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authorDana Robinson <43805+derobins@users.noreply.github.com>2023-03-23 01:41:00 (GMT)
committerGitHub <noreply@github.com>2023-03-23 01:41:00 (GMT)
commitaf2666013f548ec41263bd164ab03741086ba563 (patch)
tree012850b0dbc3351e38d0e63ee112a66c01cba108 /release_docs
parent7b5e67b0662cf128a7d1e92f7e1fbb751d2932f7 (diff)
downloadhdf5-af2666013f548ec41263bd164ab03741086ba563.zip
hdf5-af2666013f548ec41263bd164ab03741086ba563.tar.gz
hdf5-af2666013f548ec41263bd164ab03741086ba563.tar.bz2
Bring new release_docs scheme from 1.14 (#2614)
Diffstat (limited to 'release_docs')
-rw-r--r--release_docs/HISTORY-1_0-1_8_0.txt (renamed from release_docs/HISTORY-1_0-1_8_0_rc3.txt)0
-rw-r--r--release_docs/HISTORY-1_10.txt6562
-rw-r--r--release_docs/HISTORY-1_12.txt628
-rw-r--r--release_docs/HISTORY-1_12_0-1_14_0.txt (renamed from release_docs/HISTORY-1_13.txt)753
-rw-r--r--release_docs/HISTORY-1_8.txt14439
-rw-r--r--release_docs/NEWSLETTER.txt25
-rw-r--r--release_docs/README.md102
-rw-r--r--release_docs/RELEASE.txt272
8 files changed, 884 insertions, 21897 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_10.txt b/release_docs/HISTORY-1_10.txt
deleted file mode 100644
index 1fc3c60..0000000
--- a/release_docs/HISTORY-1_10.txt
+++ /dev/null
@@ -1,6562 +0,0 @@
-HDF5 History
-============
-
-This file contains development history of the HDF5 1.10 branch
-
-09. Release Information for hdf5-1.10.7
-08. Release Information for hdf5-1.10.6
-07. Release Information for hdf5-1.10.5
-06. Release Information for hdf5-1.10.4
-05. Release Information for hdf5-1.10.3
-04. Release Information for hdf5-1.10.2
-03. Release Information for hdf5-1.10.1
-02. Release Information for hdf5-1.10.0-patch1
-01. Release Information for hdf5-1.10.0
-
-[Search on the string '%%%%' for section breaks of each release.]
-
-%%%%1.10.7%%%%
-
-HDF5 version 1.10.7 released on 2020-09-11
-================================================================================
-
-
-INTRODUCTION
-
-This document describes the differences between this release and the previous
-HDF5 release. It contains information on the platforms tested and known
-problems in this release. For more details check the HISTORY*.txt files in the
-HDF5 source.
-
-Note that documentation in the links below will be updated at the time of each
-final release.
-
-Links to HDF5 documentation can be found on The HDF5 web page:
-
- https://portal.hdfgroup.org/display/HDF5/HDF5
-
-The official HDF5 releases can be obtained from:
-
- https://www.hdfgroup.org/downloads/hdf5/
-
- HDF5 binaries provided are fully tested with ZLIB and the free
- Open Source SZIP successor Libaec (with BSD license).
- The official ZLIB and SZIP/Libaec pages are at:
-
- ZLIB: http://www.zlib.net/
- http://www.zlib.net/zlib_license.html
- SZIP/Libaec: https://gitlab.dkrz.de/k202009/libaec
- https://gitlab.dkrz.de/k202009/libaec/-/blob/master/Copyright.txt
-
-Changes from Release to Release and New Features in the HDF5-1.10.x release series
-can be found at:
-
- https://portal.hdfgroup.org/display/HDF5/HDF5+Application+Developer%27s+Guide
-
-If you have any questions or comments, please send them to the HDF Help Desk:
-
- help@hdfgroup.org
-
-
-CONTENTS
-
-- New Features
-- Support for new platforms and languages
-- Bug Fixes since HDF5-1.10.6
-- Supported Platforms
-- Tested Configuration Features Summary
-- More Tested Platforms
-- Known Problems
-- CMake vs. Autotools installations
-
-
-New Features
-============
-
- Configuration:
- -------------
- - Disable memory sanity checks in the Autotools in release branches
-
- The library can be configured to use internal memory sanity checking,
- which replaces C API calls like malloc(3) and free(3) with our own calls
- which add things like heap canaries. These canaries can cause problems
- when external filter plugins reallocate canary-marked buffers.
-
- For this reason, the default will be to not use the memory allocation
- sanity check feature in release branches (e.g., hdf5_1_10_7).
- Debug builds in development branches (e.g., develop, hdf5_1_10) will
- still use them by default.
-
- This change only affects Autotools debug builds. Non-debug autotools
- builds and all CMake builds do not enable this feature by default.
-
- (DER - 2020/08/19)
-
- - Add file locking configure and CMake options
-
- HDF5 1.10.0 introduced a file locking scheme, primarily to help
- enforce SWMR setup. Formerly, the only user-level control of the scheme
- was via the HDF5_USE_FILE_LOCKING environment variable.
-
- This change introduces configure-time options that control whether
- or not file locking will be used and whether or not the library
- ignores errors when locking has been disabled on the file system
- (useful on some HPC Lustre installations).
-
- In both the Autotools and CMake, the settings have the effect of changing
- the default property list settings (see the H5Pset/get_file_locking()
- entry, below).
-
- The yes/no/best-effort file locking configure setting has also been
- added to the libhdf5.settings file.
-
- Autotools:
-
- An --enable-file-locking=(yes|no|best-effort) option has been added.
-
- yes: Use file locking.
- no: Do not use file locking.
- best-effort: Use file locking and ignore "disabled" errors.
-
- CMake:
-
- Two self-explanatory options have been added:
-
- HDF5_USE_FILE_LOCKING
- HDF5_IGNORE_DISABLED_FILE_LOCKS
-
- Setting both of these to ON is the equivalent to the Autotools'
- best-effort setting.
-
- NOTE:
- The precedence order of the various file locking control mechanisms is:
-
- 1) HDF5_USE_FILE_LOCKING environment variable (highest)
-
- 2) H5Pset_file_locking()
-
- 3) configure/CMake options (which set the property list defaults)
-
- 4) library defaults (currently best-effort)
-
- (DER - 2020/07/30, HDFFV-11092)
-
- - CMake option to link the generated Fortran MOD files into the include
- directory.
-
- The Fortran generation of MOD files by a Fortran compile can produce
- different binary files between SHARED and STATIC compiles with different
- compilers and/or different platforms. Note that it has been found that
- different versions of Fortran compilers will produce incompatible MOD
- files. Currently, CMake will locate these MOD files in subfolders of
- the include directory and add that path to the Fortran library target
- in the CMake config file, which can be used by the CMake find library
- process. For other build systems using the binary from a CMake install,
- a new CMake configuration can be used to copy the pre-chosen version
- of the Fortran MOD files into the install include directory.
