - -* Parallel tests failed with 16 processes with data inconsistency at testphdf5 - / dataset_readAll. Parallel tests also failed with 32 and 64 processes with - collective abort of all ranks at t_posix_compliant / allwrite_allread_blocks - with MPI IO. - (CMC - 2009/04/28) - -* On an Intel 64 Linux cluster (RH 4, Linux 2.6.9) with Intel 10.0 compilers, - use -mp -O1 compilation flags to build the libraries. A higher level of - optimization causes failures in several HDF5 library tests. - -* A dataset created or rewritten with a v1.6.3 library or after cannot be read - with the v1.6.2 library or before when the Fletcher32 EDC filter is enabled. - There was a bug in the calculation of the Fletcher32 checksum in the - library before v1.6.3; the checksum value was not consistent between big- - endian and little-endian systems. This bug was fixed in Release 1.6.3. - However, after fixing the bug, the checksum value was no longer the same as - before on little-endian system. Library releases after 1.6.4 can still read - datasets created or rewritten with an HDF5 library of v1.6.2 or before. - (SLU - 2005/06/30) - - -%%%%1.8.10%%%% - - -HDF5 version 1.8.10 released on 2012-10-26 -================================================================================ - -INTRODUCTION -============ - -This document describes the differences between HDF5-1.8.9 and -HDF5 1.8.10, and contains information on the platforms tested and -known problems in HDF5-1.8.10. -For more details, see the files HISTORY-1_0-1_8_0_rc3.txt -and HISTORY-1_8.txt in the release_docs/ directory of the HDF5 source. - -Links to the HDF5 1.8.10 source code, documentation, and additional materials -can be found on the HDF5 web page at: - - http://www.hdfgroup.org/products/hdf5/ - -The HDF5 1.8.10 release can be obtained from: - - http://www.hdfgroup.org/HDF5/release/obtain5.html - -User documentation for 1.8.10 can be accessed directly at this location: - - http://www.hdfgroup.org/HDF5/doc/ - -New features in the HDF5-1.8.x release series, including brief general -descriptions of some new and modified APIs, are described in the "What's New -in 1.8.0?" document: - - http://www.hdfgroup.org/HDF5/doc/ADGuide/WhatsNew180.html - -All new and modified APIs are listed in detail in the "HDF5 Software Changes -from Release to Release" document, in the section "Release 1.8.10 (current -release) versus Release 1.8.9": - - http://www.hdfgroup.org/HDF5/doc/ADGuide/Changes.html - -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, Languages, and Compilers -- Bug Fixes since HDF5-1.8.9 -- Supported Platforms -- Supported Configuration Features Summary -- More Tested Platforms -- Known Problems - - -New Features -============ - - Configuration - ------------- - - None - - Library - ------- - - Updated to latest autotools and changed all hard *.sh scripts to - configure managed *.sh.in files. Removed overloading of autotools - TESTS variable by examples and tests. Renamed configure.in to - configure.ac. (ADB - 2012/08/23 - HDFFV-8129) - - The data sieve buffer size was set for all the datasets in the file. It - could waste memory if any dataset size is smaller than the sieve buffer - size. Now the library picks the smaller one between the dataset size - and the sieve buffer size from the file access property. See Issue 7934. - (SLU - 2012/4/11) - - Parallel Library - ---------------- - - Added the H5Pget_mpio_no_collective_cause() function that retrieves - reasons why the collective I/O was broken during read/write IO access. - (JKM - 2012/08/30 HDFFV-8143) - - - Added H5Pget_mpio_actual_io_mode_f (MSB - 2012/09/27) - - Tools - ----- - - h5import: Changed to allow the use of h5dump output as input files to - h5import. h5dump must include the "-p" option to print the properties; - configuration file is captured output of h5dump. The restrictions are - that only one dataset with a simple datatype (integer, floating-point, - or string) can be processed. Integers and floating-point imports from - h5dump must use the "binary" option for the data file. The string version - uses the h5dump "-y --width=1" options to disable the indexing printouts, - print single columns, and obviously NOT use the "binary" option. - (ADB - 2012/07/19 HDFFV-721) - - High-Level APIs - --------------- - - None - - Fortran API - ----------- - - Fixed a typo in return value of the nh5dread_f_c function (was 1 - instead of 0 on success); fixed the return value to make it consistent - with other Fortran functions; cleaned debug statements from the code. - (EIP - 2012/06/23) - - C++ API - ------- - - None - - -Support for New Platforms, Languages, and Compilers -=================================================== - - None - -Bug Fixes since HDF5-1.8.9 -========================== - - Configuration - ------------- - - Fixed configure --enable-production to not use -O optimization for Lion - and Mountain Lion systems when gcc (i686-apple-darwin11-llvm-gcc-4.2 - (GCC) 4.2.1) is used. Somehow the -O optimization will cause some of - the hard conversion code in test/dt_arith.c to fail. HDFFV-8017. - (AKC - 2012/10/10) - - Fixed AIX Fortran compiler flags to use appropriate settings for - debugging, profiling, and optimization situations. HDFFV-8069. - (AKC 2012/09/27) - - Library - ------- - - Fixed a memory leak exposed when inserting/removing a property - from a property list several times. HDFFV-8022. (MSC 2012/05/18) - - The file_image test will fail in the "initial file image and callbacks in - the core VFD" sub-test if the source directory is read-only as the test - fails to create its test files in the build directory. This has been - fixed. HDFFV-8009 (AKC - 2012/07/06) - - - Parallel Library - ---------------- - - The MPI-POSIX VFD was updated to include the POSIX and Windows - correctness features added that had already been added to the other VFDs. - HDFFV-8058/7845. (DER 2012/09/17) - - Performance - ------------- - - Removed program perform/benchpar from the enable-build-all list. The - program will be retired or moved to another location. HDFFV-8156 - (AKC 2012/10/01) - - Retired program perform/mpi-perf. Its purpose has been incorporated - into h5perf. (AKC 2012/09/21) - - Tools - ----- - - h5repack: "h5repack -f NONE file1.h5 out.h5" command failed if - source file contains chunked dataset and a chunk dim is bigger than - the dataset dim. Another issue is that the command changed max dims - if chunk dim is smaller than the dataset dim. These issue occurred - when dataset size is smaller than 64k (compact size limit) Fixed both. - HDFFV-8012 (JKM 2012/09/24) - - h5diff: Fixed the counter in verbose mode (-v, -r) so that it will no - longer add together the differences between datasets and the differences - between attributes of those datasets. This change makes the output of - verbose mode consistent for datasets, groups, and committed datatypes. - HDFFV-5919 (JKM 2012/09/10) - - h5diff: Fixed the incorrect result when comparing attribute data - values and the data type has the same class but different sizes. - HDFFV-7942 (JKM 2012/08/15) - - h5dump: Replaced single element fwrite with block writes. - HDFFV-1208 (ADB 2012/08/13) - - h5diff: Fixed test failure for "make check" due to failure of - copying test files when performed in HDF5 source tree. Also applied - to other tools. HDFFV-8107 (JKM 2012/08/01) - - ph5diff: Fixed intermittent hang issue on a certain operation in - parallel mode. It was detected by daily test for comparing - non-comparable objects, but it could have occurred in other - operations depending on machine condition. HDFFV-8003 (JKM 2012/08/01) - - h5diff: Fixed the function COPY_TESTFILES_TO_TESTDIR() of testh5diff.sh - to better report when there is an error in the file copying. - HDFFV-8105 (AKC 2012/07/22) - - h5dump: Fixed the sort by name display to maintain correct parent/child - relationships between ascending/descending order. - HDFFV-8095 (ADB 2012/07/12) - - h5dump: Fixed the display by creation order when using option -n - (print contents). - HDFFV-5942 (ADB 2012/07/09) - - h5dump: Changed to allow H5T_CSET_UTF8 to be displayed in h5dump output. - Used technique similar to what was done in h5ls (matches library - options). - HDFFV-7999 (ADB 2012/05/23) - - h5diff: Fixed the tool so that it will not check and display the status - of dangling links without setting the --follow-symlinks option. This - also improved performance when comparing lots of external links without - the --follow-symlinks option. - HDFFV-7998 (JKM 2012/04/26) - - F90 API - ------- - - - Fixed a typo in return value of the nh5dread_f_c function (was 1 - instead of 0 on success); fixed the return value to make it consistent - with other Fortran functions; cleaned debug statements from the code. - (EIP - 2012/06/23) - - - Fixed a problem writing/reading control characters to a dataset; writing - a string containing alerts, backspace, carriage_return, form_feed, - horizontal_tab, vertical_tab, or new_line is now tested and working. - (MSB - 2012/09/01) - - - Corrected the integer type of H5S_UNLIMITED_F to HSIZE_T (MSB - 2012/09/01) - - - Corrected the number of continuation lines in the src files - to be less than 32 lines for F95 compliance. (MSB - 2012/10/01) - - C++ API - ------ - - None - - High-Level APIs: - ------ - - - Fixed problem with H5TBdelete_record destroying all data following the - deletion of a row. (MSB- 2012/7/26) - - - Fixed H5LTget_attribute_string not closing an object identifier when an - error occurs. (MSB- 2012/7/21) - - - Corrected the return type of H5TBAget_fill from herr_t to htri_t to - reflect that a return value of 1 indicates that a fill value is - present, 0 indicates a fill value is not present, and <0 indicates an - error. - - Fortran High-Level APIs: - ------ - - None - -Supported Platforms -=================== - AIX 5.3 xlc 10.1.0.5 - (NASA G-ADA) xlC 10.1.0.5 - xlf90 12.1.0.6 - - Linux 2.6.18-308.13.1.el5PAE GNU C (gcc), Fortran (gfortran), C++ (g++) - #1 SMP i686 i686 i386 compilers for 32-bit applications; - (jam) Version 4.1.2 20080704 (Red Hat 4.1.2-52) - Version 4.6.3 - PGI C, Fortran, C++ Compilers for 32-bit - applications; - Version 11.9-0 - Intel(R) C, C++, Fortran Compiler for 32-bit - applications; - Version 12.1 - MPICH mpich2-1.4.1p1 compiled with - gcc 4.1.2 and gfortran 4.1.2 - - Linux 2.6.18-308.16.1.el5 GNU C (gcc), Fortran (gfortran), C++ (g++) - #1 SMP x86_64 GNU/Linux compilers for 32-bit applications; - (koala) Version 4.1.2 20080704 (Red Hat 4.1.2-52) - Version 4.6.3 - PGI C, Fortran, C++ for 64-bit target on - x86-64; - Version 11.9-0 - Version 12.5-0 - Intel(R) C, C++, Fortran Compilers for - applications running on Intel(R) 64; - Version 12.1 (Build 20110811) - Version 12.1 (Build 20120212) - MPICH mpich2-1.4.1p1 compiled with - gcc 4.1.2 and gfortran 4.1.2 - - Linux 2.6.32-220.7.1.el6.ppc64 gcc (GCC) 4.4.6 20110731 (Red Hat 4.4.6-3) - #1 SMP ppc64 GNU/Linux g++ (GCC) 4.4.6 20110731 - (ostrich) GNU Fortran (GCC) 4.4.6 20110731 (Red Hat 4.4.6-3) - - Linux 2.6.32-220.23.1.1chaos Intel C, C++, Fortran Compilers - ch5.x86_64 GNU/Linux Version 12.1.5.339 - (LLNL Aztec) - - IBM Blue Gene/P XL C for Blue Gene/P, bgxlc V9.0 - (LLNL uDawn) XL C++ for Blue Gene/P, bgxlC V9.0 - XL Fortran for Blue Gene/P, bgxlf90 V11.1 - - SunOS 5.10 32- and 64-bit Sun C 5.9 Sun OS_sparc Patch 124867-16 - (linew) Sun Fortran 95 8.3 Sun OS_sparc Patch 127000-13 - Sun C++ 5.9 Sun OS_sparc Patch 124863-26 - Sun C 5.11 SunOS_sparc - Sun Fortran 95 8.5 SunOS_sparc - Sun C++ 5.11 SunOS_sparc - - Windows XP Visual Studio 2008 w/ Intel Fortran 10.1 (project files) - - Windows XP x64 Visual Studio 2008 w/ Intel Fortran 10.1 (project files) - - Windows 7 Visual Studio 2008 w/ Intel Fortran 11.1 (cmake) - Visual Studio 2010 w/ Intel Fortran 12 (cmake) - Cygwin(CYGWIN_NT-6.1 1.7.15(0.260/5/3) gcc(4.5.3) compiler and gfortran) - (cmake and autotools) - - Windows 7 x64 Visual Studio 2008 w/ Intel Fortran 11.1 (cmake) - Visual Studio 2010 w/ Intel Fortran 12 (cmake) - Cygwin(CYGWIN_NT-6.1 1.7.15(0.260/5/3) gcc(4.5.3) compiler and gfortran) - (cmake and autotools) - - Mac OS X Snow Leopard 10.6.8 gcc i686-apple-darwin11-llvm-gcc-4.2 (GCC) 4.2.1 from Xcode 3.2.6 - Darwin Kernel Version 10.8.0 g++ i686-apple-darwin11-llvm-g++-4.2 (GCC) 4.2.1 from Xcode 3.2.6 - (fred) gfortran GNU Fortran (GCC) 4.6.2 - Intel C (icc), Fortran (ifort), C++ (icpc) - 12.1.0.038 Build 20110811 - - Mac OS X Snow Leopard 10.6.8 gcc i686-apple-darwin11-llvm-gcc-4.2 (GCC) 4.2.1 from Xcode 3.2.6 - Darwin Kernel Version 10.8.0 g++ i686-apple-darwin11-llvm-g++-4.2 (GCC) 4.2.1 from Xcode 3.2.6 - Intel 32-bit gfortran GNU Fortran (GCC) 4.6.1 - (tejeda) Intel C (icc), Fortran (ifort), C++ (icpc) - 12.1.0.038 Build 20110811 - - Mac OS X Lion 10.7.3 gcc i686-apple-darwin11-llvm-gcc-4.2 (GCC) 4.2.1 from Xcode 4.2.1 - 32- and 64-bit g++ i686-apple-darwin11-llvm-g++-4.2 (GCC) 4.2.1 from Xcode 4.2.1 - (duck) gfortran GNU Fortran (GCC) 4.6.2 - - Mac OS X Mountain Lion 10.8.1 cc Apple clang version 4.0 from Xcode 4.5.1 - (owl) c++ Apple clang version 4.0 from Xcode 4.5.1 - gcc i686-apple-darwin11-llvm-gcc-4.2 (GCC) 4.2.1 from Xcode 4.5.1 - g++ i686-apple-darwin11-llvm-g++-4.2 (GCC) 4.2.1 from Xcode 4.5.1 - gfortran GNU Fortran (GCC) 4.6.2 - - -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 -Solaris2.10 32-bit n y/y n y y y -Solaris2.10 64-bit n y/n n y y y -Windows 7 y y/n n y y y -Windows 7 x64 y y/n n y y y -Mac OS X Snow Leopard 10.6.8 32-bit n y/y n y y n -Mac OS X Snow Leopard 10.6.8 64-bit n y/y n y y y -Mac OS X Lion 10.7.3 32-bit n y/y n y y n -Mac OS X Lion 10.7.3 64-bit n y/y n y y y -Mac OS X Mountain Lion 10.8.1 64-bit n y/n n y y n -AIX 5.3 32- and 64-bit y y/n y y y y -CentOS 5.5 Linux 2.6.18-308 i686 GNU y y/y y y y y -CentOS 5.5 Linux 2.6.18-308 i686 Intel n y/y n y y y -CentOS 5.5 Linux 2.6.18-308 i686 PGI n y/y n y y y -CentOS 5.5 Linux 2.6.18 x86_64 GNU y y/y y y y y -CentOS 5.5 Linux 2.6.18 x86_64 Intel n y/y n y y y -CentOS 5.5 Linux 2.6.18 x86_64 PGI n y/y n y y y -Linux 2.6.32-220.7.1.el6.ppc64 n y/n n y y y - - -Platform Shared Shared Shared Thread- - C libs F90 libs C++ libs safe -Solaris2.10 32-bit y y y y -Solaris2.10 64-bit n n n n -Windows 7 y y y y -Windows 7 x64 y y y y -Mac OS X Snow Leopard 10.6.8 32-bit y n y n -Mac OS X Snow Leopard 10.6.8 64-bit y n y n -Mac OS X Lion 10.7.3 32-bit y n y y -Mac OS X Lion 10.7.3 64-bit y n y y -Mac OS X Mountain Lion 10.8.1 64-bit y n y y -AIX 5.3 32- and 64-bit n n n y -CentOS 5.5 Linux 2.6.18-308 i686 GNU y y y y -CentOS 5.5 Linux 2.6.18-308 i686 Intel y y y n -CentOS 5.5 Linux 2.6.18-308 i686 PGI y y y n -CentOS 5.5 Linux 2.6.18 x86_64 GNU y y y y -CentOS 5.5 Linux 2.6.18 x86_64 Intel y y y n -CentOS 5.5 Linux 2.6.18 x86_64 PGI y y y n -Linux 2.6.32-220.7.1.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. - - FreeBSD 8.2-STABLE i386 gcc 4.2.1 [FreeBSD] 20070719 - (loyalty) gcc 4.6.1 20110422 - g++ 4.6.1 20110422 - gfortran 4.6.1 20110422 - - FreeBSD 8.2-STABLE amd64 gcc 4.2.1 [FreeBSD] 20070719 - (freedom) gcc 4.6.1 20110422 - g++ 4.6.1 20110422 - gfortran 4.6.1 20110422 - - Debian6.0.3 2.6.32-5-686 #1 SMP i686 GNU/Linux - gcc (Debian 4.4.5-8) 4.4.5 - GNU Fortran (Debian 4.4.5-8) 4.4.5 - (cmake and autotools) - - Debian6.0.3 2.6.32-5-amd64 #1 SMP x86_64 GNU/Linux - gcc (Debian 4.4.5-8) 4.4.5 - GNU Fortran (Debian 4.4.5-8) 4.4.5 - (cmake and autotools) - - Fedora17 3.5.2-1.fc17.i6866 #1 SMP i686 i686 i386 GNU/Linux - gcc (GCC) 4.7.0 20120507 (Red Hat 4.7.0-5) - GNU Fortran (GCC) 4.7.0 20120507 (Red Hat 4.7.0-5) - (cmake and autotools) - - Fedora17 3.5.2-1.fc17.x86_64 #1 SMP x86_64 x86_64 x86_64 GNU/Linux - gcc (GCC) 4.7.0 20120507 (Red Hat 4.7.0-5) - GNU Fortran (GCC) 4.7.0 20120507 (Red Hat 4.7.0-5) - (cmake and autotools) - - SUSE 12.2 3.4.6-2.10-desktop #1 SMP PREEMPT i686 i686 i386 GNU/Linux - gcc (SUSE Linux) 4.7.1 - GNU Fortran (SUSE Linux) 4.7.1 - (cmake and autotools) - - SUSE 12.2 3.4.6-2.10-desktop #1 SMP PREEMPT x86_64 x86_64 x86_64 GNU/Linux - gcc (SUSE Linux) 4.7.1 - GNU Fortran (SUSE Linux) 4.7.1 - (cmake and autotools) - - Ubuntu 12.04 3.2.0-29-generic #46-Ubuntu SMP i686 GNU/Linux - gcc (Ubuntu/Linaro 4.6.3-1ubuntu5) 4.6.3 - GNU Fortran (Ubuntu/Linaro 4.6.3-1ubuntu5) 4.6.3 - (cmake and autotools) - - Ubuntu 12.04 3.2.0-29-generic #46-Ubuntu SMP x86_64 GNU/Linux - gcc (Ubuntu/Linaro 4.6.3-1ubuntu5) 4.6.3 - GNU Fortran (Ubuntu/Linaro 4.6.3-1ubuntu5) 4.6.3 - (cmake and autotools) - (Use optimization level -O1) - - Cray Linux Environment (CLE) PrgEnv-pgi/4.0.46 - hopper.nersc.gov pgcc 12.5-0 64-bit target on x86-64 Linux -tp shanghai - pgf90 12.5-0 64-bit target on x86-64 Linux -tp shanghai - pgCC 12.5-0 64-bit target on x86-64 Linux -tp shanghai - - -Known Problems -============== -* The following h5stat test case fails in BG/P machines (and potentially other - machines that display extra output if an MPI task returns with a non-zero - code.) - Testing h5stat notexist.h5 - - The test actually runs and passes as expected. It is the extra output from - the MPI process that causes the test script to fail. This will be fixed - in the next release. (AKC - 2012/10/25 - HDFFV-8233) - -* The C++ and FORTRAN bindings are not currently working on FreeBSD with the - native release 8.2 compilers (4.2.1), but are working with gcc 4.6 from the - ports (and probably gcc releases after that). - (QAK - 2012/10/19) - -* The following h5dump test case fails in BG/P machines (and potentially other - machines that use a command script to launch executables): - - h5dump --no-compact-subset -d "AHFINDERDIRECT::ah_centroid_t[0] it=0 tl=0" - tno-subset.h5 - - This is due to the embedded spaces in the dataset name being interpreted - by the command script launcher as meta-characters, thus passing three - arguments to h5dump's -d flag. The command passes if run by hand, just - not via the test script. - (AKC - 2012/05/03) - -* On hopper, the build failed when RUNSERIAL and RUNPARALLEL are set - to aprun -np X, because the H5lib_settings.c file was not generated - properly. Not setting those environment variables works, because - configure was able to automatically detect that it's a Cray system - and used the proper launch commands when necessary. - (MSC - 2012/04/18) - -* The data conversion test dt_arith.c fails in "long double" to integer - conversion on Ubuntu 11.10 (3.0.0.13 kernel) with GCC 4.6.1 if the library - is built with optimization -O3 or -O2. The older GCC (4.5) or newer kernel - (3.2.2 on Fedora) doesn't have the problem. Users should lower the - optimization level (-O1 or -O0) by defining CFLAGS in the command line of - "configure" like: - - CFLAGS=-O1 ./configure - - This will overwrite the library's default optimization level. - (SLU - 2012/02/07 - HDFFV-7829) - -* The STDIO VFD does not work on some architectures, possibly due to 32/64 - bit or large file issues. The basic STDIO VFD test is known to fail on - 64-bit SunOS 5.10 on SPARC when built with -m64 and 32-bit OS X/Darwin - 10.7.0. The STDIO VFD test has been disabled while we investigate and - a fix should appear in a future release. - (DER - 2011/10/14 - HDFFV-8235) - -* h5diff can report inconsistent results when comparing datasets of enum type - that contain invalid values. This is due to how enum types are handled in - the library and will be addressed in a future release. - (DER - 2011/10/14 - HDFFV-7527) - -* The links test can fail under the stdio VFD due to some issues with external - links. This will be investigated and fixed in a future release. - (DER - 2011/10/14 - HDFFV-7768) - -* After the shared library support was fixed for some bugs, it was discovered - that "make prefix=XXX install" no longer works for shared libraries. It - still works correctly for static libraries. Therefore, if you want to - install the HDF5 shared libraries in a location such as /usr/local/hdf5, - you need to specify the location via the --prefix option during configure - time. E.g, ./configure --prefix=/usr/local/hdf5 ... - (AKC - 2011/05/07 - HDFFV-7583) - -* The parallel test, t_shapesame, in testpar/, may run for a long time and may - be terminated by the alarm signal. If that happens, one can increase the - alarm seconds (default is 1200 seconds = 20 minutes) by setting the - environment variable, $HDF5_ALARM_SECONDS, to a larger value such as 3600 - (60 minutes). Note that the t_shapesame test may fail in some systems - (see the "While working on the 1.8.6 release..." problem below). If - it does, it will waste more time if $HDF5_ALARM_SECONDS is set - to a larger value. - (AKC - 2011/05/07) - -* The C++ and FORTRAN bindings are not currently working on FreeBSD. - (QAK - 2011/04/26) - -* Shared Fortran libraries are not quite working on AIX. While they are - generated when --enable-shared is specified, the fortran and hl/fortran - tests fail. We are looking into the issue. HL and C++ shared libraries - should now be working as intended, however. - (MAM - 2011/04/20) - -* The --with-mpe configure option does not work with Mpich2. - (AKC - 2011/03/10) - -* While working on the 1.8.6 release of HDF5, a bug was discovered that can - occur when reading from a dataset in parallel shortly after it has been - written to collectively. The issue was exposed by a new test in the parallel - HDF5 test suite, but had existed before that. We believe the problem lies with - certain MPI implementations and/or file systems. - - We have provided a pure MPI test program, as well as a standalone HDF5 - program, that can be used to determine if this is an issue on your system. - They should be run across multiple nodes with a varying number of processes. - These programs can be found at: - http://www.hdfgroup.org/ftp/HDF5/examples/known_problems/ - (NAF - 2011/01/19) - -* The library's test dt_arith.c showed a compiler's rounding problem on - Cygwin when converting from unsigned long long to long double. The - library's own conversion works fine. We defined a macro for Cygwin to - skip this test until we can solve the problem. - (SLU - 2010/05/05 - HDFFV-1264) - -* All the VFL drivers aren't backward compatible. In H5FDpublic.h, the - structure H5FD_class_t changed in 1.8. There is new parameter added to - get_eoa and set_eoa callback functions. A new callback function - get_type_map was added in. The public function H5FDrealloc was taken - out in 1.8. The problem only happens when users define their own driver - for 1.6 and try to plug in 1.8 library. Because there's only one user - complaining about it, we (Elena, Quincey, and I) decided to leave it as - it is (see bug report #1279). Quincey will make a plan for 1.10. - (SLU - 2010/02/02) - -* The --enable-static-exec configure flag will only statically link libraries - if the static version of that library is present. If only the shared version - of a library exists (i.e., most system libraries on Solaris, AIX, and Mac, - for example, only have shared versions), the flag should still result in a - successful compilation, but note that the installed executables will not be - fully static. Thus, the only guarantee on these systems is that the - executable is statically linked with just the HDF5 library. - (MAM - 2009/11/04) - -* Parallel tests failed with 16 processes with data inconsistency at testphdf5 - / dataset_readAll. Parallel tests also failed with 32 and 64 processes with - collective abort of all ranks at t_posix_compliant / allwrite_allread_blocks - with MPI IO. - (CMC - 2009/04/28) - -* On an Intel 64 Linux cluster (RH 4, Linux 2.6.9) with Intel 10.0 compilers, - use -mp -O1 compilation flags to build the libraries. A higher level of - optimization causes failures in several HDF5 library tests. - -* A dataset created or rewritten with a v1.6.3 library or after cannot be read - with the v1.6.2 library or before when the Fletcher32 EDC filter is enabled. - There was a bug in the calculation of the Fletcher32 checksum in the - library before v1.6.3; the checksum value was not consistent between big- - endian and little-endian systems. This bug was fixed in Release 1.6.3. - However, after fixing the bug, the checksum value was no longer the same as - before on little-endian system. Library releases after 1.6.4 can still read - datasets created or rewritten with an HDF5 library of v1.6.2 or before. - (SLU - 2005/06/30) - - -%%%%1.8.9%%%% - - -HDF5 version 1.8.9 released on 2012-05-09 -================================================================================ - -INTRODUCTION -============ - -This document describes the differences between HDF5-1.8.8 and -HDF5 1.8.9. It also contains information on the platforms tested and -known problems in HDF5-1.8.9. - -For more details, see the files HISTORY-1_0-1_8_0_rc3.txt -and HISTORY-1_8.txt in the release_docs/ directory of the HDF5 source. - -Links to the HDF5 1.8.9 source code, documentation, and additional materials -can be found on the HDF5 web page at: - - http://www.hdfgroup.org/products/hdf5/ - -The HDF5 1.8.9 release can be obtained from: - - http://www.hdfgroup.org/HDF5/release/obtain5.html - -User documentation for 1.8.9 can be accessed directly at this location: - - http://www.hdfgroup.org/HDF5/doc/ - -New features in the HDF5-1.8.x release series, including brief general -descriptions of some new and modified APIs, are described in the "What's New -in 1.8.0?" document: - - http://www.hdfgroup.org/HDF5/doc/ADGuide/WhatsNew180.html - -All new and modified APIs are listed in detail in the "HDF5 Software Changes -from Release to Release" document, in the section "Release 1.8.9 (current -release) versus Release 1.8.8": - - http://www.hdfgroup.org/HDF5/doc/ADGuide/Changes.html - -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, Languages, and Compilers -- Bug Fixes since HDF5-1.8.8 -- Platforms Tested -- Supported Configuration Features Summary -- Known Problems - - -New Features -============ - - Configuration - ------------- - - None - - Library - ------- - - Added new feature to merge committed datatypes when copying objects, - using new H5O_COPY_MERGE_COMMITTED_DTYPE_FLAG, modified by new API - routines: H5Padd_merge_committed_dtype_path(), - H5Pfree_merge_committed_dtype_paths(), H5Pset_mcdt_search_cb() and - H5Pget_mcdt_search_cb(). (QAK - 2012/03/30) - - Added new feature which allows working with files in memory in the - same ways files are worked with on disk. New API routines include - H5Pset_file_image, H5Pget_file_image, H5Pset_file_image_callbacks, - H5Pget_file_image_callbacks, H5Fget_file_image, and - H5LTopen_file_image. (QAK - 2012/04/17) - - Parallel Library - ---------------- - - Corrected memory allocation error in MPI datatype construction code. - (QAK - 2012/04/23) - - Add two new routines to set/get the atomicity parameter in the - MPI library to perform atomic operations. Some file systems (for - example PVFS2) do not support atomic updates, so those routines - would not be supported. (MSC - 2012/03/27 - HDFFV-7961) - - Tools - ----- - - h5repack: Added ability to set the metadata block size of the output - file, with the '-M'/'--metadata_block_size' command line parameter. - (QAK - 2012/03/30) - - h5stat: Added ability to display a summary of the file space usage for a - file, with the '-S'/'--summary' command line parameter. (QAK - 2012/03/28) - - h5dump: Added capability for "-a" option to show attributes containing "/" - by using an escape character. For example, for a dataset "/dset" - containing attribute "speed(m/h)", use "h5dump -a "/dset/speed(\/h)" - to show the content of the attribute. (PC - 2012/03/12 - HDFFV-7523) - - h5dump: Added ability to apply command options across multiple files using a - wildcard in the filename. Unix example; "h5dump -H -d Dataset1 tarr*.h5". - Cross platform example; "h5dump -H -d Dataset1 tarray1.h5 tarray2.h5 tarray3.h5". - (ADB - 2012/03/12 - HDFFV-7876). - - h5dump: Added new option --no-compact-subset. This option will not - interpret the '[' character as starting the compact form of - subsetting. This is useful when the "h5dump error: unable to - open dataset "datset_name"" message is output because a dataset - name contains a '[' character. (ADB - 2012/03/05 - HDFFV-7689). - - h5repack: Improved performance for big chunked datasets (size > 128MB) - when used with the layout (-l) or compression (-f) options. - Before this change, repacking datasets with chunks with a large first - dimension would take extremely long. For example, repacking a dataset - with chunk dimensions of 1024x5x1 might take many hours to process - while changing a dataset with chunk dimensions set to 1x5x1024 - might take under an hour. After this change, processing the dataset - with chunk dimensions of 1024x5x1 takes about 15 minutes, and processing - a dataset with chunk dimensions of 1x5x1024 takes about 14 minutes. - (JKM - 2012/03/01 - HDFFV-7862) - - High-Level APIs - --------------- - - New API: H5LTpath_valid (Fortran: h5ltpath_valid_f) checks - if a path is correct, determines if a link resolves to a valid - object, and checks that the link does not dangle. (MSB - 2012/03/15) - - Fortran API - ----------- - - - Added for the C API the Fortran wrapper: - h5ocopy_f (MSB - 2012/03/22) - - C++ API - ------- - - None - - -Support for New Platforms, Languages, and Compilers -=================================================== - - None - -Bug Fixes since HDF5-1.8.8 -========================== - - Configuration - ------------- - - Fixed Makefile issue in which "-Wl," was not properly specified - prior to -rpath when building parallel Fortran libraries with - an Intel compiler. (MAM - 2012/03/26) - - Makefiles generated by other packages using h5cc as the compiler - no longer error when 'make' is invoked more than once in order - to 'rebuild' after changes to source. (MAM - 2012/03/26) - - Added code to display the version information of XL Fortran and C++ - in the summary of configure. (AKC - 2012/02/28 - HDFFV-7793) - - Updated all CMakeLists.txt files to indicate the minimum CMake version is - the current standard of 2.8.6 (ADB - 2011/12/05 - HDFFV-7854) - - Library - ------- - - Windows and STDIO correctness changes have been propagated from the SEC2 - and old Windows drivers to the STDIO VFD. (DER - 2012/03/30 - HDFFV-7917) - - Fixed an error that would occur when copying an object with attribute - creation order tracked and indexed. (NAF - 2012/03/28 - HDFFV-7762) - - Fixed a bug in H5Ocopy(): When copying an opened object, call the - object's flush class action to ensure that cached data is flushed so - that H5Ocopy will get the correct data. (VC - 2012/03/27 - HDFFV-7853) - - The istore test will now skip the sparse 50x50x50 test when the VFD does - not support sparse files on that platform. The most important platforms - on which this will be skipped are Windows (NTFS sparse files are not - supported) and Mac OS-X (HFS sparse files are not supported). This - fixes CTest timeout issues on Windows. (DER - 2012/03/27 - HDFFV-7769) - - Windows and POSIX correctness changes have been propagated from the SEC2 - VFD to the Core VFD. This mainly affects file operations on the - driver's backing store and fixes a problem on Windows where large files - could not be read. (DER - 2012/03/27 - HDFFV-7916 - HDFFV-7603) - - When an application tries to write or read many small data chunks and - runs out of memory, the library had a segmentation fault. The fix is to - return the error stack with proper information. - (SLU - 2012/03/23 - HDFFV-7785) - - H5Pset_data_transform had a segmentation fault in some cases like x*-100. - It works correctly now and handles other cases like 100-x or 2/x. - (SLU - 2012/03/15 - HDFFV-7922) - - Fixed rare corruption bugs that could occur when using the new object - header format. (NAF - 2012/03/15 - HDFFV-7879) - - Fixed an error that occurred when creating a contiguous dataset with a - zero-sized dataspace and space allocation time set to 'early'. - (QAK - 2012/03/12) - - Changed Windows thread creation to use _beginthread() instead of - CreateThread(). Threads created by the latter can be killed in - low-memory situations. (DER - 2012/02/10 - HDFFV-7780) - - Creating a dataset in a read-only file caused a segmentation fault when - the file is closed. It's fixed. The attempt to create a dataset will - fail with an error indicating the file is read-only. - (SLU - 2012/01/25 - HDFFV-7756) - - Fixed a segmentation fault that could occur when shrinking a dataset - with chunks larger than 1 MB. (NAF - 2011/11/30 - HDFFV-7833) - - Fixed a bug that could cause H5Oget_info to return the wrong address - after copying a committed (named) datatype. (NAF - 2011/11/14) - - The library allowed the conversion of strings between ASCII and UTF8 - We have corrected it to report an error under this situation. - (SLU - 2011/11/8 - HDFFV-7582) - - Fixed a segmentation fault when the library tried to shrink the size - of a compound datatype through H5Tset_size immediately after the - datatype was created. (SLU - 2011/11/4 - HDFFV-7618) - - Parallel Library - ---------------- - - None - - Tools - ----- - - h5unjam: Fixed a segmentation fault that occurred when h5unjam was used - with the -V (show version) option. (JKM - 2012/04/19 - HDFFV-8001) - - h5repack: Fixed a failure that occurred when repacking the chunk size - of a specified chunked dataset with unlimited max dims. - (JKM - 2012/04/11 - HDFFV-7993) - - h5diff: Fixed a failure when comparing groups. Before the fix, if an - object in a group was compared with an object in another group where - both had the same name but the object type was different, then h5diff - would fail. After the fix, h5diff detects such cases as non-comparable - and displays appropriate error messages. - (JKM - 2012/03/28 - HDFFV-7644) - - h5diff: If unique objects exist only in one file and if h5diff is set to - exclude the unique objects with the --exclude-path option, then h5diff - might miss excluding some objects. This was fixed to correctly exclude - objects. (JKM - 2012/03/20 - HDFFV-7837) - - h5diff: When two symbolic dangling links are compared with the - --follow-symlinks option, the result should be the same. This worked when - comparing two files, but didn't work when comparing two objects. - h5diff now works when comparing two objects. - (JKM - 2012/03/09 - HDFFV-7835) - - h5dump: Added the tools library error stack to properly catch error - information generated within the library. (ADB - 2012/03/12 - HDFFV-7958) - - h5dump: Changed the process where an open link used to fail. Now dangling - links no longer throw error messages. (ADB - 2012/03/12 - HDFFV-7839) - - h5dump: Refactored code to remove duplicated functions. Split XML - functions from DDL functions. Corrected indentation and formatting - errors. Also fixed subsetting counting overflow (HDFFV-5874). Verified - all tools call tools_init() in main. The USER_BLOCK data now correctly - displays within the SUPER_BLOCK info. NOTE: WHITESPACE IN THE OUTPUT - HAS CHANGED. (ADB - 2012/02/17 - HDFFV-7560) - - h5diff: Fixed to prevent from displaying error stack message when - comparing two dangling symbolic links with the follow-symlinks option. - (JKM - 2012/01/13 - HDFFV-7836) - - h5repack: Fixed a memory leak that occurred with the handling of - variable length strings in attributes. - (JKM - 2012/01/10 - HDFFV-7840) - - h5ls: Fixed a segmentation fault that occurred when accessing region - reference data in an attribute. (JKM - 2012/01/06 - HDFFV-7838) - - F90 API - ------- - - None - - C++ API - ------ - - None - - High-Level APIs: - ------ - - None - - Fortran High-Level APIs: - ------ - - h5ltget_attribute_string_f: The h5ltget_attribute_string_f used to return - the C NULL character in the returned character buffer. The returned - character buffer now does not return the C NULL character; the buffer - is blank-padded if needed. (MSB - 2012/03/23) - - -Platforms Tested -================ -The following platforms and compilers have been tested for this release. - - AIX 5.3 xlc 10.1.0.5 - (NASA G-ADA) xlC 10.1.0.5 - xlf90 12.1.0.6 - - FreeBSD 8.2-STABLE i386 gcc 4.2.1 [FreeBSD] 20070719 - (loyalty) g++ 4.2.1 [FreeBSD] 20070719 - gcc 4.6.1 20110422 - g++ 4.6.1 20110422 - gfortran 4.6.1 20110422 - - FreeBSD 8.2-STABLE amd64 gcc 4.2.1 [FreeBSD] 20070719 - (freedom) g++ 4.2.1 [FreeBSD] 20070719 - gcc 4.6.1 20110422 - g++ 4.6.1 20110422 - gfortran 4.6.1 20110422 - - Linux 2.6.18-194.3.1.el5PAE GNU C (gcc), Fortran (gfortran), C++ (g++) - #1 SMP i686 i686 i386 compilers for 32-bit applications; - (jam) Version 4.1.2 20080704 (Red Hat 4.1.2-52) - Version 4.5.2 - PGI C, Fortran, C++ Compilers for 32-bit - applications; - Version 11.8-0 - Version 11.9-0 - Intel(R) C, C++, Fortran Compiler for 32-bit - applications; - Version 12.0 - Version 12.1 - MPICH mpich2-1.3.1 compiled with - gcc 4.1.2 and gfortran 4.1.2 - - Linux 2.6.18-308.1.1.el5 GNU C (gcc), Fortran (gfortran), C++ (g++) - #1 SMP x86_64 GNU/Linux compilers for 32-bit applications; - (koala) Version 4.1.2 20080704 (Red Hat 4.1.2-52) - Version 4.5.2 - PGI C, Fortran, C++ for 64-bit target on - x86-64; - Version 11.9-0 (64-bit) - Version 11.8-0 (32-bit) - Intel(R) C, C++, Fortran Compilers for - applications running on Intel(R) 64; - Version 12.0 - Version 12.1 - MPICH mpich2-1.3.1 compiled with - gcc 4.1.2 and gfortran 4.1.2 - - Linux 2.6.32-220.7.1.el6.ppc64 gcc (GCC) 4.4.6 20110731 (Red Hat 4.4.6-3) - #1 SMP ppc64 GNU/Linux g++ (GCC) 4.4.6 20110731 - (ostrich) GNU Fortran (GCC) 4.4.6 20110731 (Red Hat 4.4.6-3) - - Linux 2.6.18-108chaos Intel C, C++, Fortran Compilers Version 11.1 - #1 SMP x86_64 GNU/Linux - (LLNL Aztec) - - IBM Blue Gene/P XL C for Blue Gene/P, bgxlc V9.0 - (LLNL uDawn) XL C++ for Blue Gene/P, bgxlC V9.0 - XL Fortran for Blue Gene/P, bgxlf0 V11.1 - - SunOS 5.10 32- and 64-bit Sun C 5.9 Sun OS_sparc Patch 124867-16 - (linew) Sun Fortran 95 8.3 Sun OS_sparc Patch 127000-13 - Sun C++ 5.9 Sun OS_sparc Patch 124863-26 - Sun C 5.11 SunOS_sparc - Sun Fortran 95 8.5 SunOS_sparc - Sun C++ 5.11 SunOS_sparc - - SGI Altix UV Intel(R) C, Fortran Compilers - SGI ProPack 7 Linux Version 11.1 20100806 - 2.6.32.24-0.2.1.2230.2.PTF- SGI MPT 2.02 - default #1 SMP - (NCSA ember) - - Dell NVIDIA Cluster Intel(R) C, Fortran Compilers - Red Hat Enterprise Linux 6 Version 12.0.4 20110427 - 2.6.32-131.4.1.el6.x86_64 mvapich2 1.7rc1-intel-12.0.4 - (NCSA forge) - - Windows XP Visual Studio 2008 w/ Intel Fortran 10.1 (project files) - Visual Studio 2008 w/ Intel Fortran 11.1 (cmake) - Visual Studio 2010 w/ Intel Fortran 12 (cmake) - - Windows XP x64 Visual Studio 2008 w/ Intel Fortran 10.1 (project files) - Visual Studio 2008 w/ Intel Fortran 11.1 (cmake) - Visual Studio 2010 w/ Intel Fortran 12 (cmake) - - Windows 7 Visual Studio 2008 w/ Intel Fortran 11.1 (cmake) - Visual Studio 2010 w/ Intel Fortran 12 (cmake) - Cygwin(1.7.9 native gcc(4.5.3) compiler and gfortran) - - Windows 7 x64 Visual Studio 2008 w/ Intel Fortran 11.1 (cmake) - Visual Studio 2010 w/ Intel Fortran 12 (cmake) - Cygwin(1.7.9 native gcc(4.5.3) compiler and gfortran) - - Mac OS X Snow Leopard 10.6.8 i686-apple-darwin10-gcc-4.2.1 (GCC) 4.2.1 (gcc) - Darwin Kernel Version 10.8.0 i686-apple-darwin10-g++-4.2.1 (GCC) 4.2.1 (g++) - Intel 64-bit (Apple Inc. build 5666) (dot 3) - (fred) GNU Fortran (GCC) 4.6.1 (gfortran) - Intel C (icc), Fortran (ifort), C++ (icpc) - 12.1.0.038 Build 20110811 - - Mac OS X Snow Leopard 10.6.8 i686-apple-darwin10-gcc-4.2.1 (GCC) 4.2.1 (gcc) - Darwin Kernel Version 10.8.0 i686-apple-darwin10-g++-4.2.1 (GCC) 4.2.1 (g++) - Intel 32-bit (Apple Inc. build 5666) (dot 3) - (tejeda) GNU Fortran (GCC) 4.6.1 (gfortran) - Intel C (icc), Fortran (ifort), C++ (icpc) - 12.1.0.038 Build 20110811 - - Mac OS X Lion 10.7.3 GCC 4.2.1 gcc - 32- and 64-bit GNU Fortran (GCC) 4.6.1 gfortran - (duck) GCC 4.2.1. g++ - - Debian6.0.3 2.6.32-5-686 #1 SMP i686 GNU/Linux - gcc (Debian 4.4.5-8) 4.4.5 - GNU Fortran (Debian 4.4.5-8) 4.4.5 - - Debian6.0.3 2.6.32-5-amd64 #1 SMP x86_64 GNU/Linux - gcc (Debian 4.4.5-8) 4.4.5 - GNU Fortran (Debian 4.4.5-8) 4.4.5 - - Fedora16 3.2.9-2.fc16.i6866 #1 SMP i686 i686 i386 GNU/Linux - gcc (GCC) 4.6.2 20111027 (Red Hat 4.6.2-1) - GNU Fortran (GCC) 4.6.2 20111027 (Red Hat 4.6.2-1) - - Fedora16 3.2.9-2.fc16.x86_64 #1 SMP x86_64 x86_64 x86_64 GNU/Linux - gcc (GCC) 4.6.2 20111027 (Red Hat 4.6.2-1) - GNU Fortran (GCC) 4.6.2 20111027 (Red Hat 4.6.2-1) - - SUSE 12.1 3.1.9-1.4-desktop #1 SMP PREEMPT i686 i686 i386 GNU/Linux - gcc (SUSE Linux) 4.6.2 - GNU Fortran (SUSE Linux) 4.6.2 - - SUSE 12.1 3.1.9-1.4-desktop #1 SMP PREEMPT x86_64 x86_64 x86_64 GNU/Linux - gcc (SUSE Linux) 4.6.2 - GNU Fortran (SUSE Linux) 4.6.2 - - Ubuntu 11.10 3.0.0-16-generic #29-Ubuntu SMP i686 GNU/Linux - gcc (Ubuntu/Linaro 4.6.1-9ubuntu3) 4.6.1 - GNU Fortran (Ubuntu/Linaro 4.6.4-9ubuntu3) 4.6.1 - - Ubuntu 11.10 3.0.0-16-generic #29-Ubuntu SMP x86_64 GNU/Linux - gcc (Ubuntu/Linaro 4.6.1-9ubuntu3) 4.6.1 - GNU Fortran (Ubuntu/Linaro 4.6.1-9ubuntu3) 4.6.1 - - Cray Linux Environment (CLE) PrgEnv-pgi 2.2.74 - hopper.nersc.gov pgcc 11.9-0 64-bit target on x86-64 Linux -tp k8e - pgf90 11.9-0 64-bit target on x86-64 Linux -tp k8e - pgCC 11.9-0 64-bit target on x86-64 Linux -tp k8e - - -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 parallel -Solaris2.10 32-bit n y n y y y -Solaris2.10 64-bit n y n y y y -Windows XP n y(4) n y y y -Windows XP x64 n y(4) n y y y -Windows Vista n y(4) n y y y -Windows Vista x64 n y(4) n y y y -Mac OS X Snow Leopard 10.6.8 32-bit n y n y y n -Mac OS X Snow Leopard 10.6.8 64-bit n y n y y y -Mac OS X Lion 10.7.3 32-bit n y n y y n -Mac OS X Lion 10.7.3 64-bit n y n y y y -AIX 5.3 32- and 64-bit y y y y y y -FreeBSD 8.2-STABLE 32&64 bit n x n x y y -CentOS 5.5 Linux 2.6.18-194 i686 GNU (1)W y y(2) y y y y -CentOS 5.5 Linux 2.6.18-194 i686 Intel W n y n y y y -CentOS 5.5 Linux 2.6.18-194 i686 PGI W n y n y y y -CentOS 5.5 Linux 2.6.18 x86_64 GNU (1) W y y(3) y y y y -CentOS 5.5 Linux 2.6.18 x86_64 Intel W n y n y y y -CentOS 5.5 Linux 2.6.18 x86_64 PGI W n y n y y y -Linux 2.6.32-220.7.1.el6.ppc64 n y n y y y -SGI ProPack 7 Linux 2.6.32.24 y y y y y y -Red Hat Enterprise Linux 6 y y y y y y -CLE hopper.nersc.gov y y(3) y y y n - - -Platform Shared Shared Shared Thread- - C libs F90 libs C++ libs safe -Solaris2.10 32-bit y y y y -Solaris2.10 64-bit n n n n -Windows XP y y(4) y n -Windows XP x64 y y(4) y n -Windows Vista y y(4) y y -Windows Vista x64 y y(4) y y -Mac OS X Snow Leopard 10.6.8 32-bit y n y n -Mac OS X Snow Leopard 10.6.8 64-bit y n y n -Mac OS X Lion 10.7.3 32-bit y n y y -Mac OS X Lion 10.7.3 64-bit y n y y -AIX 5.3 32- and 64-bit n n n y -FreeBSD 8.2-STABLE 32&64 bit y x x y -CentOS 5.5 Linux 2.6.18-194 i686 GNU (1)W y y(2) y y -CentOS 5.5 Linux 2.6.18-194 i686 Intel W y y y n -CentOS 5.5 Linux 2.6.18-194 i686 PGI W y y y n -CentOS 5.5 Linux 2.6.18 x86_64 GNU (1) W y y y y -CentOS 5.5 Linux 2.6.18 x86_64 Intel W y y y n -CentOS 5.5 Linux 2.6.18 x86_64 PGI W y y y n -Linux 2.6.32-220.7.1.el6.ppc64 y y y n -SGI ProPack 7 Linux 2.6.32.24 y y y n -Red Hat Enterprise Linux 6 y y y n -CLE hopper.nersc.gov n n n n - - (1) Fortran compiled with gfortran. - (2) With PGI and Absoft compilers. - (3) With PGI compiler for Fortran. - (4) Using Visual Studio 2008 w/ Intel Fortran 10.1 (Cygwin shared libraries are not supported) - (5) C and C++ shared libraries will not be built when Fortran is enabled. - Compiler versions for each platform are listed in the preceding - "Platforms Tested" table. - - -Known Problems -============== -* The h5repacktst test fails on AIX 32-bit because the test uses more - memory than the default amount. The failure message typically looks like: - - "time: 0551-010 The process was stopped abnormally. Try again." - - This is an issue with the test only and does not represent a problem with - the library. To allow the test to pass, request more memory when testing - via appropriate command such as: - - $ env LDR_CNRTL=MAXDATA=0x20000000@DSA make check - - (AKC - 2012/05/09 - HDFFV-8016) - -* The file_image test will fail in the "initial file image and callbacks in - the core VFD" sub-test if the source directory is read-only as the test - fails to create its test files in the build directory. This will be - resolved in a future release. - (AKC - 2012/05/05 - HDFFV-8009) - -* The dt_arith test reports several errors involving "long double" on - Mac OS X 10.7 Lion when any level of optimization is enabled. The test does - not fail in debug mode. This will be addressed in a future release. - (SLU - 2012/05/08) - -* The following h5dump test case fails in BG/P machines (and potentially other - machines that use a command script to launch executables): - - h5dump --no-compact-subset -d "AHFINDERDIRECT::ah_centroid_t[0] it=0 tl=0" - tno-subset.h5 - - This is due to the embedded spaces in the dataset name being interpreted - by the command script launcher as meta-characters, thus passing three - arguments to h5dump's -d flag. The command passes if run by hand, just - not via the test script. - (AKC - 2012/05/03) - -* The ph5diff (parallel h5diff) tool can intermittently hang in parallel mode - when comparing two HDF5 files that contain objects with the same names but - with different object types. - (JKM - 2012/04/27) - -* On hopper, the build failed when RUNSERIAL and RUNPARALLEL are set - to aprun -np X, because the H5lib_settings.c file was not generated - properly. Not setting those environment variables works, because - configure was able to automatically detect that it's a Cray system - and used the proper launch commands when necessary. - (MSC - 2012/04/18) - -* The data conversion test dt_arith.c fails in "long double" to integer - conversion on Ubuntu 11.10 (3.0.0.13 kernel) with GCC 4.6.1 if the library - is built with optimization -O3 or -O2. The older GCC (4.5) or newer kernel - (3.2.2 on Fedora) doesn't have the problem. Users should lower the - optimization level (-O1 or -O0) by defining CFLAGS in the command line of - "configure" like: - - CFLAGS=-O1 ./configure - - This will overwrite the library's default optimization level. - (SLU - 2012/02/07 - HDFFV-7829) - -* The STDIO VFD does not work on some architectures, possibly due to 32/64 - bit or large file issues. The basic STDIO VFD test is known to fail on - 64-bit SunOS 5.10 on SPARC when built with -m64 and 32-bit OS X/Darwin - 10.7.0. The STDIO VFD test has been disabled while we investigate and - a fix should appear in a future release. - (DER - 2011/10/14) - -* h5diff can report inconsistent results when comparing datasets of enum type - that contain invalid values. This is due to how enum types are handled in - the library and will be addressed in a future release. - (DER - 2011/10/14 - HDFFV-7527) - -* The links test can fail under the stdio VFD due to some issues with external - links. This will be investigated and fixed in a future release. - (DER - 2011/10/14 - HDFFV-7768) - -* After the shared library support was fixed for some bugs, it was discovered - that "make prefix=XXX install" no longer works for shared libraries. It - still works correctly for static libraries. Therefore, if you want to - install the HDF5 shared libraries in a location such as /usr/local/hdf5, - you need to specify the location via the --prefix option during configure - time. E.g, ./configure --prefix=/usr/local/hdf5 ... - (AKC - 2011/05/07 - HDFFV-7583) - -* The parallel test, t_shapesame, in testpar/, may run for a long time and may - be terminated by the alarm signal. If that happens, one can increase the - alarm seconds (default is 1200 seconds = 20 minutes) by setting the - environment variable, $HDF5_ALARM_SECONDS, to a larger value such as 3600 - (60 minutes). Note that the t_shapesame test may fail in some systems - (see the "While working on the 1.8.6 release..." problem below). If - it does, it will waste more time if $HDF5_ALARM_SECONDS is set - to a larger value. - (AKC - 2011/05/07) - -* The C++ and FORTRAN bindings are not currently working on FreeBSD. - (QAK - 2011/04/26) - -* Shared Fortran libraries are not quite working on AIX. While they are - generated when --enable-shared is specified, the fortran and hl/fortran - tests fail. We are looking into the issue. HL and C++ shared libraries - should now be working as intended, however. - (MAM - 2011/04/20) - -* The --with-mpe configure option does not work with Mpich2. - (AKC - 2011/03/10) - -* While working on the 1.8.6 release of HDF5, a bug was discovered that can - occur when reading from a dataset in parallel shortly after it has been - written to collectively. The issue was exposed by a new test in the parallel - HDF5 test suite, but had existed before that. We believe the problem lies with - certain MPI implementations and/or file systems. - - We have provided a pure MPI test program, as well as a standalone HDF5 - program, that can be used to determine if this is an issue on your system. - They should be run across multiple nodes with a varying number of processes. - These programs can be found at: - http://www.hdfgroup.org/ftp/HDF5/examples/known_problems/ - (NAF - 2011/01/19) - -* The library's test dt_arith.c showed a compiler's rounding problem on - Cygwin when converting from unsigned long long to long double. The - library's own conversion works fine. We defined a macro for Cygwin to - skip this test until we can solve the problem. - (SLU - 2010/05/05 - HDFFV-1264) - -* All the VFL drivers aren't backward compatible. In H5FDpublic.h, the - structure H5FD_class_t changed in 1.8. There is new parameter added to - get_eoa and set_eoa callback functions. A new callback function - get_type_map was added in. The public function H5FDrealloc was taken - out in 1.8. The problem only happens when users define their own driver - for 1.6 and try to plug in 1.8 library. Because there's only one user - complaining about it, we (Elena, Quincey, and I) decided to leave it as - it is (see bug report #1279). Quincey will make a plan for 1.10. - (SLU - 2010/02/02) - -* MinGW has a missing libstdc++.dll.a library file and will not successfully link - C++ applications/tests. Do not use the enable-cxx configure option. Read all of - the INSTALL_MINGW.txt file for all restrictions. - (ADB - 2009/11/11) - -* The --enable-static-exec configure flag will only statically link libraries - if the static version of that library is present. If only the shared version - of a library exists (i.e., most system libraries on Solaris, AIX, and Mac, - for example, only have shared versions), the flag should still result in a - successful compilation, but note that the installed executables will not be - fully static. Thus, the only guarantee on these systems is that the - executable is statically linked with just the HDF5 library. - (MAM - 2009/11/04) - -* The PathScale MPI implementation, accessing a Panasas file system, would - cause H5Fcreate() with H5F_ACC_EXCL to fail even when the file does not - exist. This is due to the MPI_File_open() call failing if the mode has - the MPI_MODE_EXCL bit set. - (AKC - 2009/08/11 - HDFFV-988) - -* Parallel tests failed with 16 processes with data inconsistency at testphdf5 - / dataset_readAll. Parallel tests also failed with 32 and 64 processes with - collective abort of all ranks at t_posix_compliant / allwrite_allread_blocks - with MPI IO. - (CMC - 2009/04/28) - -* For Red Storm, a Cray XT3 system, the tools/h5ls/testh5ls.sh and - tools/h5copy/testh5copy.sh will fail some of its sub-tests. These sub-tests - are expected to fail and should exit with a non-zero code but the yod - command does not propagate the exit code of the executables. Yod always - returns 0 if it can launch the executable. The test suite shell expects - a non-zero for this particular test, therefore it concludes the test has - failed when it receives 0 from yod. Skip all the "failing" test for now - by changing them as following. - - ======== Original tools/h5ls/testh5ls.sh ========= - TOOLTEST tgroup-1.ls 1 -w80 -r -g tgroup.h5 - ======== Change to =============================== - echo SKIP TOOLTEST tgroup-1.ls 1 -w80 -r -g tgroup.h5 - ================================================== - - ======== Original tools/h5copy/testh5copy.sh ========= - TOOLTEST_FAIL -i $TESTFILE -o $FILEOUT -v -s grp_dsets -d grp_rename - TOOLTEST_FAIL -i $TESTFILE -o $FILEOUT -v -s grp_dsets -d /grp_rename/grp_dsets - TOOLTEST_FAIL -i $TESTFILE -o $FILEOUT -vp -s /grp_dsets -d /E/F/grp_dsets - TOOLTEST_FAIL -i $TESTFILE -o $FILEOUT -vp -s /grp_nested -d /G/H/grp_nested - H5LSTEST $FILEOUT - ======== Change to =============================== - echo SKIP TOOLTEST_FAIL -i $TESTFILE -o $FILEOUT -v -s grp_dsets -d grp_rename - echo SKIP TOOLTEST_FAIL -i $TESTFILE -o $FILEOUT -v -s grp_dsets -d /grp_rename/grp_dsets - echo SKIP TOOLTEST_FAIL -i $TESTFILE -o $FILEOUT -vp -s /grp_dsets -d /E/F/grp_dsets - echo SKIP TOOLTEST_FAIL -i $TESTFILE -o $FILEOUT -vp -s /grp_nested -d /G/H/grp_nested - echo SKIP H5LSTEST $FILEOUT - ================================================== - (AKC - 2008/11/10) - -* For Red Storm, a Cray XT3 system, the yod command sometimes gives the - message, "yod allocation delayed for node recovery". This interferes with - test suites that do not expect to see this message. See the section of "Red - Storm" in file INSTALL_parallel for a way to deal with this problem. - (AKC - 2008/05/28) - -* On an Intel 64 Linux cluster (RH 4, Linux 2.6.9) with Intel 10.0 compilers, - use -mp -O1 compilation flags to build the libraries. A higher level of - optimization causes failures in several HDF5 library tests. - -* On mpich 1.2.5 and 1.2.6, if more than two processes contribute no IO and - the application asks to do collective IO, we have found that when using 4 - processors, a simple collective write will sometimes be hung. This can be - verified with t_mpi test under testpar. - -* A dataset created or rewritten with a v1.6.3 library or after cannot be read - with the v1.6.2 library or before when the Fletcher32 EDC filter is enabled. - There was a bug in the calculation of the Fletcher32 checksum in the - library before v1.6.3; the checksum value was not consistent between big- - endian and little-endian systems. This bug was fixed in Release 1.6.3. - However, after fixing the bug, the checksum value was no longer the same as - before on little-endian system. Library releases after 1.6.4 can still read - datasets created or rewritten with an HDF5 library of v1.6.2 or before. - (SLU - 2005/06/30) - -* On IBM AIX systems, parallel HDF5 mode will fail some tests with error - messages like "INFO: 0031-XXX ...". This is from the command `poe'. - Set the environment variable MP_INFOLEVEL to 0 to minimize the messages - and run the tests again. - - The tests may fail with messages like "The socket name is already in use", - but HDF5 does not use sockets. This failure is due to problems with the - poe command trying to set up the debug socket. To resolve this problem, - check to see whether there are many old /tmp/s.pedb.* files staying around. - These are sockets used by the poe command and left behind due to failed - commands. First, ask your system administrator to clean them out. - Lastly, request IBM to provide a means to run poe without the debug socket. - (AKC - 2004/12/08) - - -%%%%1.8.8%%%% - - -HDF5 version 1.8.8 released on 2011-11-15 -================================================================================ - -INTRODUCTION -============ - -This document describes the differences between HDF5-1.8.7 and -HDF5 1.8.8, and contains information on the platforms tested and -known problems in HDF5-1.8.8. -For more details, see the files HISTORY-1_0-1_8_0_rc3.txt -and HISTORY-1_8.txt in the release_docs/ directory of the HDF5 source. - -Links to the HDF5 1.8.8 source code, documentation, and additional materials -can be found on the HDF5 web page at: - - http://www.hdfgroup.org/products/hdf5/ - -The HDF5 1.8.8 release can be obtained from: - - http://www.hdfgroup.org/HDF5/release/obtain5.html - -User documentation for 1.8.8 can be accessed directly at this location: - - http://www.hdfgroup.org/HDF5/doc/ - -New features in the HDF5-1.8.x release series, including brief general -descriptions of some new and modified APIs, are described in the "What's New -in 1.8.0?" document: - - http://www.hdfgroup.org/HDF5/doc/ADGuide/WhatsNew180.html - -All new and modified APIs are listed in detail in the "HDF5 Software Changes -from Release to Release" document, in the section "Release 1.8.8 (current -release) versus Release 1.8.7": - - http://www.hdfgroup.org/HDF5/doc/ADGuide/Changes.html - -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, Languages, and Compilers -- Bug Fixes since HDF5-1.8.7 -- Platforms Tested -- Supported Configuration Features Summary -- Known Problems - - -New Features -============ - - Configuration - ------------- - - Added the --enable-fortran2003 flag to enable Fortran2003 support - in the HDF5 Fortran library. The flag should be used along with the - --enable-fortran flag and takes affect only when the Fortran compiler - is Fortran2003 compliant. (EIP - 2011/11/14) - - Added checks for clock_gettime and mach/mach_time.h to both configure and - CMake. This will support the move from gettimeofday to clock_gettime's - monotonic timer in the profiling code in a future release. - (DER - 2011/10/12) - - Library - ------- - - The Windows VFD code has been removed with the exception of the functions - which set it (H5Pset_fapl_windows, for example). Setting the Windows - VFD now really sets the SEC2 VFD. The WINDOWS_MAX_BUF and - WINDOWS_USE_STDIO configuration options and #defines have also been - removed. NOTE: Since the Windows VFD was a clone of the SEC2 VFD, this - change should be transparent to users. - (DER - 2011/10/12 - HDFFV-7740, HDFFV-7744) - - H5Tcreate now supports the string type (fixed-length and variable- - length). (SLU - 2011/05/20) - - Parallel Library - ---------------- - - Added new H5Pget_mpio_actual_chunk_opt_mode and - H5Pget_mpio_actual_io_mode API routines for querying whether/how - a collective I/O operation completed. (QAK - 2011/10/12) - - Tools - ----- - - None - - High-Level APIs - --------------- - - Added the following Fortran wrappers for the Dimension Scale APIs: - h5dsset_scale_f - h5dsattach_scale_f - h5dsdetach_scale_f - h5dsis_attached_f - h5dsis_scale_f - h5dsset_label_f - h5dsget_label_f - h5dsget_scale_name_f - h5dsget_num_scales_f - (EIP for SB - 2011/10/13 - HDFFV-3797) - - Fortran API - ----------- - - The HDF5 Fortran library was enhanced to support the Fortran 2003 standard. - The following features are available when the HDF5 library is configured - using the --enable-fortran and --enable-fortran2003 configure flags AND - if the Fortran compiler is Fortran 2003 compliant: - - - Subroutines overloaded with the C_PTR derived type: - h5pget_f - h5pget_fill_value_f - h5pinsert_f - h5pregister_f - h5pset_f - h5pset_fill_value_f - h5rcreate_f - h5rderefrence_f - h5rget_name_f - h5rget_obj_type_f - - Subroutines overloaded with the C_PTR derived type - and simplified signatures: - h5aread_f - h5awrite_f - h5dread_f - h5dwrite_f - - New subroutines - h5dvlen_reclaim_f - h5literate_by_name_f - h5literate_f - h5ovisit_f - h5tconvert_f - h5pset_nbit_f - h5pset_scaleoffset_f - - Subroutines with additional optional parameters: - h5pcreate_class_f - (EIP - 2011/10/14) - - C++ API - ------- - - None - - -Support for New Platforms, Languages, and Compilers -=================================================== - - None - -Bug Fixes since HDF5-1.8.7 -========================== - - Configuration - ------------- - - Changed the size of H5_SIZEOF_OFF_T to 4 bytes (was 8) in the VMS - h5pubconf.h based on the output of a test program. (DER - 2011/10/12) - - The Windows and VMS versions of H5pubconf.h were brought into sync with - the linux/posix version. (DER - 2011/10/12) - - Fixed a bug in the bin/trace Perl script where API functions - that take a variable number of arguments were not processed for - trace statement fixup. (DER - 2011/08/25) - - The --enable-h5dump-packed-bits configure option has been removed. - The h5dump code that this option conditionally enabled is now always - compiled into h5dump. Please refer to the h5dump reference manual for - usage of the packed bits feature. (MAM - 2011/06/23 - HDFFV-7592) - - Configure now uses the same flags and symbols in its tests that are - used to build the library. (DER - 2011/05/24) - - Library - ------- - - Corrected the error when copying attributes between files which are using - different versions of the file format. (QAK - 2011/10/20 - HDFFV-7718) - - Corrected the error when loading local heaps from the file, which could - cause the size of the local heap's data block to increase dramatically. - (QAK - 2011/10/14 - HDFFV-7767) - - An application does not need to do H5O_move_msgs_forward() when writing - attributes. Tests were checked into the performance suite. - (VC - 2011/10/13 - HDFFV-7640) - - Fixed a bug that occurred when using H5Ocopy on a committed datatype - containing an attribute using that committed datatype. - (NAF - 2011/10/13 - HDFFV-5854) - - Added generic VFD I/O types to the SEC2 and log VFDs to ensure correct - I/O sizes (and remove compiler warnings) between Windows and true POSIX - systems. (DER - 2011/10/12) - - Corrected some Windows behavior in the SEC2 and log VFDs. This mainly - involved datatype correctness fixes, Windows API call error checks, - and adding the volume serial number to the VFD cmp functions. - (DER - 2011/10/12) - - Converted post-checks for the appropriate POSIX I/O sizes to pre-checks - in order to avoid platform-specific or undefined behavior. - (DER - 2011/10/12) - - #ifdef _WIN32 instances have been changed to #ifdef H5_HAVE_WIN32_API. - H5_HAVE_VISUAL_STUDIO checks have been added where necessary. This is in - CMake only as configure never sets _WIN32. (ADB - 2011/09/12) - - CLANG compiler with the options -fcatch-undefined-behavior and -ftrapv - discovered 3 problems in tests and tools' library: - 1. In dsets.c, left shifting an unsigned int for 32 bits or more - caused undefined behavior. - 2. In dt_arith.c, the INIT_INTEGER macro definition has an overflow - when the value is a negative minimal and is being subtracted from one. - 3. In tools/lib/h5tools_str.c, right shifting an int value for 32 bits - or more caused undefined behavior. - All the problems have been corrected. (SLU - 2011/09/02 - HDFFV-7674) - - H5Epush2() now has the correct trace functionality (this is related to the - bin/trace Perl script bug noted in the configure section). - (DER - 2011/08/25) - - Corrected mismatched function name typo of h5pget_dxpl_mpio_c and - h5pfill_value_defined_c. (AKC - 2011/08/22 - HDFFV-7641) - - Corrected an internal error in the library where objects that use committed - (named) datatypes and were accessed from two different file IDs could confuse - the two and cause erroneous failures. (QAK - 2011/07/18 - HDFFV-7638) - - In v1.6 of the library, there was an EOA for the whole MULTI file saved in the - super block. We took it out in v1.8 of the library because it's meaningless - for the MULTI file. v1.8 of the library saves the EOA for the metadata file - instead, but this caused a backward compatibility problem. - A v1.8 library couldn't open the file created with the v1.6 library. We - fixed the problem by checking the EOA value to detect the file - created with v1.6 library. (SLU - 2011/06/22) - - When a dataset had filters and reading data failed, the error message - didn't say which filter wasn't registered. It's fixed now. (SLU - 2011/06/03) - - Parallel Library - ---------------- - - The Special Collective IO (IO when some processes do not contribute to the - IO) and the Complex Derived Datatype MPI functionalities are no longer - conditionally enabled in the library by configure. They are always - enabled in order to take advantage of performance boosts from these - behaviors. Older MPI implementations that do not allow for these - functionalities can no longer by used by HDF5. - (MAM - 2011/07/08 - HDFFV-7639). - - Tools - ----- - - h5diff: fixed segfault over non-comparable attribute with different - dimension or rank, along with '-c' option to display details. - (JKM - 2011/10/24 - HDFFV-7770) - - Fixed h5diff to display all the comparable objects and attributes - regardless of detecting non-comparables. (JKM - 2011/09/16 - HDFFV-7693) - - Fixed h5repack to update the values of references(object and region) of - attributes in h5repack for 1) references, 2) arrays of references, - 3) variable-length references, and 4) compound references. - (PC - 2011/09/14 - HDFFV-5932) - - h5diff: fixed a segfault over a dataset with container types - array and variable-length (vlen) along with multiple nested compound types. - Example: compound->array->compound, compound->vlen->compound. - (JKM - 2011/09/01 - HDFFV-7712) - - h5repack: added macro to handle a failure in H5Dread/write when memory - allocation failed inside the library. (PC - 2011/08/19) - - Fixed h5jam to not to allow the specifying of an HDF5 formatted file as - an input file for the -u (user block file) option. The original HDF5 file - would not be accessible if this behavior was allowed. - (JKM - 2011/08/19 - HDFFV-5941) - - Revised the command help pages of h5jam and h5unjam. The descriptions - were not up to date and some were missing. - (JKM - 2011/08/15 - HDFFV-7515) - - Fixed h5dump to correct the schema location: - <hdf5:HDF5-File - xmlns:hdf5="http://hdfgroup.org/HDF5/XML/schema/HDF5-File" - xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" - xsi:schemaLocation="http://hdfgroup.org/HDF5/XML/schema/HDF5-File - http://www.hdfgroup.org/HDF5/XML/schema/HDF5-File.xsd"> - (ADB - 2011/08/10) - - h5repack: h5repack failed to copy a dataset if the layout is changed - from chunked with unlimited dimensions to contiguous. - (PC - 2011/07/15 - HDFFV-7649) - - Fixed h5diff: the "--delta" option considers two NaN of the same type - are different. This is wrong based on the h5diff description in the - Reference Manual. (PC - 2011/07/15 - HDFFV-7656) - - Fixed h5diff to display an instructive error message and exit with - an instructive error message when mutually exclusive options - (-d, -p and --use-system-epsilon) are used together. - (JKM - 2011/07/07 - HDFFV-7600) - - Fixed h5dump so that it displays the first line of each element in correct - position for multiple dimension array types. Before this fix, - the first line of each element in an array was - displayed after the last line of previous element without - moving to the next line (+indentation). - (JKM - 2011/06/15 - HDFFV-5878) - - Fixed h5dump so that it will display the correct value for - H5T_STD_I8LE datasets on the Blue-gene system (ppc64, linux, Big-Endian, - clustering). (AKC & JKM - 2011/05/12 - HDFFV-7594) - - Fixed h5diff to compare a file to itself correctly. Previously h5diff - reported either the files were different or not compatible in certain - cases even when comparing a file to itself. This fix also improves - performance when comparing the same target objects through verifying - the object and file addresses before comparing the details - in the objects. Examples of details are datasets and attributes. - (XCAO & JKM - 2011/05/06 - HDFFV-5928) - - F90 API - ------- - - Modified the h5open_f and h5close_f subroutines to not to call H5open - and H5close correspondingly. While the H5open call just adds overhead, - the H5close call called by a Fortran application shuts down the HDF5 - library. This makes the library inaccessible to the application. - (EIP & SB - 2011/10/13 - HDFFV-915) - - Fixed h5tget_tag_f where the length of the C string was used to - repack the C string into the Fortran string. This lead to memory - corruption in the calling program. (SB - 2011/07/26) - - Added defined constants: - H5T_ORDER_MIXED_F (HDFFV-2767) - H5Z_SO_FLOAT_DSCALE_F - H5Z_SO_FLOAT_ESCALE_F - H5Z_SO_INT_F - H5Z_SO_INT_MINBITS_DEFAULT_F - H5O_TYPE_UNKNOWN_F - H5O_TYPE_GROUP_F - H5O_TYPE_DATASET_F - H5O_TYPE_NAMED_DATATYPE_F - H5O_TYPE_NTYPES_F - - C++ API - ------ - - None - - High-Level APIs: - ------ - - Fixed the H5LTdtype_to_text function. It had some memory problems when - dealing with some complicated data types. (SLU - 2011/10/19 - HDFFV-7701) - - Fixed H5DSset_label seg faulting when retrieving the length of a - dimension label that was not set. (SB - 2011/08/07 - HDFFV-7673) - - Fixed a dimension scale bug where if you create a dimscale, attach two - datasets to it, and then unattach them, you get an error if they are - unattached in order, but no error if you unattach them in reverse order. - (SB - 2011/06/07 - HDFFV-7605) - - Fortran High-Level APIs: - ------ - - None - - -Platforms Tested -================ -The following platforms and compilers have been tested for this release. - - AIX 5.3 xlc 10.1.0.5 - (NASA G-ADA) xlC 10.1.0.5 - xlf90 12.1.0.6 - - FreeBSD 8.2-STABLE i386 gcc 4.2.1 [FreeBSD] 20070719 - (loyalty) g++ 4.2.1 [FreeBSD] 20070719 - gcc 4.6.1 20110422 - g++ 4.6.1 20110422 - gfortran 4.6.1 20110422 - - FreeBSD 8.2-STABLE amd64 gcc 4.2.1 [FreeBSD] 20070719 - (freedom) g++ 4.2.1 [FreeBSD] 20070719 - gcc 4.6.1 20110422 - g++ 4.6.1 20110422 - gfortran 4.6.1 20110422 - - IBM Blue Gene/P bgxlc 9.0.0.9 - (LLNL uDawn) bgxlf90 11.1.0.7 - bgxlC 9.0.0.9 - - Linux 2.6.16.60-0.54.5-smp Intel(R) C, C++, Fortran Compilers - x86_64 Version 11.1 20090630 - (INL Icestorm) - - Linux 2.6.18-194.el5 x86_64 Intel(R) C, C++, Fortran Compilers - (INL Fission) Version 12.0.2 20110112 - - Linux 2.6.18-108chaos x86_64 Intel(R) C, C++, Fortran Compilers - (LLNL Aztec) Version 11.1 20090630 - - Linux 2.6.18-194.3.1.el5PAE gcc (GCC) 4.1.2 and 4.4.2 - #1 SMP i686 i686 i386 GNU Fortran (GCC) 4.1.2 20080704 - (jam) (Red Hat 4.1.2-48) and 4.4.2 - PGI C, Fortran, C++ 10.4-0 32-bit - PGI C, Fortran, C++ 10.6-0 32-bit - Intel(R) C Compiler for 32-bit - applications, Version 11.1 - Intel(R) C++ Compiler for 32-bit - applications, Version 11.1 - Intel(R) Fortran Compiler for 32-bit - applications, Version 11.1 - MPICH mpich2-1.3.1 compiled with - gcc 4.1.2 and gfortran 4.1.2 - - Linux 2.6.18-238.12.1.el5 gcc 4.1.2 and 4.4.2 - #1 SMP x86_64 GNU/Linux GNU Fortran (GCC) 4.1.2 20080704 - (koala) (Red Hat 4.1.2-46) and 4.4.2 - tested for both 32- and 64-bit binaries - Intel(R) C, C++, Fortran Compilers for - applications running on Intel(R) 64, - Version 11.1. - PGI C, Fortran, C++ Version 9.0-4 - for 64-bit target on x86-64 - MPICH mpich2-1.3.1 compiled with - gcc 4.1.2 and gfortran 4.1.2 - - SGI Altix UV Intel(R) C, Fortran Compilers - SGI ProPack 7 Linux Version 11.1 20100806 - 2.6.32.24-0.2.1.2230.2.PTF- SGI MPT 2.02 - default #1 SMP - (NCSA ember) - - Dell NVIDIA Cluster Intel(R) C, Fortran Compilers - Red Hat Enterprise