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| author | Dana Robinson <43805+derobins@users.noreply.github.com> | 2023-03-18 04:21:44 (GMT) |
|---|---|---|
| committer | GitHub <noreply@github.com> | 2023-03-18 04:21:44 (GMT) |
| commit | 7c5d0a3756032a3f5f2cbbdf56b8824177584223 (patch) | |
| tree | 93a295fb8d99ea76434c98e0d4117db8f8de1722 | |
| parent | ebdbd503ca1d1a50701937542c6a9e66a3885458 (diff) | |
| download | hdf5-7c5d0a3756032a3f5f2cbbdf56b8824177584223.zip hdf5-7c5d0a3756032a3f5f2cbbdf56b8824177584223.tar.gz hdf5-7c5d0a3756032a3f5f2cbbdf56b8824177584223.tar.bz2 | |
Use new scheme in release_docs (#2585)
* Add README.md and NEWSLETTER.txt files
* Remove HISTORY-1_8.txt
* Rename HISTORY-1_0-1_8_0_rc3.txt to HISTORY-1_0-1_8_0.txt
| -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_8.txt | 14439 | ||||
| -rw-r--r-- | release_docs/NEWSLETTER.txt | 25 | ||||
| -rw-r--r-- | release_docs/README.md | 102 |
4 files changed, 127 insertions, 14439 deletions
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_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. |