-
- The default will depend on the configuration of
- BUILD_STATIC_LIBS and BUILD_SHARED_LIBS:
- YES YES Default to SHARED
- YES NO Default to STATIC
- NO YES Default to SHARED
- NO NO Default to SHARED
- The defaults can be overridden by setting the config option
- HDF5_INSTALL_MOD_FORTRAN to one of NO, SHARED, or STATIC
-
- (ADB - 2020/07/09, HDFFV-11116)
-
- - CMake option to use AEC (open source SZip) library instead of SZip
-
- The open source AEC library is a replacement library for SZip. In
- order to use it for hdf5, the libaec CMake source was changed to add
- "-fPIC" and exclude test files. A new option USE_LIBAEC is required
- to compensate for the different files produced by AEC build.
-
- Autotools does not build the compression libraries within hdf5 builds,
- but will use an installed libaec when configured as before with the
- option --with-libsz=<path to libaec directory>.
-
- (ADB - 2020/04/22, OESS-65)
-
- - CMake ConfigureChecks.cmake file now uses CHECK_STRUCT_HAS_MEMBER
-
- Some handcrafted tests in HDFTests.c have been removed and the CMake
- CHECK_STRUCT_HAS_MEMBER module has been used.
-
- (ADB - 2020/03/24, TRILAB-24)
-
- - Both build systems use same set of warnings flags
-
- GNU C, C++ and gfortran warnings flags were moved to files in a config
- sub-folder named gnu-warnings. Flags that only are available for a specific
- version of the compiler are in files named with that version.
- Clang C warnings flags were moved to files in a config sub-folder
- named clang-warnings.
- Intel C, Fortran warnings flags were moved to files in a config sub-folder
- named intel-warnings.
-
- There are flags in named "error-xxx" files with warnings that may
- be promoted to errors. Some source files may still need fixes.
-
- There are also pairs of files named "developer-xxx" and "no-developer-xxx"
- that are chosen by the CMake option:HDF5_ENABLE_DEV_WARNINGS or the
- configure option:--enable-developer-warnings.
-
- In addition, CMake no longer applies these warnings for examples.
-
- (ADB - 2020/03/24, TRILAB-192)
-
- - Update CMake minimum version to 3.12
-
- Updated CMake minimum version to 3.12 and added version checks
- for Windows features.
-
- (ADB - 2020/02/05, TRILABS-142)
-
- - Fixed CMake include properties for Fortran libraries
-
- Corrected the library properties for Fortran to use the
- correct path for the Fortran module files.
-
- (ADB - 2020/02/04, HDFFV-11012)
-
- - Added common warnings files for gnu and intel
-
- Added warnings files to use one common set of flags
- during configure for both autotools and CMake build
- systems. The initial implementation only affects a
- general set of flags for gnu and intel compilers.
-
- (ADB - 2020/01/17)
-
- - Added new options to CMake for control of testing
-
- Added CMake options (default ON);
- HDF5_TEST_SERIAL AND/OR HDF5_TEST_PARALLEL
- combined with:
- HDF5_TEST_TOOLS
- HDF5_TEST_EXAMPLES
- HDF5_TEST_SWMR
- HDF5_TEST_FORTRAN
- HDF5_TEST_CPP
- HDF5_TEST_JAVA
-
- (ADB - 2020/01/15, HDFFV-11001)
-
- - Added Clang sanitizers to CMake for analyzer support if compiler is clang.
-
- Added CMake code and files to execute the Clang sanitizers if
- HDF5_ENABLE_SANITIZERS is enabled and the USE_SANITIZER option
- is set to one of the following:
- Address
- Memory
- MemoryWithOrigins
- Undefined
- Thread
- Leak
- 'Address;Undefined'
-
- (ADB - 2019/12/12, TRILAB-135)
-
-
- Library:
- --------
- - Add metadata cache optimization to reduce skip list usage
-
- On file flush or close, the metadata cache attempts to write out
- all dirty entries in increasing address order. To do this, it needs
- an address sorted list of metadata entries. Further, since flushing
- one metadata cache entry can dirty another, this list must support
- efficient insertion and deletion.
-
- The metadata cache uses a skip list of all dirty entries for this
- purpose. Before this release, this skip list was maintained at all
- times. However, since profiling indicates that this imposes a
- significant cost, we now construct and maintain the skip list only
- when needed. Specifically, we enable the skip list and load it with
- a list of all dirty entries in the metadata cache just before a flush,
- and disable it after the flush.
-
- (JRM - 2020/08/17, HDFFV-11034)
-
- - Add BEST_EFFORT value to HDF5_USE_FILE_LOCKING environment variable
-
- This change adds a BEST_EFFORT to the TRUE/FALSE, 1/0 settings that
- were previously accepted. This option turns on file locking but
- ignores locking errors when the library detects that file locking
- has been disabled on a file system (useful on some HPC Lustre
- installations).
-
- The capitalization of BEST_EFFORT is mandatory.
-
- See the configure option discussion for HDFFV-11092 (above) for more
- information on the file locking feature and how it's controlled.
-
- (DER - 2020/07/30, HDFFV-11092)
-
-
- - Add H5Pset/get_file_locking() API calls
-
- This change adds new API calls which can be used to set or get the
- file locking parameters. The single API call sets both the "use file
- locking" flag and the "ignore disabled file locking" flag.
-
- When opening a file multiple times without closing, the file MUST be
- opened with the same file locking settings. Opening a file with different
- file locking settings will fail (this is similar to the behavior of
- H5Pset_fclose_degree()).
-
- See the configure option discussion for HDFFV-11092 (above) for more
- information on the file locking feature and how it's controlled.
-
- (DER - 2020/07/30, HDFFV-11092)
-
- - Add Mirror VFD
-
- Use TCP/IP sockets to perform write-only (W/O) file I/O on a remote
- machine. Must be used in conjunction with the Splitter VFD.
-
- (JOS - 2020/03/13, TBD)
-
- - Add Splitter VFD
-
- Maintain separate R/W and W/O channels for "concurrent" file writes
- to two files using a single HDF5 file handle.
-
- (JOS - 2020/03/13, TBD)
-
- - Fixed an assertion failure in the parallel library when collectively
- filling chunks. As it is required that chunks be written in
- monotonically non-decreasing order of offset in the file, this assertion
- was being triggered when the list of chunk file space allocations being
- passed to the collective chunk filling routine was not sorted according
- to this particular requirement.
-
- The addition of a sort of the out of order chunks trades a bit of
- performance for the elimination of this assertion and of any complaints
- from MPI implementations about the file offsets used being out of order.
-
- (JTH - 2019/10/07)
-
- Fortran Library:
- ----------------
- - Add wrappers for H5Pset/get_file_locking() API calls
-
- h5pget_file_locking_f()
- h5pset_file_locking_f()
-
- See the configure option discussion for HDFFV-11092 (above) for more
- information on the file locking feature and how it's controlled.