Linux 6 Version 12.0.4 20110427 - 2.6.32-131.4.1.el6.x86_64 mvapich2 1.7rc1-intel-12.0.4 - (NCSA forge) - - SunOS 5.10 32- and 64-bit Sun C 5.11 SunOS_sparc 2010/08/13 - Sun Fortran 95 8.5 SunOS_sparc 2010/08/13 - Sun C++ 5.11 SunOS_sparc 2010/08/13 - - Windows XP Visual Studio 2008 w/ Intel Fortran 10.1 (project files) - Visual Studio 2008 w/ Intel Fortran 11.1 (cmake) - Visual Studio 2010 (cmake) - Cygwin(1.7.9 native gcc(4.5.3) compiler and gfortran) - - Windows XP x64 Visual Studio 2008 w/ Intel Fortran 10.1 (project files) - Visual Studio 2008 w/ Intel Fortran 11.1 (cmake) - Visual Studio 2010 (cmake) - Cygwin(1.7.9 native gcc(4.5.3) compiler and gfortran) - - Windows Vista Visual Studio 2008 w/ Intel Fortran 11.1 (cmake) - - Windows Vista x64 Visual Studio 2008 w/ Intel Fortran 11.1 (cmake) - - Windows 7 Visual Studio 2008 w/ Intel Fortran 11.1 (cmake) - - Windows 7 x64 Visual Studio 2008 w/ Intel Fortran 11.1 (cmake) - - Mac OS X 10.8.0 (Intel 64-bit) i686-apple-darwin10-gcc-4.2.1 (GCC) 4.2.1 (Apple Inc. build 5666) (dot 3) - Darwin Kernel Version 10.8.0 GNU Fortran (GCC) 4.6.1 - Intel C, C++ and Fortran compilers 12.1.0 - - Mac OS X 10.8.0 (Intel 32-bit) i686-apple-darwin10-gcc-4.2.1 (GCC) 4.2.1 (Apple Inc. build 5666) (dot 3) - Darwin Kernel Version 10.8.0 GNU Fortran (GCC) version 4.6.1 - Intel C, C++ and Fortran compilers 12.1.0 - - Fedora 12 2.6.32.16-150.fc12.ppc64 #1 SMP ppc64 GNU/Linux - gcc (GCC) 4.4.4 20100630 (Red Hat 4.4.4-10) - GNU Fortran (GCC) 4.4.4 20100630 (Red Hat 4.4.4-10) - - Debian6.0.3 2.6.32-5-686 #1 SMP i686 GNU/Linux - gcc (Debian 4.4.5-8) 4.4.5 - GNU Fortran (Debian 4.4.5-8) 4.4.5 - - Debian6.0.3 2.6.32-5-amd64 #1 SMP x86_64 GNU/Linux - gcc (Debian 4.4.5-8) 4.4.5 - GNU Fortran (Debian 4.4.5-8) 4.4.5 - - Fedora15 2.6.40.6-0.fc15.i686.PAE #1 SMP i686 i686 i386 GNU/Linux - gcc (GCC) 4.6.1 20110908 (Red Hat 4.6.1-9) - GNU Fortran (GCC) 4.6.1 20110908 (Red Hat 4.6.1-9) - - Fedora15 2.6.40.6-0.fc15.x86_64 #1 SMP x86_64 x86_64 x86_64 GNU/Linux - gcc (GCC) 4.6.1 20110908 (Red Hat 4.6.1-9) - GNU Fortran (GCC) 4.6.1 20110908 (Red Hat 4.6.1-9) - - SUSE 11.4 2.6.37.6-0.7-desktop #1 SMP PREEMPT i686 i686 i386 GNU/Linux - gcc (SUSE Linux) 4.5.1 20101208 - GNU Fortran (SUSE Linux) 4.5.1 20101208 - - SUSE 11.4 2.6.37.6-0.7-desktop #1 SMP PREEMPT x86_64 x86_64 x86_64 GNU/Linux - gcc (SUSE Linux) 4.5.1 20101208 - GNU Fortran (SUSE Linux) 4.5.1 20101208 - - Ubuntu 11.10 3.0.0-12-generic #20-Ubuntu SMP i686 GNU/Linux - gcc (Ubuntu/Linaro 4.6.1-9ubuntu3) 4.6.1 - GNU Fortran (Ubuntu/Linaro 4.6.4-9ubuntu3) 4.6.1 - - Ubuntu 11.10 3.0.0-12-generic #20-Ubuntu SMP x86_64 GNU/Linux - gcc (Ubuntu/Linaro 4.6.1-9ubuntu3) 4.6.1 - GNU Fortran (Ubuntu/Linaro 4.6.1-9ubuntu3) 4.6.1 - - OpenVMS Alpha 8.3 HP C V7.3-009 - HP Fortran V8.2-104679-48H9K - HP C++ V7.3-009 - - Cray Linux Environment (CLE) PrgEnv-pgi 2.2.74 - hopper.nersc.gov pgcc 11.7-0 64-bit target on x86-64 Linux -tp k8e - franklin.nersc.gov pgf90 11.7-0 64-bit target on x86-64 Linux -tp k8e - pgCC 11.7-0 64-bit target on x86-64 Linux -tp k8e - -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 parallel -Solaris2.10 32-bit n y n y y y -Solaris2.10 64-bit n y n y y y -Windows XP n y(4) n y y y -Windows XP x64 n y(4) n y y y -Windows Vista n y(4) n y y y -Windows Vista x64 n y(4) n y y y -OpenVMS Alpha n y n y y n -Mac OS X 10.8 Intel 32-bit n y n y y y -Mac OS X 10.8 Intel 64-bit n y n y y y -AIX 5.3 32- and 64-bit n y n y y y -FreeBSD 8.2-STABLE 32&64 bit n x n x y y -CentOS 5.5 Linux 2.6.18-194 i686 GNU (1)W y y(2) y y y y -CentOS 5.5 Linux 2.6.18-194 i686 Intel W n y n y y n -CentOS 5.5 Linux 2.6.18-194 i686 PGI W n y n y y n -CentOS 5.5 Linux 2.6.16 x86_64 GNU (1) W y y(3) y y y y -CentOS 5.5 Linux 2.6.16 x86_64 Intel W n y n y y n -CentOS 5.5 Linux 2.6.16 x86_64 PGI W n y n y y y -Fedora 12 Linux 2.6.32.16-150.fc12.ppc64 n y n y y y -SGI ProPack 7 Linux 2.6.32.24 y y y y y y -Red Hat Enterprise Linux 6 y y y y y y -CLE hopper.nersc.gov y y(3) y y y n -CLE franklin.nersc.gov y y(3) y y y n - - -Platform Shared Shared Shared Thread- - C libs F90 libs C++ libs safe -Solaris2.10 32-bit y y y y -Solaris2.10 64-bit y y y y -Windows XP y y(4) y n -Windows XP x64 y y(4) y n -Windows Vista y y(4) y y -Windows Vista x64 y y(4) y y -OpenVMS Alpha n n n n -Mac OS X 10.8 Intel 32-bit y(5) n y n -Mac OS X 10.8 Intel 64-bit y(5) n y n -AIX 5.3 32- and 64-bit n n n y -FreeBSD 8.2-STABLE 32&64 bit y x x y -CentOS 5.5 Linux 2.6.18-128 i686 GNU (1)W y y(2) y y -CentOS 5.5 Linux 2.6.18-128 i686 Intel W y y y n -CentOS 5.5 Linux 2.6.18-128 i686 PGI W y y y n -CentOS 5.5 Linux 2.6.16 x86_64 GNU (1) W y y y y -CentOS 5.5 Linux 2.6.16 x86_64 Intel W y y y n -CentOS 5.5 Linux 2.6.16 x86_64 PGI W y y y n -Fedora 12 Linux 2.6.32.16-150.fc12.ppc64 y y y y -SGI ProPack 7 Linux 2.6.32.24 y y y n -Red Hat Enterprise Linux 6 y y y n -CLE hopper.nersc.gov n n n n -CLE franklin.nersc.gov n n n n - - (1) Fortran compiled with gfortran. - (2) With PGI and Absoft compilers. - (3) With PGI compiler for Fortran. - (4) Using Visual Studio 2008 w/ Intel Fortran 10.1 (Cygwin shared libraries are not supported) - (5) C and C++ shared libraries will not be built when Fortran is enabled. - Compiler versions for each platform are listed in the preceding - "Platforms Tested" table. - - -Known Problems -============== - -* The STDIO VFD does not work on some architectures, possibly due to 32/64 - bit or large file issues. The basic STDIO VFD test is known to fail on - 64-bit SunOS 5.10 on SPARC when built with -m64 and 32-bit OS X/Darwin - 10.7.0. The STDIO VFD test has been disabled while we investigate and - a fix should appear in a future release, possibly 1.8.9. - (DER - 2011/10/14) - -* h5diff can report inconsistent results when comparing datasets of enum type - that contain invalid values. This is due to how enum types are handled in - the library and will be addressed in the next release. - (DER - 2011/10/14 - HDFFV-7527) - -* The links test can fail under the stdio VFD due to some issues with external - links. This will be investigated and fixed in a future release. - (DER - 2011/10/14 - HDFFV-7768) - -* After the shared library support was fixed for some bugs, it was discovered - that "make prefix=XXX install" no longer works for shared libraries. It - still works correctly for static libraries. Therefore, if you want to - install the HDF5 shared libraries in a location such as /usr/local/hdf5, - you need to specify the location via the --prefix option during configure - time. E.g, ./configure --prefix=/usr/local/hdf5 ... - (AKC - 2011/05/07 - HDFFV-7583) - -* The parallel test, t_shapesame, in testpar/, may run for a long time and may - be terminated by the alarm signal. If that happens, one can increase the - alarm seconds (default is 1200 seconds = 20 minutes) by setting the - environment variable, $HDF5_ALARM_SECONDS, to a larger value such as 3600 - (60 minutes). Note that the t_shapesame test may fail in some systems - (see the "While working on the 1.8.6 release..." problem below). If - it does, it will waste more time if $HDF5_ALARM_SECONDS is set - to a larger value. (AKC - 2011/05/07) - -* The C++ and FORTRAN bindings are not currently working on FreeBSD. - (QAK - 2011/04/26) - -* Shared Fortran libraries are not quite working on AIX. While they are - generated when --enable-shared is specified, the fortran and hl/fortran - tests fail. We are looking into the issue. HL and C++ shared libraries - should now be working as intended, however. (MAM - 2011/04/20) - -* The --with-mpe configure option does not work with Mpich2. (AKC - 2011/03/10) - -* While working on the 1.8.6 release of HDF5, a bug was discovered that can - occur when reading from a dataset in parallel shortly after it has been - written to collectively. The issue was exposed by a new test in the parallel - HDF5 test suite, but had existed before that. We believe the problem lies with - certain MPI implementations and/or file systems. - - We have provided a pure MPI test program, as well as a standalone HDF5 - program, that can be used to determine if this is an issue on your system. - They should be run across multiple nodes with a varying number of processes. - These programs can be found at: - http://www.hdfgroup.org/ftp/HDF5/examples/known_problems/ - (NAF - 2011/01/19) - -* The library's test dt_arith.c showed a compiler's rounding problem on - Cygwin when converting from unsigned long long to long double. The - library's own conversion works fine. We defined a macro for Cygwin to - skip this test until we can solve the problem. - (SLU - 2010/05/05 - HDFFV-1264) - -* All the VFL drivers aren't backward compatible. In H5FDpublic.h, the - structure H5FD_class_t changed in 1.8. There is new parameter added to - get_eoa and set_eoa callback functions. A new callback function - get_type_map was added in. The public function H5FDrealloc was taken - out in 1.8. The problem only happens when users define their own driver - for 1.6 and try to plug in 1.8 library. Because there's only one user - complaining about it, we (Elena, Quincey, and I) decided to leave it as - it is (see bug report #1279). Quincey will make a plan for 1.10. - (SLU - 2010/02/02) - -* MinGW has a missing libstdc++.dll.a library file and will not successfully link - C++ applications/tests. Do not use the enable-cxx configure option. Read all of - the INSTALL_MINGW.txt file for all restrictions. (ADB - 2009/11/11) - -* The --enable-static-exec configure flag will only statically link libraries - if the static version of that library is present. If only the shared version - of a library exists (i.e., most system libraries on Solaris, AIX, and Mac, - for example, only have shared versions), the flag should still result in a - successful compilation, but note that the installed executables will not be - fully static. Thus, the only guarantee on these systems is that the - executable is statically linked with just the HDF5 library. - (MAM - 2009/11/04) - -* The PathScale MPI implementation, accessing a Panasas file system, would - cause H5Fcreate() with H5F_ACC_EXCL to fail even when the file does not - exist. This is due to the MPI_File_open() call failing if the mode has - the MPI_MODE_EXCL bit set. (AKC - 2009/08/11 - HDFFV-988) - -* Parallel tests failed with 16 processes with data inconsistency at testphdf5 - / dataset_readAll. Parallel tests also failed with 32 and 64 processes with - collective abort of all ranks at t_posix_compliant / allwrite_allread_blocks - with MPI IO. (CMC - 2009/04/28) - -* For Red Storm, a Cray XT3 system, the tools/h5ls/testh5ls.sh and - tools/h5copy/testh5copy.sh will fail some of its sub-tests. These sub-tests - are expected to fail and should exit with a non-zero code but the yod - command does not propagate the exit code of the executables. Yod always - returns 0 if it can launch the executable. The test suite shell expects - a non-zero for this particular test, therefore it concludes the test has - failed when it receives 0 from yod. Skip all the "failing" test for now - by changing them as following. - - ======== Original tools/h5ls/testh5ls.sh ========= - TOOLTEST tgroup-1.ls 1 -w80 -r -g tgroup.h5 - ======== Change to =============================== - echo SKIP TOOLTEST tgroup-1.ls 1 -w80 -r -g tgroup.h5 - ================================================== - - ======== Original tools/h5copy/testh5copy.sh ========= - TOOLTEST_FAIL -i $TESTFILE -o $FILEOUT -v -s grp_dsets -d grp_rename - TOOLTEST_FAIL -i $TESTFILE -o $FILEOUT -v -s grp_dsets -d /grp_rename/grp_dsets - TOOLTEST_FAIL -i $TESTFILE -o $FILEOUT -vp -s /grp_dsets -d /E/F/grp_dsets - TOOLTEST_FAIL -i $TESTFILE -o $FILEOUT -vp -s /grp_nested -d /G/H/grp_nested - H5LSTEST $FILEOUT - ======== Change to =============================== - echo SKIP TOOLTEST_FAIL -i $TESTFILE -o $FILEOUT -v -s grp_dsets -d grp_rename - echo SKIP TOOLTEST_FAIL -i $TESTFILE -o $FILEOUT -v -s grp_dsets -d /grp_rename/grp_dsets - echo SKIP TOOLTEST_FAIL -i $TESTFILE -o $FILEOUT -vp -s /grp_dsets -d /E/F/grp_dsets - echo SKIP TOOLTEST_FAIL -i $TESTFILE -o $FILEOUT -vp -s /grp_nested -d /G/H/grp_nested - echo SKIP H5LSTEST $FILEOUT - ================================================== - (AKC - 2008/11/10) - -* For Red Storm, a Cray XT3 system, the yod command sometimes gives the - message, "yod allocation delayed for node recovery". This interferes with - test suites that do not expect to see this message. See the section of "Red - Storm" in file INSTALL_parallel for a way to deal with this problem. - (AKC - 2008/05/28) - -* On an Intel 64 Linux cluster (RH 4, Linux 2.6.9) with Intel 10.0 compilers, - use -mp -O1 compilation flags to build the libraries. A higher level of - optimization causes failures in several HDF5 library tests. - -* On mpich 1.2.5 and 1.2.6, if more than two processes contribute no IO and - the application asks to do collective IO, we have found that when using 4 - processors, a simple collective write will sometimes be hung. This can be - verified with t_mpi test under testpar. - -* A dataset created or rewritten with a v1.6.3 library or after cannot be read - with the v1.6.2 library or before when the Fletcher32 EDC filter is enabled. - There was a bug in the calculation of the Fletcher32 checksum in the - library before v1.6.3; the checksum value was not consistent between big- - endian and little-endian systems. This bug was fixed in Release 1.6.3. - However, after fixing the bug, the checksum value was no longer the same as - before on little-endian system. Library releases after 1.6.4 can still read - datasets created or rewritten with an HDF5 library of v1.6.2 or before. - (SLU - 2005/06/30) - -* On IBM AIX systems, parallel HDF5 mode will fail some tests with error - messages like "INFO: 0031-XXX ...". This is from the command `poe'. - Set the environment variable MP_INFOLEVEL to 0 to minimize the messages - and run the tests again. - - The tests may fail with messages like "The socket name is already in use", - but HDF5 does not use sockets. This failure is due to problems with the - poe command trying to set up the debug socket. To resolve this problem, - check to see whether there are many old /tmp/s.pedb.* files staying around. - These are sockets used by the poe command and left behind due to failed - commands. First, ask your system administrator to clean them out. - Lastly, request IBM to provide a means to run poe without the debug socket. - (AKC - 2004/12/08) - - -%%%%1.8.7%%%% - - -HDF5 version 1.8.7 released on Tue May 10 09:24:44 CDT 2011 -================================================================================ - -INTRODUCTION -============ - -This document describes the differences between HDF5-1.8.6 and -HDF5 1.8.7, and contains information on the platforms tested and -known problems in HDF5-1.8.7. -For more details, see the files HISTORY-1_0-1_8_0_rc3.txt -and HISTORY-1_8.txt in the release_docs/ directory of the HDF5 source. - -Links to the HDF5 1.8.7 source code, documentation, and additional materials -can be found on the HDF5 web page at: - - http://www.hdfgroup.org/products/hdf5/ - -The HDF5 1.8.7 release can be obtained from: - - http://www.hdfgroup.org/HDF5/release/obtain5.html - -User documentation for 1.8.7 can be accessed directly at this location: - - http://www.hdfgroup.org/HDF5/doc/ - -New features in the HDF5-1.8.x release series, including brief general -descriptions of some new and modified APIs, are described in the "What's New -in 1.8.0?" document: - - http://www.hdfgroup.org/HDF5/doc/ADGuide/WhatsNew180.html - -All new and modified APIs are listed in detail in the "HDF5 Software Changes -from Release to Release" document, in the section "Release 1.8.7 (current -release) versus Release 1.8.6": - - http://www.hdfgroup.org/HDF5/doc/ADGuide/Changes.html - -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, Languages, and Compilers -- Bug Fixes since HDF5-1.8.6 -- Platforms Tested -- Supported Configuration Features Summary -- Known Problems - - -New Features -============ - - Configuration - ------------- - - Configure now generates Makefiles that build in "silent make mode" - by default in which compile and link lines are significantly - simplified for clarity. To override this and view actual compile and - link lines during building, the --disable-silent-rules flag can be used - at configure time, or the 'make' command can be followed by V=1, to - indicate a "verbose" make. (MAM - 2011/4/14). - - Added mpicc and mpif90 as the default C and Fortran compilers for Linux - systems when --enable-parallel is specified but no $CC or $FC is defined. - (AKC - 2011/2/7) - - Added a new configure option, "--enable-unsupported", which can - be used to stop configure from preventing the use of unsupported - configure option combinations, such as c++ in parallel or Fortran - with threadsafe. Use at your own risk, as it may result in a - library that won't compile or run as expected! - (MAM - 2010/11/17 - Bug 2061) - - Library - ------- - - The library allows the dimension size of a dataspace to be zero. In - the past, the library would allow this only if the maximal dimension - size was unlimited. Now there is no such restriction, but no data - can be written to this kind of dataset. (SLU - 2011/4/20) - - We added two new macros, H5_VERSION_GE and H5_VERSION_LE, to let users - compare certain version numbers with the library being used. (SLU - - 2011/4/20) - - Added ability to cache files opened through external links. Added new - public functions H5Pset_elink_file_cache_size(), - H5Pget_elink_file_cache_size(), and H5Fclear_elink_file_cache(). - (NAF - 2011/02/17) - - Finished implementing all options for 'log' VFD. (QAK - 2011/1/25) - - Removed all old code for Metrowerks compilers, bracketed by - __MWERKS__). Metrowerks compiler is long gone. (AKC - 2010/11/17) - - Parallel Library - ---------------- - - None - - Tools - ----- - - h5diff: Added new "verbose with levels" option, '-vN, --verbose=N'. - The old '-v, --verbose' option is deprecated but remains available; - it is exactly equivalent to '-v0, --verbose=0'. - The new levels 1 ('-v1' or '--verbose=1') and 2 ('-v2' or - '--verbose=2') can be specified to view more information regarding - attributes differences. Bug #2121 (JKM 2011/3/23) - - h5dump: Added new option --enable-error-stack. This option will - display error stack information in the output stream. This is - useful when the "h5dump: Unable to print data" message is output. - (ADB - 2011/03/03) - - High-Level APIs - --------------- - - Fortran LT make datasets routines (H5LTmake_dataset_f, - h5ltmake_dataset_int_f, h5ltmake_dataset_float_f, h5ltmake_dataset_double_f) - and LT read datasets routines (h5ltread_dataset_f,h5ltread_dataset_int_f, - h5ltread_dataset_float_f, 5ltread_dataset_double_f) can now handle - 4-dimensional to 7-dimensional rank datasets. HDFFV-1217 (MSB-2011/4/24/2011) - - F90 API - ------- - - None - - C++ API - ------- - - None - - -Support for New Platforms, Languages, and Compilers -=================================================== - - Intel V11.1 uses now -O3 optimization in production mode (EIP - 2010/10/08) - - - -Bug Fixes since HDF5-1.8.6 -========================== - - Configuration - ------------- - - Shared C++ and HL libraries on AIX should now be working correctly. - Note that Fortran shared libraries are still not working on AIX. - (See the Known Problems section, below). (MAM - 2011/4/20) - - Removed config/ibm-aix6.x. All IBM-AIX settings are in one file, - ibm-aix. (AKC - 2011/4/14) - - Shared C libraries are no longer disabled on Mac when Fortran - is enabled. Shared Fortran libraries are still not supported on Mac, - so configure will disable them by default, but this is overridable - with the new --enable-unsupported configure option. The configure - summary has been updated to reflect the fact that the shared-ness of - the C++/Fortran wrapper libraries may not align with the C library. - (MAM - 2011/04/11 - HDFFV-4353). - - Library - ------- - - Changed assertion failure when decoding a compound datatype with no - fields into a normal error failure. Also prohibit using this sort - of datatype for creating an attribute (as is already the case for - datasets and committed (named) datatypes). (QAK - 2011/04/15, Jira - issue #HDFFV-2766) - - Tell the VFL flush call that the file will be closing, allowing - the VFDs to avoid sync'ing the file (particularly valuable in parallel). - (QAK - 2011/03/09) - - The datatype handler created with H5Tencode/decode used to have the - reference count 0 (zero); it now has the reference count 1 (one). - (SLU - 2011/2/18) - - Fixed the definition of H5_HAVE_GETTIMEOFDAY on Windows so that - HDgettimeofday() is defined and works properly. Bug HDFFV-5931 - (DER - 2011/04/14) - - Added basic VFD tests for the Windows, STDIO and log VFD tests. - (DER - 2011/04/11) - - Parallel Library - ---------------- - - None - - Tools - ----- - - Updated h5dump test case script to prevent entire test failure when - source directory is read-only. Bug #HDFFV-4342 (JKM 2011/4/12) - - Fixed h5dump displaying incorrect values for H5T_STD_I8BE type data in - attribute on Big-Endian machine. H5T_STD_I8BE is unsigned 8bit type, - so h5dump is supposed to display -2 instead of 254. It worked correctly - on Little-Endian system , but not on Big-Endian system. Bug #HDFFV-4358 - (JKM 04/08/2011) - - Updated some HDF5 tools to standardize the option name as - '--enable-error-stack' for printing HDF5 error stack messages. h5ls and - h5dump have been updated. For h5ls, this replaces "-e/--errors" option, - which is deprecated. For h5dump, this is a new option. Bug #2182 - (JKM 2011/3/30) - - Fixed the h5diff --use-system-epsilon option. The formula used in the - calculation was changed from ( |a - b| / b ) to ( |a - b| ). - This was done to improve performance. Bug #2184 (JKM 2011/3/24) - - Fixed output for H5T_REFERENCE in h5dump. According to the BNF document - the output of a H5T_REFERENCE should be followed by the type; - <reference> ::= H5T_REFERENCE { <ref_type> } - <ref_type> ::= H5T_STD_REF_OBJECT | H5T_STD_REF_DSETREG - Previously this was only displayed if the -R option was used. - Bug #1725 (ADB 2011/3/28) - - Fixed two h5diff issues. 1) h5diff compared attributes correctly only - when two objects had the same number of attributes and the attribute - names were identical. 2) h5diff did not display useful information about - attribute differences. Bug #2121 (JKM 2011/3/17) - - Fixed a memory leak in h5diff that occurred when accessing symbolic links - with the --follow-symlink option. Bug #2214 (JKM 2011/3/18) - - Fixed a memory leak in h5diff that occurred when accessing variable length - string data. Bug #2216 (JKM 2011/3/18) - - Fixed and improved the help page for h5ls -a, --address option. - Bug #1904 (JKM 2011/3/11) - - Fixed h5copy to enable copying an object into the same HDF5 file. - Previously h5copy displayed an error message when the target file - was the same as the source file. (XCAO 2011/3/8) - - Fixed an h5dump problem that caused the tool to skip some data elements - in large datasets with a large array datatype on Windows. This issue - arose only on Windows due to the different return behavior of the - _vsnprintf() function. Bug #2161 (JKM 2011/3/3) - - Fixed h5dump which was skipping some array indices in large datasets - with a relatively large array datatype. The interval of skipped indices - varied according to the size of the array. Bug #2092 (JKM 2011/2/15) - - Fixed h5diff which was segfaulting when comparing compound datasets - with a combination of fixed-length string datatypes and variable-length - string datatypes in certain orders. Bug #2089 (JKM 2010/12/28) - - Improved h5diff performance. 1) Now use HDmemcmp() before comparing two - elements. 2) Replace expensive H5Tequals() calls. 3) Retrieve datatype - information at dataset level, not at each element level for compound - datasets. HDFFV-7516 (JKM 2011/4/18) - - Fixed h5ls to display nested compound types with curly brackets - when -S (--simple) option is used with -l (--label), so it shows - which members (in curly brackets) belong to which nested compound type, - making the output clearer. Bug #1979 (JKM 2010/11/09) - - Fixed h5diff to handle variable-length strings in a compound dataset - and variable-length string arrays in a compound dataset correctly. - Garbage values were previously displayed when h5diff compared multiple - variable-length strings in a compound type dataset. - Bug #1989 (JKM 2010/10/28) - - Fixed h5copy to fail gracefully when copying an object to a non- - existing group without the -p option. Bug #2040 (JKM 2010/10/18) - - F90 API - ------ - - None - - C++ API - ------ - - None - - High-Level APIs: - ------ - - None - - Fortran High-Level APIs: - ------ - - h5tbmake_table_f: Fixed error in passing an array of characters with different - length field names. - - h5tget_field_info_f: Fixed error with packing the C strings into a Fortran - array of strings. Added optional argument called 'maxlen_out' which returns - the maximum string character length in a field name element. - Bug HDFFV-1255 (MSB- 4/17/2011) - - - - -Platforms Tested -================ -The following platforms and compilers have been tested for this release. - - AIX 6.1 xlc 11.1.0.3 - (NCSA BP) xlC 11.1.0.3 - xlf90 13.1.0.3 - mpcc_r 11.1.0.3 - mpxlf90_r 13.1.0.3 - - FreeBSD 8.2-STABLE i386 gcc 4.2.1 [FreeBSD] 20070719 - (loyalty) g++ 4.2.1 [FreeBSD] 20070719 - gcc 4.6.1 20110422 - g++ 4.6.1 20110422 - gfortran 4.6.1 20110422 - - FreeBSD 8.2-STABLE amd64 gcc 4.2.1 [FreeBSD] 20070719 - (freedom) g++ 4.2.1 [FreeBSD] 20070719 - gcc 4.6.1 20110422 - g++ 4.6.1 20110422 - gfortran 4.6.1 20110422 - - Linux 2.6.18-194.3.1.el5PAE gcc (GCC) 4.1.2 and 4.4.2 - #1 SMP i686 i686 i386 G95 (GCC 4.0.3 (g95 0.93!) Apr 21 2010) - (jam) GNU Fortran (GCC) 4.1.2 20080704 - (Red Hat 4.1.2-48) and 4.4.2 - PGI C, Fortran, C++ 10.4-0 32-bit - PGI C, Fortran, C++ 10.6-0 32-bit - Intel(R) C Compiler for 32-bit - applications, Version 11.1 - Intel(R) C++ Compiler for 32-bit - applications, Version 11.1 - Intel(R) Fortran Compiler for 32-bit - applications, Version 11.1 - Absoft 32-bit Fortran 95 10.0.7 - MPICH mpich2-1.3.1 compiled with - gcc 4.1.2 and gfortran 4.1.2 - - Linux 2.6.18-194.17.1.el5 gcc 4.1.2 and 4.4.2 - #1 SMP x86_64 GNU/Linux G95 (GCC 4.0.3 (g95 0.93!) Apr 21 2010) - (amani) tested for both 32- and 64-bit binaries - GNU Fortran (GCC) 4.1.2 20080704 - (Red Hat 4.1.2-46) and 4.4.2 - Intel(R) C, C++, Fortran Compilers for - applications running on Intel(R) 64, - Version 11.1. - PGI C, Fortran, C++ Version 9.0-4 - for 64-bit target on x86-64 - MPICH mpich2-1.3.1 compiled with - gcc 4.1.2 and gfortran 4.1.2 - - SGI ProPack 7 Linux Intel(R) C++ Version 11.1 20100806 - 2.6.32.24-0.2.1.2230.2.PTF- Intel(R) Fortran Version 11.1 20100806 - default #1 SMP SGI MPT 2.01 - SGI Altix UV - (NCSA ember) - - SunOS 5.10 32- and 64-bit Sun C 5.9 Sun OS_sparc Patch 124867-16 - (linew) Sun Fortran 95 8.3 Sun OS_sparc Patch 127000-13 - Sun C++ 5.9 Sun OS_sparc Patch 124863-26 - Sun C 5.10 SunOS_sparc Patch 141861-07 - Sun Fortran 95 8.4 SunOS_sparc Patch 128231-06 - Sun C++ 5.10 SunOS_sparc 128228-11 - - Intel Xeon Linux 2.6.18- gcc 4.2.4 - 92.1.10.el5_lustre.1.6.6smp- Intel(R) C++ Version 10.1.017 - perfctr #8 SMP Intel(R) Fortran Compiler Version 10.1.017 - (NCSA abe) Open MPI 1.3.2 - MVAPICH2-1.5.1_pgi-10.8 - - Windows XP Visual Studio 2008 w/ Intel Fortran 10.1 (project files) - Visual Studio 2008 w/ Intel Fortran 11.1 (cmake) - Visual Studio 2010 (cmake) - Cygwin(1.7.7 native gcc(4.3.4) compiler and gfortran) - - Windows XP x64 Visual Studio 2008 w/ Intel Fortran 10.1 (project files) - Visual Studio 2008 w/ Intel Fortran 11.1 (cmake) - Visual Studio 2010 (cmake) - Cygwin(1.7.7 native gcc(4.3.4) compiler and gfortran) - - Windows Vista Visual Studio 2008 w/ Intel Fortran 11.1 (cmake) - - Windows Vista x64 Visual Studio 2008 w/ Intel Fortran 11.1 (cmake) - - Windows 7 Visual Studio 2008 w/ Intel Fortran 11.1 (cmake) - - Windows 7 x64 Visual Studio 2008 w/ Intel Fortran 11.1 (cmake) - - Mac OS X 10.7.0 (Intel 64-bit) i686-apple-darwin10-gcc-4.2.1 (GCC) 4.2.1 - Darwin Kernel Version 10.7.0 GNU Fortran (GCC) 4.6.0 20101106 (experimental) - Intel C, C++ and Fortran compilers 12.0.1.122 20101110 - - Mac OS X 10.7.0 (Intel 32-bit) i686-apple-darwin10-gcc-4.2.1 (GCC) 4.2.1 (Apple Inc. build 5666) (dot 3) - Darwin Kernel Version 10.7.0 GNU Fortran (GCC) version 4.4.0 20090123 (experimental) - [trunk revision 143587] - - Fedora 12 2.6.32.16-150.fc12.ppc64 #1 SMP ppc64 GNU/Linux - gcc (GCC) 4.4.4 20100630 (Red Hat 4.4.4-10) - GNU Fortran (GCC) 4.4.4 20100630 (Red Hat 4.4.4-10) - - Debian6.01 2.6.32-5-686 #1 SMP i686 GNU/Linux - gcc (Debian 4.4.5-8) 4.4.5 - GNU Fortran (Debian 4.4.5-8) 4.4.5 - - Debian6.01 2.6.32-5-amd64 #1 SMP x86_64 GNU/Linux - gcc (Debian 4.4.5-8) 4.4.5 - GNU Fortran (Debian 4.4.5-8) 4.4.5 - - Fedora14 2.6.35.12-88.fc14.i686.PAE #1 SMP i686 i686 i386 GNU/Linux - gcc (GCC) 4.5.1 20100924 (Red Hat 4.5.1-4) - GNU Fortran (GCC) 4.5.1 20100924 (Red Hat 4.5.1-4) - - Fedora14 2.6.35.12-88.fc14.x86_64 #1 SMP x86_64 x86_64 x86_64 GNU/Linux - gcc (GCC) 4.5.1 20100924 (Red Hat 4.5.1-4) - GNU Fortran (GCC) 4.5.1 20100924 (Red Hat 4.5.1-4) - - SUSE 11.4 2.6.37.1-1.2-desktop #1 SMP PREEMPT i686 i686 i386 GNU/Linux - gcc (SUSE Linux) 4.5.1 20101208 - GNU Fortran (SUSE Linux) 4.5.1 20101208 - - SUSE 11.4 2.6.37.1-1.2-desktop #1 SMP PREEMPT x86_64 x86_64 x86_64 GNU/Linux - gcc (SUSE Linux) 4.5.1 20101208 - GNU Fortran (SUSE Linux) 4.5.1 20101208 - - Ubuntu 10.10 2.6.35-28-generic #50-Ubuntu SMP i686 GNU/Linux - gcc (Ubuntu/Linaro 4.4.4-14ubuntu5) 4.4.5 - GNU Fortran (Ubuntu/Linaro 4.4.4-14ubuntu5) 4.4.5 - - Ubuntu 10.10 2.6.35-28-generic #50-Ubuntu SMP x86_64 GNU/Linux - gcc (Ubuntu/Linaro 4.4.4-14ubuntu5) 4.4.5 - GNU Fortran (Ubuntu/Linaro 4.4.4-14ubuntu5) 4.4.5 - - OpenVMS Alpha 8.3 HP C V7.3-009 - HP Fortran V8.2-104679-48H9K - HP C++ V7.3-009 - -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 parallel -Solaris2.10 32-bit n y n y y y -Solaris2.10 64-bit n y n y y y -Windows XP n y(4) n y y y -Windows XP x64 n y(4) n y y y -Windows Vista n y(4) n y y y -Windows Vista x64 n y(4) n y y y -OpenVMS Alpha n y n y y n -Mac OS X 10.7 Intel 32-bit n y n y y y -Mac OS X 10.7 Intel 64-bit n y n y y y -AIX 6.1 32- and 64-bit y y y y y y -FreeBSD 8.2-STABLE 32&64 bit n x n x y y -CentOS 5.5 Linux 2.6.18-194 i686 GNU (1)W y y(2) y y y y -CentOS 5.5 Linux 2.6.18-194 i686 Intel W n y n y y n -CentOS 5.5 Linux 2.6.18-194 i686 PGI W n y n y y n -CentOS 5.5 Linux 2.6.16 x86_64 GNU (1) W y y(3) y y y y -CentOS 5.5 Linux 2.6.16 x86_64 Intel W n y n y y n -CentOS 5.5 Linux 2.6.16 x86_64 PGI W n y n y y y -RedHat EL4 2.6.18 Xeon Lustre C y y y y y n -Fedora 12 Linux 2.6.32.16-150.fc12.ppc64 n y n y y y -SGI Linux 2.6.32.19 y y y y y y - - -Platform Shared Shared Shared Thread- - C libs F90 libs C++ libs safe -Solaris2.10 32-bit y y y y -Solaris2.10 64-bit y y y y -Windows XP y y(4) y n -Windows XP x64 y y(4) y n -Windows Vista y y(4) y y -Windows Vista x64 y y(4) y y -OpenVMS Alpha n n n n -Mac OS X 10.7 Intel 32-bit y(5) n y n -Mac OS X 10.7 Intel 64-bit y(5) n y n -AIX 6.1 32- and 64-bit n n n y -FreeBSD 8.2-STABLE 32&64 bit y x x y -CentOS 5.5 Linux 2.6.18-128 i686 GNU (1)W y y(2) y y -CentOS 5.5 Linux 2.6.18-128 i686 Intel W y y y n -CentOS 5.5 Linux 2.6.18-128 i686 PGI W y y y n -CentOS 5.5 Linux 2.6.16 x86_64 GNU (1) W y y y y -CentOS 5.5 Linux 2.6.16 x86_64 Intel W y y y n -CentOS 5.5 Linux 2.6.16 x86_64 PGI W y y y n -RedHat EL4 2.6.18 Xeon Lustre C y y y n -Fedora 12 Linux 2.6.32.16-150.fc12.ppc64 y y y y -SGI Linux 2.6.32.19 y y y y - - (1) Fortran compiled with gfortran. - (2) With PGI and Absoft compilers. - (3) With PGI compiler for Fortran. - (4) Using Visual Studio 2008 w/ Intel Fortran 10.1 (Cygwin shared libraries are not supported) - (5) C and C++ shared libraries will not be built when Fortran is enabled. - Compiler versions for each platform are listed in the preceding - "Platforms Tested" table. - - -Known Problems -============== -* After the shared library support was fixed for some bugs, it was discovered - that "make prefix=XXX install" no longer works for shared libraries. It - still works correctly for static libraries. Therefore, if you want to - install the HDF5 shared libraries in a location such as /usr/local/hdf5, - you need to specify the location via the --prefix option during configure - time. E.g, ./configure --prefix=/usr/local/hdf5 ... - (AKC - 2011/05/07 HDFFV-7583) - -* The parallel test, t_shapesame, in testpar/, may run for a long time and may - be terminated by the alarm signal. If that happens, one can increase the - alarm seconds (default is 1200 seconds = 20 minutes) by setting the - environment variable, $HDF5_ALARM_SECONDS, to a larger value such as 3600 - (60 minutes). Note that the t_shapesame test may fail in some systems - (see the "While working on the 1.8.6 release..." problem below). If - it does, it will waste more time if $HDF5_ALARM_SECONDS is set - to a larger value. (AKC - 2011/05/07) - -* The C++ and FORTRAN bindings are not currently working on FreeBSD. - (QAK - 2011/04/26) - -* Shared Fortran libraries are not quite working on AIX. While they are - generated when --enable-shared is specified, the fortran and hl/fortran - tests fail. We are looking into the issue. HL and C++ shared libraries - should now be working as intended, however. (MAM - 2011/04/20) - -* The --with-mpe configure option does not work with Mpich2. AKC - 2011/03/10 - -* If parallel gmake (e.g., gmake -j 4) is used, the "gmake clean" command - sometimes fails in the perform directory due to the attempt to remove the - executable of h5perf or h5perf_serial by two "parallel" commands. This error - has no consequence on the functionality of the HDF5 library or install. It - is fixed in the next release. AKC - 2011/01/25 - -* While working on the 1.8.6 release of HDF5, a bug was discovered that can - occur when reading from a dataset in parallel shortly after it has been - written to collectively. The issue was exposed by a new test in the parallel - HDF5 test suite, but had existed before that. We believe the problem lies with - certain MPI implementations and/or file systems. - - We have provided a pure MPI test program, as well as a standalone HDF5 - program, that can be used to determine if this is an issue on your system. - They should be run across multiple nodes with a varying number of processes. - These programs can be found at: - http://www.hdfgroup.org/ftp/HDF5/examples/known_problems/ - -* The library's test dt_arith.c showed a compiler's rounding problem on - Cygwin when converting from unsigned long long to long double. The - library's own conversion works fine. We defined a macro for Cygwin to - skip this test until we can solve the problem. Please see bug #1813. - SLU - 2010/5/5 - -* All the VFL drivers aren't backward compatible. In H5FDpublic.h, the - structure H5FD_class_t changed in 1.8. There is new parameter added to - get_eoa and set_eoa callback functions. A new callback function - get_type_map was added in. The public function H5FDrealloc was taken - out in 1.8. The problem only happens when users define their own driver - for 1.6 and try to plug in 1.8 library. Because there's only one user - complaining about it, we (Elena, Quincey, and I) decided to leave it as - it is (see bug report #1279). Quincey will make a plan for 1.10. - SLU - 2010/2/2 - -* MinGW has a missing libstdc++.dll.a library file and will not successfully link - C++ applications/tests. Do not use the enable-cxx configure option. Read all of - the INSTALL_MINGW.txt file for all restrictions. ADB - 2009/11/11 - -* The PathScale MPI implementation, accessing a Panasas file system, would - cause H5Fcreate() with H5F_ACC_EXCL to fail even when the file does not - exist. This is due to the MPI_File_open() call failing if the mode has - the MPI_MODE_EXCL bit set. (See bug 1468 for details.) AKC - 2009/8/11 - -* Parallel tests failed with 16 processes with data inconsistency at testphdf5 - / dataset_readAll. Parallel tests also failed with 32 and 64 processes with - collective abort of all ranks at t_posix_compliant / allwrite_allread_blocks - with MPI IO. CMC - 2009/04/28 - -* For Red Storm, a Cray XT3 system, the tools/h5ls/testh5ls.sh and - tools/h5copy/testh5copy.sh will fail some of its sub-tests. These sub-tests - are expected to fail and should exit with a non-zero code but the yod - command does not propagate the exit code of the executables. Yod always - returns 0 if it can launch the executable. The test suite shell expects - a non-zero for this particular test, therefore it concludes the test has - failed when it receives 0 from yod. Skip all the "failing" test for now - by changing them as following. - - ======== Original tools/h5ls/testh5ls.sh ========= - TOOLTEST tgroup-1.ls 1 -w80 -r -g tgroup.h5 - ======== Change to =============================== - echo SKIP TOOLTEST tgroup-1.ls 1 -w80 -r -g tgroup.h5 - ================================================== - - ======== Original tools/h5copy/testh5copy.sh ========= - TOOLTEST_FAIL -i $TESTFILE -o $FILEOUT -v -s grp_dsets -d grp_rename - TOOLTEST_FAIL -i $TESTFILE -o $FILEOUT -v -s grp_dsets -d /grp_rename/grp_dsets - TOOLTEST_FAIL -i $TESTFILE -o $FILEOUT -vp -s /grp_dsets -d /E/F/grp_dsets - TOOLTEST_FAIL -i $TESTFILE -o $FILEOUT -vp -s /grp_nested -d /G/H/grp_nested - H5LSTEST $FILEOUT - ======== Change to =============================== - echo SKIP TOOLTEST_FAIL -i $TESTFILE -o $FILEOUT -v -s grp_dsets -d grp_rename - echo SKIP TOOLTEST_FAIL -i $TESTFILE -o $FILEOUT -v -s grp_dsets -d /grp_rename/grp_dsets - echo SKIP TOOLTEST_FAIL -i $TESTFILE -o $FILEOUT -vp -s /grp_dsets -d /E/F/grp_dsets - echo SKIP TOOLTEST_FAIL -i $TESTFILE -o $FILEOUT -vp -s /grp_nested -d /G/H/grp_nested - echo SKIP H5LSTEST $FILEOUT - ================================================== - AKC - 2008/11/10 - -* For Red Storm, a Cray XT3 system, the yod command sometimes gives the - message, "yod allocation delayed for node recovery". This interferes with - test suites that do not expect to see this message. See the section of "Red - Storm" in file INSTALL_parallel for a way to deal with this problem. - AKC - 2008/05/28 - -* On an Intel 64 Linux cluster (RH 4, Linux 2.6.9) with Intel 10.0 compilers, - use -mp -O1 compilation flags to build the libraries. A higher level of - optimization causes failures in several HDF5 library tests. - -* On mpich 1.2.5 and 1.2.6, if more than two processes contribute no IO and - the application asks to do collective IO, we have found that when using 4 - processors, a simple collective write will sometimes be hung. This can be - verified with t_mpi test under testpar. - -* A dataset created or rewritten with a v1.6.3 library or after cannot be read - with the v1.6.2 library or before when the Fletcher32 EDC filter is enabled. - There was a bug in the calculation of the Fletcher32 checksum in the - library before v1.6.3; the checksum value was not consistent between big- - endian and little-endian systems. This bug was fixed in Release 1.6.3. - However, after fixing the bug, the checksum value was no longer the same as - before on little-endian system. Library releases after 1.6.4 can still read - datasets created or rewritten with an HDF5 library of v1.6.2 or before. - SLU - 2005/6/30 - -* On IBM AIX systems, parallel HDF5 mode will fail some tests with error - messages like "INFO: 0031-XXX ...". This is from the command `poe'. - Set the environment variable MP_INFOLEVEL to 0 to minimize the messages - and run the tests again. - - The tests may fail with messages like "The socket name is already in use", - but HDF5 does not use sockets. This failure is due to problems with the - poe command trying to set up the debug socket. To resolve this problem, - check to see whether there are many old /tmp/s.pedb.* files staying around. - These are sockets used by the poe command and left behind due to failed - commands. First, ask your system administrator to clean them out. - Lastly, request IBM to provide a means to run poe without the debug socket. - -* The --enable-static-exec configure flag will only statically link libraries - if the static version of that library is present. If only the shared version - of a library exists (i.e., most system libraries on Solaris, AIX, and Mac, - for example, only have shared versions), the flag should still result in a - successful compilation, but note that the installed executables will not be - fully static. Thus, the only guarantee on these systems is that the - executable is statically linked with just the HDF5 library. - -* There is also a configure error on Altix machines that incorrectly reports - when a version of Szip without an encoder is being used. - -* On cobalt, an SGI Altix SMP ia64 system, Intel compiler version 10.1 (which - is the default on that system) does not work properly and results in - failures during make check (in a static build) and make installcheck (during - a shared build). This appears to be a compiler optimization problem. - Reducing optimization by setting CFLAGS to -O1 or below resolves the issue. - Alternatively, using a newer version of the compiler (11.0) also works as - intended. MAM - 2010/06/01 - -* h5diff will not report enum value differences when one or both of the values - is not a valid enumeration value. The source of this bug has been identified - and it will be fixed in 1.8.8. DER - 2011/04/27 - - -%%%%1.8.6%%%% - - -HDF5 version 1.8.6 released on Mon Feb 14 10:26:30 CST 2011 -================================================================================ - -INTRODUCTION -============ - -This document describes the differences between HDF5-1.8.5 and -HDF5 1.8.6, and contains information on the platforms tested and -known problems in HDF5-1.8.6. -For more details, see the files HISTORY-1_0-1_8_0_rc3.txt -and HISTORY-1_8.txt in the release_docs/ directory of the HDF5 source. - -Links to the HDF5 1.8.6 source code, documentation, and additional materials -can be found on the HDF5 web page at: - - http://www.hdfgroup.org/products/hdf5/ - -The HDF5 1.8.6 release can be obtained from: - - http://www.hdfgroup.org/HDF5/release/obtain5.html - -User documentation for 1.8.6 can be accessed directly at this location: - - http://www.hdfgroup.org/HDF5/doc/ - -New features in the HDF5-1.8.x release series, including brief general -descriptions of some new and modified APIs, are described in the "What's New -in 1.8.0?" document: - - http://www.hdfgroup.org/HDF5/doc/ADGuide/WhatsNew180.html - -All new and modified APIs are listed in detail in the "HDF5 Software Changes -from Release to Release" document, in the section "Release 1.8.6 (current -release) versus Release 1.8.5": - - http://www.hdfgroup.org/HDF5/doc/ADGuide/Changes.html - -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, Languages, and Compilers -- Bug Fixes since HDF5-1.8.5 -- Platforms Tested -- Supported Configuration Features Summary -- Known Problems - - -New Features -============ - - Configuration - ------------- - - CMake: Improved CPack packaging, added parallel commands, improved - configuration options (better similarity to configure), added more - tests, better support for use in external cmake projects. - (ADB - 2010/10/07) - - The default configuration setting for official releases is - --enable-production. For unofficial releases, the default configuration - setting has been --disable-production. (AKC - 2010/05/28) - Library - ------- - - Added support for thread safety on Windows using the Windows threads - library. Use the HDF5_ENABLE_THREADSAFE option in CMake on a Windows - platform to enable this functionality. This is supported on Windows - Vista and newer Windows operating systems. (MAM - 2010/09/10) - - H5Tset_order and H5Tget_order now support all datatypes. A new byte - order, H5T_ORDER_MIXED, has been added specifically for a compound - datatype and its derived type. (SLU - 2010/8/23) - - Improved performance of metadata I/O by changing the default algorithm - to perform I/O from all processes (instead of just process 0) when using - parallel I/O drivers. (QAK - 2010/07/19) - - Improved performance of I/O on datasets with the same shape, but - different rank. (QAK - 2010/07/19) - - Improved performance of the chunk cache by avoiding unnecessary b-tree - lookups of chunks already in cache. (NAF - 2010/06/15) - - Parallel Library - ---------------- - - None - - Tools - ----- - - h5diff: Added a new flag: --exclude-path. The specified path to an - object will be excluded when comparing two files or two groups. If a - group is specified to be excluded, all member objects of that group - will be excluded. (JKM - 2010/09/16). - - h5ls: Added a new flag: --no-dangling-links. See --help output for - details. (JKM - 2010/06/15) - - h5ls: Added a new flag --follow-symlinks. See --help output for - details. (JKM - 2010/05/25) - - High-Level APIs - --------------- - - None - - F90 API - ------- - - None - - C++ API - ------- - - None - - -Support for New Platforms, Languages, and Compilers -=================================================== - - Sun C and C++ 5.10 and Sun Fortran 95 8.4. - - Mac OS X 10.6.4 with gcc 4.2.1 and gfortran 4.6 - - -Bug Fixes since HDF5-1.8.5 -========================== - - Configuration - ------------- - - The default number of MPI processes for testing purposes has been - changed from 3 to 6. (AKC - 2010/11/11) - - Some tests in tools/h5repack may fail in AIX systems when -q32 mode is - used. The error is caused by not requesting enough memory in default. - Added "env LDR_CNTRL=MAXDATA=0x20000000@DSA" into the $RUNSERIAL and - $RUNPARALLE in the AIX config file so that executables are tested with - more memory. (AKC - 2010/11/11) - - Removed recognition of the parallel compilers of LAM(hcc) and - ChMPIon(cmpicc) since we have no access to these two MPI implementations - and cannot verify their correctness. (AKC - 2010/07/14 - Bug 1921) - - PHDF5 was changed to use "mpiexec" instead of mpirun as the default - MPI applications startup command as defined in the MPI-2 definition, - section 4.1. (AKC - 2010/06/11 - Bug 1921) - - Library - ------- - - Fixed a bug that caused big endian machines to generate corrupt files - when using the scale-offset filter with floating point data or fill - values. Note that such datasets will no longer be readable by any - by any machine after this patch. (NAF - 2010/02/02 - Bug 2131) - - Retrieving a link's name by index in the case where the link is external - and the file that the link refers to doesn't exist will now fail - gracefully rather than cause a segmentation fault. (MAM - 2010/11/17) - - Modified metadata accumulator to better track accumulated dirty metadata - in an effort to reduce unnecessary I/O in certain situations and to - fix some other corner cases which were prone to error. (MAM - 2010/10/15) - - Added a new set of unit tests that are run during 'make check' to verify - the behavior of the metadata accumulator. (MAM - 2010/10/15) - - Modified library to always cache symbol table information. Libraries - from version 1.6.3 and earlier have a bug which causes them to require - this information for some operations. (NAF - 2010/09/21 - Bug 1864) - - Fixed a bug where the library could generate an assertion/core dump when - a file that had been created with H5Pset_libver_bounds(fapl, - H5F_LIBVER_LATEST, H5F_LIBVER_LATEST) but didn't have a superblock - extension was later reopened. (QAK - 2010/09/16 - Bug 1968) - - Fixed a bug that could occur when getting information for a new-style - group that was previously opened through a file handle that was later - closed. (NAF - 2010/09/15) - - Added define check in H5public.h if stdint.h is supported by the C++ - compiler. This define is only available on Windows with VS2010 and using - CMake to build the library. (ADB - 2010/09/13 - Bug 1938) - - When a mandatory filter failed to write data chunks, the dataset - couldn't close (bug 1260). The fix releases all resources and closes - the dataset but returns a failure. (SLU - 2010/09/08) - - H5Eset_current_stack now also closes the error stack set as the - default. This is to avoid a potential problem. - (SLU - 2010/09/07 - Bug 1799) - - Corrected situation where 1-D chunked dataset could get created by an - application without calling H5Pset_chunk(). H5Pset_chunk is now - required for creating all chunked datasets. (QAK - 2010/09/02) - - Fixed many memory issues that valgrind exposed. (QAK - 2010/08/24) - - Fixed the bug in the filter's public CAN_APPLY function. The return - value should be htri_t not herr_t. (SLU - 2010/08/05 - Bug 1239) - - Fixed the STDIO VFD to use fseeko64 instead of fseek64 for 64-bit I/O - support. (AKC - 2010/7/30) - - Fixed a bug in the direct I/O driver that could render files with certain - kinds of unaligned data unreadable or corrupt them. (NAF - 2010/07/28) - - valgrind reported an error of copying data to itself when a new attribute - is written. Fixed by taking out the memcpy step in the attribute code. - (SLU - 2010/07/28 - Bug 1956) - - Corrected various issues in the MPI datatype creation code which could - cause resource leaks or incorrect behavior (and may improve the - performance as well). (QAK - 2010/07/19) - - Fixed a bug that could cause file corruption when using non-default sizes - of addresses and/or lengths. This bug could also cause uncorrupted files - with this property to be unreadable. This bug was introduced in 1.8.5. - (NAF - 2010/07/16 - Bug 1951) - - Parallel Library - ---------------- - - None - - Tools - ----- - - Fixed h5diff to compare member objects and groups recursively when - two files or groups are compared. (JKM - 2010/9/16 - Bug 1975) - - Fixed h5repack to be able to convert a dataset to COMPACT layout. - (JKM - 2010/09/15 - Bug 1896) - - Changed h5ls to not interpret special characters in object or attribute - names for output. (JKM - 2010/06/28 - Bug 1784) - - Revised the order of arguments for h5cc, h5fc, h5c++, h5pcc and h5pfc. - CPPFLAGS, CFLAGS, LDFLAGS, and LIBS have been duplicated with an H5BLD_ - prefix to put the flags and paths from the hdf5 build in the correct - places and allow the script user to add entries in CPPFLAGS, CFLAGS, - LDFLAGS, and LIBS that will take precedence over those from the hdf5 - build. The user can make these entries persistent by editing - CFLAGSBASE, CPPFLAGSBASE, LDFLAGSBASE, and LIBSBASE near the top of - the script or temporary by setting HDF5_CFLAGS, HDF5_CPPFLAGS, - HDF5_LDFLAGS, or HDF5_LIBS in the environment. The new order of - arguments in these scripts is $CLINKER $H5BLD_CPPFLAGS $CPPFLAGS - $H5BLD_CFLAGS $CFLAGS $LDFLAGS $clibpath $link_objs $LIBS $link_args - $shared_link. (LRK - 2010/10/25 - Bug 1973) - - F90 API - ------ - - None - - C++ API - ------ - - None - - High-Level APIs: - ------ - - None - - Fortran High-Level APIs: - ------ - - None - - -Platforms Tested -================ -The following platforms and compilers have been tested for this release. - - AIX 6.1 xlc 11.1.0.3 - (NCSA BP) xlC 11.1.0.3 - xlf 13.1.0.3 - mpcc_r 11.1.0.3 - mpxlf_r 13.1.0.3 - - FreeBSD 6.3-STABLE i386 gcc 3.4.6 [FreeBSD] 20060305 - (duty) g++ 3.4.6 [FreeBSD] 20060305 - gcc 4.4.5 20100803 - g++ 4.4.5 20100803 - gfortran 4.4.5 20100803 - - FreeBSD 6.3-STABLE amd64 gcc 3.4.6 [FreeBSD] 20060305 - (liberty) g++ 3.4.6 [FreeBSD] 20060305 - gcc 4.4.5 20100803 - g++ 4.4.5 20100803 - gfortran 4.4.5 20100803 - - Linux 2.6.18-194.3.1.el5PAE gcc (GCC) 4.1.2 and 4.4.2 - #1 SMP i686 i686 i386 G95 (GCC 4.0.3 (g95 0.93!) Apr 21 2010) - (jam) GNU Fortran (GCC) 4.1.2 20080704 - (Red Hat 4.1.2-48) and 4.4.2 - PGI C, Fortran, C++ 10.4-0 32-bit - PGI C, Fortran, C++ 10.6-0 32-bit - Intel(R) C Compiler for 32-bit - applications, Version 11.1 - Intel(R) C++ Compiler for 32-bit - applications, Version 11.1 - Intel(R) Fortran Compiler for 32-bit - applications, Version 11.1 - Absoft 32-bit Fortran 95 10.0.7 - MPICH mpich2-1.3.1 compiled with - gcc 4.1.2 and gfortran 4.1.2 - - Linux 2.6.18-194.17.1.el5 gcc 4.1.2 and 4.4.2 - #1 SMP x86_64 GNU/Linux G95 (GCC 4.0.3 (g95 0.93!) Apr 21 2010) - (amani) tested for both 32- and 64-bit binaries - GNU Fortran (GCC) 4.1.2 20080704 - (Red Hat 4.1.2-46) and 4.4.2 - Intel(R) C, C++, Fortran Compilers for - applications running on Intel(R) 64, - Version 11.1. - PGI C, Fortran, C++ Version 9.0-4 - for 64-bit target on x86-64 - MPICH mpich2-1.3.1 compiled with - gcc 4.1.2 and gfortran 4.1.2 - - SGI ProPack 7 Linux Intel(R) C++ Version 11.1 20100806 - 2.6.32.19-0.3.1.1982.0.PTF- Intel(R) Fortran Version 11.1 20100806 - default #1 SMP SGI MPT 2.01 - SGI Altix UV - (NCSA ember) - - SunOS 5.10 32- and 64-bit Sun C 5.9 Sun OS_sparc Patch 124867-16 - (linew) Sun Fortran 95 8.3 Sun OS_sparc Patch 127000-13 - Sun C++ 5.9 Sun OS_sparc Patch 124863-62 - Sun C 5.10 SunOS_sparc Patch 141861-07 - Sun Fortran 95 8.4 SunOS_sparc Patch 128231-06 - Sun C++ 5.10 SunOS_sparc 128228-11 - - Intel Xeon Linux 2.6.18- gcc 4.2.4 - 92.1.10.el5_lustre.1.6.6smp- Intel(R) C++ Version 10.1.017 - perfctr #8 SMP Intel(R) Fortran Compiler Version 10.1.017 - (NCSA abe) Open MPI 1.3.2 - MVAPICH2-1.5.1_pgi-10.8 - - Windows XP Visual Studio 2008 w/ Intel Fortran 10.1 (project files) - Visual Studio 2008 w/ Intel Fortran 11.1 (cmake) - Visual Studio 2010 (cmake) - Cygwin(1.7.7 native gcc(4.3.4) compiler and gfortran) - - Windows XP x64 Visual Studio 2008 w/ Intel Fortran 10.1 (project files) - Visual Studio 2008 w/ Intel Fortran 11.1 (cmake) - Visual Studio 2010 (cmake) - Cygwin(1.7.7 native gcc(4.3.4) compiler and gfortran) - - Windows Vista Visual Studio 2008 w/ Intel Fortran 10.1 (project files) - Visual Studio 2008 w/ Intel Fortran 11.1 (cmake) - - Windows Vista x64 Visual Studio 2008 w/ Intel Fortran 10.1 (project files) - Visual Studio 2008 w/ Intel Fortran 11.1 (cmake) - - Windows 7 Visual Studio 2008 w/ Intel Fortran 11.1 (cmake) - - Windows 7 x64 Visual Studio 2008 w/ Intel Fortran 11.1 (cmake) - - Mac OS X 10.6.3 (Intel 64-bit) i686-apple-darwin10-gcc-4.2.1 (GCC) 4.2.1 - Darwin Kernel Version 10.3.1 GNU Fortran (GCC) 4.5.0 20090910 - Intel C, C++ and Fortran compilers 11.1 20100806 - - Mac OS X 10.6.4 (Intel 32-bit) i686-apple-darwin10-gcc-4.2.1 (GCC) 4.2.1 - Darwin Kernel Version 10.4.0 GNU Fortran (GCC) 4.6.0 20101106 - Intel C, C++ and Fortran compilers 12.0.0 20101110 - - Mac OS X 10.6.4 (Intel 64-bit) i686-apple-darwin10-gcc-4.2.1 (GCC) 4.2.1 (Apple Inc. build 5659) - Darwin Kernel Version 10.6.0 GNU Fortran (GCC) 4.5.0 20090910 - Intel C, C++ and Fortran compilers 11.1 20100806 - - Fedora 12 2.6.32.16-150.fc12.ppc64 #1 SMP ppc64 GNU/Linux - gcc (GCC) 4.4.4 20100630 (Red Hat 4.4.4-10) - GNU Fortran (GCC) 4.4.4 20100630 (Red Hat 4.4.4-10) - - Debian5.06 2.6.26-2-686 #1 SMP i686 GNU/Linux - gcc (Debian 4.3.2-1.1) 4.3.2 - GNU Fortran (Debian 4.3.2-1.1) 4.3.2 - - Debian5.06 2.6.26-2-amd64 #1 SMP x86_64 GNU/Linux - gcc (Debian 4.3.2-1.1) 4.3.2 - GNU Fortran (Debian 4.3.2-1.1) 4.3.2 - - Fedora14 2.6.35.6-48.fc14.i686.PAE #1 SMP i686 i686 i386 GNU/Linux - gcc (GCC) 4.5.1 20100924 (Red Hat 4.5.1-4) - GNU Fortran (GCC) 4.5.1 20100924 (Red Hat 4.5.1-4) - - Fedora14 2.6.35.6-48.fc14.x86_64 #1 SMP x86_64 x86_64 x86_64 GNU/Linux - gcc (GCC) 4.5.1 20100924 (Red Hat 4.5.1-4) - GNU Fortran (GCC) 4.5.1 20100924 (Red Hat 4.5.1-4) - - SUSE 11.3 2.6.34.7-0.7-desktop #1 SMP PREEMPT i686 i686 i386 GNU/Linux - gcc (SUSE Linux) 4.5.0 20100604 [gcc-4_5-branch revision 160292] - GNU Fortran (SUSE Linux) 4.5.0 20100604 [gcc-4_5-branch revision 160292] - - SUSE 11.3 2.6.34.7-0.7-desktop #1 SMP PREEMPT x86_64 x86_64 x86_64 GNU/Linux - gcc (SUSE Linux) 4.5.0 20100604 [gcc-4_5-branch revision 160292] - GNU Fortran (SUSE Linux) 4.5.0 20100604 [gcc-4_5-branch revision 160292] - - Ubuntu 10.10 2.6.35-25-generic #44-Ubuntu SMP i686 GNU/Linux - gcc (Ubuntu/Linaro 4.4.4-14ubuntu5) 4.4.5 - GNU Fortran (Ubuntu/Linaro 4.4.4-14ubuntu5) 4.4.5 - - Ubuntu 10.10 2.6.35-25-generic #44-Ubuntu SMP x86_64 GNU/Linux - gcc (Ubuntu/Linaro 4.4.4-14ubuntu5) 4.4.5 - GNU Fortran (Ubuntu/Linaro 4.4.4-14ubuntu5) 4.4.5 - - OpenVMS Alpha 8.3 HP C V7.3-009 - HP Fortran V8.2-104679-48H9K - HP C++ V7.3-009 - -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 parallel -Solaris2.10 32-bit n y n y y y -Solaris2.10 64-bit n y n y y y -Windows XP n y(4) n y y y -Windows XP x64 n y(4) n y y y -Windows Vista n y(4) n y y y -Windows Vista x64 n y(4) n y y y -OpenVMS Alpha n y n y y n -Mac OS X 10.6 Intel n y n y y y -AIX 6.1 32- and 64-bit y y y y y y -FreeBSD 6.3-STABLE 32&64 bit n y n y y y -CentOS 5.5 Linux 2.6.18-194 i686 GNU (1)W y y(2) y y y y -CentOS 5.5 Linux 2.6.18-194 i686 Intel W n y n y y n -CentOS 5.5 Linux 2.6.18-194 i686 PGI W n y n y y n -CentOS 5.5 Linux 2.6.16 x86_64 GNU (1) W y y(3) y y y y -CentOS 5.5 Linux 2.6.16 x86_64 Intel W n y n y y n -CentOS 5.5 Linux 2.6.16 x86_64 PGI W n y n y y y -RedHat EL4 2.6.18 Xeon Lustre C y y y y y n -Fedora 12 Linux 2.6.32.16-150.fc12.ppc64 n y n y y y -SGI Linux 2.6.32.19 y y y y y y - - -Platform Shared Shared Shared Thread- - C libs F90 libs C++ libs safe -Solaris2.10 32-bit y y y y -Solaris2.10 64-bit y y y y -Windows XP y y(4) y n -Windows XP x64 y y(4) y n -Windows Vista y y(4) y y -Windows Vista x64 y y(4) y y -OpenVMS Alpha n n n n -Mac OS X 10.6 y(5) n y n -AIX 6.1 32- and 64-bit n n n y -FreeBSD 6.3-STABLE 32&64 bit y n y y -CentOS 5.5 Linux 2.6.18-128 i686 GNU (1)W y y(2) y y -CentOS 5.5 Linux 2.6.18-128 i686 Intel W y y y n -CentOS 5.5 Linux 2.6.18-128 i686 PGI W y y y n -CentOS 5.5 Linux 2.6.16 x86_64 GNU (1) W y y y y -CentOS 5.5 Linux 2.6.16 x86_64 Intel W y y y n -CentOS 5.5 Linux 2.6.16 x86_64 PGI W y y y n -RedHat EL4 2.6.18 Xeon Lustre C y y y n -Fedora 12 Linux 2.6.32.16-150.fc12.ppc64 y y y y -SGI Linux 2.6.32.19 y y y y - - (1) Fortran compiled with gfortran. - (2) With PGI and Absoft compilers. - (3) With PGI compiler for Fortran. - (4) Using Visual Studio 2008 w/ Intel Fortran 10.1 (Cygwin shared libraries are not supported) - (5) C and C++ shared libraries will not be built when Fortran is enabled. - Compiler versions for each platform are listed in the preceding - "Platforms Tested" table. - - -Known Problems -============== -* examples/run-all-ex.sh does not work on Cygwin. (NAF - 2011/02/11) - -* Parallel test, t_shapesame in testpar, is rather unstable as it continues to - have occasional errors in AIX and quite often in NCSA Abe. It is being built - but it is not run automatically in the "make check" command. One would have to - run it by hand to see if it works in a particular machine. AKC - 2011/01/28 - -* Although OpenVMS Alpha is supported, there are several problems with the C - test suite - getname.c, lheap.c, lheap.c, mtime.c, and stab.c. The test - suite for h5diff also fails. These failures are from the tests, not the - library. We have fixed these failures. But it's too late to put the fixes - into this release. If you install the 1.8.6 library, it should still work - despite of these test failures. If you want the working copy without any - test failure, you can request it from us. SLU - 2011/01/26 - -* If parallel gmake (e.g., gmake -j 4) is used, the "gmake clean" command - sometimes fails in the perform directory due to the attempt to remove the - executable of h5perf or h5perf_serial by two "parallel" commands. This error - has no consequence on the functionality of the HDF5 library or install. It - is fixed in the next release. AKC - 2011/01/25 - -* While working on the 1.8.6 release of HDF5, a bug was discovered that can - occur when reading from a dataset in parallel shortly after it has been - written to collectively. The issue was exposed by a new test in the parallel - HDF5 test suite, but had existed before that. We believe the problem lies with - certain MPI implementations and/or filesystems. - - We have provided a pure MPI test program, as well as a standalone HDF5 - program, that can be used to determine if this is an issue on your system. - They should be run across multiple nodes with a varying number of processes. - These programs can be found at: - http://www.hdfgroup.org/ftp/HDF5/examples/known_problems/ - -* The h5diff tool can display garbage values when variable-length strings in - a compound type dataset are compared. This also occurs with variable-length - string arrays in a compound type dataset. See bug #1989. This will be fixed - in the next release. JKM - 2010/11/05 - -* The AIX --enable-shared setting does not quite work. It can produce a shared - library, but there cannot be more than one shared library that is - interlinked. This means that the high level APIs will not work which is not - very useful. We hope to have a solution in the next release. - (AKC - 2010/10/15) - -* H5Eset_auto can cause a seg fault for a library API call if the application - compiles with -DH5_USE_16_API (see bug 1707). It will be fixed in the - next release. SLU - 2010/10/5 - -* The library's test dt_arith.c showed a compiler's rounding problem on - Cygwin when converting an unsigned long long to a long double. The - library's own conversion works fine. We defined a macro for Cygwin to - skip this test until we can solve the problem. Please see bug #1813. - SLU - 2010/5/5 - -* All the VFL drivers aren't backwardly compatible. In H5FDpublic.h, the - structure H5FD_class_t changed in 1.8. A new parameter was added to the - get_eoa and set_eoa callback functions, and a new callback function - get_type_map was added. The public function H5FDrealloc was taken out in - 1.8. The problem only happens when users define their own driver for 1.6 - and try to plug in a 1.8 library. This will be fixed in 1.10. SLU - 2010/2/2 - -* MinGW has a missing libstdc++.dll.a library file and will not successfully link - C++ applications/tests. Do not use the enable-cxx configure option. Read all of - the INSTALL_MINGW.txt file for all restrictions. ADB - 2009/11/11 - -* The PathScale MPI implementation, accessing a Panasas file system, would - cause H5Fcreate() with H5F_ACC_EXCL to fail even when the file does not - exist. This is due to the MPI_File_open() call failing if the amode has - the MPI_MODE_EXCL bit set. (See bug 1468 for details.) AKC - 2009/8/11 - -* Parallel tests failed with 16 processes with data inconsistency at testphdf5 - / dataset_readAll. Parallel tests also failed with 32 and 64 processes with - collective abort of all ranks at t_posix_compliant / allwrite_allread_blocks - with MPI IO. CMC - 2009/04/28 - -* For Red Storm, a Cray XT3 system, the tools/h5ls/testh5ls.sh and - tools/h5copy/testh5copy.sh will fail some of their sub-tests. These - sub-tests are expected to fail and should exit with a non-zero code but - the yod command does not propagate the exit code of the executables. Yod - always returns 0 if it can launch the executable. The test suite shell - expects a non-zero for this particular test. Therefore, it concludes the - test has failed when it receives 0 from yod. To skip all the "failing" - tests for now, change them as shown below. - - ======== Original tools/h5ls/testh5ls.sh ========= - TOOLTEST tgroup-1.ls 1 -w80 -r -g tgroup.h5 - ======== Change to =============================== - echo SKIP TOOLTEST tgroup-1.ls 1 -w80 -r -g tgroup.h5 - ================================================== - - ======== Original tools/h5copy/testh5copy.sh ========= - TOOLTEST_FAIL -i $TESTFILE -o $FILEOUT -v -s grp_dsets -d grp_rename - TOOLTEST_FAIL -i $TESTFILE -o $FILEOUT -v -s grp_dsets -d /grp_rename/grp_dsets - TOOLTEST_FAIL -i $TESTFILE -o $FILEOUT -vp -s /grp_dsets -d /E/F/grp_dsets - TOOLTEST_FAIL -i $TESTFILE -o $FILEOUT -vp -s /grp_nested -d /G/H/grp_nested - H5LSTEST $FILEOUT - ======== Change to =============================== - echo SKIP TOOLTEST_FAIL -i $TESTFILE -o $FILEOUT -v -s grp_dsets -d grp_rename - echo SKIP TOOLTEST_FAIL -i $TESTFILE -o $FILEOUT -v -s grp_dsets -d /grp_rename/grp_dsets - echo SKIP TOOLTEST_FAIL -i $TESTFILE -o $FILEOUT -vp -s /grp_dsets -d /E/F/grp_dsets - echo SKIP TOOLTEST_FAIL -i $TESTFILE -o $FILEOUT -vp -s /grp_nested -d /G/H/grp_nested - echo SKIP H5LSTEST $FILEOUT - ================================================== - AKC - 2008/11/10 - -* For Red Storm, a Cray XT3 system, the yod command sometimes gives the - message "yod allocation delayed for node recovery." This interferes - with test suites that do not expect to see this message. See the "Red Storm" - section in file INSTALL_parallel for a way to deal with this problem. - AKC - 2008/05/28 - -* On an Intel 64 Linux cluster (RH 4, Linux 2.6.9) with Intel 10.0 compilers, - use the -mp -O1 compilation flags to build the libraries. A higher level - of optimization causes failures in several HDF5 library tests. - -* On mpich 1.2.5 and 1.2.6 on a system using four processors, if more than - two processes contribute no I/O and the application asks to do collective - I/O, we have found that a simple collective write will sometimes hang. This - can be verified with the t_mpi test under testpar. - -* A dataset created or rewritten with a v1.6.3 or later library cannot be - read with the v1.6.2 or earlier library when the Fletcher32 EDC filter - is enabled. There was a bug in the calculation of the Fletcher32 checksum - in the library before v1.6.3; the checksum value was not consistent - between big-endian and little-endian systems. This bug was fixed in - Release 1.6.3. However, after fixing the bug, the checksum value was no - longer the same as before on little-endian system. Library releases after - 1.6.4 can still read datasets created or rewritten with an HDF5 library of - v1.6.2 or earlier. SLU - 2005/6/30 - -* On IBM AIX systems, parallel HDF5 mode will fail some tests with error - messages like "INFO: 0031-XXX ...". This is from the command `poe'. To - work around this, set the environment variable MP_INFOLEVEL to 0 to - minimize the messages and run the tests again. The tests may fail with - messages like "The socket name is already in use", but HDF5 does not use - sockets. This failure is due to problems with the poe command trying to - set up the debug socket. To resolve this problem, check to see whether - there are any old /tmp/s.pedb.* files around. These are sockets used by - the poe command and left behind if the command failed at some point. To - resolve this, ask your system administrator to remove the - old/tmp/s.pedb.