-
- (DER - 2020/07/30, HDFFV-11092)
-
- - Added new Fortran parameters:
-
- H5F_LIBVER_ERROR_F
- H5F_LIBVER_NBOUNDS_F
- H5F_LIBVER_V18_F
- H5F_LIBVER_V110_F
-
- - Added new Fortran API: h5pget_libver_bounds_f
-
- (MSB - 2020/02/11, HDFFV-11018)
-
- C++ Library:
- ------------
- - Add wrappers for H5Pset/get_file_locking() API calls
-
- FileAccPropList::setFileLocking()
- FileAccPropList::getFileLocking()
-
- See the configure option discussion for HDFFV-11092 (above) for more
- information on the file locking feature and how it's controlled.
-
- (DER - 2020/07/30, HDFFV-11092)
-
- Java Library:
- ----------------
- - Add wrappers for H5Pset/get_file_locking() API calls
-
- H5Pset_file_locking()
- H5Pget_use_file_locking()
- H5Pget_ignore_disabled_file_locking()
-
- Unlike the C++ and Fortran wrappers, there are separate getters for the
- two file locking settings, each of which returns a boolean value.
-
- See the configure option discussion for HDFFV-11092 (above) for more
- information on the file locking feature and how it's controlled.
-
- (DER - 2020/07/30, HDFFV-11092)
-
- Tools:
- ------
- - h5repack added options to control how external links are handled.
-
- Currently h5repack preserves external links and cannot copy and merge
- data from the external files. Two options, merge and prune, were added to
- control how to merge data from an external link into the resulting file.
- --merge Follow external soft link recursively and merge data.
- --prune Do not follow external soft links and remove link.
- --merge --prune Follow external link, merge data and remove dangling link.
-
- (ADB - 2020/08/05, HDFFV-9984)
-
- High-Level APIs:
- ---------------
- - None
-
- C Packet Table API
- ------------------
- - None
-
- Internal header file
- --------------------
- - None
-
- Documentation
- -------------
- - None
-
-
-Support for new platforms, languages and compilers.
-=======================================
- - None
-
-
-Bug Fixes since HDF5-1.10.6 release
-==================================
-
- Library
- -------
- - Fix bug and simplify collective metadata write operation when some ranks
- have no entries to contribute. This fixes parallel regression test
- failures with IBM SpectrumScale MPI on the Summit system at ORNL.
-
- (QAK - 2020/09/02)
-
- - Avoid setting up complex MPI types with 0-length vectors, which some
- MPI implementations don't handle well. (In particular, IBM
- SpectrumScale MPI on the Summit system at ORNL)
-
- (QAK - 2020/08/21)
-
- - Fixed use-of-uninitialized-value error
-
- Appropriate initialization of local structs was added to remove the
- use-of-uninitialized-value errors reported by MemorySanitizer.
-
- (BMR - 2020/8/13, HDFFV-11101)
-
- - Creation of dataset with optional filter
-
- When the combination of type, space, etc doesn't work for filter
- and the filter is optional, it was supposed to be skipped but it was
- not skipped and the creation failed.
-
- A fix is applied to allow the creation of a dataset in such
- situation, as specified in the user documentation.
-
- (BMR - 2020/8/13, HDFFV-10933)
-
- - Explicitly declared dlopen to use RTLD_LOCAL
-
- dlopen documentation states that if neither RTLD_GLOBAL nor
- RTLD_LOCAL are specified, then the default behavior is unspecified.
- The default on linux is usually RTLD_LOCAL while macos will default
- to RTLD_GLOBAL.
-
- (ADB - 2020/08/12, HDFFV-11127)
-
- - Fixed issues CVE-2018-13870 and CVE-2018-13869
-
- When a buffer overflow occurred because a name length was corrupted
- and became very large, h5dump crashed on memory access violation.
-
- A check for reading past the end of the buffer was added to multiple
- locations to prevent the crashes and h5dump now simply fails with an
- error message when this error condition occurs.
-
- (BMR - 2020/7/31, HDFFV-11120 and HDFFV-11121)
-
- - H5Sset_extent_none() sets the dataspace class to H5S_NO_CLASS which
- causes asserts/errors when passed to other dataspace API calls.
-
- H5S_NO_CLASS is an internal class value that should not have been
- exposed via a public API call.
-
- In debug builds of the library, this can cause asserts to trip. In
- non-debug builds, it will produce normal library errors.
-
- The new library behavior is for H5Sset_extent_none() to convert
- the dataspace into one of type H5S_NULL, which is better handled
- by the library and easier for developers to reason about.
-
- (DER - 2020/07/27, HDFFV-11027)
-
- - Fixed the segmentation fault when reading attributes with multiple threads
-
- It was reported that the reading of attributes with variable length string
- datatype will crash with segmentation fault particularly when the number
- of threads is high (>16 threads). The problem was due to the file pointer
- that was set in the variable length string datatype for the attribute.
- That file pointer was already closed when the attribute was accessed.
-
- The problem was fixed by setting the file pointer to the current opened
- file pointer when the attribute was accessed. Similar patch up was done
- before when reading dataset with variable length string datatype.
-
- (VC - 2020/07/13, HDFFV-11080)
-
- - Fixed issue CVE-2018-17438
-
- A division by zero was discovered in H5D__select_io() of H5Dselect.c.
- https://security-tracker.debian.org/tracker/CVE-2018-17438
-
- A check was added to protect against division by zero. When such
- situation occurs again, the normal HDF5 error handling will be invoked,
- instead of segmentation fault.
-
- (BMR, DER - 2020/07/09, HDFFV-10587)
-
- - Fixed CVE-2018-17435
-
- The tool h52gif produced a segfault when the size of an attribute message
- was corrupted and caused a buffer overflow.
-
- The problem was fixed by verifying the attribute message's size against the
- buffer size before accessing the buffer. h52gif was also fixed to display
- the failure instead of silently exiting after the segfault was eliminated.
-
- (BMR - 2020/6/19, HDFFV-10591)
-
- - Don't allocate an empty (0-dimensioned) chunked dataset's chunk
- index, until the dataset's dimensions are increased.
-
- (QAK - 2020/05/07)
-
- Configuration
- -------------
- - Stopped addition of szip header and include directory path for
- incompatible libsz
-
- szlib.h is the same for both 32-bit and 64-bit szip, and the header file
- and its path were added to the HDF5 binary even though the configure
- check of a function in libsz later failed and szip compression was not
- enabled. The header file and include path are now added only when the
- libsz function passes the configure check.
-
- (LRK - 2020/08/17, HDFFV-10830)
-
- - Added -fsanitize=address autotools configure option for Clang compiler
-
- Clang sanitizer options were also added for Clang compilers with CMake.
-
- (LRK, 2020/08/05, HDFFV-10836)
-
- - Updated testh5cc.sh.in for functions versioned in HDF5 1.10.
-
- testh5cc.sh previously tested that the correct version of a function
- versioned in HDF5 1.6 or 1.8 was compiled when one of
- H5_NO_DEPRECATED_SYMBOLS or H5_USE_16_API_DEFAULT were defined. This
- test was extended for additional testing with H5_USE_18_API_DEFAULT.