* files, and then ask IBM to provide a means to run poe - without the debug socket. - -* The --enable-static-exec configure flag will only statically link - libraries if the static version of that library is present. If only the - shared version of a library exists (i.e., most system libraries on - Solaris, AIX, and Mac, for example, only have shared versions), the flag - should still result in a successful compilation, but note that the - installed executables will not be fully static. Thus, the only guarantee - on these systems is that the executable is statically linked with just - the HDF5 library. - -* On an SGI Altix SMP ia64 system, the Intel compiler version 10.1 (which - is the default on that system) does not work properly and results in - failures during the make check (in a static build) and the make - installcheck (in a shared build). This appears to be a compiler - optimization problem. Reducing the optimization by setting CFLAGS to - -O1 or below resolves the issue. Using a newer version of the compiler - (11.0) avoids the issue. MAM - 2010/06/01 - -* On solaris systems, when running the examples with the scripts installed in - .../share/hdf5_examples, two of the c tests, h5_extlink and h5_elink_unix2win - may fail or generate HDF5 errors because the script commands in c/run-c-ex.sh - fail to create test directories red, blue, and u2w. Moving the '!' in lines - 67, 70, 73 of run-c-ex.sh will fix the problem. For example the script command - "if ! test -d red; then" will work on solaris if changed to - "if test ! -d red; then". - - -%%%%1.8.5%%%% - - -HDF5 version 1.8.5 released on Fri Jun 4 13:27:31 CDT 2010 -================================================================================ - -INTRODUCTION -============ - -This document describes the differences between HDF5-1.8.4 and HDF5 1.8.5, and -contains information on the platforms tested and known problems in HDF5-1.8.5. -For more details, see the files HISTORY-1_0-1_8_0_rc3.txt and HISTORY-1_8.txt -in the release_docs/ directory of the HDF5 source. - -Links to the HDF5 1.8.5 source code, documentation, and additional materials -can be found on the HDF5 web page at: - - http://www.hdfgroup.org/products/hdf5/ - -The HDF5 1.8.5 release can be obtained from: - - http://www.hdfgroup.org/HDF5/release/obtain5.html - -User documentation for 1.8.5 can be accessed directly at this location: - - http://www.hdfgroup.org/HDF5/doc/ - -New features in the HDF5-1.8.x release series, including brief general -descriptions of some new and modified APIs, are described in the "What's New -in 1.8.0?" document: - - http://www.hdfgroup.org/HDF5/doc/ADGuide/WhatsNew180.html - -All new and modified APIs are listed in detail in the "HDF5 Software Changes -from Release to Release" document, in the section "Release 1.8.5 (current -release) versus Release 1.8.4": - - http://www.hdfgroup.org/HDF5/doc/ADGuide/Changes.html - -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, Languages, and Compilers -- Bug Fixes since HDF5-1.8.4 -- Platforms Tested -- Supported Configuration Features Summary -- Known Problems - - -New Features -============ - - Configuration - ------------- - - CMake Early Access: This release adds support for building HDF5 using - the CMake system. Initial work has targeted Windows, but other platforms - can be used. See the CMake.TXT file for more information. Version - 2.8.1 of CMake is required. - - Configure now adds appropriate defines for supporting large (64-bit) - files on all systems, where supported, by default, instead of only Linux. - This large file support is controllable with the --enable-largefile - configure option. The Linux-specific --enable-linux-lfs option has been - deprecated in favor of this new option. Please note that specifying - --disable-large does NOT attempt to "turn off" largefile support if it - is natively supported by the compiler, but rather just disables - configure from actively trying to add any additional compiler flags. - (MAM - 2010/05/05 - Bug # 1772/1434) - - Fixed an signal handling mask error in H5detect that might result in - SIGBUS or SIGSEGV failures in some platforms such as Linux on Sparc. - (AKC - 2010/4/28 - Bug # 1764) - - Fixed various "strict aliasing" problems, allowing higher levels - of compiler optimization (in particular, allowing '-O3' to work - with recent versions of GCC). (QAK - 2010/04/26) - - Upgraded versions of autotools used to generate configuration suite. - We now use Automake 1.11.1, Autoconf 2.65, and Libtool 2.2.6b. - (MAM - 2010/04/15) - - Added the xlc-* and mpcc_r-* BASENAME patterns to be recognized as IBM - compilers so that the IBM compiler options can be added properly. This - allows non-system-default compiler command names (e.g. xlc-m.n.k.l) be - recognized. (AKC - 2009/11/26) - - Library - ------- - - Performance is substantially improved when extending a dataset with early - allocation. (NAF - 2010/03/24 - Bug # 1637) - - Added support for filtering densely stored groups. Many of the API - functions related to filters have been extended to support dense groups - as well as datasets. Pipeline messages can now be stored in a group's - object header. (NAF/QAK - 2009/11/3) - - Parallel Library - ---------------- - - None - - Tools - ----- - - h5dump: Added the new packed bits feature which prints packed bits stored - in an integer dataset. (AKC/ADB - 2010/5/7) - - h5diff: Fixed incorrect behavior (hang) in parallel mode when specifying - invalid options (ex: -v and -q). (JKM - 2010/02/17) - - h5diff: Added new flag --no-dangling-links (see --help for details). - (JKM - 2010/02/10) - - h5diff: Added new flag --follow-symlinks (see --help for details). - (JKM - 2010/01/25) - - h5diff: Added a fix to correct the display of garbage values when - displaying big-endian data on a little-endian machine. (JKM - 2009/11/20) - - High-Level APIs - --------------- - - None - - F90 API - ------- - - None - - C++ API - ------- - - New member functions - + Overloaded CommonFG::getObjnameByIdx to take char* for name. - + Overloaded CommonFG::getObjTypeByIdx to return type name as a char*. - (BMR - 2010/05/10) - + Added DataSet::getInMemDataSize() to simplify getting the dataset's - data size in memory. (BMR - 2009/07/26) - - -Support for New Platforms, Languages, and Compilers -=================================================== - - AIX 6.1 has been added. (AKC - 2010/1/4) - - -Bug Fixes since HDF5-1.8.4 -========================== - - Configuration - ------------- - - Fixed various "strict aliasing" problems, allowing higher levels - of compiler optimization (in particular, allowing '-O3' to work - with recent versions of GCC). (QAK - 2010/04/26) - - Library - ------- - - Fixed a file corruption bug that could happen when shrinking a compressed - dataset. (NAF - 2010/05/20) - - Fixed some memory leaks in VL datatype conversion when strings are - used as fill values. (MAM - 2010/05/12 - Bug # 1826) - - Fixed an H5Rcreate failure when passing in a -1 for the dataspace - identifier. (ADB - 2010/4/28) - - Fixed a bug when copying objects with NULL references with the - H5O_COPY_EXPAND_REFERENCE_FLAG flag set. (NAF - 2010/04/08 - Bug # 1815) - - Added a mechanism to the H5I interface to save returned object identifier - structures for immediate re-use if needed. This addresses a potential - performance issue by delaying the case when the next identifier to be - registered has grown so large that it wraps around and needs to be - checked to see whether it is available for distribution. - (MAM - 2010/03/15 - Bug # 1730) - - Files can now be concurrently opened more than once using the core file - driver, as long as the backing store is used. (NAF - 2010/03/09) - - Added support for H5O_COPY_EXPAND_EXT_LINK_FLAG to H5Ocopy. External - links will now be expanded if this flag is set. - (NAF - 2010/03/05 - Bug # 1733) - - Fixed a bug where the library, when traversing an external link, would - reopen the source file if nothing else worked. (NAF - 2010/03/05) - - Fixed a bug where fractal heap identifiers for attributes and shared - object header messages could be incorrectly encoded in the file for - files created on big-endian platforms. - Please see http://www.hdfgroup.org/HDF5/release/known_problems if you - suspect you have a file with this problem. - (QAK - 2010/02/23 - Bug # 1755) - - Fixed an intermittent bug in the b-tree code which could be triggered - by expanding and shrinking chunked datasets in certain ways. - (NAF - 2010/02/16) - - H5Tdetect_class said a VL string is a string type. But when it's in - a compound type, it said it's a VL type. THis has been fixed to be - consistent; it now always returns a string type. - (SLU - 2009/12/10 - Bug # 1584) - - Allow "child" files from external links to be correctly located when - relative to a "parent" file that is opened through a symbolic link. - (QAK - 2009/12/01) - - Parallel Library - ---------------- - - Parallel mode in AIX will fail some of the testcheck_version.sh tests - where it treats "exit(134) the same as if process 0 had received an abort - signal. Fixed. (AKC - 2009/11/3) - - Tools - ----- - - Fixed h5ls to return exit code 1 (error) when a non-existent file is - specified. (JKM - 2010/04/27 - Bug # 1793) - - Fixed h5copy failure when copying a dangling link that is specified - directly. (JKM - 2010/04/22 - Bug # 1817) - - Fixed an h5repack failure that lost attributes from a dataset of - reference type. (JKM - 2010/3/25 - Bug # 1726) - - Fixed h5repack error that set NULL for object reference values for - datasets, groups, or named datatypes. (JKM - 2010/03/19 - Bug # 1814) - - F90 API - ------ - - None - - C++ API - ------ - - The constructor PropList::PropList(id) was fixed to act properly - according to the nature of 'id'. When 'id' is a property class - identifier, a new property list will be created. When 'id' is a - property list identifier, a copy of the property list will be made. - (BMR - 2010/5/9) - - The parameters 'size' and 'bufsize' in CommonFG::getLinkval and - CommonFG::getComment, respectively, now have default values for the - user's convenience. (BMR - 2009/10/23) - - NULL pointer accessing was fixed. (BMR - 2009/10/05 - Bug # 1061) - - Read/write methods of DataSet and Attribute classes were fixed - to handle string correctly. (BMR - 2009/07/26) - - High-Level APIs: - ------ - - Fixed a bug in H5DSattach_scale, H5DSis_attached, and H5DSdetach_scale - caused by using the H5Tget_native_type function to determine the native - type for reading the REFERENCE_LIST attribute. This bug was exposed - on Mac PPC. (EIP - 2010/05/22 - Bug # 1851) - - Fixed a bug in the H5DSdetach_scale function when 0 bytes were - allocated after the last reference to a dimension scale was removed - from the list of references in a VL element of the DIMENSION_LIST - attribute. Modified the function to comply with the specification: - the DIMENSION_LIST attribute is now deleted when no dimension scales - are left attached. (EIP - 2010/05/14 - Bug # 1822) - - Fortran High-Level APIs: - ------ - - None - - -Platforms Tested -================ -The following platforms and compilers have been tested for this release. - - AIX 5.3 xlc 7.0.0.9, 8.0.0.20, 9.0.0.4 - (LLNL Up) xlC 7.0.0.9, 8.0.0.20, 9.0.0.4 - xlf 9.1.0.9, 10.1.0.9, 11.1.0.7 - mpcc_r 7.0.0.9 - mpxlf_r 09.01.0000.0008 - - AIX 6.1 xlc 10.1.0.6 - (NCSA BP) xlC 10.1.0.6 - xlf 12.1.0.7 - - Cray XT3 (2.1.56) cc (pgcc) 10.0-0 - (SNL red storm) ftn (pgf90) 10.0-0 - CC (pgCC) 10.0-0 - - FreeBSD 6.3-STABLE i386 gcc 3.4.6 [FreeBSD] 20060305 - (duty) g++ 3.4.6 [FreeBSD] 20060305 - gcc 4.3.4 20090419 - g++ 4.3.4 20090419 - gfortran 4.3.4 20090419 - - FreeBSD 6.3-STABLE amd64 gcc 3.4.6 [FreeBSD] 20060305 - (liberty) g++ 3.4.6 [FreeBSD] 20060305 - gcc 4.4.1 20090421 - g++ 4.4.1 20090421 - gfortran 4.4.1 20090421 - - Linux 2.6.18-128.1.6.el5xen gcc (GCC) 4.1.2 20080704 and 4.4.2 - #1 SMP i686 i686 i386 GNU Fortran (GCC) 4.1.2 20080704 and 4.4.2 - (jam) g++ (GCC) 4.1.2 20080704 and 4.4.2 - G95 (GCC 4.0.3 (g95 0.93!) Apr 21 2010) - Absoft 32-bit Fortran 95 10.0.7 - PGI C, Fortran, C++ 10.4-0 32-bit - Intel(R) C, C++, Fortran Compilers for 32-bit - applications, Version 11.1 Build 20090827 - MPICH mpich2-1.0.8 compiled with - gcc 4.1.2 and GNU Fortran (GCC) 4.1.2 - - Linux 2.6.18-164.el5 #1 SMP gcc 4.1.2 20080704 and gcc 4.4.2 - x86_64 GNU/Linux GNU Fortran (GCC) 4.1.2 20080704 and 4.4.2 - (amani) g++ (GCC) 4.1.2 20080704 and 4.4.2 - G95 (GCC 4.0.3 (g95 0.93!) Apr 21 2010) - Intel(R) C, C++, Fortran Compilers for - applications running on Intel(R) 64, - Version 11.1 Build 20090827. - PGI C, Fortran, C++ Version 10.4-0 - for 32 & 64-bit target on x86-64 - MPICH mpich2-1.0.8 compiled with - gcc 4.1.2 and GNU Fortran (GCC) 4.1.2 - - Linux 2.6.16.54-0.2.5 #1 Intel(R) C++ Version 11.0.074 - SGI Altix SMP ia64 Intel(R) Fortran Itanium(R) Version 11.0.074 - (cobalt) SGI MPI 1.38 - - SunOS 5.10 32- and 64-bit Sun C 5.9 SunOS_sparc Patch 124867-14 - (linew) Sun Fortran 95 8.3 SunOS_sparc - Patch 127000-13 - Sun C++ 5.9 SunOS_sparc Patch 124863-23 - - Intel Xeon Linux 2.6.18- Intel(R) C++ Version 10.0.026 - 92.1.10.el5_lustre.1.6.6smp- Intel(R) Fortran Compiler Version 10.0.026 - perfctr #7 SMP Open MPI 1.2.2 - (abe) MVAPICH2-0.9.8p28p2patched-intel-ofed-1.2 - compiled with icc v10.0.026 and ifort 10.0.026 - - Linux 2.6.18-76chaos #1 SMP Intel(R) C, C++, Fortran Compilers for - SMP x86_64 GNU/Linux applications running on Intel(R) 64, - (SNL Glory) Versions 11.1. - - Windows XP Visual Studio 2008 w/ Intel Fortran 10.1 - Cygwin(1.7.5 native gcc(4.3.4) compiler and - gfortran) - - Windows XP x64 Visual Studio 2008 w/ Intel Fortran 10.1 - - Windows Vista Visual Studio 2008 w/ Intel Fortran 10.1 - - Windows Vista x64 Visual Studio 2008 w/ Intel Fortran 10.1 - - MAC OS 10.6.3 (Intel) i686-apple-darwin10-gcc-4.2.1 (GCC) 4.2.1 - (pahra) GNU Fortran (GCC) 4.5.0 20090910 - i686-apple-darwin10-g++-4.2.1 (GCC) 4.2.1 - Intel C, C++ and Fortran compilers 11.1 - - MAC OS 10.5.8 (Intel) i686-apple-darwin9-gcc-4.0.1 (GCC) 4.0.1 - (tejeda) - - MAC OS 10.5 (PPC) powerpc-apple-darwin9-gcc-4.0.1 (GCC) 4.0.1 - (juniper-w) - - OpenVMS Alpha V8.3 HP C V7.3-009 - HP C++ V7.3-009 - HP Fortran V8.0-1-104669-48GBT - -Supported Configuration Features Summary -======================================== - - In the tables below - y = tested and supported - n = not supported or 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 parallel -Solaris2.10 32-bit n y n y y y -Solaris2.10 64-bit n y n y y y -Windows XP n y(4) n(4) y y y -Windows XP x64 n y(4) n(4) y y y -Windows Vista n y(4) n(4) y y y -Windows Vista x64 n y(4) n(4) y y y -Mac OS X 10.5 PPC n n n n y n -Mac OS X 10.5 Intel n y n y y y -Mac OS X 10.6 Intel n y n y y y -AIX 5.3 32- and 64-bit n y n y y n -AIX 6.1 32- and 64-bit n y n y y n -FreeBSD 6.3-STABLE 32&64 bit n y n y y y -RedHat EL4 2.6.9-42 i686 GNU (1) W y y y y y y -RedHat EL5 2.6.18-128 i686 GNU (1)W y y(2) y y y y -RedHat EL5 2.6.18-128 i686 Intel W n y n y y n -RedHat EL5 2.6.18-128 i686 PGI W n y n y y n -SuSe Linux 2.6.16 x86_64 GNU (1) W y y(3) y y y y -SuSe Linux 2.6.16 x86_64 Intel W n y n y y n -SuSe Linux 2.6.16 x86_64 PGI W n y n y y y -SuSe Linux 2.6.16 SGI Altix ia64 C y y y y y y -RedHat EL4 2.6.18 Xeon Lustre C y y y y y n -Cray XT3 2.1.56 y y y y y n -OpenVMS Alpha V8.3 n y n y y n - -Platform Shared Shared Shared Thread- - C libs F90 libs C++ libs safe -Solaris2.10 32-bit y y y y -Solaris2.10 64-bit y y y y -Windows XP y y(4) y n -Windows XP x64 y y(4) y n -Windows Vista y y(4) y n -Windows Vista x64 y y(4) y n -Mac OS X 10.5 PPC y n n n -Mac OS X 10.5 (Intel) y(5) n y n -Mac OS X 10.6 (Intel) y(5) n y n -AIX 5.3 32- and 64-bit n n n n -AIX 6.1 32- and 64-bit n n n n -FreeBSD 6.3-STABLE 32&64 bit y n y y -RedHat EL4 2.6.9-42 i686 GNU (1) W y y y y -RedHat EL5 2.6.18-128 i686 GNU (1)W y y(2) y y -RedHat EL5 2.6.18-128 i686 Intel W y y y n -RedHat EL5 2.6.18-128 i686 PGI W y y y n -SuSe Linux 2.6.16 x86_64 GNU (1) W y y y y -SuSe Linux 2.6.16 x86_64 Intel W y y y n -SuSe Linux 2.6.16 x86_64 PGI W y y y n -SuSe Linux 2.6.16 SGI Altix ia64 C y n -RedHat EL4 2.6.18 Xeon Lustre C y y y n -Cray XT3 2.1.56 n n n n -OpenVMS Alpha V8.3 n n n n - - (1) Fortran compiled with g95. - (2) With PGI and Absoft compilers. - (3) With PGI compiler for Fortran. - (4) Using Visual Studio 2008. (Cygwin shared libraries are not - supported.) - (5) Shared C and C++ are disabled when Fortran is configured in. - Compiler versions for each platform are listed in the preceding - "Platforms Tested" table. - - -Known Problems -============== -* The library's test dt_arith.c exposed a compiler's rounding problem on - Cygwin when converting from unsigned long long to long double. The - library's own conversion works correctly. A macro is defined for Cygwin - to skip this test until we can solve the problem. (Please see bug #1813.) - SLU - 2010/5/5 - -* All the VFL drivers aren't backward compatible. In H5FDpublic.h, the - structure H5FD_class_t changed in 1.8. There is a new parameter added to - get_eoa and set_eoa callback functions. A new callback function - get_type_map was added. The public function H5FDrealloc was taken - out in 1.8. The problem only happens when users define their own driver - for 1.6 and try to plug it into a 1.8 library. This affects a very small - number of users. (See bug report #1279.) SLU - 2010/2/2 - -* MinGW has a missing libstdc++.dll.a library file and will not successfully - link C++ applications/tests. Do not use the enable-cxx configure option. - Read all of the INSTALL_MINGW.txt file for all restrictions. - ADB - 2009/11/11 - -* Some tests in tools/h5repack may fail in AIX systems when -q32 mode is used. - The error is due to insufficient memory requested. Request a large amount - of runtime memory by setting the following environment variable for more - memory. - LDR_CNTRL=MAXDATA=0x20000000@DSA - AKC - 2009/10/31 - -* The PathScale MPI implementation, accessing a Panasas file system, would - cause H5Fcreate() with H5F_ACC_EXCL to fail even when the file is not - existing. This is due to the MPI_File_open() call failing if the amode has - the MPI_MODE_EXCL bit set. (See bug 1468 for details.) AKC - 2009/8/11 - -* Parallel tests failed with 16 processes with data inconsistency at testphdf5 - / dataset_readAll. Parallel tests also failed with 32 and 64 processes with - collective abort of all ranks at t_posix_compliant / allwrite_allread_blocks - with MPI IO. CMC - 2009/04/28 - -* For gcc v4.3 and v4.4, with production mode, if -O3 is used, H5Tinit.c - would fail to compile. Actually bad H5Tinit.c is produced. If -O (same - as -O1) is used, H5Tinit.c compiled okay but test/dt_arith would fail. - When -O0 (no optimizatio) is used, H5Tinit.c compilete okay and all - tests passed. Therefore, -O0 is imposed for v4.3 and v4.4 of gcc. - AKC - 2009/04/20 - -* For Red Storm, a Cray XT3 system, the tools/h5ls/testh5ls.sh and - tools/h5copy/testh5copy.sh will fail some of its sub-tests. These sub-tests - are expected to fail and should exit with a non-zero code but the yod - command does not propagate the exit code of the executables. Yod always - returns 0 if it can launch the executable. The test suite shell expects - a non-zero for this particular test, therefore it concludes the test has - failed when it receives 0 from yod. Skip all the "failing" test for now - by changing them as following. - - ======== Original tools/h5ls/testh5ls.sh ========= - TOOLTEST tgroup-1.ls 1 -w80 -r -g tgroup.h5 - ======== Change to =============================== - echo SKIP TOOLTEST tgroup-1.ls 1 -w80 -r -g tgroup.h5 - ================================================== - - ======== Original tools/h5copy/testh5copy.sh ========= - TOOLTEST_FAIL -i $TESTFILE -o $FILEOUT -v -s grp_dsets -d grp_rename - TOOLTEST_FAIL -i $TESTFILE -o $FILEOUT -v -s grp_dsets -d /grp_rename/grp_dsets - TOOLTEST_FAIL -i $TESTFILE -o $FILEOUT -vp -s /grp_dsets -d /E/F/grp_dsets - TOOLTEST_FAIL -i $TESTFILE -o $FILEOUT -vp -s /grp_nested -d /G/H/grp_nested - H5LSTEST $FILEOUT - ======== Change to =============================== - echo SKIP TOOLTEST_FAIL -i $TESTFILE -o $FILEOUT -v -s grp_dsets -d grp_rename - echo SKIP TOOLTEST_FAIL -i $TESTFILE -o $FILEOUT -v -s grp_dsets -d /grp_rename/grp_dsets - echo SKIP TOOLTEST_FAIL -i $TESTFILE -o $FILEOUT -vp -s /grp_dsets -d /E/F/grp_dsets - echo SKIP TOOLTEST_FAIL -i $TESTFILE -o $FILEOUT -vp -s /grp_nested -d /G/H/grp_nested - echo SKIP H5LSTEST $FILEOUT - ================================================== - AKC - 2008/11/10 - -* For Red Storm, a Cray XT3 system, the yod command sometimes gives the - message, "yod allocation delayed for node recovery". This interferes with - test suites that do not expect seeing this message. See the section of "Red - Storm" in file INSTALL_parallel for a way to deal with this problem. - AKC - 2008/05/28 - -* On Intel 64 Linux cluster (RH 4, Linux 2.6.9) with Intel 10.0 compilers, - use -mp -O1 compilation flags to build the libraries. A higher level of - optimization causes failures in several HDF5 library tests. - -* On mpich 1.2.5 and 1.2.6, if more than two processes contribute no IO and - the application asks to do collective IO, we have found that when using 4 - processors, a simple collective write will sometimes be hung. This can be - verified with t_mpi test under testpar. - -* A dataset created or rewritten with a v1.6.3 library or after cannot be read - with the v1.6.2 library or before when the Fletcher32 EDC filter is enabled. - There was a bug in the calculation of the Fletcher32 checksum in the - library before v1.6.3; the checksum value was not consistent between big- - endian and little-endian systems. This bug was fixed in Release 1.6.3. - However, after fixing the bug, the checksum value was no longer the same as - before on little-endian system. Library releases after 1.6.4 can still read - datasets created or rewritten with an HDF5 library of v1.6.2 or before. - SLU - 2005/6/30 - -* On IBM AIX systems, parallel HDF5 mode will fail some tests with error - messages like "INFO: 0031-XXX ...". This is from the command `poe'. - Set the environment variable MP_INFOLEVEL to 0 to minimize the messages - and run the tests again. - - The tests may fail with messages like "The socket name is already in use," - but HDF5 does not use sockets. This failure is due to problems with the - poe command trying to set up the debug socket. To resolve this problem, - check to see whether there are many old /tmp/s.pedb.* files staying around. - These are sockets used by the poe command and left behind due to failed - commands. First, ask your system administrator to clean them out. - Lastly, request IBM to provide a means to run poe without the debug socket. - -* The --enable-static-exec configure flag will only statically link libraries - if the static version of that library is present. If only the shared version - of a library exists (i.e., most system libraries on Solaris, AIX, and Mac, - for example, only have shared versions), the flag should still result in a - successful compilation, but note that the installed executables will not be - fully static. Thus, the only guarantee on these systems is that the - executable is statically linked with just the HDF5 library. - -* There is also a configure error on Altix machines that incorrectly reports - when a version of Szip without an encoder is being used. - -* On FREE-BSD systems when shared libraries are disabled, make install fails - in install-examples with the error '"Makefile", line 635: Need an operator'. - When this error occurs removing or commenting out the line "export - LD_LIBRARY_PATH=$(LL_PATH)" (line 635 in examples/Makefile) will allow make - install to finish installing examples. The problem will be fixed in the - next release. LRK - 2010/05/26 - -* On cobalt, an SGI Altix SMP ia64 system, Intel compiler version 10.1 (which - is the default on that system) does not work properly and results in - failures during make check (in a static build) and make installcheck (during - a shared build). This appears to be a compiler optimization problem. - Reducing optimization by setting CFLAGS to -O1 or below resolves the issue. - Alternatively, using a newer version of the compiler (11.0) also works as - intended. MAM - 2010/06/01 - - -%%%%1.8.4%%%% - - -HDF5 version 1.8.4 released on Tue Nov 10 15:33:14 CST 2009 -================================================================================ - -INTRODUCTION -============ - -This document describes the differences between HDF5-1.8.3 and -HDF5 1.8.4, and contains information on the platforms tested and -known problems in HDF5-1.8.4 -For more details, see the files HISTORY-1_0-1_8_0_rc3.txt -and HISTORY-1_8.txt in the release_docs/ directory of the HDF5 source. - -Links to the HDF5 1.8.4 source code, documentation, and additional materials -can be found on the HDF5 web page at: - - http://www.hdfgroup.org/products/hdf5/ - -The HDF5 1.8.4 release can be obtained from: - - http://www.hdfgroup.org/HDF5/release/obtain5.html - -User documentation for 1.8.4 can be accessed directly at this location: - - http://www.hdfgroup.org/HDF5/doc/ - -New features in the HDF5-1.8.x release series, including brief general -descriptions of some new and modified APIs, are described in the "What's New -in 1.8.0?" document: - - http://www.hdfgroup.org/HDF5/doc/ADGuide/WhatsNew180.html - -All new and modified APIs are listed in detail in the "HDF5 Software Changes -from Release to Release" document, in the section "Release 1.8.4 (current -release) versus Release 1.8.3": - - http://www.hdfgroup.org/HDF5/doc/ADGuide/Changes.html - -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, Languages, and Compilers -- Bug Fixes since HDF5-1.8.3 -- Platforms Tested -- Supported Configuration Features Summary -- Known Problems - - -New Features -============ - - Configuration - ------------- - - Configuration suite now uses Automake 1.11 and Autoconf 2.64. - MAM 2009/08/31. - - Changed default Gnu fortran compiler from g95 to gfortran since - gfortran is more likely installed with gcc now. -AKC 2009/07/19- - - Library - ------- - - The embedded library information is displayed by H5check_version() if a - version mismatch is detected. Also changed H5check_version() to - suppress the warning message totally if $HDF5_DISABLE_VERSION_CHECK is 2 - or higher. (Old behavior treated 3 or higher the same as 1, that is - print a warning and allows the program to continue. (AKC - 2009/9/28) - - If a user does not care for the extra library information insert - in the executables, he may turn it off by --disable-embedded-libinfo - during configure. (AKC - 2009/9/15) - - Parallel Library - ---------------- - - None - - Tools - ----- - - h5diff: h5diff treats two INFINITY values different. Fixed by checking - (value==expect) before call ABS(...) at h5diff_array.c. This will make - that (INF==INF) is true (INF is treated as an number instead of NaN) - (PC -- 2009/07/28) - - h5diff: add option "--use-system-epsilon" to print difference if - (|a-b| > EPSILON). - Change default to use strict equality (PC -- 2009/09/12) - - High-Level APIs - --------------- - - None - - F90 API - ------- - - Added H5Oopen_by_addr_f MSB - 9/14/09 - - C++ API - ------- - - None - - -Support for New Platforms, Languages, and Compilers -=================================================== - - PathScale compilers are recognized and can build the HDF5 library - properly. AKC - 2009/7/28 - - - -Bug Fixes since HDF5-1.8.3 -========================== - - Configuration - ------------- - - Removed the following config files, as we no longer support them: - config/dec-osf*, config/hpux11.00, config/irix5.x, - config/powerpc-ibm-aix4.x config/rs6000-ibm-aix5.x config/unicos* - MAM - 2009/10/08 - - Modified configure and make process to properly preserve user's CFLAGS - (and company) environment variables. Build will now properly use - automake's AM_CFLAGS for any compiler flags set by the configure - process. Configure will no longer modify CFLAGS directly, nor will - setting CFLAGS during make completely replace what configure has set up. - MAM - 2009/10/08 - - Support for TFLOPS, config/intel-osf1, is removed since the TFLOPS - machine has long retired. AKC - 2009/10/06. - - Added $(EXEEXT) extension to H5detect when it's executed in the - src/Makefile to generate H5Tinit.c so it works correctly on platforms - that require the full extension when running executables. - MAM - 2009/10/01 - BZ #1613 - - Configure will now set FC and CXX to "no" when fortran and c++ - are not being compiled, respectively, so configure will not run - some of the compiler tests for these languages when they are not - being used. MAM - 2009/10/01 - - The --enable-static-exec flag will now properly place the -static flag - on the link line of all installed executables. This will force the - executable to link with static libraries over shared libraries, provided - the static libraries are available. MAM - 2009/08/31 - BZ #1583 - - The PathScale compiler (v3.2) was mistaken as gcc v4.2.0 but it fails to - recognize some gcc options. Fixed. (see bug 1301). AKC - 2009/7/28 - - - Library - ------- - - Fixed a bug where writing and deleting many global heap objects (i.e. - variable length data) would render the file unreadable. Previously - created files exhibiting this problem should now be readable. - NAF - 2009/10/27 - 1483 - - Fixed error in library's internal caching mechanisms which could cause - an assertion failure (and attendant core dump) when encountering an - unusually formatted file. (QAK - 2009/10/13) - - Fixed incorrect return value for H5Pget_preserve. AKC - 2009/10/08 - 1628 - - Fixed an assertion failure that occurred when H5Ocopy was called on a - dataset using a vlen inside a compound. NAF - 2009/10/02 - 1597 - - Fixed incorrect return value for H5Pget_filter_by_id1/2 in H5Ppublic.h. - NAF - 2009/09/25 - 1620 - - Fixed a bug where properties weren't being compared with the registered - compare callback. NAF - 2009/09/25 - 1555 - - Corrected problem where library would re-write the superblock in a file - opened for R/W access, even when no changes were made to the file. - (QAK - 2009/08/20, Bz#1473) - - Fixed a bug where H5Pget_filter_by_id would succeed when called for a - filter that wasn't present. NAF - 2009/06/25 - 1250 - - Fixed an issue with committed compound datatypes containing a vlen. Also - fixed memory leaks involving committed datatypes. NAF - 2009/06/10 - 1593 - - Parallel Library - ---------------- - - None - - Tools - ----- - - h5dump/h5ls display buffer resize fixed in tools library. - ADB - 2009/7/21 - 1520 - - perf_serial test added to Windows projects and check batch file. - ADB - 2009/06/11 -1504 - - - F90 API - ------ - - Fixed bug in h5lget_info_by_idx_f by adding missing arguments, - consequently changing the API. New API is: - - SUBROUTINE h5lget_info_by_idx_f(loc_id, group_name, index_field, order, n, & - link_type, f_corder_valid, corder, cset, address, val_size, hdferr, lapl_id) - - MSB - 2009/9/17 - 1652 - - - Corrected the values for the H5L_flags FORTRAN constants: - H5L_LINK_ERROR_F, H5L_LINK_HARD_F, H5L_LINK_SOFT_F, H5L_LINK_EXTERNAL_F - MSB - 2009-09-17 - 1653 - - - Added FORTRAN equivalent of C constant H5T_ORDER_NONE: H5T_ORDER_NONE_F - MSB - 2009-9-24 - 1471 - - C++ API - ------ - - None - - High-Level APIs: - ------ - - Fixed a bug where the H5TB API would forget the order of fields when added - out of offset order. NAF - 2009/10/27 - 1582 - - H5DSis_attached failed to account for different platform types. Added a - get native type call. ADB - 2009/9/29 - 1562 - - Fortran High-Level APIs: - ------ - - Lite: the h5ltread_dataset_string_f and h5ltget_attribute_string_f functions - had memory problems with the g95 fortran compiler. (PVN � 5/13/2009) 1522 - - - -Platforms Tested -================ -The following platforms and compilers have been tested for this release. - - AIX 5.3 xlc 7.0.0.8 - (LLNL Up) xlf 09.01.0000.0008 - xlC 7.0.0.8 - mpcc_r 7.0.0.8 - mpxlf_r 09.01.0000.0008 - - Cray XT3 (2.0.41) cc (pgcc) 7.1-4 - (SNL red storm) ftn (pgf90) 7.1-4 - CC (pgCC) 7.1-4 - - FreeBSD 6.3-STABLE i386 gcc 3.4.6 [FreeBSD] 20060305 - (duty) g++ 3.4.6 [FreeBSD] 20060305 - gcc 4.3.5 20091004 - g++ 4.3.5 20091004 - gfortran 4.3.5 20091004 - - FreeBSD 6.3-STABLE amd64 gcc 3.4.6 [FreeBSD] 20060305 - (liberty) g++ 3.4.6 [FreeBSD] 20060305 - gcc 4.4.2 20091006 - g++ 4.4.2 20091006 - gfortran 4.4.2 20091006 - - Linux 2.6.18-164.el5 gcc (GCC) 4.1.2 20080704 - #1 SMP i686 i686 i386 G95 (GCC 4.0.3 (g95 0.92!) Jun 24 2009) - (jam) GNU Fortran (GCC) 4.1.2 20080704 - (Red Hat 4.1.2-46) - PGI C, Fortran, C++ 8.0-5 32-bit - PGI C, Fortran, C++ 8.0-1 32-bit - Intel(R) C Compiler for 32-bit - applications, Versions 11.0, 11.1 - Intel(R) C++ Compiler for 32-bit - applications, Version 11.0, 11.1 - Intel(R) Fortran Compiler for 32-bit - applications, Version 11.0, 11.1 - Absoft 32-bit Fortran 95 10.0.7 - MPICH mpich2-1.0.8 compiled with - gcc (GCC) 4.1.2 and G95 - (GCC 4.0.3 (g95 0.92!) - - Linux 2.6.18-164.el5 #1 SMP gcc 4.1.2 20080704 - x86_64 GNU/Linux G95 (GCC 4.0.3 (g95 0.92!) Jun 24 2009) - (amani) tested for both 32- and 64-bit binaries - Intel(R) C, C++, Fortran Compilers for - applications running on Intel(R) 64, - Versions 11.1. - PGI C, Fortran, C++ Version 9.0-4 - for 64-bit target on x86-64 - gcc 4.1.2 and G95 (GCC 4.0.3 (g95 0.92!) - MPICH mpich2-1.0.8 compiled with - gcc 4.1.2 and G95 (GCC 4.0.3 (g95 0.92!) - GNU Fortran (GCC) 4.1.2 20080704 - (Red Hat 4.1.2-46) - - - Linux 2.6.16.60-0.42.5 #1 Intel(R) C++ Version 10.1.017 - SGI Altix SMP ia64 Intel(R) Fortran Itanium(R) Version 10.1.017 - (cobalt) SGI MPI 1.38 - - SunOS 5.10 32- and 64-bit Sun C 5.9 SunOS_sparc Patch 124867-11 2009/04/30 - (linew) Sun Fortran 95 8.3 SunOS_sparc - Patch 127000-11 2009/10/06 - Sun C++ 5.9 SunOS_sparc - Patch 124863-16 2009/09/15 - - Intel Xeon Linux 2.6.18- Intel(R) C++ Version 10.0.026 - 92.1.10.el5_lustre.1.6.6smp- Intel(R) Fortran Compiler Version 10.0.026 - perfctr #6 SMP Open MPI 1.2.2 - (abe) MVAPICH2-0.9.8p28p2patched-intel-ofed-1.2 - compiled with icc v10.0.026 and ifort 10.0.026 - - IA-64 Linux 2.4.21-309.tg1 gcc (GCC) 3.2.2 - #1 SMP ia64 Intel(R) C++ Version 8.1.037 - (NCSA tg-login) Intel(R) Fortran Compiler Version 8.1.033 - mpich-gm-1.2.7p1..16-intel-8.1.037-r1 - - Linux 2.6.9-55.0.9.EL_lustre Intel(R) C, C++, Fortran Compilers for - .1.4.11.1smp #1 SMP applications running on Intel(R) 64, - SMP x86_64 GNU/Linux Versions 10.1. - (SNL Thunderbird) - - Linux 2.6.18-76chaos #1 SMP Intel(R) C, C++, Fortran Compilers for - SMP x86_64 GNU/Linux applications running on Intel(R) 64, - (SNL Glory) Versions 10.1. - - Windows XP Visual Studio 2005 w/ Intel Fortran 9.1 - Cygwin(native gcc compiler and g95) - - Windows XP x64 Visual Studio 2005 w/ Intel Fortran 9.1 - - Windows Vista Visual Studio 2005 w/ Intel Fortran 9.1 - - Windows Vista x64 Visual Studio 2005 w/ Intel Fortran 9.1 - - MAC OS 10.5.6 (Intel) i686-apple-darwin9-gcc-4.0.1 (GCC) 4.0.1 - GNU Fortran (GCC) 4.3.0 20070810 - G95 (GCC 4.0.3 (g95 0.91!) Apr 24 2008) - Intel C, C++ and Fortran compilers 10.1 - - -Supported Configuration Features Summary -======================================== - - In the tables below - y = tested and supported - n = not supported or 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 parallel -Solaris2.10 32-bit n y n y y y -Solaris2.10 64-bit n y n y y y -Windows XP n y(4) n(4) y y y -Windows XP x64 n y(4) n(4) y y y -Windows Vista n n n y y y -Mac OS X 10.5 Intel n y n y y y -AIX 5.3 32- and 64-bit n y n y y n -FreeBSD 6.3-STABLE 32&64 bit n y n y y y -RedHat EL5 2.6.18-164 i686 GNU (1)W y y(2) y y y y -RedHat EL5 2.6.18-164 i686 Intel W n y n y y n -RedHat EL5 2.6.18-164 i686 PGI W n y n y y n -RedHat EL5 2.6.18-164 x86_64 GNU(1)W y y(3) y y y y -RedHat EL5 2.6.18-164 x86_64 IntelW n y n y y n -RedHat EL5 2.6.18-164 x86_64 PGI W n y n y y y -SuSe Linux 2.6.16 SGI Altix ia64 C y y y y y y -RedHat EL4 2.6.18 Xeon Lustre C y y y y y n -SuSe Linux 2.4.21 ia64 Intel C y y y y y n -Cray XT3 2.0.62 y y y y y n - - -Platform Shared Shared Shared Thread- - C libs F90 libs C++ libs safe -Solaris2.10 32-bit y y y y -Solaris2.10 64-bit y y y y -Windows XP y y(4) y y -Windows XP x64 y y(4) y y -Windows Vista y n n y -Mac OS X 10.5 y n y n -AIX 5.3 32- and 64-bit n n n n -FreeBSD 6.3-STABLE 32&64 bit y y y y -RedHat EL5 2.6.18-164 i686 GNU (1)W y y(2) y y -RedHat EL5 2.6.18-164 i686 Intel W y y y n -RedHat EL5 2.6.18-164 i686 PGI W y y y n -RedHat EL5 2.6.18-164 x86_64 GNU(1)W y y y y -RedHat EL5 2.6.18-164 x86_64 IntelW y y y n -RedHat EL5 2.6.18-164 x86_64 PGI W y y y n -SuSe Linux 2.6.16 SGI Altix ia64 C y n -RedHat EL4 2.6.18 Xeon Lustre C y y y n -SuSe Linux 2.4.21 ia64 Intel C y y y n -Cray XT3 2.0.62 n n n n - - (1) Fortran compiled with g95. - (2) With PGI and Absoft compilers. - (3) With PGI compiler for Fortran. - (4) Using Visual Studio 2005 or Cygwin - Compiler versions for each platform are listed in the preceding - "Platforms Tested" table. - - -Known Problems -============== -* Parallel mode in AIX will fail some of the testcheck_version.sh tests where - it treats "exit(134) the same as if process 0 had received an abort signal. - This is fixed and will be available in the next release. AKC - 2009/11/3 - -* Some tests in tools/h5repack may fail in AIX systems when -q32 mode is used. - The error is due to insufficient memory requested. Request a large amount - of runtime memory by setting the following environment variable for more - memory. - LDR_CNTRL=MAXDATA=0x20000000@DSA - AKC - 2009/10/31 - -* The PathScale MPI implementation, accessing a Panasas file system, would - cause H5Fcreate() with H5F_ACC_EXCL to fail even when the file is not - existing. This is due to the MPI_File_open() call failing if the amode has - the MPI_MODE_EXCL bit set. (See bug 1468 for details.) AKC - 2009/8/11 - -* Parallel tests failed with 16 processes with data inconsistency at testphdf5 - / dataset_readAll. Parallel tests also failed with 32 and 64 processes with - collective abort of all ranks at t_posix_compliant / allwrite_allread_blocks - with MPI IO. CMC - 2009/04/28 - -* There is a known issue in which HDF5 will change the timestamp on a file - simply by opening it with read/write permissions, even if the file is not - modified in any way. This is due to the way in which HDF5 manages the file - superblock. A fix is currently underway and should be included in the 1.8.4 - release of HDF5. MAM - 2009/04/28 - -* For gcc v4.3 and v4.4, with production mode, if -O3 is used, H5Tinit.c - would fail to compile. Actually bad H5Tinit.c is produced. If -O (same - as -O1) is used, H5Tinit.c compiled okay but test/dt_arith would fail. - When -O0 (no optimizatio) is used, H5Tinit.c compilete okay and all - tests passed. Therefore, -O0 is imposed for v4.3 and v4.4 of gcc. - AKC - 2009/04/20 - -* For Red Storm, a Cray XT3 system, the tools/h5ls/testh5ls.sh and - tools/h5copy/testh5copy.sh will fail some of its sub-tests. These sub-tests - are expected to fail and should exit with a non-zero code but the yod - command does not propagate the exit code of the executables. Yod always - returns 0 if it can launch the executable. The test suite shell expects - a non-zero for this particular test, therefore it concludes the test has - failed when it receives 0 from yod. Skip all the "failing" test for now - by changing them as following. - - ======== Original tools/h5ls/testh5ls.sh ========= - TOOLTEST tgroup-1.ls 1 -w80 -r -g tgroup.h5 - ======== Change to =============================== - echo SKIP TOOLTEST tgroup-1.ls 1 -w80 -r -g tgroup.h5 - ================================================== - - ======== Original tools/h5copy/testh5copy.sh ========= - TOOLTEST_FAIL -i $TESTFILE -o $FILEOUT -v -s grp_dsets -d grp_rename - TOOLTEST_FAIL -i $TESTFILE -o $FILEOUT -v -s grp_dsets -d /grp_rename/grp_dsets - TOOLTEST_FAIL -i $TESTFILE -o $FILEOUT -vp -s /grp_dsets -d /E/F/grp_dsets - TOOLTEST_FAIL -i $TESTFILE -o $FILEOUT -vp -s /grp_nested -d /G/H/grp_nested - H5LSTEST $FILEOUT - ======== Change to =============================== - echo SKIP TOOLTEST_FAIL -i $TESTFILE -o $FILEOUT -v -s grp_dsets -d grp_rename - echo SKIP TOOLTEST_FAIL -i $TESTFILE -o $FILEOUT -v -s grp_dsets -d /grp_rename/grp_dsets - echo SKIP TOOLTEST_FAIL -i $TESTFILE -o $FILEOUT -vp -s /grp_dsets -d /E/F/grp_dsets - echo SKIP TOOLTEST_FAIL -i $TESTFILE -o $FILEOUT -vp -s /grp_nested -d /G/H/grp_nested - echo SKIP H5LSTEST $FILEOUT - ================================================== - AKC - 2008/11/10 - -* For Red Storm, a Cray XT3 system, the yod command sometimes gives the - message, "yod allocation delayed for node recovery". This interferes with - test suites that do not expect seeing this message. See the section of "Red - Storm" in file INSTALL_parallel for a way to deal with this problem. - AKC - 2008/05/28 - -* On Intel 64 Linux cluster (RH 4, Linux 2.6.9) with Intel 10.0 compilers, - use -mp -O1 compilation flags to build the libraries. A higher level of - optimization causes failures in several HDF5 library tests. - -* On mpich 1.2.5 and 1.2.6, if more than two processes contribute no IO and - the application asks to do collective IO, we have found that when using 4 - processors, a simple collective write will sometimes be hung. This can be - verified with t_mpi test under testpar. - -* A dataset created or rewritten with a v1.6.3 library or after cannot be read - with the v1.6.2 library or before when the Fletcher32 EDC filter is enabled. - There was a bug in the calculation of the Fletcher32 checksum in the - library before v1.6.3; the checksum value was not consistent between big- - endian and little-endian systems. This bug was fixed in Release 1.6.3. - However, after fixing the bug, the checksum value was no longer the same as - before on little-endian system. Library releases after 1.6.4 can still read - datasets created or rewritten with an HDF5 library of v1.6.2 or before. - SLU - 2005/6/30 - -* On IBM AIX systems, parallel HDF5 mode will fail some tests with error - messages like "INFO: 0031-XXX ...". This is from the command `poe'. - Set the environment variable MP_INFOLEVEL to 0 to minimize the messages - and run the tests again. - - The tests may fail with messages like "The socket name is already in use", - but HDF5 does not use sockets. This failure is due to problems with the - poe command trying to set up the debug socket. To resolve this problem, - check to see whether there are many old /tmp/s.pedb.* files staying around. - These are sockets used by the poe command and left behind due to failed - commands. First, ask your system administrator to clean them out. - Lastly, request IBM to provide a means to run poe without the debug socket. - -* The --enable-static-exec configure flag will only statically link libraries - if the static version of that library is present. If only the shared version - of a library exists (i.e., most system libraries on Solaris, AIX, and Mac, - for example, only have shared versions), the flag should still result in a - successful compilation, but note that the installed executables will not be - fully static. Thus, the only guarantee on these systems is that the - executable is statically linked with just the HDF5 library. - -* There is also a configure error on Altix machines that incorrectly reports - when a version of Szip without an encoder is being used. - -%%%%1.8.3%%%% - - -HDF5 version 1.8.3 released on Mon May 4 09:21:00 CDT 2009 -================================================================================ - -INTRODUCTION -============ - -This document describes the differences between HDF5-1.8.2 and -HDF5 1.8.3, and contains information on the platforms tested and -known problems in HDF5-1.8.3. -For more details, see the files HISTORY-1_0-1_8_0_rc3.txt -and HISTORY-1_8.txt in the release_docs/ directory of the HDF5 source. - -Links to the HDF5 1.8.3 source code, documentation, and additional materials -can be found on the HDF5 web page at: - - http://www.hdfgroup.org/products/hdf5/ - -The HDF5 1.8.3 release can be obtained from: - - http://www.hdfgroup.org/HDF5/release/obtain5.html - -User documentation for 1.8.3 can be accessed directly at this location: - - http://www.hdfgroup.org/HDF5/doc/ - -New features in the HDF5-1.8.x release series, including brief general -descriptions of some new and modified APIs, are described in the "What's New -in 1.8.0?" document: - - http://www.hdfgroup.org/HDF5/doc/ADGuide/WhatsNew180.html - -All new and modified APIs are listed in detail in the "HDF5 Software Changes -from Release to Release" document, in the section "Release 1.8.3 (current -release) versus Release 1.8.2": - - http://www.hdfgroup.org/HDF5/doc/ADGuide/Changes.html - -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, Languages, and Compilers -- Bug Fixes since HDF5-1.8.2 -- Platforms Tested -- Supported Configuration Features Summary -- Known Problems - - -New Features -============ - - Configuration - ------------- - - Added libtool version numbers to generated c++, fortran, and - hl libraries. MAM 2009/04/19. - - Regenerated Makefile.ins using Automake 1.10.2. MAM 2009/04/19. - - Added a Make target of check-all-install to test the correctness of - installing via the prefix= or $DESTDIR options. AKC - 2009/04/14 - - Library - ------- - - Embed the content of libhdf5.settings into the hdf5 executables - so that an "orphaned" executables can display (via the Unix - strings command, for example) the library settings used to build - the executables. This is a prototype implementation. Improvement will - be added in next release. AKC - 2009/04/20 - - Separated "factory" free list class from block free lists. These free - lists are dynamically created and manage blocks of a fixed size. - H5set_free_list_limits() will use the same settings specified for block - free lists for factory free lists. NAF - 2009/04/08 - - Added support for dense attributes to H5Ocopy. XCao/NAF - 2009/01/29 - - Added H5Pset_elink_cb and H5Pget_elink_cb functions to support a - user-defined callback function for external link traversal. - NAF - 2009/01/08 - - Added H5Pset_elink_acc_flags and H5Pget_elink_acc_flags functions to - allow the user to specify the file access flags used to open the target - file of an external link. NAF - 2009/01/08 - - Added H5Pset_chunk_cache() and H5Pget_chunk_cache() functions to allow - individual rdcc configuration for each dataset. Added - H5Dget_access_plist() function to retrieve a dataset access property - list from a dataset. NAF - 2008/11/12 - - Added H5Iis_valid() function to check if an id is valid without - producing an error message. NAF - 2008/11/5 - - Added code to maintain a min_clean_fraction in the metadata cache when - in serial mode. MAM - 2009/01/9 - - Parallel Library - ---------------- - - Modified parallel tests to run with arbitrary number of processes. The - modified tests are testphdf5 (parallel dataset access), t_chunk_alloc - (chunk allocation), and t_posix_compliant (posix compliance). The rest of - the parallel tests already use in the code the number of processes - available in the communicator. (CMC - 2009/04/28) - - Tools - ----- - - h5diff new flag, -c, --compare, list objects that are not comparable. - PVN - 2009/4/2 - 1368 - - h5diff new flag, -N, --nan, avoids NaNs detection. PVN - 2009/4/2 - - h5dump correctly specifies XML dtd / schema urls ADB - 2009/4/3 - 1519 - - h5repack now handles group creation order. PVN - 2009/4/2 - 1402 - - h5repack: When user doesn't specify a chunk size, h5repack now - defines a default chunk size as the same size of the size of the - hyperslab used to read the chunks. The size of the hyperslabs are - defined as the size of each dimension or a predefined constant, - whatever is smaller. This assures that the chunk read fits in the - chunk cache. PVN - 2008/11/21 - - High-Level APIs - --------------- - - Table: In version 3.0 of Table, the writing of the "NROWS" attribute - (used to store number of records) was deprecated. PVN - 2008/11/24 - - F90 API - ------- - - Added for the C APIs the Fortran wrappers: - h5dget_access_plist_f - h5iis_valid_f - h5pset_chunk_cache_f - h5pget_chunk_cache_f - MSB - 2009/04/17 - - C++ API - ------- - - None - - -Support for New Platforms, Languages, and Compilers -=================================================== - - -Bug Fixes since HDF5-1.8.2 -========================== - - Configuration - ------------- - - The --includedir=DIR configuration option now works as intended, and - can be used to specify the location to install C header files. The - default location remains unchanged, residing at ${prefix}/include. - MAM - 2009/03/10 - BZ #1381 - - Configure no longer removes the '-g' flag from CFLAGS when in production - mode if it has been explicitly set in the CFLAGS environment variable - prior to configuration. MAM - 2009/03/09 - BZ #1401 - - Library - ------- - - Added versioning to H5Z_class_t struct to allow compatibility with 1.6 - API. NAF - 2009/04/20 - 1533 - - Fixed a problem with using data transforms with non-native types in the - file. NAF - 2009/04/20 - 1548 - - Added direct.h include file to windows section of H5private.h - to fix _getcwd() warning. ADB - 2009/04/14 - 1536 - - Fixed a bug that prevented external links from working after calling - H5close(). NAF - 2009/04/10 - 1539 - - Modified library to write cached symbol table information to the - superblock, to allow library versions 1.3.0 to 1.6.3 to read files created - by this version. NAF - 2009/04/08 - 1423 - - Changed skip lists to use a deterministic algorithm. The library should - now never call rand() or srand(). NAF - 2009/04/08 - 503 - - Fixed a bug where H5Lcopy and H5Lmove wouldn't create intermediate groups - when that property was set. NAF - 2009/04/07 - 1526 - - Fixed a bug that caused files with a user block to grow by the size of the - user block every time they were opened. NAF - 2009/03/26 - 1499 - - Fixed a rare problem that could occur with files using the old (pre 1.4) - array datatype. NAF - 2009/03/23 - - Modified library to be able to open files with corrupt root group symbol - table messages, and correct these errors if they are found. Such files - can only be successfully opened with write access. NAF - 2009/03/23 - 1189 - - Removed the long_long #define and replaced all instances with - "long long". This caused problems with third party products. All - currently supported compilers support the type. ADB - 2009/03/05 - - Fixed various bugs that could prevent the fill value from being written - in certain rare cases. NAF - 2009/02/26 - 1469 - - Fixed a bug that prevented more than one dataset chunk from being cached - at a time. NAF - 2009/02/12 - 1015 - - Fixed an assertion failure caused by opening an attribute multiple times - through multiple file handles. NAF - 2009/02/12 - 1420 - - Fixed a problem that could prevent the user from adding attributes (or any - object header message) in some circumstances. NAF - 2009/02/12 - 1427 - - Fixed a bug that could cause problems when an attribute was added to a - committed datatype using the committed datatype's datatype. - NAF - 2009/02/12 - - Fixed a bug that could cause problems when copying an object with a shared - message in its own object header. NAF - 2009/01/29 - - Changed H5Tset_order to properly reject H5T_ORDER_NONE for most datatypes. - NAF - 2009/01/27 - 1443 - - Fixed a bug where H5Tpack wouldn't remove trailing space from an otherwise - packed compound type. NAF - 2009/01/14 - - Fixed up some old v2 btree assertions that get run in debug mode that - were previously failing on compilation, and removed some of the - more heavily outdated and non-rewritable ones. MAM - 2008/12/15 - - Fixed a bug that could cause problems when "automatically" unmounting - multiple files. NAF - 2008/11/17 - - H5Dset_extent: when shrinking dimensions, some chunks were not deleted. - PVN - 2009/01/8 - - Parallel Library - ---------------- - - None - - Tools - ----- - - Fixed many problems that could occur when using h5repack with named - datatypes. NAF - 2009/4/20 - 1516/1466 - - h5dump, h5diff, h5repack were not reading (by hyperslabs) datasets - that have a datatype datum size greater than H5TOOLS_BUFSIZE, a constant - defined as 1024Kb, such as array types with large dimensions. - PVN - 2009/4/1 - 1501 - - h5import: By selecting a compression type, a big endian byte order - was being selected. PVN - 2009/3/11 - 1462 - - zip_perf.c had missing argument on one of the open() calls. Fixed. - AKC - 2008/12/9 - - F90 API - ------ - - None - - C++ API - ------ - - None - - High-Level APIs: - ------ - - Dimension scales: The scale index return value in H5DSiterate_scales - was not always incremented. PVN - 2009/4/8 - 1538 - - Fortran High-Level APIs: - ------ - - Lite: The h5ltget_dataset_info_f function (gets information about - a dataset) was not correctly returning the dimension array - PVN - 2009/3/23 - - -Platforms Tested -================ -The following platforms and compilers have been tested for this release. - - AIX 5.3 xlc 7.0.0.8 - (LLNL Up) xlf 09.01.0000.0008 - xlC 7.0.0.8 - mpcc_r 7.0.0.8 - mpxlf_r 09.01.0000.0008 - - Cray XT3 (2.0.41) cc (pgcc) 7.1-4 - (SNL red storm) ftn (pgf90) 7.1-4 - CC (pgCC) 7.1-4 - - FreeBSD 6.3-STABLE i386 gcc 3.4.6 [FreeBSD] 20060305 - (duty) g++ 3.4.6 [FreeBSD] 20060305 - gcc 4.3.4 20090419 - g++ 4.3.4 20090419 - gfortran 4.3.4 20090419 - - FreeBSD 6.3-STABLE amd64 gcc 3.4.6 [FreeBSD] 20060305 - (liberty) g++ 3.4.6 [FreeBSD] 20060305 - gcc 4.4.1 20090421 - g++ 4.4.1 20090421 - gfortran 4.4.1 20090421 - - IRIX64 6.5 (64 & n32) MIPSpro cc 7.4.4m - F90 MIPSpro 7.4.4m - C++ MIPSpro cc 7.4.4m - - Linux 2.6.18-128.1.6.el5xen gcc (GCC) 4.1.2 - #1 SMP i686 i686 i386 G95 (GCC 4.0.3 (g95 0.92!) Feb 4 2009) - (jam) PGI C, Fortran, C++ 7.2-1 32-bit - PGI C, Fortran, C++ 8.0-1 32-bit - Intel(R) C Compiler for 32-bit - applications, Versions 10.1, 11.0 - Intel(R) C++ Compiler for 32-bit - applications, Version 10.1, 11.0 - Intel(R) Fortran Compiler for 32-bit - applications, Version 10.1, 11.0 - Absoft 32-bit Fortran 95 10.0.7 - MPICH mpich2-1.0.8 compiled with - gcc 4.1.2 and G95 (GCC 4.0.3 (g95 0.92!) - - Linux 2.6.9-42.0.10.ELsmp #1 gcc (GCC) 3.4.6 - SMP i686 i686 i386 G95 (GCC 4.0.3 (g95 0.92!) Feb 4 2009) - (kagiso) MPICH mpich2-1.0.8 compiled with - gcc 3.4.6 and G95 (GCC 4.0.3 (g95 0.92!) - - Linux 2.6.16.60-0.37-smp #1 gcc 4.1.2 - SMP x86_64 GNU/Linux G95 (GCC 4.0.3 (g95 0.92!) Feb 4 2009) - (smirom) Intel(R) C, C++, Fortran Compilers for - applications running on Intel(R) 64, - Versions 10.1, 11.0. - PGI C, Fortran, C++ Version 7.2-1, 8.0-1 - for 64-bit target on x86-64 - gcc 4.1.2 and G95 (GCC 4.0.3 (g95 0.92!) - MPICH mpich2-1.0.8 compiled with - gcc 4.1.2 and G95 (GCC 4.0.3 (g95 0.92!) - tested for both 32- and 64-bit binaries - - Linux 2.6.16.54-0.2.5 #1 Intel(R) C++ Version 10.1.017 - SGI Altix SMP ia64 Intel(R) Fortran Itanium(R) Version 10.1.017 - (cobalt) SGI MPI 1.38 - - SunOS 5.10 32- and 64-bit Sun WorkShop 6 update 2 C 5.9 Patch 124867-09 - (linew) Sun WorkShop 6 update 2 Fortran 95 8.3 - Patch 127000-07 - Sun WorkShop 6 update 2 C++ 5.8 - Patch 124863-11 - - Intel Xeon Linux 2.6.18- gcc 3.4.6 20060404 - 92.1.10.el5_lustre.1.6.6smp- Intel(R) C++ Version 10.0.026 - perfctr #2 SMP Intel(R) Fortran Compiler Version 10.0.026 - (abe) Open MPI 1.2.2 - MVAPICH2-0.9.8p28p2patched-intel-ofed-1.2 - compiled with icc v10.0.026 and ifort 10.0.026 - - IA-64 Linux 2.4.21-309.tg1 gcc (GCC) 3.2.2 - #1 SMP ia64 Intel(R) C++ Version 8.1.037 - (NCSA tg-login) Intel(R) Fortran Compiler Version 8.1.033 - mpich-gm-1.2.7p1..16-intel-8.1.037-r1 - - Linux 2.6.9-55.0.9.EL_lustre Intel(R) C, C++, Fortran Compilers for - .1.4.11.1smp #1 SMP applications running on Intel(R) 64, - SMP x86_64 GNU/Linux Versions 9.1. - (SNL Spirit) - - Linux 2.6.9-55.0.9.EL_lustre Intel(R) C, C++, Fortran Compilers for - .1.4.11.1smp #1 SMP applications running on Intel(R) 64, - SMP x86_64 GNU/Linux Versions 10.1. - (SNL Thunderbird) - - Linux 2.6.18-63chaos #1 SMP Intel(R) C, C++, Fortran Compilers for - SMP x86_64 GNU/Linux applications running on Intel(R) 64, - (SNL Glory) Versions 10.1. - - Linux 2.6.18-63chaos #1 SMP Intel(R) C, C++, Fortran Compilers for - SMP x86_64 GNU/Linux applications running on Intel(R) 64, - (LLNL Zeus) Versions 9.1. - gcc/gfortran/g++ (GCC) 4.1.2. - - Windows XP Visual Studio .NET - Visual Studio 2005 w/ Intel Fortran 9.1 - Cygwin(native gcc compiler and g95) - - Windows XP x64 Visual Studio 2005 w/ Intel Fortran 9.1 - - Windows Vista Visual Studio 2005 - - MAC OS 10.5.6 (Intel) i686-apple-darwin9-gcc-4.0.1 (GCC) 4.0.1 - GNU Fortran (GCC) 4.3.0 20070810 - G95 (GCC 4.0.3 (g95 0.91!) Apr 24 2008) - Intel C, C++ and Fortran compilers 10.1 - - -Supported Configuration Features Summary -======================================== - - In the tables below - y = tested and supported - n = not supported or 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 parallel -Solaris2.10 32-bit n y n y y y -Solaris2.10 64-bit n y n y y y -IRIX64_6.5 32-bit n n n n y y -IRIX64_6.5 64-bit n y y y y y -Windows XP n y(4) n(4) y y y -Windows XP x64 n y(4) n(4) y y y -Windows Vista n n n y y y -Mac OS X 10.5 Intel n y n y y y -AIX 5.3 32- and 64-bit n y n y y n -FreeBSD 6.3-STABLE 32&64 bit n y n y y y -RedHat EL4 2.6.9-42 i686 GNU (1) W y y y y y y -RedHat EL5 2.6.18-128 i686 GNU (1)W y y(2) y y y y -RedHat EL5 2.6.18-128 i686 Intel W n y n y y n -RedHat EL5 2.6.18-128 i686 PGI W n y n y y n -SuSe Linux 2.6.16 x86_64 GNU (1) W y y(3) y y y y -SuSe Linux 2.6.16 x86_64 Intel W n y n y y n -SuSe Linux 2.6.16 x86_64 PGI W n y n y y y -SuSe Linux 2.6.16 SGI Altix ia64 C y y y y y y -RedHat EL4 2.6.18 Xeon Lustre C y y y y y n -SuSe Linux 2.4.21 ia64 Intel C y y y y y n -Cray XT3 2.0.41 y y y y y n - - -Platform Shared Shared Shared Thread- - C libs F90 libs C++ libs safe -Solaris2.10 32-bit y y y y -Solaris2.10 64-bit y y y y -IRIX64_6.5 32-bit y dna y y -IRIX64_6.5 64-bit y y n y -Windows XP y y(4) y y -Windows XP x64 y y(4) y y -Windows Vista y n n y -Mac OS X 10.5 y n y n -AIX 5.3 32- and 64-bit n n n n -FreeBSD 6.3-STABLE 32&64 bit y n y y -RedHat EL4 2.6.9-42 i686 GNU (1) W y y y y -RedHat EL5 2.6.18-128 i686 GNU (1)W y y(2) y y -RedHat EL5 2.6.18-128 i686 Intel W y y y n -RedHat EL5 2.6.18-128 i686 PGI W y y y n -SuSe Linux 2.6.16 x86_64 GNU (1) W y y y y -SuSe Linux 2.6.16 x86_64 Intel W y y y n -SuSe Linux 2.6.16 x86_64 PGI W y y y n -SuSe Linux 2.6.16 SGI Altix ia64 C y n -RedHat EL4 2.6.18 Xeon Lustre C y y y n -SuSe Linux 2.4.21 ia64 Intel C y y y n -Cray XT3 2.0.41 n n n n - - (1) Fortran compiled with g95. - (2) With PGI and Absoft compilers. - (3) With PGI compiler for Fortran. - (4) Using Visual Studio 2005 or Cygwin - Compiler versions for each platform are listed in the preceding - "Platforms Tested" table. - - -Known Problems -============== -* Parallel tests failed with 16 processes with data inconsistency at testphdf5 - / dataset_readAll. Parallel tests also failed with 32 and 64 processes with - collective abort of all ranks at t_posix_compliant / allwrite_allread_blocks - with MPI IO. CMC - 2009/04/28 - -* There is a known issue in which HDF5 will change the timestamp on a file - simply by opening it with read/write permissions, even if the file is not - modified in any way. This is due to the way in which HDF5 manages the file - superblock. A fix is currently underway and should be included in the 1.8.4 - release of HDF5. MAM - 2009/04/28 - -* For gcc v4.3 and v4.4, with production mode, if -O3 is used, H5Tinit.c - would fail to compile. Actually bad H5Tinit.c is produced. If -O (same - as -O1) is used, H5Tinit.c compiled okay but test/dt_arith would fail. - When -O0 (no optimizatio) is used, H5Tinit.c compilete okay and all - tests passed. Therefore, -O0 is imposed for v4.3 and v4.4 of gcc. - AKC - 2009/04/20 - -* For Red Storm, a Cray XT3 system, the tools/h5ls/testh5ls.sh and - tools/h5copy/testh5copy.sh will fail some of its sub-tests. These sub-tests - are expected to fail and should exit with a non-zero code but the yod - command does not propagate the exit code of the executables. Yod always - returns 0 if it can launch the executable. The test suite shell expects - a non-zero for this particular test, therefore it concludes the test has - failed when it receives 0 from yod. Skip all the "failing" test for now - by changing them as following. - - ======== Original tools/h5ls/testh5ls.sh ========= - TOOLTEST tgroup-1.ls 1 -w80 -r -g tgroup.h5 - ======== Change to =============================== - echo SKIP TOOLTEST tgroup-1.ls 1 -w80 -r -g tgroup.h5 - ================================================== - - ======== Original tools/h5copy/testh5copy.sh ========= - TOOLTEST_FAIL -i $TESTFILE -o $FILEOUT -v -s grp_dsets -d grp_rename - TOOLTEST_FAIL -i $TESTFILE -o $FILEOUT -v -s grp_dsets -d /grp_rename/grp_dsets - TOOLTEST_FAIL -i $TESTFILE -o $FILEOUT -vp -s /grp_dsets -d /E/F/grp_dsets - TOOLTEST_FAIL -i $TESTFILE -o $FILEOUT -vp -s /grp_nested -d /G/H/grp_nested - H5LSTEST $FILEOUT - ======== Change to =============================== - echo SKIP TOOLTEST_FAIL -i $TESTFILE -o $FILEOUT -v -s grp_dsets -d grp_rename - echo SKIP TOOLTEST_FAIL -i $TESTFILE -o $FILEOUT -v -s grp_dsets -d /grp_rename/grp_dsets - echo SKIP TOOLTEST_FAIL -i $TESTFILE -o $FILEOUT -vp -s /grp_dsets -d /E/F/grp_dsets - echo SKIP TOOLTEST_FAIL -i $TESTFILE -o $FILEOUT -vp -s /grp_nested -d /G/H/grp_nested - echo SKIP H5LSTEST $FILEOUT - ================================================== - AKC - 2008/11/10 - -* For Red Storm, a Cray XT3 system, the yod command sometimes gives the - message, "yod allocation delayed for node recovery". This interferes with - test suites that do not expect seeing this message. See the section of "Red - Storm" in file INSTALL_parallel for a way to deal with this problem. - AKC - 2008/05/28 - -* We have discovered two problems when running collective IO parallel HDF5 - tests with chunking storage on the ChaMPIon MPI compiler on tungsten, a - Linux cluster at NCSA. - - Under some complex selection cases: - 1) MPI_Get_element returns the wrong value. - 2) MPI_Type_struct also generates the wrong derived datatype and corrupt - data may be generated. - These issues arise only when turning on collective IO with chunking storage - with some complex selections. We have not found these problems on other - MPI-IO compilers. If you encounter these problems, you may use independent - IO instead. - - To avoid this behavior, change the following line in your code - H5Pset_dxpl_mpio(xfer_plist, H5FD_MPIO_COLLECTIVE); - to - H5Pset_dxpl_mpio(xfer_plist, H5FD_MPIO_INDEPENDENT); - KY - 2007/08/24 - -* On Intel 64 Linux cluster (RH 4, Linux 2.6.9) with Intel 10.0 compilers, - use -mp -O1 compilation flags to build the libraries. A higher level of - optimization causes failures in several HDF5 library tests. - -* For LLNL, uP: both serial and parallel tests pass. - Zeus: Serial tests pass but parallel tests fail with a known problem in MPI. - ubgl: Serial tests pass but parallel tests fail. - -* On mpich 1.2.5 and 1.2.6, if more than two processes contribute no IO and - the application asks to do collective IO, we have found that when using 4 - processors, a simple collective write will sometimes be hung. This can be - verified with t_mpi test under testpar. - -* On IRIX6.5, when the C compiler version is greater than 7.4, complicated - MPI derived datatype code will work. However, the user should increase - the value of the MPI_TYPE_MAX environment variable to some appropriate value - to use collective irregular selection code. For example, the current - parallel HDF5 test needs to raise MPI_TYPE_MAX to 200,000 to pass the test. - -* A dataset created or rewritten with a v1.6.3 library or after cannot be read - with the v1.6.2 library or before when the Fletcher32 EDC filter is enabled. - There was a bug in the calculation of the Fletcher32 checksum in the - library before v1.6.3; the checksum value was not consistent between big- - endian and little-endian systems. This bug was fixed in Release 1.6.3. - However, after fixing the bug, the checksum value was no longer the same as - before on little-endian system. Library releases after 1.6.4 can still read - datasets created or rewritten with an HDF5 library of v1.6.2 or before. - SLU - 2005/6/30 - -* On IBM AIX systems, parallel HDF5 mode will fail some tests with error - messages like "INFO: 0031-XXX ...". This is from the command `poe'. - Set the environment variable MP_INFOLEVEL to 0 to minimize the messages - and run the tests again. - - The tests may fail with messages like "The socket name is already in use", - but HDF5 does not use sockets. This failure is due to problems with the - poe command trying to set up the debug socket. To resolve this problem, - check to see whether there are many old /tmp/s.pedb.* files staying around. - These are sockets used by the poe command and left behind due to failed - commands. First, ask your system administrator to clean them out. - Lastly, request IBM to provide a means to run poe without the debug socket. - -* The --enable-static-exec configure flag fails to compile for Solaris - platforms. This is due to the fact that not all of the system libraries on - Solaris are available in a static format. - - The --enable-static-exec configure flag also fails to correctly compile - on IBM SP2 platforms for serial mode. The parallel mode works fine with - this option. - - It is suggested that you do not use this option on these platforms - during configuration. - -* There is also a configure error on Altix machines that incorrectly reports - when a version of Szip without an encoder is being used. - -* Information about building with PGI and Intel compilers is available in - the INSTALL file sections 4.7 and 4.8. - - -%%%%1.8.2%%%% - - -HDF5 version 1.8.2 released on Mon Nov 10 15:43:09 CST 2008 -================================================================================ - -INTRODUCTION -============ - -This document describes the differences between HDF5-1.8.1 and HDF5 1.8.2, -and contains information on the platforms tested and known problems in -HDF5-1.8.2. For more details, see the files HISTORY-1_0-1_8_0_rc3.txt -and HISTORY-1_8.txt in the release_docs/ directory of the HDF5 source. - -Links to the HDF5 1.8.2 source code, documentation, and additional materials -can be found on the HDF5 web page at: - - http://www.hdfgroup.org/products/hdf5/ - -The HDF5 1.8.2 release can be obtained from: - - http://www.hdfgroup.org/HDF5/release/obtain5.html - -User documentation for 1.8.2 can be accessed directly at this location: - - http://www.hdfgroup.org/HDF5/doc/ - -New features in the HDF5-1.8.x release series, including brief general -descriptions of some new and modified APIs, are described in the "What's New -in 1.8.0?" document: - - http://www.hdfgroup.org/HDF5/doc/ADGuide/WhatsNew180.html - -All new and modified APIs are listed in detail in the "HDF5 Software Changes -from Release to Release" document, in the section "Release 1.8.2 (current -release) versus Release 1.8.1": - - http://www.hdfgroup.org/HDF5/doc/ADGuide/Changes.html - -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 HDF5-1.8.1 -- Platforms Tested -- Supported Configuration Features Summary -- Known Problems - - -New Features -============ - - Configuration - ------------- - - Upgraded libtool to version 2.2.6a. (MAM - 2008/10/15). - - Library - ------- - - Added two new public routines: H5Pget_elink_fapl() and - H5Pset_elink_fapl(). (see bug #1247) (VC - 2008/10/13) - - Improved free space tracking in file to be faster. (QAK - 2008/10/06) - - Added 'mounted' field to H5G_info_t struct. (QAK - 2008/07/15) - - Parallel Library - ---------------- - - None - - Tools - ----- - - h5repack: added new options -u and -b to add a userblock to an HDF5 - file during the repack. (PVN - 2008/08/26) - - h5repack: added options -t and -a to call H5Pset_alignment while - creating a repacked file. (PVN - 2008/08/29) - - h5ls: added capability to traverse through external links when the -r - (recursive) flag is given. (NAF - 2008/09/16) - - h5ls: added -E option to enable traversal of external links. - h5ls will not traverse external links without this flag being set. - (NAF - 2008/10/06) - - h5dump: when -b flag is used without a keyword after it, binary - output defaults to NATIVE. MEMORY keyword was deprecated - and replaced by NATIVE keyword. (PVN - 2008/10/30) - - h5diff: returns 1 when file graphs differ by any object. - Error return code was changed to 2 from -1. (PVN - 2008/10/30) - - h5import: TEXTFPE (scientific format) was deprecated. Use TEXTFP - instead (PVN - 2008/10/30) - - - - F90 API - ------ - - Added optional parameter 'mounted' to H5Gget_info_f, - H5Gget_info_by_idx_f, H5Gget_info_by_name_f (MSB - 2008/09/24) - - Added H5Tget_native_type_f (MSB - 2008/09/30) - - - C++ API - ------ - - These member functions were added as wrapper for H5Rdereference to - replace the incorrect IdComponent::dereference(). - void H5Object::dereference(H5Object& obj, void* ref, - H5R_type_t ref_type=H5R_OBJECT) - void H5Object::dereference(H5File& h5file, void* ref, - H5R_type_t ref_type=H5R_OBJECT) - void H5Object::dereference(Attribute& obj, void* ref, - H5R_type_t ref_type=H5R_OBJECT) - - In addition, these constructors were added to create the associated - objects by way of dereference: - DataSet(H5Object& obj, void* ref, H5R_type_t ref_type=H5R_OBJECT) - DataSet(H5File& file, void* ref, H5R_type_t ref_type=H5R_OBJECT) - DataSet(Attribute& attr, void* ref, H5R_type_t ref_type=H5R_OBJECT) - Group(H5Object& obj, void* ref, H5R_type_t ref_type=H5R_OBJECT) - Group(H5File& obj, void* ref, H5R_type_t ref_type=H5R_OBJECT) - Group(Attribute& attr, void* ref, H5R_type_t ref_type=H5R_OBJECT) - DataType(H5Object& obj, void* ref, H5R_type_t ref_type=H5R_OBJECT) - DataType(H5File& file, void* ref, H5R_type_t ref_type=H5R_OBJECT) - DataType(Attribute& attr, void* ref, H5R_type_t ref_type=H5R_OBJECT) - (BMR - 2008/10/29) - - -Support for New Platforms, Languages, and Compilers -=================================================== - - Intel 10.1 is supported on Mac OS X 10.5.4. - Note: - When Fortran is enabled, configure automatically - disables the build of shared libraries (i.e., only - static C and C++ HDF5 libraries will be built - along with the static HDF5 Fortran library). - Intel 10.1 C and C++ compilers require - "-no-multibyte-chars" compilation flag due to the known - bug in the compilers. - (EIP - 2008/10/30) - - -Bug Fixes since HDF5-1.8.1 -========================== - - Configuration - ------------- - - Fixed error with 'make check install' failing due to h5dump - needing other tools built first. (MAM - 2008/10/15). - - When using shared szip, it is no longer necessary to specify - the path to the shared szip libraries in LD_LIBRARY_PATH. - (MAM - 2008/10/15). - - The file libhdf5_fortran.settings is not installed since its content - is included in libhdf5.settings now. (AKC - 2008/10/21) - - "make DESTDIR=xxx install" failed to install some tools and files - (e.g., h5cc and fortran modules). Fixed. (AKC - 2008/10/8). - - Library - ------- - - H5Ovisit and H5Ovisit_by_name will now properly terminate when the - callback function returns a positive value on the starting object. - (NAF - 2008/11/03) - - Fixed an error where a null message could be created that was larger - than could be written to the file. (NAF - 2008/10/23) - - Corrected error with family/split/multi VFD not updating driver info - when "latest" version of the file format used. (QAK - 2008/10/14) - - Corrected alignment+threshold errors to work correctly when metadata - aggregation is enabled. (QAK - 2008/10/06) - - Changed H5Fget_obj_count and H5Fget_obj_ids to ignore objects - registered by the library for internal library use. - (NAF - 2008/10/06) - - Fixed potential memory leak during compound conversion. - (NAF - 2008/10/06) - - Changed the return value of H5Fget_obj_count from INT to SSIZE_T. - Also changed the return value of H5Fget_obj_ids from HERR_T to - SSIZE_T and the type of the parameter MAX_OBJS from INT to SIZE_T. - (SLU - 2008/09/26) - - Fixed an issue that could cause data to be improperly overwritten - during compound type conversion. (NAF - 2008/09/19) - - Fixed pointer alignment violations that could occur during vlen - conversion. (NAF - 2008/09/16) - - Fixed problem where library could cause a segmentation fault when - an invalid location ID was given to H5Giterate(). (QAK - 2008/08/19) - - Fixed improper shutdown when objects have reference count > 1. The - library now tracks reference count due to the application separately - from that due to internal library routines. (NAF - 2008/08/19) - - Fixed assertion failure caused by incorrect array datatype version. - (NAF - 2008/08/08) - - Fixed an issue where mount point traversal would fail when using - multiple handles for the child. (NAF - 2008/08/07) - - Fixed an issue where mount points were inaccessible when using - multiple file handles for the parent. The mount table is now in - the shared file structure (the parent pointer is still in the - top structure). (NAF - 2008/08/07) - - Fixed assertion failure caused by incorrect array datatype version. - (NAF - 2008/08/04) - - Fixed issue where a group could have a file mounted on it twice. - (QAK - 2008/07/15) - - When an attribute was opened twice and data was written with - one of the handles, the file didn't have the data. It happened - because each handle had its own object structure, and the empty - one overwrote the data with fill value. This is fixed by making - some attribute information like the data be shared in the - attribute structure. (SLU - 2008/07/07) - - Fixed a Windows-specific issue in the ohdr test which was causing - users in some timezones to get false errors. This a deficiency in - the Windows mktime() function, and has been handled properly. - (SJW - 2008/06/19) - - Parallel Library - ---------------- - - None - - Tools - ----- - - h5dump now checks for uniqueness of committed datatypes. - (NAF - 2008/10/15) - - Fixed unnecessary indentation of committed datatypes in h5dump. - (NAF - 2008/10/15) - - Fixed bugs in h5stat: segmemtation fault when printing groups and - print warning message when traversal of objects is unsuccessful. - (see bug #1253) (VC- 2008/10/13) - - Fixed bug in h5ls that prevented relative group listings (like - "h5ls foo.h5/bar") from working correctly (QAK - 2008/06/03) - - h5dump: when doing binary output (-b), the stdout printing of - attributes was done incorrectly. Removed printing of attributes - when doing binary output. (PVN - 2008/06/05) - - - F90 API - ------ - - h5sselect_elements_f: Added additional operators H5S_SELECT_APPEND - and H5S_SELECT_PREPEND (MSB - 2008/09/30) - - h5sget_select_elem_pointlist: Fixed list of returned points by - rearranging the point list correctly by accounting for C - conventions. (MSB - 2008/09/30) - - h5sget_select_hyper_blocklist_f: Fixed error in transposed dimension - of arrays.