-
- (LRK, 2020/06/22, HDFFV-11000)
-
- - Fixed CMake include properties for Fortran libraries
-
- Corrected the library properties for Fortran to use the
- correct path for the Fortran module files.
-
- (ADB - 2020/02/04, HDFFV-11012)
-
- Performance
- -------------
- - None
-
- Java Library:
- ----------------
- - None
-
- Fortran
- --------
- - Corrected INTERFACE INTENT(IN) to INTENT(OUT) for buf_size in h5fget_file_image_f.
-
- (MSB - 2020/2/18, HDFFV-11029)
-
- - Fixed configure issue when building HDF5 with NAG Fortran 7.0.
-
- HDF5 now accounts for the addition of half-precision floating-point
- in NAG 7.0 with a KIND=16.
-
- (MSB - 2020/02/28, HDFFV-11033)
-
- Tools
- -----
- - The tools library was updated by standardizing the error stack process.
-
- General sequence is:
- h5tools_setprogname(PROGRAMNAME);
- h5tools_setstatus(EXIT_SUCCESS);
- h5tools_init();
- ... process the command-line (check for error-stack enable) ...
- h5tools_error_report();
- ... (do work) ...
- h5diff_exit(ret);
-
- (ADB - 2020/07/20, HDFFV-11066)
-
- - h5diff fixed a command line parsing error.
-
- h5diff would ignore the argument to -d (delta) if it is smaller than DBL_EPSILON.
- The macro H5_DBL_ABS_EQUAL was removed and a direct value comparison was used.
-
- (ADB - 2020/07/20, HDFFV-10897)
-
- - h5diff added a command line option to ignore attributes.
-
- h5diff would ignore all objects with a supplied path if the exclude-path argument is used.
- Adding the exclude-attribute argument will only eclude attributes, with the supplied path,
- from comparison.
-
- (ADB - 2020/07/20, HDFFV-5935)
-
- - h5diff added another level to the verbose argument to print filenames.
-
- Added verbose level 3 that is level 2 plus the filenames. The levels are:
- 0 : Identical to '-v' or '--verbose'
- 1 : All level 0 information plus one-line attribute status summary
- 2 : All level 1 information plus extended attribute status report
- 3 : All level 2 information plus file names
-
- (ADB - 2020/07/20, HDFFV-10005)
-
- - h5repack was fixed to repack the reference attributes properly.
- The code line that checks if the update of reference inside a compound
- datatype is misplaced outside the code block loop that carries out the
- check. In consequence, the next attribute that is not the reference
- type was repacked again as the reference type and caused the failure of
- repacking. The fix is to move the corresponding code line to the correct
- code block.
-
- (KY -2020/02/10, HDFFV-11014)
-
- High-Level APIs:
- ------
- - The H5DSis_scale function was updated to return "not a dimension scale" (0)
- instead of failing (-1), when CLASS or DIMENSION_SCALE attributes are
- not written according to Dimension Scales Specification.
-
- (EIP - 2020/08/12, HDFFV-10436)
-
- Fortran High-Level APIs:
- ------
- - None
-
- Documentation
- -------------
- - None
-
- F90 APIs
- --------
- - None
-
- C++ APIs
- --------
- - None
-
- Testing
- -------
- - Stopped java/test/junit.sh.in installing libs for testing under ${prefix}
-
- Lib files needed are now copied to a subdirectory in the java/test
- directory, and on Macs the loader path for libhdf5.xxxs.so is changed
- in the temporary copy of libhdf5_java.dylib.
-
- (LRK, 2020/7/2, HDFFV-11063)
-
-
-Supported Platforms
-===================
-
- Linux 3.10.0-1127.10.1.el7 gcc (GCC) 4.8.5 20150623 (Red Hat 4.8.5-39)
- #1 SMP ppc64 GNU/Linux g++ (GCC) 4.8.5 20150623 (Red Hat 4.8.5-39)
- (echidna) GNU Fortran (GCC) 4.8.5 20150623 (Red Hat 4.8.5-39)
-
- Linux 2.6.32-754.31.1.el6 IBM XL C/C++ V13.1
- #1 SMP ppc64 GNU/Linux IBM XL Fortran V15.1
- (ostrich)
-
- Linux 3.10.0-327.18.2.el7 GNU C (gcc), Fortran (gfortran), C++ (g++)
- #1 SMP x86_64 GNU/Linux compilers:
- (jelly/kituo/moohan) Version 4.8.5 20150623 (Red Hat 4.8.5-4)
- Version 4.9.3, Version 5.3.0, Version 6.3.0,
- Version 7.2.0, Version 8.3.0, Version 9.1.0
- Intel(R) C (icc), C++ (icpc), Fortran (icc)
- compilers:
- Version 17.0.0.098 Build 20160721
- MPICH 3.3 compiled with GCC 7.2.0
- OpenMPI 4.0.0 compiled with GCC 7.2.0
-
- SunOS 5.11 11.4.5.12.5.0 Sun C 5.15 SunOS_sparc 2017/05/30
- 32- and 64-bit Studio 12.6 Fortran 95 8.8 SunOS_sparc 2017/05/30
- (hedgehog) Sun C++ 5.15 SunOS_sparc 2017/05/30
-
- Windows 7 x64 Visual Studio 2015 w/ Intel C, Fortran 2018 (cmake)
-
- Windows 10 x64 Visual Studio 2015 w/ Intel Fortran 18 (cmake)
- Visual Studio 2017 w/ Intel Fortran 19 (cmake)
- Visual Studio 2019 w/ Intel Fortran 19 (cmake)
- Visual Studio 2019 w/ MSMPI 10.1 (cmake)
-
- macOS Mojave 10.14.6 Apple LLVM version 10.0.1 (clang-1001.0.46.4)
- 64-bit gfortran GNU Fortran (GCC) 6.3.0
- (swallow) Intel icc/icpc/ifort version 19.0.4.233 20190416
-
-Tested Configuration Features Summary
-=====================================
-
- In the tables below
- y = tested
- n = not tested in this release
- C = Cluster
- W = Workstation
- x = not working in this release
- dna = does not apply
- ( ) = footnote appears below second table
- <blank> = testing incomplete on this feature or platform
-
-Platform C F90/ F90 C++ zlib SZIP
- parallel F2003 parallel
-Solaris2.11 32-bit n y/y n y y y
-Solaris2.11 64-bit n y/n n y y y
-Windows 7 x64 y y/y y y y y
-Windows 10 y y/y n y y y
-Windows 10 x64 y y/y n y y y
-MacOS Sierra 10.12.6 64-bit n y/y n y y y
-MacOS High Sierra 10.13.6 64-bit n y/y n y y y
-MacOS Mojave 10.14.6 64-bit n y/y n y y y
-CentOS 7.2 Linux 3.10.0 x86_64 PGI n y/y n y y y
-CentOS 7.2 Linux 3.10.0 x86_64 GNU y y/y y y y y
-CentOS 7.2 Linux 3.10.0 x86_64 Intel n y/y n y y y
-Linux 2.6.32-754.31.1.el6.ppc64 XL n y/y n y y y
-
-
-Platform Shared Shared Shared Thread-
- C libs F90 libs C++ libs safe
-Solaris2.11 32-bit y y y y
-Solaris2.11 64-bit y y y y
-Windows 7 x64 y y y y
-Windows 10 y y y y
-Windows 10 x64 y y y y
-MacOS Sierra 10.12.6 64-bit y n y y
-MacOS High Sierra 10.13.6 64-bit y n y y
-MacOS Mojave 10.14.6 64-bit y n y y
-CentOS 7.2 Linux 3.10.0 x86_64 PGI y y y n
-CentOS 7.2 Linux 3.10.0 x86_64 GNU y y y y
-CentOS 7.2 Linux 3.10.0 x86_64 Intel y y y n
-Linux 2.6.32-754.31.1.el6.ppc64 XL y y y n
-
-Compiler versions for each platform are listed in the preceding
-"Supported Platforms" table.