(MSB - 2008/9/30) - - h5sget_select_bounds_f: Swapped array bounds to account for C and - Fortran reversed array notation (MSB - 2008/9/30) - - Changed to initializing string to a blank character instead of a - null type in tH5P.f90 to fix compiling error using AIX 5.3.0 - (MSB - 2008/7/29) - - Fixed missing commas in H5test_kind.f90 detected by NAG compiler - (MSB - 2008/7/29) - - Fixed passing and array to a scalar in tH5A_1_8.f90 detected by - NAG compiler (MSB - 2008/7/29) - - Added the ability of the test programs to use the status of - HDF5_NOCLEANUP to determine if the *.h5 files should be removed - or not after the tests are completed (MSB - 2008/10/1) - - In nh5tget_offset_c: (MSB 9/12/2008) - If offset was equal to 0 it returned the error code of -1, - this was changed to return an error code of -1 when the offset - value is < 0. - - Uses intrinsic Fortran function SIZEOF if available when detecting - type of INTEGERs and REALs in H5test_kind.f90 (MSB - 2008/9/3) - - Put the DOUBLE PRECISION interfaces in a separate module and - added a USE statement for the module. The interfaces are - included/excluded depending on the state of FORTRAN_DEFAULT_REAL - is DBLE_F which detects if the default REAL is DOUBLE PRECISION. - This allows the library to be compiled with -r8 Fortran flag - without the user needing to edit the source code. - (MSB - 200/8/27) - - Enable building shared library for fortran by adding the flag -fPIC - to the compile flags for versions of Intel Fortran compiler >=9 - (MSB - 2008/8/26) - - C++ API - ------ - - Fixed a design bug which allowed an Attribute object to create/modify - attributes (bugzilla #1068). The API class hierarchy was revised - to address the problem. Classes AbstractDS and Attribute are moved - out of H5Object. Class Attribute now multiply inherits from - IdComponent and AbstractDs and class DataSet from H5Object and - AbstractDs. In addition, the data member IdComponent::id was - moved into subclasses: Attribute, DataSet, DataSpace, DataType, - H5File, Group, and PropList. (BMR - 2008/05/20) - - IdComponent::dereference was incorrect and replaced as described - in "New Features" section. - (BMR - 2008/10/29) - - -Platforms Tested -================ -The following platforms and compilers have been tested for this release. - - AIX 5.3 xlc 7.0.0.8 - xlf 09.01.0000.0008 - xlC 7.0.0.8 - mpcc_r 7.0.0.8 - mpxlf_r 09.01.0000.0008 - - Cray XT3 (2.0.41) cc (pgcc) 7.1-4 - (red storm) ftn (pgf90) 7.1-4 - CC (pgCC) 7.1-4 - - FreeBSD 6.3-STABLE i386 gcc 3.4.6 [FreeBSD] 20060305 - (duty) g++ 3.4.6 [FreeBSD] 20060305 - gcc 4.2.5 20080702 - g++ 4.2.5 20080702 - gfortran 4.2.5 20080702 - - FreeBSD 6.3-STABLE amd64 gcc 3.4.6 [FreeBSD] 20060305 - (liberty) g++ 3.4.6 [FreeBSD] 20060305 - gcc 4.2.5 20080702 - g++ 4.2.5 20080702 - gfortran 4.2.5 20080702 - - IRIX64 6.5 (64 & n32) MIPSpro cc 7.4.4m - F90 MIPSpro 7.4.4m - C++ MIPSpro cc 7.4.4m - - Linux 2.6.9-42.0.10.ELsmp #1 gcc (GCC) 3.4.6 - SMP i686 i386 G95 (GCC 4.0.3 (g95 0.92!) April 18 2007) - (kagiso) PGI C, Fortran, C++ 7.2-1 32-bit - Intel(R) C Compiler for 32-bit - applications, Version 10.1 - Intel(R) C++ Compiler for 32-bit - applications, Version 10.1 - Intel(R) Fortran Compiler for 32-bit - applications, Version 10.1 - Absoft 32-bit Fortran 95 10.0.4 - MPICH mpich-1.2.7 compiled with - gcc 3.4.6 and G95 (GCC 4.0.3 (g95 0.92!) - MPICH mpich2-1.0.6p1 compiled with - gcc 3.4.6 and G95 (GCC 4.0.3 (g95 0.92!) - - Linux 2.6.16.46-0.14-smp #1 Intel(R) C++ for Intel(R) EM64T - SMP x86_64 GNU/Linux Ver. 10.1.013 - (smirom) Intel(R) Fortran Intel(R) EM64T - Ver. 10.1.013 - PGI C, Fortran, C++ Version 7.2-1 - for 64-bit target on x86-64 - MPICH mpich-1.2.7 compiled with - gcc 4.1.2 and G95 (GCC 4.0.3 (g95 0.92!) - MPICH mpich2-1.0.7 compiled with - gcc 4.1.2 and G95 (GCC 4.0.3 (g95 0.92!) - tested for both 32- and 64-bit binaries - - Linux 2.6.16.54-0.2.5 #1 Intel(R) C++ Version 10.1.017 - Altix SMP ia64 Intel(R) Fortran Itanium(R) Version 10.1.017 - (cobalt) SGI MPI 1.16 - - SunOS 5.10 32- and 64-bit Sun WorkShop 6 update 2 C 5.8 - (linew) Sun WorkShop 6 update 2 Fortran 95 8.2 - Sun WorkShop 6 update 2 C++ 5.8 - Patch 121019-06 - - Xeon Linux 2.6.9-42.0.10.EL_lustre-1.4.10.1smp - (abe) Intel(R) C++ Version 10.0.026 - Intel(R) Fortran Compiler Version 10.0.026 - Open MPI 1.2.2 - MVAPICH2-0.9.8p28p2patched-intel-ofed-1.2 - compiled with icc v10.0.026 and - ifort 10.0.026 - - IA-64 Linux 2.4.21-309.tg1 #1 SMP - ia64 gcc (GCC) 3.2.2 - (NCSA tg-login) Intel(R) C++ Version 8.1.037 - Intel(R) Fortran Compiler Version 8.1.033 - mpich-gm-1.2.7p1..16-intel-8.1.037-r1 - - Intel 64 Linux 2.6.9-42.0.10.EL_lustre-1.4.10.1smp - (abe) gcc 3.4.6 20060404 - Intel(R) C++ Version 10.0 - Intel (R) Fortran Compiler Version 10.0 - mvapich2-0.9.8p2patched-intel-ofed-1.2 - - Windows XP Visual Studio .NET - Visual Studio 2005 w/ Intel Fortran 9.1 - Cygwin(native gcc compiler and g95) - - Windows XP x64 Visual Studio 2005 w/ Intel Fortran 9.1 - - Windows Vista Visual Studio 2005 - - MAC OS 10.5.4 (Intel) i686-apple-darwin9-gcc-4.0.1 (GCC) 4.0.1 - GNU Fortran (GCC) 4.3.0 20070810 - G95 (GCC 4.0.3 (g95 0.91!) Apr 24 2008) - Intel C, C++ and Fortran compilers 10.1 - - -Supported Configuration Features Summary -======================================== - - In the tables below - y = tested and supported - n = not supported or not tested in this release - 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 parallel -Solaris2.10 32-bit n y n y y y -Solaris2.10 64-bit n y n y y y -IRIX64_6.5 32-bit n n n n y y -IRIX64_6.5 64-bit n y y y y y -Windows XP n y(15) n(15) y y y -Windows XP x64 n y(15) n(15) y y y -Windows Vista n n n y y y -Mac OS X 10.5 Intel n y n y y y -AIX 5.3 32- and 64-bit n y n y y n -FreeBSD 6.3-STABLE -32&64 bit n y n y y y -RedHat EL4 (3) W y(1) y(10) y(1) y y y -RedHat EL4 Intel (3) W n y n y y n -RedHat EL4 PGI (3) W n y n y y n -SuSe x86_64 gcc(3,12) W y(2) y(11) y(2) y y y -SuSe x86_64 Int(3,12) W n y(13) n y y n -SuSe x86_64 PGI(3,12) W n y(8) n y y y -Linux 2.6 SuSE ia64 C - Intel (3,7) y y y y y n -Linux 2.6 SGI Altix - ia64 Intel (3) y y y y y y -Linux 2.6 RHEL C - Lustre Intel (5) y(4) y y(4) y y n -Cray XT3 2.0.41 y y y y y n - - -Platform Shared Shared Shared Thread- - C libs F90 libs C++ libs safe -Solaris2.10 32-bit y y y y -Solaris2.10 64-bit y y y y -IRIX64_6.5 32-bit y dna y y -IRIX64_6.5 64-bit y y n y -Windows XP y y(15) y y -Windows XP x64 y y(15) y y -Windows Vista y n n y -Mac OS X 10.5 y n y n -AIX 5.3 32- and 64-bit n n n n -FreeBSD 6.2 32&64 bit y n y y -RedHat EL4 (3) W y y(10) y y -RedHat EL4 Intel (3) W y y y n -RedHat EL4 PGI (3) W y y y n -SuSe x86_64 GNU(3,12) W y y y y -SuSe x86_64 Int(3,12) W y y y n -SuSe x86_64 PGI(3,12) W y y y n -Linux 2.4 SuSE C - ia64 C Intel (7) y y y n -Linux 2.4 SGI Altix C - ia64 Intel y n -Linux 2.6 RHEL C - Lustre Intel (5) y y y n -Cray XT3 2.0.41 n n n n - - Notes: (1) Using mpich2 1.0.6. - (2) Using mpich2 1.0.7. - (3) Linux 2.6 with GNU, Intel, and PGI compilers, as indicated. - W or C indicates workstation or cluster, respectively. - (4) Using mvapich2 0.9.8. - (5) Linux 2.6.9-42.0.10. Xeon cluster with ELsmp_perfctr_lustre - and Intel compilers - (6) Linux 2.4.21-32.0.1. Xeon cluster with ELsmp_perfctr_lustre - and Intel compilers - (7) Linux 2.4.21, SuSE_292.till. Ia64 cluster with Intel compilers - (8) pgf90 - (9) With Compaq Visual Fortran 6.6c compiler. - (10) With PGI and Absoft compilers. - (11) PGI and Intel compilers for both C and Fortran - (12) AMD Opteron x86_64 - (13) ifort - (14) Yes with C and Fortran, but not with C++ - (15) Using Visual Studio 2005 or Cygwin - (16) Not tested for this release. - Compiler versions for each platform are listed in the preceding - "Platforms Tested" table. - - -Known Problems -============== -* For Red Storm, a Cray XT3 system, the tools/h5ls/testh5ls.sh and - tools/h5copy/testh5copy.sh will fail some of its sub-tests. These sub-tests - are expected to fail and should exit with a non-zero code but the yod - command does not propagate the exit code of the executables. Yod always - returns 0 if it can launch the executable. The test suite shell expects - a non-zero for this particular test, therefore it concludes the test has - failed when it receives 0 from yod. Skip all the "failing" test for now - by changing them as following. - - ======== Original tools/h5ls/testh5ls.sh ========= - TOOLTEST tgroup-1.ls 1 -w80 -r -g tgroup.h5 - ======== Change to =============================== - echo SKIP TOOLTEST tgroup-1.ls 1 -w80 -r -g tgroup.h5 - ================================================== - - ======== Original tools/h5copy/testh5copy.sh ========= - TOOLTEST_FAIL -i $TESTFILE -o $FILEOUT -v -s grp_dsets -d grp_rename - TOOLTEST_FAIL -i $TESTFILE -o $FILEOUT -v -s grp_dsets -d /grp_rename/grp_dsets - TOOLTEST_FAIL -i $TESTFILE -o $FILEOUT -vp -s /grp_dsets -d /E/F/grp_dsets - TOOLTEST_FAIL -i $TESTFILE -o $FILEOUT -vp -s /grp_nested -d /G/H/grp_nested - H5LSTEST $FILEOUT - ======== Change to =============================== - echo SKIP TOOLTEST_FAIL -i $TESTFILE -o $FILEOUT -v -s grp_dsets -d grp_rename - echo SKIP TOOLTEST_FAIL -i $TESTFILE -o $FILEOUT -v -s grp_dsets -d /grp_rename/grp_dsets - echo SKIP TOOLTEST_FAIL -i $TESTFILE -o $FILEOUT -vp -s /grp_dsets -d /E/F/grp_dsets - echo SKIP TOOLTEST_FAIL -i $TESTFILE -o $FILEOUT -vp -s /grp_nested -d /G/H/grp_nested - echo SKIP H5LSTEST $FILEOUT - ================================================== - AKC - 2008/11/10 - -* For Red Storm, a Cray XT3 system, the yod command sometimes gives the - message, "yod allocation delayed for node recovery". This interferes with - test suites that do not expect seeing this message. See the section of "Red - Storm" in file INSTALL_parallel for a way to deal with this problem. - AKC - 2008/05/28 - -* We have discovered two problems when running collective IO parallel HDF5 - tests with chunking storage on the ChaMPIon MPI compiler on tungsten, a - Linux cluster at NCSA. - - Under some complex selection cases: - 1) MPI_Get_element returns the wrong value. - 2) MPI_Type_struct also generates the wrong derived datatype and corrupt - data may be generated. - These issues arise only when turning on collective IO with chunking storage - with some complex selections. We have not found these problems on other - MPI-IO compilers. If you encounter these problems, you may use independent - IO instead. - - To avoid this behavior, change the following line in your code - H5Pset_dxpl_mpio(xfer_plist, H5FD_MPIO_COLLECTIVE); - to - H5Pset_dxpl_mpio(xfer_plist, H5FD_MPIO_INDEPENDENT); - - KY - 2007/08/24 - -* On Intel 64 Linux cluster (RH 4, Linux 2.6.9) with Intel 10.0 compilers, - use -mp -O1 compilation flags to build the libraries. A higher level of - optimization causes failures in several HDF5 library tests. - -* For LLNL, uP: both serial and parallel tests pass. - Zeus: Serial tests pass but parallel tests fail with a known problem in MPI. - ubgl: Serial tests pass but parallel tests fail. - -* On mpich 1.2.5 and 1.2.6, if more than two processes contribute no IO and - the application asks to do collective IO, we have found that when using 4 - processors, a simple collective write will sometimes be hung. This can be - verified with t_mpi test under testpar. - -* On IRIX6.5, when the C compiler version is greater than 7.4, complicated - MPI derived datatype code will work. However, the user should increase - the value of the MPI_TYPE_MAX environment variable to some appropriate value - to use collective irregular selection code. For example, the current - parallel HDF5 test needs to raise MPI_TYPE_MAX to 200,000 to pass the test. - -* A dataset created or rewritten with a v1.6.3 library or after cannot be read - with the v1.6.2 library or before when the Fletcher32 EDC filter is enabled. - There was a bug in the calculation of the Fletcher32 checksum in the - library before v1.6.3; the checksum value was not consistent between big- - endian and little-endian systems. This bug was fixed in Release 1.6.3. - However, after fixing the bug, the checksum value was no longer the same as - before on little-endian system. Library releases after 1.6.4 can still read - datasets created or rewritten with an HDF5 library of v1.6.2 or before. - SLU - 2005/6/30 - -* On IBM AIX systems, parallel HDF5 mode will fail some tests with error - messages like "INFO: 0031-XXX ...". This is from the command `poe'. - Set the environment variable MP_INFOLEVEL to 0 to minimize the messages - and run the tests again. - - The tests may fail with messages like "The socket name is already in use", - but HDF5 does not use sockets. This failure is due to problems with the - poe command trying to set up the debug socket. To resolve this problem, - check to see whether there are many old /tmp/s.pedb.* files staying around. - These are sockets used by the poe command and left behind due to failed - commands. First, ask your system administrator to clean them out. - Lastly, request IBM to provide a means to run poe without the debug socket. - -* The --enable-static-exec configure flag fails to compile for Solaris - platforms. This is due to the fact that not all of the system libraries on - Solaris are available in a static format. - - The --enable-static-exec configure flag also fails to correctly compile - on IBM SP2 platforms for serial mode. The parallel mode works fine with - this option. - - It is suggested that you do not use this option on these platforms - during configuration. - -* There is also a configure error on Altix machines that incorrectly reports - when a version of Szip without an encoder is being used. - -* Information about building with PGI and Intel compilers is available in - the INSTALL file sections 4.7 and 4.8. - - - - -%%%%1.8.1%%%% - - -HDF5 version 1.8.1 released on Thu May 29 15:28:55 CDT 2008 -================================================================================ - -INTRODUCTION -============ - -This document describes the differences between the HDF5-1.8.1 release -and HDF5 1.8.0, and contains information on the platforms tested and known -problems in HDF5-1.8.1. For more details, see the files -HISTORY-1_0-1_8_0_rc3.txt and HISTORY-1_8.txt in the release_docs/ directory -of the HDF5 source. - -Links to the HDF5 1.8.1 source code, documentation, and additional materials -can be found on the HDF5 web page at: - - http://www.hdfgroup.org/products/hdf5/ - -The HDF5 1.8.1 release can be obtained from: - - http://www.hdfgroup.org/HDF5/release/obtain5.html - -User documentation for 1.8.1 can be accessed directly at this location: - - http://www.hdfgroup.org/HDF5/doc/ - -New features in the HDF5-1.8.x release series, including brief general -descriptions of some new and modified APIs, are described in the "What's New -in 1.8.0?" document: - - http://www.hdfgroup.org/HDF5/doc/ADGuide/WhatsNew180.html - -All new and modified APIs are listed in detail in the "HDF5 Software Changes -from Release to Release" document, in the section "Release 1.8.1 (current -release) versus Release 1.8.0": - - http://www.hdfgroup.org/HDF5/doc/ADGuide/Changes.html - -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 HDF5-1.8.0 -- Platforms Tested -- Supported Configuration Features Summary -- Known Problems - - -New Features -============ - - Configuration - ------------- - - The lib/libhdf5.settings file contains much more configure - information. (AKC - 2008/05/18) - - - The new configure option "--disable-sharedlib-rpath" disables - embedding the '-Wl,-rpath' information into executables when - shared libraries are produced, and instead solely relies on the - information in LD_LIBRARY_PATH. (MAM - 2008/05/15) - - - Configuration suite now uses Autoconf 2.61, Automake 1.10.1, and - Libtool 2.2.2 (MAM - 2008/05/01) - - Source code distribution - ======================== - - Library - ------- - - None - - Parallel Library - ---------------- - - None - - Tools - ----- - - h5repack: Reinstated the -i and -o command line flags to specify - input and output files. h5repack now understands both the old - syntax (with -i and -o) and the new syntax introduced in Release - 1.8.0. (PVN - 2008/05/23) - - h5dump: Added support for external links, displaying the object that - an external link points to. (PVN - 2008/05/12) - - h5dump: Added an option, -m, to allow user-defined formatting in the - output of floating point numbers. (PVN - 2008/05/06) - - h5dump, in output of the -p option: Added effective data compression - ratio to the dataset storage layout output when a compression filter - has been applied to a dataset. (PVN - 2008/05/01) - - F90 API - ------ - - New H5A, H5G, H5L, H5O, and H5P APIs to enable 1.8 features were - added. See "Release 1.8.1 (current release) versus Release 1.8.0" in - the document "HDF5 Software Changes from Release to Release" - (http://hdfgroup.org/HDF5/doc/ADGuide/Changes.html) for the - complete list of the new APIs. - - C++ API - ------ - - None - - -Support for New Platforms, Languages, and Compilers -=================================================== - - Both serial and parallel HDF5 are supported for the Red Storm machine - which is a Cray XT3 system. - - - The Fortran library will work correctly if compiled with the -i8 - flag. This has been tested with the g95, PGI and Intel Fortran - compilers. - - -Bug Fixes since HDF5-1.8.0 -========================== - - Configuration - ------------- - - None - - Source code distribution - ======================== - - Library - ------- - - Chunking: Chunks greater than 4GB are disallowed. - (QAK - 2008/05/16) - - Fixed the problem with searching for a target file when following - an external link. The search pattern will depend on whether the - target file's pathname is an absolute or a relative path. - Please see the H5Lcreate_external description in the "HDF5 - Reference Manual" (http://hdfgroup.org/HDF5/doc/RM/RM_H5L.html). - (VC - 2008/04/08) - - Fixed possible file corruption bug when encoding datatype - descriptions for compound datatypes whose size was between - 256 and 511 bytes and the file was opened with the "use the - latest format" property enabled (with H5Pset_libver_bounds). - (QAK - 2008/03/13) - - Fixed bug in H5Aget_num_attrs() routine to correctly handle an - invalid location identifier. (QAK - 2008/03/11) - - Parallel Library - ---------------- - - None - - Tools - ----- - - Fixed bug in h5diff that prevented datasets and attributes with - variable-length string elements from comparing correctly. - (QAK - 2008/02/28) - - Fixed bug in h5dump that caused binary output to be made only for - the first dataset, when several datasets were requested. - (PVN - 2008/04/07) - - F90 API - ------ - - The h5tset(get)_fields subroutines were missing the parameter to - specify a sign position; fixed. (EIP - 2008/05/23) - - Many APIs were fixed to work with the 8-byte integers in Fortran vs. - 4-byte integers in C. This change is transparent to user applications. - - C++ API - ------ - - The class hierarchy was revised to address the problem reported - in bugzilla #1068, Attribute should not be derived from base - class H5Object. Classes AbstractDS was moved out of H5Object. - Class Attribute now multiply inherits from IdComponent and - AbstractDs and class DataSet from H5Object and AbstractDs. - In addition, data member IdComponent::id was moved into subclasses: - Attribute, DataSet, DataSpace, DataType, H5File, Group, and PropList. - (BMR - 2008/05/20) - - IdComponent::dereference was incorrect; it was changed from: - void IdComponent::dereference(IdComponent& obj, void* ref) - to: - void H5Object::dereference(H5File& h5file, void* ref) - void H5Object::dereference(H5Object& obj, void* ref) - (BMR - 2008/05/20) - - Revised Attribute::write and Attribute::read wrappers to handle - memory allocation/deallocation properly. (bugzilla 1045) - (BMR - 2008/05/20) - - -Platforms Tested -================ -The following platforms and compilers have been tested for this release. - - Cray XT3 (2.0.41) cc (pgcc) 7.1-4 - (red storm) ftn (pgf90) 7.1-4 - CC (pgCC) 7.1-4 - mpicc 1.0.2 - mpif90 1.0.2 - - FreeBSD 6.2-STABLE i386 gcc 3.4.6 [FreeBSD] 20060305 - (duty) g++ 3.4.6 [FreeBSD] 20060305 - gcc 4.2.1 20080123 - g++ 4.2.1 20080123 - gfortran 4.2.1 20070620 - - FreeBSD 6.2-STABLE amd64 gcc 3.4.6 [FreeBSD] 20060305 - (liberty) g++ 3.4.6 [FreeBSD] 20060305 - gcc 4.2.1 20080123 - g++ 4.2.1 20080123 - gfortran 4.2.1 20080123 - - IRIX64 6.5 (64 & n32) MIPSpro cc 7.4.4m - F90 MIPSpro 7.4.4m - C++ MIPSpro cc 7.4.4m - - Linux 2.6.9 (RHEL4) Intel 10.0 compilers - (abe.ncsa.uiuc.edu) - - Linux 2.4.21-47 gcc 3.2.3 20030502 - (osage) - - Linux 2.6.9-42.0.10 gcc,g++ 3.4.6 20060404, G95 (GCC 4.0.3) - (kagiso) PGI 7.1-6 (pgcc, pgf90, pgCC) - Intel 9.1 (icc, ifort, icpc) - - Linux 2.6.16.27 x86_64 AMD gcc 4.1.0 (SuSE Linux), g++ 4.1.0, - (smirom) g95 (GCC 4.0.3) - PGI 7.1-6 (pgcc, pgf90, pgCC) - Intel 9.1 (icc, ifort, icpc) - - Linux 2.6.5-7.252.1-rtgfx #1 Intel(R) C++ Version 9.0 - SMP ia64 Intel(R) Fortran Itanium(R) Version 9.0 - (cobalt) SGI MPI - - SunOS 5.8 32,46 Sun WorkShop 6 update 2 C 5.3 - (Solaris 2.8) Sun WorkShop 6 update 2 Fortran 95 6.2 - Sun WorkShop 6 update 2 C++ 5.3 - - SunOS 5.10 cc: Sun C 5.8 - (linew) f90: Sun Fortran 95 8.2 - CC: Sun C++ 5.8 - - Xeon Linux 2.4.21-32.0.1.ELsmp-perfctr-lustre - (tungsten) gcc 3.2.2 20030222 - Intel(R) C++ Version 9.0 - Intel(R) Fortran Compiler Version 9.0 - - IA-64 Linux 2.4.21.SuSE_309.tg1 ia64 - (NCSA tg-login) gcc 3.2.2 - Intel(R) C++ Version 8.1 - Intel(R) Fortran Compiler Version 8.1 - mpich-gm-1.2.6..14b-intel-r2 - - Intel 64 Linux 2.6.9-42.0.10.EL_lustre-1.4.10.1smp - (abe) gcc 3.4.6 20060404 - Intel(R) C++ Version 10.0 - Intel (R) Fortran Compiler Version 10.0 - mvapich2-0.9.8p2patched-intel-ofed-1.2 - - Windows XP Visual Studio .NET - Visual Studio 2005 w/ Intel Fortran 9.1 - Cygwin(native gcc compiler and g95) - MinGW(native gcc compiler and g95) - - Windows XP x64 Visual Studio 2005 w/ Intel Fortran 9.1 - - Windows Vista Visual Studio 2005 - - MAC OS 10.5.2 (Intel) i686-apple-darwin9-gcc-4.0.1 (GCC) 4.0.1 - GNU Fortran (GCC) 4.3.0 20070810 - G95 (GCC 4.0.3 (g95 0.91!) Apr 24 2008) - - -Supported Configuration Features Summary -======================================== - - In the tables below - y = tested and supported - n = not supported or not tested in this release - 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 parallel -SunOS5.10 64-bit n y n y y y -SunOS5.10 32-bit n y n y y y -IRIX64_6.5 64-bit n y y y y y -IRIX64_6.5 32-bit n n n n y y -Windows XP n y(15) n(15) y y y -Windows XP x64 n y(15) n(15) y y y -Windows Vista n n n y y y -Mac OS X 10.5 Intel n y n y y y -FreeBSD 4.11 n n n y y y -RedHat EL3 W (3) y(1) y(10) y(1) y y y -RedHat EL3 W Intel (3) n y n y y n -RedHat EL3 W PGI (3) n y n y y n -SuSe x86_64 gcc (3,12) y(2) y(11) y(2) y y y -SuSe x86_64 Int (3,12) n y(13) n y y n -SuSe x86_64 PGI (3,12) n y(8) n y y y -Linux 2.4 Xeon C - Lustre Intel (3,6) n y n y y n -Linux 2.6 SuSE ia64 C - Intel (3,7) y y y y y n -Linux 2.6 SGI Altix - ia64 Intel (3) y y y y y y -Linux 2.6 RHEL C - Lustre Intel (5) y(4) y y(4) y y n -Cray XT3 2.0.41 y y y y y n - - -Platform Shared Shared Shared Thread- - C libs F90 libs C++ libs safe -Solaris2.10 64-bit y y y y -Solaris2.10 32-bit y y y y -IRIX64_6.5 64-bit y y n y -IRIX64_6.5 32-bit y dna y y -Windows XP y y(15) y y -Windows XP x64 y y(15) y y -Windows Vista y n n y -Mac OS X 10.3 y n -FreeBSD 4.11 y n y y -RedHat EL3 W (3) y y(10) y y -RedHat EL3 W Intel (3) y y y n -RedHat EL3 W PGI (3) y y y n -SuSe x86_64 W GNU (3,12) y y y y -SuSe x86_64 W Int (3,12) y y y n -SuSe x86_64 W PGI (3,12) y y y n -Linux 2.4 Xeon C - Lustre Intel (6) y y y n -Linux 2.4 SuSE - ia64 C Intel (7) y y y n -Linux 2.4 SGI Altix - ia64 Intel y n -Linux 2.6 RHEL C - Lustre Intel (5) y y y n -Cray XT3 2.0.41 n n n n n - - Notes: (1) Using mpich2 1.0.6. - (2) Using mpich2 1.0.7. - (3) Linux 2.6 with GNU, Intel, and PGI compilers, as indicated. - W or C indicates workstation or cluster, respectively. - (4) Using mvapich2 0.9.8. - (5) Linux 2.6.9-42.0.10. Xeon cluster with ELsmp_perfctr_lustre - and Intel compilers - (6) Linux 2.4.21-32.0.1. Xeon cluster with ELsmp_perfctr_lustre - and Intel compilers - (7) Linux 2.4.21, SuSE_292.till. Ia64 cluster with Intel compilers - (8) pgf90 - (9) With Compaq Visual Fortran 6.6c compiler. - (10) With PGI and Absoft compilers. - (11) PGI and Intel compilers for both C and Fortran - (12) AMD Opteron x86_64 - (13) ifort - (14) Yes with C and Fortran, but not with C++ - (15) Using Visual Studio 2005 or Cygwin - (16) Not tested for this release. - Compiler versions for each platform are listed in the preceding - "Platforms Tested" table. - - -Known Problems -============== -* For Red Storm, a Cray XT3 system, the yod command sometimes gives the - message, "yod allocation delayed for node recovery". This interferes with - test suites that do not expect seeing this message. See the section of "Red - Storm" in file INSTALL_parallel for a way to deal with this problem. - AKC - 2008/05/28 - -* For Red Storm, a Cray XT3 system, the tools/h5ls/testh5ls.sh will fail on - the test "Testing h5ls -w80 -r -g tgroup.h5" fails. This test is - expected to fail and exit with a non-zero code but the yod command does - not propagate the exit code of the executables. Yod always returns 0 if it - can launch the executable. The test suite shell expects a non-zero for - this particular test, therefore it concludes the test has failed when it - receives 0 from yod. To bypass this problem for now, change the following - lines in the tools/h5ls/testh5ls.sh. - ======== Original ========= - # The following combination of arguments is expected to return an error message - # and return value 1 - TOOLTEST tgroup-1.ls 1 -w80 -r -g tgroup.h5 - ======== Skip the test ========= - echo SKIP TOOLTEST tgroup-1.ls 1 -w80 -r -g tgroup.h5 - ======== end of bypass ======== - AKC - 2008/05/28 - -* We have discovered two problems when running collective IO parallel HDF5 - tests with chunking storage on the ChaMPIon MPI compiler on tungsten, a - Linux cluster at NCSA. - - Under some complex selection cases: - 1) MPI_Get_element returns the wrong value. - 2) MPI_Type_struct also generates the wrong derived datatype and corrupt - data may be generated. - These issues arise only when turning on collective IO with chunking storage - with some complex selections. We have not found these problems on other - MPI-IO compilers. If you encounter these problems, you may use independent - IO instead. - - To avoid this behavior, change the following line in your code - H5Pset_dxpl_mpio(xfer_plist, H5FD_MPIO_COLLECTIVE); - to - H5Pset_dxpl_mpio(xfer_plist, H5FD_MPIO_INDEPENDENT); - - KY - 2007/08/24 - -* For SNL, spirit/liberty/thunderbird: The serial tests pass but parallel - tests failed with MPI-IO file locking message. AKC - 2007/6/25 - -* On Intel 64 Linux cluster (RH 4, Linux 2.6.9) with Intel 10.0 compilers, - use -mp -O1 compilation flags to build the libraries. A higher level of - optimization causes failures in several HDF5 library tests. - -* For LLNL, uP: both serial and parallel tests pass. - Zeus: Serial tests pass but parallel tests fail with a known problem in MPI. - ubgl: Serial tests pass but parallel tests fail. - -* Configuring with --enable-debug=all produces compiler errors on most - platforms: Users who want to run HDF5 in debug mode should use - --enable-debug rather than --enable-debug=all to enable debugging - information on most modules. - -* On Mac OS 10.4, test/dt_arith.c has some errors in conversion from long - double to (unsigned) long long and from (unsigned) long long to long double. - -* On Altix SGI with Intel 9.0, testmeta.c would not compile with -O3 - optimization flag. - -* On VAX, the Scaleoffset filter is not supported. The Scaleoffset filter - supports only the IEEE standard for floating-point data; it cannot be applied - to HDF5 data generated on VAX. - -* On Cray X1, a lone colon on the command line of h5dump --xml (as in - the testh5dumpxml.sh script) is misinterpereted by the operating system - and causes an error. - -* On mpich 1.2.5 and 1.2.6, if more than two processes contribute no IO and - the application asks to do collective IO, we have found that when using 4 - processors, a simple collective write will sometimes be hung. This can be - verified with t_mpi test under testpar. - -* On IRIX6.5, when the C compiler version is greater than 7.4, complicated - MPI derived datatype code will work. However, the user should increase - the value of the MPI_TYPE_MAX environment variable to some appropriate value - to use collective irregular selection code. For example, the current - parallel HDF5 test needs to raise MPI_TYPE_MAX to 200,000 to pass the test. - -* A dataset created or rewritten with a v1.6.3 library or after cannot be read - with the v1.6.2 library or before when the Fletcher32 EDC filter is enabled. - There was a bug in the calculation of the Fletcher32 checksum in the - library before v1.6.3; the checksum value was not consistent between big- - endian and little-endian systems. This bug was fixed in Release 1.6.3. - However, after fixing the bug, the checksum value was no longer the same as - before on little-endian system. Library releases after 1.6.4 can still read - datasets created or rewritten with an HDF5 library of v1.6.2 or before. - SLU - 2005/6/30 - -* For version 6 (6.02 and 6.04) of the Portland Group compiler on the AMD - Opteron processor, there is a bug in the compiler for optimization(-O2). - The library failed in several tests, all related to the MULTI driver. - The problem has been reported to the vendor. - -* On IBM AIX systems, parallel HDF5 mode will fail some tests with error - messages like "INFO: 0031-XXX ...". This is from the command `poe'. - Set the environment variable MP_INFOLEVEL to 0 to minimize the messages - and run the tests again. - - The tests may fail with messages like "The socket name is already in use", - but HDF5 does not use sockets. This failure is due to problems with the - poe command trying to set up the debug socket. To resolve this problem, - check to see whether there are many old /tmp/s.pedb.* files staying around. - These are sockets used by the poe command and left behind due to failed - commands. First, ask your system administrator to clean them out. - Lastly, request IBM to provide a means to run poe without the debug socket. - -* The --enable-static-exec configure flag fails to compile for Solaris - platforms. This is due to the fact that not all of the system libraries on - Solaris are available in a static format. - - The --enable-static-exec configure flag also fails to correctly compile - on IBM SP2 platforms for serial mode. The parallel mode works fine with - this option. - - It is suggested that you do not use this option on these platforms - during configuration. - -* With the gcc 2.95.2 compiler, HDF5 uses the `-ansi' flag during - compilation. The ANSI version of the compiler complains about not being - able to handle the `long long' datatype with the warning: - - warning: ANSI C does not support `long long' - - This warning is innocuous and can be safely ignored. - -* The ./dsets tests fail on the TFLOPS machine if the test program, - dsets.c, is compiled with the -O option. The HDF5 library still works - correctly with the -O option. The test program works fine if it is - compiled with -O1 or -O0. Only -O (same as -O2) causes the test - program to fail. - -* Not all platforms behave correctly with Szip's shared libraries. Szip is - disabled in these cases, and a message is relayed at configure time. Static - libraries should be working on all systems that support Szip and should be - used when shared libraries are unavailable. - - There is also a configure error on Altix machines that incorrectly reports - when a version of Szip without an encoder is being used. - -* On some platforms that use Intel and Absoft compilers to build the HDF5 - Fortran library, compilation may fail for fortranlib_test.f90, fflush1.f90 - and fflush2.f90 complaining about the exit subroutine. Comment out the line - IF (total_error .ne. 0) CALL exit (total_error). - -* Information about building with PGI and Intel compilers is available in - the INSTALL file sections 4.7 and 4.8. - -* On at least one system, SDSC DataStar, the scheduler (in this case - LoadLeveler) sends job status updates to standard error when you run - any executable that was compiled with the parallel compilers. - - This causes problems when running "make check" on parallel builds, as - many of the tool tests function by saving the output from test runs, - and comparing it to an exemplar. - - The best solution is to reconfigure the target system so it no longer - inserts the extra text. However, this may not be practical. - - In such cases, one solution is to "setenv HDF5_Make_Ignore yes" prior to - the configure and build. This will cause "make check" to continue after - detecting errors in the tool tests. However, in the case of SDSC DataStar, - it also leaves you with some 150 "failed" tests to examine by hand. - - A second solution is to write a script to run serial tests and filter - out the text added by the scheduler. A sample script used on SDSC - DataStar is given below, but you will probably have to customize it - for your installation. - - Observe that the basic idea is to insert the script as the first item - on the command line which executes the the test. The script then - executes the test and filters out the offending text before passing - it on. - - #!