-
-
-More Tested Platforms
-=====================
-The following platforms are not supported but have been tested for this release.
-
- Linux 2.6.32-573.22.1.el6 GNU C (gcc), Fortran (gfortran), C++ (g++)
- #1 SMP x86_64 GNU/Linux compilers:
- (platypus) Version 4.4.7 20120313
- Version 4.9.3, 5.3.0, 6.2.0
- PGI C, Fortran, C++ for 64-bit target on
- x86-64;
- Version 19.10-0
- MPICH 3.1.4 compiled with GCC 4.9.3
-
- Linux 2.6.32-754.31.1.el6 gcc (GCC) 4.4.7 20120313 (Red Hat 4.4.7-18)
- #1 SMP ppc64 GNU/Linux g++ (GCC) 4.4.7 20120313 (Red Hat 4.4.7-18)
- (ostrich) GNU Fortran (GCC) 4.4.7 20120313 (Red Hat 4.4.7-18)
-
- Linux 3.10.0-327.18.2.el7 GNU C (gcc) and C++ (g++) compilers
- #1 SMP x86_64 GNU/Linux Version 4.8.5 20150623 (Red Hat 4.8.5-4)
- (jelly) with NAG Fortran Compiler Release 6.1(Tozai)
- GCC Version 7.1.0
- OpenMPI 2.1.6-GCC-7.2.0-2.29,
- 3.1.3-GCC-7.2.0-2.29
- Intel(R) C (icc) and C++ (icpc) compilers
- Version 17.0.0.098 Build 20160721
- with NAG Fortran Compiler Release 6.1(Tozai)
-
- Linux 3.10.0-327.10.1.el7 MPICH 3.1.4 compiled with GCC 4.9.3
- #1 SMP x86_64 GNU/Linux
- (moohan)
-
- Linux-3.10.0-1127.0.0.1chaos openmpi-4.0.0
- #1 SMP x86_64 GNU/Linux clang/3.9.0, 8.0.1
- (quartz) gcc/7.3.0, 8.1.0
- intel/16.0.4
-
- Linux-4.14.0-115.10.1.1 spectrum-mpi/rolling-release
- #1 SMP ppc64le GNU/Linux clang/coral-2018.08.08
- (lassen) gcc/7.3.1
- xl/2019.02.07
-
- Linux-4.12.14-150.52-default cray-mpich/7.7.10
- #1 SMP x86_64 GNU/Linux gcc/7.3.0, 8.2.0
- (cori) intel/19.0.3
-
- Linux-4.4.180-94.107-default cray-mpich/7.7.6
- # 1SMP x86_64 GNU/Linux gcc/7.2.0, 8.2.0
- (mutrino) intel/17.0.4, 18.0.2, 19.0.4
-
- Fedora 32 5.7.15-200.fc32.x86_64 Clang version 10.0.0 (Fedora 10.0.0-2.fc32)
- #1 SMP x86_64 GNU/Linux GNU gcc (GCC) 10.2.1 20200723 (Red Hat 10.2.1-1)
- GNU Fortran (GCC) 10.2.1 20200723 (Red Hat 10.2.1)
- (cmake and autotools)
-
- Mac OS X El Capitan 10.11.6 Apple clang version 7.3.0 from Xcode 7.3
- 64-bit gfortran GNU Fortran (GCC) 5.2.0
- (osx1011test) Intel icc/icpc/ifort version 16.0.2
-
- macOS Sierra 10.12.6 Apple LLVM version 9.0.0 (clang-900.39.2)
- 64-bit gfortran GNU Fortran (GCC) 7.4.0
- (kite) Intel icc/icpc/ifort version 17.0.2
-
- macOS High Sierra 10.13.6 Apple LLVM version 10.0.0 (clang-1000.10.44.4)
- 64-bit gfortran GNU Fortran (GCC) 6.3.0
- (bear) Intel icc/icpc/ifort version 19.0.4.233 20190416
-
- SunOS 5.11 11.3 Sun C 5.15 SunOS_sparc
- 32- and 64-bit Sun Fortran 95 8.8 SunOS_sparc
- (emu) Sun C++ 5.15 SunOS_sparc
-
-
-Known Problems
-==============
- CMake files do not behave correctly with paths containing spaces.
- Do not use spaces in paths because the required escaping for handling spaces
- results in very complex and fragile build files.
- ADB - 2019/05/07
-
- At present, metadata cache images may not be generated by parallel
- applications. Parallel applications can read files with metadata cache
- images, but since this is a collective operation, a deadlock is possible
- if one or more processes do not participate.
-
- Two tests fail attempting collective writes with OpenMPI 3.0.0/GCC-7.2.0-2.29:
- testphdf5 (ecdsetw, selnone, cchunk1, cchunk3, cchunk4, and actualio)
- t_shapesame (sscontig2)
-
- CPP ptable test fails on both VS2017 and VS2019 with Intel compiler, JIRA
- issue: HDFFV-10628. This test will pass with VS2015 with Intel compiler.
-
- Known problems in previous releases can be found in the HISTORY*.txt files
- in the HDF5 source. Please report any new problems found to
- help@hdfgroup.org.
-
-
-CMake vs. Autotools installations
-=================================
-While both build systems produce similar results, there are differences.
-Each system produces the same set of folders on linux (only CMake works
-on standard Windows); bin, include, lib and share. Autotools places the
-COPYING and RELEASE.txt file in the root folder, CMake places them in
-the share folder.
-
-The bin folder contains the tools and the build scripts. Additionally, CMake
-creates dynamic versions of the tools with the suffix "-shared". Autotools
-installs one set of tools depending on the "--enable-shared" configuration
-option.
- build scripts
- -------------
- Autotools: h5c++, h5cc, h5fc
- CMake: h5c++, h5cc, h5hlc++, h5hlcc
-
-The include folder holds the header files and the fortran mod files. CMake
-the share folder.
-
-The bin folder contains the tools and the build scripts. Additionally, CMake
-places the fortran mod files into separate shared and static subfolders,
-while Autotools places one set of mod files into the include folder. Because
-CMake produces a tools library, the header files for tools will appear in
-the include folder.
-
-The lib folder contains the library files, and CMake adds the pkgconfig
-subfolder with the hdf5*.pc files used by the bin/build scripts created by
-the CMake build. CMake separates the C interface code from the fortran code by
-creating C-stub libraries for each Fortran library. In addition, only CMake
-installs the tools library. The names of the szip libraries are different
-between the build systems.
-
-The share folder will have the most differences because CMake builds include
-a number of CMake specific files for support of CMake's find_package and support
-for the HDF5 Examples CMake project.
-
-
-
-%%%%1.10.6%%%%
-
-HDF5 version 1.10.6 released on 2019-12-23
-================================================================================
-
-
-INTRODUCTION
-
-This document describes the differences between this release and the previous
-HDF5 release. It contains information on the platforms tested and known
-problems in this release. For more details check the HISTORY*.txt files in the
-HDF5 source.
-
-Note that documentation in the links below will be updated at the time of each
-final release.
-
-Links to HDF5 documentation can be found on The HDF5 web page:
-
- https://portal.hdfgroup.org/display/HDF5/HDF5
-
-The official HDF5 releases can be obtained from:
-
- https://www.hdfgroup.org/downloads/hdf5/
-
-Changes from Release to Release and New Features in the HDF5-1.10.x release series
-can be found at:
-
- https://portal.hdfgroup.org/display/HDF5/HDF5+Application+Developer%27s+Guide
-
-If you have any questions or comments, please send them to the HDF Help Desk:
-
- help@hdfgroup.org
-
-
-CONTENTS
-
-- New Features
-- Support for new platforms and languages
-- Bug Fixes since HDF5-1.10.5
-- Supported Platforms
-- Tested Configuration Features Summary
-- More Tested Platforms
-- Known Problems
-- CMake vs. Autotools installations
-
-
-New Features
-============
-
- Configuration:
- -------------
- - Update CMake for VS2019 support
-
- CMake added support for VS2019 in version 3.15. Changes to the CMake
- generator setting required changes to scripts. Also updated version
- references in CMake files as necessary.
-
- (ADB - 2019/11/18, HDFFV-10962)
-
- - Update CMake options to match new autotools options
-
- Add configure options (autotools - CMake):
- enable-asserts HDF5_ENABLE_ASSERTS
- enable-symbols HDF5_ENABLE_SYMBOLS
- enable-profiling HDF5_ENABLE_PROFILING
- enable-optimization HDF5_ENABLE_OPTIMIZATION
- In addition NDEBUG is no longer forced defined and relies on the CMake
- process.
-
- (ADB - 2019/10/07, HDFFV-100901, HDFFV-10637, TRILAB-97)
-
- - Update CMake tests to use FIXTURES
-
- CMake test fixtures allow setup/cleanup tests and other dependency
- requirements as properties for tests. This is more flexible for
- modern CMake code.
-
- (ADB - 2019/07/23, HDFFV-10529)
-
- - Windows PDB files are always installed
-
- There are build configuration or flag settings for Windows that may not
- generate PDB files. If those files are not generated then the install
- utility will fail because those PDB files are not found. An optional
- variable, DISABLE_PDB_FILES, was added to not install PDB files.
-
- (ADB - 2019/07/17, HDFFV-10424)
-
- - Add mingw CMake support with a toolchain file
-
- There have been a number of mingw issues that have been linked under
- HDFFV-10845. It has been decided to implement the CMake cross-compiling
- technique of toolchain files. We will use a linux platform with the mingw
- compiler stack for testing. Only the C language is fully supported, and
- the error tests are skipped. The C++ language works for static but shared
- builds have a shared library issue with the mingw Standard Exception Handling
- library, which is not available on Windows. Fortran has a common cross-compile
- problem with the fortran configure tests.
-
- (ADB - 2019/07/12, HDFFV-10845, HDFFV-10595)
-
- - Windows PDB files are installed incorrectly
-
- For static builds, the PDB files for windows should be installed next
- to the static libraries in the lib folder. Also the debug versions of
- libraries and PDB files are now correctly built using the default
- CMAKE_DEBUG_POSTFIX setting.
-
- (ADB - 2019/07/09, HDFFV-10581)
-
- - Add option to build only shared libs
-
- A request was made to prevent building static libraries and only build
- shared. A new option was added to CMake, ONLY_SHARED_LIBS, which will
- skip building static libraries. Certain utility functions will build with
- static libs but are not published. Tests are adjusted to use the correct
- libraries depending on SHARED/STATIC settings.
-
- (ADB - 2019/06/12, HDFFV-10805)
-
- - Add options to enable or disable building tools and tests
-
- Configure options --enable-tests and --enable-tools were added for
- autotools configure. These options are enabled by default, and can be
- disabled with either --disable-tests (or tools) or --enable-tests=no
- (or --enable-tools=no). Build time is reduced ~20% when tools are
- disabled, 35% when tests are disabled, 45% when both are disabled.
- Re-enabling them after the initial build requires running configure
- again with the option(s) enabled.
-
- (LRK - 2019/06/12, HDFFV-9976)
-
- - Change tools tests to search the error stack
-
- There are some use cases which can cause the error stack of tools to be
- different then the expected output. These tests now use grepTest.cmake;
- this was changed to allow the error file to be searched for an expected string.
-
- (ADB - 2019/04/15, HDFFV-10741)
-
-
- Library:
- --------
- - Added S3 and HDFS Virtual File Drivers (VFDs) to HDF5
-
- These new VFDs have been introduced in HDF5-1.10.6. Instructions to
- enable them when configuring HDF5 on Linux and Mac may be found at
- https://portal.hdfgroup.org/display/HDF5/Virtual+File+Drivers+-+S3+and+HDFS.
-
- Installing on Windows requires CMake 3.13 and the following additional setup.
- Install openssl library (with dev files);
- from "Shining Light Productions". msi package preferred.
-
- PATH should have been updated with the installation dir.
- set ENV variable OPENSSL_ROOT_DIR to the installation dir.
- set ENV variable OPENSSL_CONF to the cfg file, likely %OPENSSL_ROOT_DIR%\bin\openssl.cfg
- Install libcurl library (with dev files);
- download the latest released version using git: https://github.com/curl/curl.git
-
- Open a Visual Studio Command prompt
- change to the libcurl root folder
- run the "buildconf.bat" batch file
- change to the winbuild directory
- nmake /f Makefile.vc mode=dll MACHINE=x64
- copy libcurl-vc-x64-release-dll-ipv6-sspi-winssl dir to C:\curl (installation dir)
- set ENV variable CURL_ROOT to C:\curl (installation dir)
- update PATH ENV variable to %CURL_ROOT%\bin (installation bin dir).