/bin/csh - - set STDOUT_FILE=~/bin/serial_filter.stdout - set STDERR_FILE=~/bin/serial_filter.stderr - - rm -f $STDOUT_FILE $STDERR_FILE - - ($* > $STDOUT_FILE) >& $STDERR_FILE - - set RETURN_VALUE=$status - - cat $STDOUT_FILE - - tail +3 $STDERR_FILE - - exit $RETURN_VALUE - - You get the HDF5 make files and test scripts to execute your filter script - by setting the environment variable "RUNSERIAL" to the full path of the - script prior to running configure for parallel builds. Remember to - "unsetenv RUNSERIAL" before running configure for a serial build. - - Note that the RUNSERIAL environment variable exists so that we can - prefix serial runs as necessary on the target system. On DataStar, - no prefix is necessary. However on an MPICH system, the prefix might - have to be set to something like "/usr/local/mpi/bin/mpirun -np 1" to - get the serial tests to run at all. - - In such cases, you will have to include the regular prefix in your - filter script. - -* H5Ocopy() does not copy reg_ref attributes correctly when shared-message - is turn on. The value of the reference in the destination attriubte is - wrong. This H5Ocopy problem will affect the h5copy tool. - -* In the C++ API, it appears that there are bugs in Attribute::write/read - and DataSet::write/read for fixed- and variable-len strings. The problems - are being worked on and a patch will be provided when the fixes are - available. - - -%%%%1.8.0%%%% - - -HDF5 version 1.8.0 released on Tue Feb 12 20:41:19 CST 2008 -================================================================================ - -INTRODUCTION -============ - -This document describes the differences between the HDF5-1.6.x release series -and HDF5 1.8.0, and contains information on the platforms tested and known -problems in HDF5-1.8.0. For more details, see the HISTORY-1_0-1_8_0_rc3.txt -file in the -release_docs/ directory of the HDF5 source. - -Links to the HDF5 1.8.0 source code, documentation, and additional materials -can be found on the HDF5 web page at: - - http://www.hdfgroup.org/products/hdf5/ - -The HDF5 1.8.0 release can be obtained from: - - http://www.hdfgroup.org/HDF5/release/obtain5.html - -User documentation for 1.8.0 can be accessed directly at this location: - - http://www.hdfgroup.org/HDF5/doc/ - -New features in 1.8.0, including brief general descriptions of some new -and modified APIs, are described in the "What's New in 1.8.0?" document: - - http://www.hdfgroup.org/HDF5/doc/ADGuide/WhatsNew180.html - -All new and modified APIs are listed in detail in the "HDF5 Software Changes -from Release to Release" document, in the section "Release 1.8.0 (current -release) versus Release 1.6.x": - - http://www.hdfgroup.org/HDF5/doc/ADGuide/Changes.html - -If you have any questions or comments, please send them to the HDF Help Desk: - - help@hdfgroup.org - - -CONTENTS -======== - -- New Features -- Removed Feature -- Support for new platforms and languages -- Bug Fixes since HDF5-1.6.0 -- Platforms Tested -- Supported Configuration Features Summary -- Known Problems - - -New Features -============ - - HDF5 Release 1.8.0 is a major release with many changes and new features. - - New format and interface features discussed in the "What's New in - HDF5 1.8.0" document include the following: - - Enhanced group object management - Enhanced attribute management and more efficient meta data handling - Expanded datatype features - Creation order tracking and indexing - Improved meta data caching and cache control - UTF-8 encoding - New I/O filters: n-bit and scale+offset compression - New link (H5L) and object (H5O) interfaces and features - External and user-defined links - New high-level APIs: - HDF5 Packet Table (H5PT) and HDF5 Dimension Scale (H5DS) - C++ and Fortran interfaces for older high-level APIs: - H5Lite (H5LT), H5Image (H5IM), and H5Table (H5TB) - New and improved tools - And more... - - http://hdfgroup.org/HDF5/doc/ADGuide/WhatsNew180.html - - - New APIs associated with these features, other interface changes - (e.g., ENUM and struct definitions), and new library configuration flags - are listed in the "Release 1.8.0 (current release) versus Release 1.6.x" - section of "HDF5 Software Changes from Release to Release." - - http://hdfgroup.org/HDF5/doc/ADGuide/Changes.html - -Compatibility -------------- - Many HDF5 users and user communities have existing applications that - they may wish to port to Release 1.8.0. Alternatively, some users may - wish to take advantage of Release 1.8.0's improved performance without - having to port such applications. To facilitate managing application - compatibility and porting applications from release to release, the HDF - Team has implemented the following features: - Individually-configurable macros that selectively map common - interface names to the old and new interfaces - Library configuration options to configure the macro mappings - - Two related documents accompany this release: - "API Compatibility Macros in HDF5" discusses the specifics of the - new individually-configurable macros and library configuration - options. - http://hdfgroup.org/HDF5/doc/RM/APICompatMacros.html - - "New Features in HDF5 Release 1.8.0 and Backward/Forward Format - Compatibility Issues" discusses each new feature with regard to - its impact on format compatibility. - http://hdfgroup.org/HDF5/doc/ADGuide/CompatFormat180.html - -Referenced documents --------------------- - http://hdfgroup.org/HDF5/doc/ADGuide/WhatsNew180.html - "What's New in HDF5 1.8.0" - - http://hdfgroup.org/HDF5/doc/ADGuide/Changes.html - The "Release 1.8.0 (current release) versus Release 1.6.x " - section in "HDF5 Software Changes from Release to Release" - - http://hdfgroup.org/HDF5/doc/RM/APICompatMacros.html - "API Compatibility Macros in HDF5" - - http://hdfgroup.org/HDF5/doc/ADGuide/CompatFormat180.html - "New Features in HDF5 Release 1.8.0 and Backward/Forward Format - Compatibility Issues" - - -Removed Feature -=============== -The stream virtual file driver (H5FD_STREAM) have been removed in this -release. This affects the functions H5Pset_fapl_stream and H5Pget_fapl_stream -and the constant H5FD_STREAM. - -This virtual file driver will be available at -http://hdf5-addons.origo.ethz.ch/. Note that at the time of this release, -the transition is still in progress; the necessary integration tools may -not be available when HDF5 Release 1.8.0 first comes out. - - -Support for New Platforms, Languages, and Compilers -=================================================== - - Support for Open VMS 7.3 was added. - - -Bug Fixes since HDF5-1.6.0 -========================== - This release contains numerous bug fixes. For details, see the - "Changes from 1.6.0 to 1.8.0-rc3" section of the HISTORY.txt file for - this release. - - -Platforms Tested -================ -The following platforms and compilers have been tested for for this release. - - AIX 5.2 (32/64 bit) xlc 8.0.0.11 - xlC 8.0 - xlf 10.01.0000.0 - mpcc_r 6.0.0.8 - mpxlf_r 8.1.1.7 - - FreeBSD 6.2-STABLE i386 gcc 3.4.6 [FreeBSD] 20060305 - (duty) g++ 3.4.6 [FreeBSD] 20060305 - gcc 4.2.1 20080123 - g++ 4.2.1 20080123 - gfortran 4.2.1 20070620 - - FreeBSD 6.2-STABLE amd64 gcc 3.4.6 [FreeBSD] 20060305 - (liberty) g++ 3.4.6 [FreeBSD] 20060305 - gcc 4.2.1 20080123 - g++ 4.2.1 20080123 - gfortran 4.2.1 20080123 - - IRIX64 6.5 (64 & n32) MIPSpro cc 7.4.4m - F90 MIPSpro 7.4.4m - C++ MIPSpro cc 7.4.4m - - Linux 2.6.9 (RHEL4) Intel 10.0 compilers - (abe.ncsa.uiuc.edu) - - Linux 2.4.21-47 gcc 3.2.3 20030502 - (osage) - - Linux 2.6.9-42.0.10 gcc 3.4.6 20060404 - (kagiso) PGI 7.0-7 (pgcc, pgf90, pgCC) - Intel 9.1 (icc, ifort, icpc) - - Linux 2.6.16.27 x86_64 AMD gcc 4.1.0 (SuSE Linux), g++ 4.1.0, - (smirom) g95 (GCC 4.0.3) - PGI 6.2-5 (pgcc, pgf90, pgCC) - Intel 9.1 (icc, iort, icpc) - - Linux 2.6.5-7.252.1-rtgfx #1 Intel(R) C++ Version 9.0 - SMP ia64 Intel(R) Fortran Itanium(R) Version 9.0 - (cobalt) SGI MPI - - SunOS 5.8 32,46 Sun WorkShop 6 update 2 C 5.3 - (Solaris 2.8) Sun WorkShop 6 update 2 Fortran 95 6.2 - Sun WorkShop 6 update 2 C++ 5.3 - - SunOS 5.10 cc: Sun C 5.8 - (linew) f90: Sun Fortran 95 8.2 - CC: Sun C++ 5.8 - - Xeon Linux 2.4.21-32.0.1.ELsmp-perfctr-lustre - (tungsten) gcc 3.2.2 20030222 - Intel(R) C++ Version 9.0 - Intel(R) Fortran Compiler Version 9.0 - - IA-64 Linux 2.4.21.SuSE_292.til1 ia64 - (NCSA tg-login) gcc 3.2.2 - Intel(R) C++ Version 8.1 - Intel(R) Fortran Compiler Version 8.1 - mpich-gm-1.2.5..10-intel-r2 - - Windows XP Visual Studio .NET - Visual Studio 2005 w/ Intel Fortran 9.1 - Cygwin(native gcc compiler and g95) - MinGW(native gcc compiler and g95) - - Windows XP x64 Visual Studio 2005 w/ Intel Fortran 9.1 - - Windows Vista Visual Studio 2005 - - MAC OS 10.4 (Intel) gcc i686-apple-darwin8-gcc-4.0.1 (GCC) 4.0.1 - G95 (GCC 4.0.3 (g95 0.91!) Nov 21 2006) - - Alpha Open VMS 7.3 Compaq C V6.5-001-48BCD - HP Fortran V7.6-3276 - Compaq C++ V6.5-004 - - -Supported Configuration Features Summary -======================================== - - In the tables below - y = tested and supported - n = not supported or not tested in this release - 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 parallel -SunOS5.8 64-bit n y n y y y -SunOS5.8 32-bit n y n y y y -SunOS5.10 64-bit y(1) y n y y y -SunOS5.10 32-bit y(1) y n y y y -IRIX64_6.5 64-bit n y y y y y -IRIX64_6.5 32-bit n n n n y y -AIX-5.2 32-bit y y y y y y -AIX-5.2 64-bit y y y y y y -Windows XP n y(15) n(15) y y y -Windows XP x64 n y(15) n(15) y y y -Windows Vista n n n y y y -Mac OS X 10.4 PowerPC n n -Mac OS X 10.4 Intel n y n y y y -FreeBSD 4.11 n n n y y y -RedHat EL3 W (3) y(1a) y(10) y(1a) y y y -RedHat EL3 W Intel (3) n y n y y n -RedHat EL3 W PGI (3) n y n y y n -SuSe x86_64 gcc (3,12) y(1a) y(11) n y y y -SuSe x86_64 Int (3,12) n y(13) n y y n -SuSe x86_64 PGI (3,12) n y(8) n y y y -Linux 2.4 Xeon C - Lustre Intel (3,6) n y n y y n -Linux 2.6 SuSE ia64 C - Intel (3,7) y y y y y n -Linux 2.6 SGI Altix - ia64 Intel (3) y y y y y y -Alpha OpenVMS 7.3.2 n y n y n n - - - -Platform Shared Shared Shared static- Thread- - C libs F90 libs C++ libs exec safe -Solaris2.8 64-bit y y y x y -Solaris2.8 32-bit y y y x y -Solaris2.10 64-bit y x y -Solaris2.10 32-bit y x y -IRIX64_6.5 64-bit y y n y y -IRIX64_6.5 32-bit y dna y y y -AIX-5.2 & 5.3 32-bit n n n y n -AIX-5.2 & 5.3 64-bit n n n y n -Windows XP y y(15) y y y -Windows XP x64 y y(15) y y y -Windows Vista y n n y y -Mac OS X 10.3 y y n -FreeBSD 4.11 y n y y y -RedHat EL3 W (3) y y(10) y y y -RedHat EL3 W Intel (3) y y y y n -RedHat EL3 W PGI (3) y y y y n -SuSe x86_64 W GNU (3,12) y y y y y -SuSe x86_64 W Int (3,12) y y y y(14) n -SuSe x86_64 W PGI (3,12) y y y y(14) n -Linux 2.4 Xeon C - Lustre Intel (6) y y y y n -Linux 2.4 SuSE - ia64 C Intel (7) y y y y n -Linux 2.4 SGI Altix - ia64 Intel y y n -Alpha OpenVMS 7.3.2 n n n y n - - Notes: (1) Using mpich 1.2.6. - (1a) Using mpich2 1.0.6. - (2) Using mpt and mpich 1.2.6. - (3) Linux 2.6 with GNU, Intel, and PGI compilers, as indicated. - W or C indicates workstation or cluster, respectively. - - (6) Linux 2.4.21-32.0.1. Xeon cluster with ELsmp_perfctr_lustre - and Intel compilers - (7) Linux 2.4.21, SuSE_292.till. Ia64 cluster with Intel -compilers - (8) pgf90 - (9) With Compaq Visual Fortran 6.6c compiler. - (10) With PGI and Absoft compilers. - (11) PGI and Intel compilers for both C and Fortran - (12) AMD Opteron x86_64 - (13) ifort - (14) Yes with C and Fortran, but not with C++ - (15) Using Visual Studio 2005 or Cygwin - (16) Not tested for this release. - Compiler versions for each platform are listed in the preceding - "Platforms Tested" table. - - -Known Problems -============== -* We have discovered two problems when running collective IO parallel HDF5 - tests with chunking storage on the ChaMPIon MPI compiler on tungsten, a - Linux cluster at NCSA. - - Under some complex selection cases: - 1) MPI_Get_element returns the wrong value. - 2) MPI_Type_struct also generates the wrong derived datatype and corrupt - data may be generated. - These issues arise only when turning on collective IO with chunking storage - with some complex selections. We have not found these problems on other - MPI-IO compilers. If you encounter these problems, you may use independent - IO instead. - - To avoid this behavior, change the following line in your code - H5Pset_dxpl_mpio(xfer_plist, H5FD_MPIO_COLLECTIVE); - - to - H5Pset_dxpl_mpio(xfer_plist, H5FD_MPIO_INDEPENDENT); - - KY - 2007/08/24 - -* For SNL, spirit/liberty/thunderbird: The serial tests pass but parallel - tests failed with MPI-IO file locking message. AKC - 2007/6/25 - -* On Intel 64 Linux cluster (RH 4, Linux 2.6.9) with Intel 10.0 compilers, - use -mp -O1 compilation flags to build the libraries. A higher level of - optimization causes failures in several HDF5 library tests. - -* For SNL, Red Storm: Only parallel HDF5 is supported. The serial tests pass - when run against the parallel library; the parallel tests also pass, but - with lots of non-fatal error messages. - -* For LLNL, uP: both serial and parallel tests pass. - Zeus: Serial tests pass but parallel tests fail with a known problem in MPI. - ubgl: Serial tests pass but parallel tests fail. - -* On SUN 5.10 C++, testing fails in the "Testing Shared Datatypes with - Attributes" test. - -* Configuring with --enable-debug=all produces compiler errors on most - platforms: Users who want to run HDF5 in debug mode should use - --enable-debug rather than --enable-debug=all to enable debugging - information on most modules. - -* On Mac OS 10.4, test/dt_arith.c has some errors in conversion from long - double to (unsigned) long long and from (unsigned) long long to long double. - -* On Altix SGI with Intel 9.0, testmeta.c would not compile with -O3 - optimization flag. - -* On VAX, the Scaleoffset filter is not supported. The filter cannot be - applied to HDF5 data generated on VAX. The Scaleoffset filter only supports - the IEEE standard for floating-point data. - -* On Cray X1, a lone colon on the command line of h5dump --xml (as in - the testh5dumpxml.sh script) is misinterpereted by the operating system - and causes an error. - -* On mpich 1.2.5 and 1.2.6, if more than two processes contribute no IO and - the application asks to do collective IO, we have found that when using 4 - processors, a simple collective write will sometimes be hung. This can be - verified with t_mpi test under testpar. - -* On IRIX6.5, when the C compiler version is greater than 7.4, complicated - MPI derived datatype code will work. However, the user should increase - the value of the MPI_TYPE_MAX environment variable to some appropriate value - to use collective irregular selection code. For example, the current - parallel HDF5 test needs to raise MPI_TYPE_MAX to 200,000 to pass the test. - -* A dataset created or rewritten with a v1.6.3 library or after cannot be read - with the v1.6.2 library or before when the Fletcher32 EDC filter is enabled. - There was a bug in the calculating code of the Fletcher32 checksum in the - library before v1.6.3; the checksum value was not consistent between big- - endian and little-endian systems. This bug was fixed in Release 1.6.3. - However, after fixing the bug, the checksum value was no longer the same as - before on little-endian system. Library releases after 1.6.4 can still read - datasets created or rewritten with an HDF5 library of v1.6.2 or before. - SLU - 2005/6/30 - -* For version 6 (6.02 and 6.04) of the Portland Group compiler on the AMD - Opteron processor, there is a bug in the compiler for optimization(-O2). - The library failed in several tests, all related to the MULTI driver. - The problem has been reported to the vendor. - -* On IBM AIX systems, parallel HDF5 mode will fail some tests with error - messages like "INFO: 0031-XXX ...". This is from the command `poe'. - Set the environment variable MP_INFOLEVEL to 0 to minimize the messages - and run the tests again. - - The tests may fail with messages like "The socket name is already in use", - but HDF5 does not use sockets. This failure is due to problems with the - poe command trying to set up the debug socket. To resolve this problem, - check to see whether there are many old /tmp/s.pedb.* files staying around. - These are sockets used by the poe command and left behind due to failed - commands. First, ask your system administrator to clean them out. - Lastly, request IBM to provide a means to run poe without the debug socket. - -* The --enable-static-exec configure flag fails to compile for Solaris - platforms. This is due to the fact that not all of the system libraries on - Solaris are available in a static format. - - The --enable-static-exec configure flag also fails to correctly compile - on IBM SP2 platform for the serial mode. The parallel mode works fine with - this option. - - It is suggested that you do not use this option on these platforms - during configuration. - -* With the gcc 2.95.2 compiler, HDF5 uses the `-ansi' flag during - compilation. The ANSI version of the compiler complains about not being - able to handle the `long long' datatype with the warning: - - warning: ANSI C does not support `long long' - - This warning is innocuous and can be safely ignored. - -* The ./dsets tests fail on the TFLOPS machine if the test program, - dsets.c, is compiled with the -O option. The HDF5 library still works - correctly with the -O option. The test program works fine if it is - compiled with -O1 or -O0. Only -O (same as -O2) causes the test - program to fail. - -* Not all platforms behave correctly with Szip's shared libraries. Szip is - disabled in these cases, and a message is relayed at configure time. Static - libraries should be working on all systems that support Szip and should be - used when shared libraries are unavailable. - - There is also a configure error on Altix machines that incorrectly reports - when a version of Szip without an encoder is being used. - -* On some platforms that use Intel and Absoft compilers to build the HDF5 - Fortran library, compilation may fail for fortranlib_test.f90, fflush1.f90 - and fflush2.f90 complaining about the exit subroutine. Comment out the line - IF (total_error .ne. 0) CALL exit (total_error). - -* Information about building with PGI and Intel compilers is available in - the INSTALL file sections 4.7 and 4.8. - -* On at least one system, SDSC DataStar, the scheduler (in this case - LoadLeveler) sends job status updates to standard error when you run - any executable that was compiled with the parallel compilers. - - This causes problems when running "make check" on parallel builds, as - many of the tool tests function by saving the output from test runs, - and comparing it to an exemplar. - - The best solution is to reconfigure the target system so it no longer - inserts the extra text. However, this may not be practical. - - In such cases, one solution is to "setenv HDF5_Make_Ignore yes" prior to - the configure and build. This will cause "make check" to continue after - detecting errors in the tool tests. However, in the case of SDSC DataStar, - it also leaves you with some 150 "failed" tests to examine by hand. - - A second solution is to write a script to run serial tests and filter - out the text added by the scheduler. A sample script used on SDSC - DataStar is given below, but you will probably have to customize it - for your installation. - - Observe that the basic idea is to insert the script as the first item - on the command line which executes the the test. The script then - executes the test and filters out the offending text before passing - it on. - - #!/bin/csh - - set STDOUT_FILE=~/bin/serial_filter.stdout - set STDERR_FILE=~/bin/serial_filter.stderr - - rm -f $STDOUT_FILE $STDERR_FILE - - ($* > $STDOUT_FILE) >& $STDERR_FILE - - set RETURN_VALUE=$status - - cat $STDOUT_FILE - - tail +3 $STDERR_FILE - - exit $RETURN_VALUE - - You get the HDF5 make files and test scripts to execute your filter script - by setting the environment variable "RUNSERIAL" to the full path of the - script prior to running configure for parallel builds. Remember to - "unsetenv RUNSERIAL" before running configure for a serial build. - - Note that the RUNSERIAL environment variable exists so that we can - can prefix serial runs as necessary on the target system. On DataStar, - no prefix is necessary. However on an MPICH system, the prefix might - have to be set to something like "/usr/local/mpi/bin/mpirun -np 1" to - get the serial tests to run at all. - - In such cases, you will have to include the regular prefix in your - filter script. - -* H5Ocopy() does not copy reg_ref attributes correctly when shared-message - is turn on. The value of the reference in the destination attriubte is - wrong. This H5Ocopy problem will affect the h5copy tool. - diff --git a/release_docs/NEWSLETTER.txt b/release_docs/NEWSLETTER.txt new file mode 100644 index 0000000..f03f710 --- /dev/null +++ b/release_docs/NEWSLETTER.txt @@ -0,0 +1,25 @@ +INTRODUCTION +============ + +This purpose of this document is to contain entries that can be used to quickly +produce a release newsletter. When something is added to the library that is +"newsletter worthy" (i.e., new feature, CVE fix, etc.) a summary note should +be added here. + +The format should look like this: + +* SUMMARY OF NEWSLETTER-WORTHY THING + + Here is where you describe the summary. Summarize the feature, fix, or + change in general language. Remember, RELEASE.txt is for communicating + technical specifics. Text entered here is more like advertising. + + (GitHub #123, #125) + +The GitHub #s could be relevant issues or PRs. They will probably not appear +in the final newsletter, but are so that the person writing the newsletter +has easy access to context if they have questions. + +Every entry in RELEASE.txt does NOT require an entry here. The newsletter is +for communicating major changes that are of interest to anyone. Minor bugfixes, +memory leak fixes, etc. do not require entries. diff --git a/release_docs/README.md b/release_docs/README.md new file mode 100644 index 0000000..1532f1a --- /dev/null +++ b/release_docs/README.md @@ -0,0 +1,102 @@ +# The `release_docs` directory + +## Intro + +This directory contains instructions for building and using the library as +well as the HDF5 history files. + +## HISTORY files + +The `HISTORY` files contain the history of this branch of HDF5. They fall into +three categories. + +### HISTORY-\[VERSION 1\]-\[VERSION 2\].txt + +These files are created when we release a new major version and include all +the changes that were made to the `develop` branch while creating a major release. + +### HISTORY-\[VERSION\].txt + +This file contains the changes that were made to a maintenance branch since +it split off from `develop`. It will also be found in the `develop` branch +when experimental releases have been created. + +### RELEASE.txt + +This is the changelog for the current version of the library. + +For a MAJOR release (or in `develop`) this files lists all the changes since the +last major version. For a MINOR release (or in a maintenance branch), this file +lists all the changes since the last release in the maintenance branch. + +Examples: + +* The file for HDF5 1.14.0 includes all the changes since HDF5 1.12.0 +* The file for HDF5 1.10.9 includes all the changes since HDF5 1.10.8 +* The file in `develop` includes all the changes since the last major release +* The file in `hdf5_1_14` includes all the changes since the last minor HDF5 1.14 release + +Note that we make no effort to bring maintenance branch `HISTORY` files back to +develop. If you want to compare, say, 1.10.4 with 1.12.3, you'd have to get +the history files from those releases and compare them by hand. + +## Creating new releases + +### MAJOR release + +* If there were experimental releases, merge the experimental `HISTORY` file + and the current `RELEASE.txt` by category to create a separate, unified + file that ignores the experimental releases. Don't check this in yet or + clobber any existing `HISTORY`/`RELEASE` files, but put it someplace handy for + use in later steps. + +* Create the new maintenance branch + +In develop: +* Create the new `HISTORY-\[VERSION 1\]-\[VERSION 2\].txt` file + * If there is an experimental `HISTORY` file, add `RELEASE.txt` to the beginning of it and use that + * Otherwise, start with `RELEASE.txt` + * Add the introduction boilerplate like in the other `HISTORY` files (TOC, etc.) +* Delete any experimental `HISTORY` file +* Clear out `RELEASE.txt` + +Note that we're KEEPING any experimental release history information in the +`HISTORY-\[VERSION 1\]-\[VERSION 2\].txt` file, so do NOT use the merged file in +the above steps! + +In the new maintenance branch: +* Create the new `HISTORY-\[VERSION\].txt` file + * If there is an experimental `HISTORY` file use the combined file you created earlier + * Otherwise, start with `RELEASE.txt` + * Add the introduction boilerplate like in the other `HISTORY` files (TOC, etc.) +* Delete any experimental `HISTORY` file +* Clear out `RELEASE.txt` + +* Create the new release branch + +In the new release branch: +* If there were experimental releases, use the combined file you created earlier as `RELEASE.txt` +* Otherwise the `RELEASE.txt` will be used as-is + +### MINOR release + +* Create the release branch + +In the maintenance branch: +* Add the contents of `RELEASE.txt` to the beginnnig of `HISTORY-\[VERSION\].txt` +* Clear out `RELEASE.txt` + +### EXPERIMENTAL release + +* Add the contents of `RELEASE.txt` to the beginnnig of `HISTORY-\[VERSION\].txt` +* Clear out `RELEASE.txt` + +## INSTALL files + +These files include instructions for building and installing HDF5 on various +platforms. + +## USING files + +These files document how to build HDF5 applications with an installed HDF5 +library. diff --git a/release_docs/RELEASE.txt b/release_docs/RELEASE.txt index 2cef92d..052428a 100644 --- a/release_docs/RELEASE.txt +++ b/release_docs/RELEASE.txt @@ -21,7 +21,7 @@ The official HDF5 releases can be obtained from: https://www.hdfgroup.org/downloads/hdf5/ -Changes from Release to Release and New Features in the HDF5-1.13.x release series +Changes from release to release and new features in the HDF5-1.14.x release series can be found at: https://portal.hdfgroup.org/display/HDF5/Release+Specific+Information @@ -36,7 +36,7 @@ CONTENTS - New Features - Support for new platforms and languages -- Bug Fixes since HDF5-1.13.3 +- Bug Fixes since HDF5-1.14.0 - Platforms Tested - Known Problems - CMake vs. Autotools installations @@ -47,108 +47,13 @@ New Features Configuration: ------------- - - Removal of MPE support - - The ability to build with MPE instrumentation has been removed along with - the following configure options: - - Autotools: - --with-mpe= - - CMake has never supported building with MPE support. - - (DER - 2022/11/08) - - - Removal of dmalloc support - - The ability to build with dmalloc support has been removed along with - the following configure options: - - Autotools: - --with-dmalloc= - - CMake: - HDF5_ENABLE_USING_DMALLOC - - (DER - 2022/11/08) - - - Removal of memory allocation sanity checks configure options - - With the removal of the memory allocation sanity checks feature, the - following configure options are no longer necessary and have been - removed: - - Autotools: - --enable-memory-alloc-sanity-check - - CMake: - HDF5_MEMORY_ALLOC_SANITY_CHECK - HDF5_ENABLE_MEMORY_STATS + - - (DER - 2022/11/03) Library: -------- - - Overhauled the Virtual Object Layer (VOL) - - The virtual object layer (VOL) was added in HDF5 1.12.0 but the initial - implementation required API-breaking changes to better support optional - operations and pass-through VOL connectors. The original VOL API is - now considered deprecated and VOL users and connector authors should - target the 1.14 VOL API. - - The specific changes are too extensive to document in a release note, so - VOL users and connector authors should consult the updated VOL connector - author's guide and the 1.12-1.14 VOL migration guide. - - (DER - 2022/12/28) - - - H5VLquery_optional() signature change - - The last parameter of this API call has changed from a pointer to hbool_t - to a pointer to uint64_t. Due to the changes in how optional operations - are handled in the 1.14 VOL API, we cannot make the old API call work - with the new scheme, so there is no API compatibility macro for it. - - (DER - 2022/12/28) - - - H5I_free_t callback signature change - - In order to support asynchronous operations and future IDs, the signature - of the H5I_free_t callback has been modified to take a second 'request' - parameter. Due to the nature of the internal library changes, no API - compatibility macro is available for this change. - - (DER - 2022/12/28) - - - Fix for CVE-2019-8396 - - Malformed HDF5 files may have truncated content which does not match - the expected size. When H5O__pline_decode() attempts to decode these it - may read past the end of the allocated space leading to heap overflows - as bounds checking is incomplete. - - The fix ensures each element is within bounds before reading. - - (2022/11/09 - HDFFV-10712, CVE-2019-8396, GitHub #2209) - - - Removal of memory allocation sanity checks feature - - This feature added heap canaries and statistics tracking for internal - library memory operations. Unfortunately, the heap canaries caused - problems when library memory operations were mixed with standard C - library memory operations (such as in the filter pipeline, where - buffers may have to be reallocated). Since any platform with a C - compiler also usually has much more sophisticated memory sanity - checking tools than the HDF5 library provided (e.g., valgrind), we - have decided to to remove the feature entirely. - - In addition to the configure changes described above, this also removes - the following from the public API: - H5get_alloc_stats() - H5_alloc_stats_t + - - (DER - 2022/11/03) Parallel Library: ----------------- @@ -198,132 +103,13 @@ New Features Support for new platforms, languages and compilers ================================================== - - -Bug Fixes since HDF5-1.13.3 release + + +Bug Fixes since HDF5-1.14.0 release =================================== Library ------- - - Seg fault on file close - - h5debug fails at file close with core dump on a file that has an - illegal file size in its cache image. In H5F_dest(), the library - performs all the closing operations for the file and keeps track of - the error encountered when reading the file cache image. - At the end of the routine, it frees the file's file structure and - returns error. Due to the error return, the file object is not removed - from the ID node table. This eventually causes assertion failure in - H5VL__native_file_close() when the library finally exits and tries to - access that file object in the table for closing. - - The closing routine, H5F_dest(), will not free the file structure if - there is error, keeping a valid file structure in the ID node table. - It will be freed later in H5VL__native_file_close() when the - library exits and terminates the file package. - - (VC - 2022/12/14, HDFFV-11052, CVE-2020-10812) - - - Fix CVE-2018-13867 / GHSA-j8jr-chrh-qfrf - - Validate location (offset) of the accumulated metadata when comparing. - - Initially, the accumulated metadata location is initialized to HADDR_UNDEF - - the highest available address. Bogus input files may provide a location - or size matching this value. Comparing this address against such bogus - values may provide false positives. Thus make sure, the value has been - initialized or fail the comparison early and let other parts of the - code deal with the bogus address/size. - Note: To avoid unnecessary checks, it is assumed that if the 'dirty' - member in the same structure is true the location is valid. - - (EFE - 2022/10/10 GH-2230) - - - Fix CVE-2018-16438 / GHSA-9xmm-cpf8-rgmx - - Make sure info block for external links has at least 3 bytes. - - According to the specification, the information block for external links - contains 1 byte of version/flag information and two 0 terminated strings - for the object linked to and the full path. - Although not very useful, the minimum string length for each (with - terminating 0) would be one byte. - Checking this helps to avoid SEGVs triggered by bogus files. - - (EFE - 2022/10/09 GH-2233) - - - CVE-2021-46244 / GHSA-vrxh-5gxg-rmhm - - Compound datatypes may not have members of size 0 - - A member size of 0 may lead to an FPE later on as reported in - CVE-2021-46244. To avoid this, check for this as soon as the - member is decoded. - - (EFE - 2022/10/05 GEH-2242) - - - - Fix CVE-2021-45830 / GHSA-5h2h-fjjr-x9m2 - - Make H5O__fsinfo_decode() more resilient to out-of-bound reads. - - When decoding a file space info message in H5O__fsinfo_decode() make - sure each element to be decoded is still within the message. Malformed - hdf5 files may have trunkated content which does not match the - expected size. Checking this will prevent attempting to decode - unrelated data and heap overflows. So far, only free space manager - address data was checked before decoding. - - (EFE - 2022/10/05 GH-2228) - - - Fix CVE-2021-46242 / GHSA-x9pw-hh7v-wjpf - - When evicting driver info block, NULL the corresponding entry. - - Since H5C_expunge_entry() called (from H5AC_expunge_entry()) sets the flag - H5C__FLUSH_INVALIDATE_FLAG, the driver info block will be freed. NULLing - the pointer in f->shared->drvinfo will prevent use-after-free when it is - used in other functions (like H5F__dest()) - as other places will check - whether the pointer is initialized before using its value. - - (EFE - 2022/09/29 GH-2254) - - - Fix CVE-2021-45833 / GHSA-x57p-jwp6-4v79 - - Report error if dimensions of chunked storage in data layout < 2 - - For Data Layout Messages version 1 & 2 the specification state - that the value stored in the data field is 1 greater than the - number of dimensions in the dataspace. For version 3 this is - not explicitly stated but the implementation suggests it to be - the case. - Thus the set value needs to be at least 2. For dimensionality - < 2 an out-of-bounds access occurs. - - (EFE - 2022/09/28 GH-2240) - - - Fix CVE-2018-14031 / GHSA-2xc7-724c-r36j - - Parent of enum datatype message must have the same size as the - enum datatype message itself. - Functions accessing the enumeration values use the size of the - enumeration datatype to determine the size of each element and - how much data to copy. - Thus the size of the enumeration and its parent need to match. - Check in H5O_dtype_decode_helper() to avoid unpleasant surprises - later. - - (EFE - 2022/09/28 GH-2236) - - - Fix CVE-2018-17439 / GHSA-vcxv-vp43-rch7 - - H5IMget_image_info(): Make sure to not exceed local array size - - Malformed hdf5 files may provide more dimensions than the array dim[] in - H5IMget_image_info() is able to hold. Check number of elements first by calling - H5Sget_simple_extent_dims() with NULL for both 'dims' and 'maxdims' arguments. - This will cause the function to return only the number of dimensions. - The fix addresses a stack overflow on write. - - (EFE - 2022/09/27 HDFFV-10589, GH-2226) + - Java Library @@ -333,49 +119,12 @@ Bug Fixes since HDF5-1.13.3 release Configuration ------------- - - Remove Javadoc generation - - The use of doxygen now supersedes the requirement to build javadocs. We do not - have the resources to continue to support two documentation methods and have - chosen doxygen as our standard. - - (ADB - 2022/12/19) - - - Change the default for building the high-level tools - - The gif2hdf5 and hdf2gif high-level tools are deprecated and will be removed - in a future release. The default build setting for them have been changed from enabled - to disabled. A user can enable the build of these tools if needed. - autotools: --enable-hlgiftools - cmake: HDF5_BUILD_HL_GIF_TOOLS=ON - - (ADB - 2022/12/16) - - - Change the settings of the *pc files to use the correct format - - The pkg-config files generated by CMake uses incorrect syntax for the 'Requires' - settings. Changing the set to use 'lib-name = version' instead 'lib-name-version' - fixes the issue - - (ADB - 2022/12/06 HDFFV-11355) - - - Move MPI libraries link from PRIVATE to PUBLIC - - The install dependencies were not including the need for MPI libraries when - an application or library was built with the C library. Also updated the - CMake target link command to use the newer style MPI::MPI_C link variable. - - (ADB - 2022/10/27) + - Tools ----- - - Fix h5repack to only print output when verbose option is selected - - When timing option was added to h5repack, the check for verbose was - incorrectly implemented. - - (ADB - 2022/12/02, GH #2270) + - Performance @@ -387,6 +136,7 @@ Bug Fixes since HDF5-1.13.3 release ----------- - + High-Level Library ------------------ - |