- the aws credentials file should be in %USERPROFILE%\.aws folder
- set the ENV variable "HDF5_ROS3_TEST_BUCKET_URL=https://s3.us-east-2.amazonaws.com/hdf5ros3"
-
- (ADB - 2019/09/12, HDFFV-10854)
-
- C++ Library:
- ------------
- - Added new wrappers for H5Pset/get_create_intermediate_group()
- LinkCreatPropList::setCreateIntermediateGroup()
- LinkCreatPropList::getCreateIntermediateGroup()
-
- (BMR - 2019/04/22, HDFFV-10622)
-
-
- Java Library:
- ----------------
- - Fixed a failure in JUnit-TestH5P on 32-bit architectures
-
- (JTH - 2019/04/30)
-
-
-Support for new platforms, languages and compilers.
-=======================================
- - CMake added support for VS2019 in version 3.15. Updated scripts.
-
- - macOS 10.13.6 Darwin 17.7.0 with Apple clang LLVM version 10.0.0
-
- - macOS 10.14.6 Darwin 18.7.0 with Apple clang LLVM version 10.0.1
-
-
-Bug Fixes since HDF5-1.10.5 release
-==================================
-
- Library
- -------
- - Improved performance when creating a large number of small datasets by
- retrieving default property values from the API context instead of doing
- skip list searches. More work is required to achieve parity with HDF5 1.8.
-
- (CJH - 2019/12/10, HDFFV-10658)
-
- - Fixed user-created data access properties not existing in the property list
- returned by H5Dget_access_plist. Thanks to Steven Varga for submitting a
- reproducer and a patch.
-
- (CJH - 2019/12/9, HDFFV-10934)
-
- - Inappropriate linking with deprecated MPI C++ libraries
-
- HDF5 does not define *_SKIP_MPICXX in the public headers, so applications
- can inadvertently wind up linking to the deprecated MPI C++ wrappers.
-
- MPICH_SKIP_MPICXX and OMPI_SKIP_MPICXX have both been defined in H5public.h
- so this should no longer be an issue. HDF5 makes no use of the deprecated
- MPI C++ wrappers.
-
- (DER - 2019/09/17, HDFFV-10893)
-
- - fcntl(2)-based file locking incorrectly passed the lock argument struct
- instead of a pointer to the struct, causing errors on systems where
- flock(2) is not available.
-
- File locking is used when files are opened to enforce SWMR semantics. A
- lock operation takes place on all file opens unless the
- HDF5_USE_FILE_LOCKING environment variable is set to the string "FALSE".
- flock(2) is preferentially used, with fcntl(2) locks as a backup if
- flock(2) is unavailable on a system (if neither is available, the lock
- operation fails). On these systems, the file lock will often fail, which
- causes HDF5 to not open the file and report an error.
-
- This bug only affects POSIX systems. Win32 builds on Windows use a no-op
- locking call which always succeeds. Systems which exhibit this bug will
- have H5_HAVE_FCNTL defined but not H5_HAVE_FLOCK in the configure output.
-
- This bug affects HDF5 1.10.0 through 1.10.5.
-
- fcntl(2)-based file locking now correctly passes the struct pointer.
-
- (DER - 2019/08/27, HDFFV-10892)
-
- - Fixed a bug caused by a bad tag value when condensing object header
- messages
-
- There was an assertion failure when moving messages from running a
- user test program with library release HDF5 1.10.4. It was because
- the tag value (object header's address) was not set up when entering
- the library routine H5O__chunk_update_idx(), which eventually
- verifies the metadata tag value when protecting the object header.
-
- The problem was fixed by replacing FUNC_ENTER_PACKAGE in H5O__chunk_update_idx()
- with FUNC_ENTER_PACKAGE_TAG(oh->cache_info.addr) to set up the metadata tag.
-
- (VC - 2019/08/23, HDFFV-10873)
-
- - Fixed the test failure from test_metadata_read_retry_info() in
- test/swmr.c
-
- The test failure is due to an incorrect number of bins returned for
- retry info (info.nbins). The # of bins expected for 101 read attempts
- is 3 instead of 2. The routine H5F_set_retries() in src/H5Fint.c
- calculates the # of bins by first obtaining the log10 value for
- (read attempts - 1). For PGI/19, the log10 value for 100 read attempts
- is 1.9999999999999998 instead of 2.00000. When casting the log10 value
- to unsigned later on, the decimal part is chopped off causing the test
- failure.
-
- This was fixed by obtaining the rounded integer value (HDceil) for the
- log10 value of read attempts first before casting the result to unsigned.
-
- (VC - 2019/8/14, HDFFV-10813)
-
- - Fixed an issue when creating a file with non-default file space info
- together with library high bound setting to H5F_LIBVER_V18.
-
- When setting non-default file space info in fcpl via
- H5Pset_file_space_strategy() and then creating a file with both high and
- low library bounds set to H5F_LIBVER_V18 in fapl, the library succeeds in
- creating the file. File creation should fail because the feature of
- setting non-default file space info does not exist in library release 1.8
- or earlier.
-
- This was fixed by setting and checking the proper version in the file
- space info message based on the library low and high bounds when creating
- and opening the HDF5 file.
-
- (VC - 2019/6/25, HDFFV-10808)
-
- - Fixed an issue where copying a version 1.8 dataset between files using
- H5Ocopy fails due to an incompatible fill version
-
- When using the HDF5 1.10.x H5Ocopy() API call to copy a version 1.8
- dataset to a file created with both high and low library bounds set to
- H5F_LIBVER_V18, the H5Ocopy() call will fail with the error stack indicating
- that the fill value version is out of bounds.
-
- This was fixed by changing the fill value message version to H5O_FILL_VERSION_3
- (from H5O_FILL_VERSION_2) for H5F_LIBVER_V18.
-
- (VC - 2019/6/14, HDFFV-10800)
-
- - Fixed a bug that would cause an error or cause fill values to be
- incorrectly read from a chunked dataset using the "single chunk" index if
- the data was held in cache and there was no data on disk.
-
- (NAF - 2019/03/06)
-
- - Fixed a bug that could cause an error or cause fill values to be
- incorrectly read from a dataset that was written to using H5Dwrite_chunk
- if the dataset was not closed after writing.
-
- (NAF - 2019/03/06, HDFFV-10716)
-
- - Fixed memory leak in scale offset filter
-
- In a special case where the MinBits is the same as the number of bits in
- the datatype's precision, the filter's data buffer was not freed, causing
- the memory usage to grow. In general the buffer was freed correctly. The
- Minbits are the minimal number of bits to store the data values. Please
- see the reference manual for H5Pset_scaleoffset for the details.
-
- (RL - 2019/3/4, HDFFV-10705)
-
-
- Configuration
- -------------
- - Correct option for default API version
-
- CMake options for default API version are not mutually exclusive.
- Change the multiple BOOL options to a single STRING option with the
- strings; v16, v18, v110.
-
- (ADB - 2019/08/12, HDFFV-10879)
-
- Tools
- -----
- - h5repack was fixed to repack datasets with external storage
- to other types of storage.
-
- New test added to repack files and verify the correct data using h5diff.
-
- (JS - 2019/09/25, HDFFV-10408)
- (ADB - 2019/10/02, HDFFV-10918)
-
-
-Supported Platforms
-===================
-
- Linux 2.6.32-696.20.1.el6.ppc64 gcc (GCC) 4.4.7 20120313 (Red Hat 4.4.7-23)
- #1 SMP ppc64 GNU/Linux g++ (GCC) 4.4.7 20120313 (Red Hat 4.4.7-23)
- (ostrich) GNU Fortran (GCC) 4.4.7 20120313 (Red Hat 4.4.7-23)
- IBM XL C/C++ V13.1
- IBM XL Fortran V15.1
-
- Linux 3.10.0-327.10.1.el7 GNU C (gcc), Fortran (gfortran), C++ (g++)
- #1 SMP x86_64 GNU/Linux compilers:
- (jelly/kituo/moohan) Version 4.8.5 20150623 (Red Hat 4.8.5-4)
- Version 4.9.3, Version 5.2.0
- Intel(R) C (icc), C++ (icpc), Fortran (icc)
- compilers:
- Version 17.0.0.098 Build 20160721
- MPICH 3.1.4 compiled with GCC 4.9.3
-
- SunOS 5.11 32- and 64-bit Sun C 5.12 SunOS_sparc
- (emu) Sun Fortran 95 8.6 SunOS_sparc
- Sun C++ 5.12 SunOS_sparc
-
- Windows 7 Visual Studio 2015 w/ Intel Fortran 18 (cmake)
-
- Windows 7 x64 Visual Studio 2015 w/ Intel C, Fortran 2018 (cmake)
- Visual Studio 2015 w/ MSMPI 8 (cmake)
-
- Windows 10 Visual Studio 2015 w/ Intel Fortran 18 (cmake)
-
- Windows 10 x64 Visual Studio 2015 w/ Intel Fortran 18 (cmake)
- Visual Studio 2017 w/ Intel Fortran 19 (cmake)
- Visual Studio 2019 w/ Intel Fortran 19 (cmake)
-
- macOS 10.13.6, Darwin, Apple clang LLVM version 10.0.0
- 17.7.0, x86_64 gfortran GNU Fortran (GCC) 6.3.0
- (bear) Intel icc/icpc/ifort version 19.0.4
-
- macOS 10.14.6, Darwin Apple clang LLVM version 10.0.1
- 18.7.0, x86_64 gfortran GNU Fortran (GCC) 6.3.0
- (bobcat) Intel icc/icpc/ifort version 19.0.4
-
-
-Tested Configuration Features Summary
-=====================================
-
- In the tables below
- y = tested
- n = not tested in this release
- C = Cluster
- W = Workstation
- x = not working in this release
- dna = does not apply
- ( ) = footnote appears below second table
- <blank> = testing incomplete on this feature or platform
-
-Platform C F90/ F90 C++ zlib SZIP
- parallel F2003 parallel
-Solaris2.11 32-bit n y/y n y y y
-Solaris2.11 64-bit n y/n n y y y
-Windows 7 y y/y n y y y
-Windows 7 x64 y y/y y y y y
-Windows 7 Cygwin n y/n n y y y
-Windows 7 x64 Cygwin n y/n n y y y
-Windows 10 y y/y n y y y
-Windows 10 x64 y y/y n y y y
-Mac OS X Yosemite 10.10.5 64-bit n y/y n y y y
-Mac OS X El Capitan 10.11.6 64-bit n y/y n y y y
-MacOS High Sierra 10.13.6 64-bit n y/y n y y y
-CentOS 7.2 Linux 3.10.0 x86_64 PGI n y/y n y y y
-CentOS 7.2 Linux 3.10.0 x86_64 GNU y y/y y y y y
-CentOS 7.2 Linux 3.10.0 x86_64 Intel n y/y n y y y
-Linux 2.6.32-573.18.1.el6.ppc64 n y/y n y y y
-
-
-Platform Shared Shared Shared Thread-
- C libs F90 libs C++ libs safe
-Solaris2.11 32-bit y y y y
-Solaris2.11 64-bit y y y y
-Windows 7 y y y y
-Windows 7 x64 y y y y
-Windows 7 Cygwin n n n y
-Windows 7 x64 Cygwin n n n y
-Windows 10 y y y y
-Windows 10 x64 y y y y
-Mac OS X Yosemite 10.10.5 64-bit y y y y
-Mac OS X El Capitan 10.11.6 64-bit y y y y
-MacOS High Sierra 10.13.6 64-bit y y y y
-CentOS 7.2 Linux 3.10.0 x86_64 PGI y y y n
-CentOS 7.2 Linux 3.10.0 x86_64 GNU y y y y
-CentOS 7.2 Linux 3.10.0 x86_64 Intel y y y n
-Linux 2.6.32-573.18.1.el6.ppc64 y y y n
-
-Compiler versions for each platform are listed in the preceding
-"Supported Platforms" table.
-
-
-More Tested Platforms
-=====================
-The following configurations are not supported but have been tested for this release.
-
- Linux 2.6.32-754.11.1.el6 GNU C (gcc), Fortran (gfortran), C++ (g++)
- #1 SMP x86_64 GNU/Linux compilers:
- (mayll/platypus) Version 4.4.7 20120313
- Version 4.9.3, 5.3.0, 6.2.0
- PGI C, Fortran, C++ for 64-bit target on
- x86-64;
- Version 17.10-0
- Intel(R) C (icc), C++ (icpc), Fortran (icc)
- compilers:
- Version 17.0.4.196 Build 20170411
- MPICH 3.1.4 compiled with GCC 4.9.3
-
- Linux 3.10.0-327.18.2.el7 GNU C (gcc) and C++ (g++) compilers
- #1 SMP x86_64 GNU/Linux Version 4.8.5 20150623 (Red Hat 4.8.5-4)
- (jelly) with NAG Fortran Compiler Release 6.2(Chiyoda)
- GCC Version 7.1.0
- MPICH 3.2-GCC-4.9.3
- MPICH 3.2.1-GCC-7.2.0-2.29
- OpenMPI 2.1.5-GCC-7.2.0-2.29
- Intel(R) C (icc) and C++ (icpc) compilers
- Version 17.0.0.098 Build 20160721
- with NAG Fortran Compiler Release 6.2(Chiyoda)
-
- Linux 3.10.0-327.10.1.el7 MPICH 3.2 compiled with GCC 5.3.0
- #1 SMP x86_64 GNU/Linux
- (moohan)
-
- Linux 2.6.32-573.18.1.el6.ppc64 MPICH mpich 3.1.4 compiled with
- #1 SMP ppc64 GNU/Linux IBM XL C/C++ for Linux, V13.1
- (ostrich) and IBM XL Fortran for Linux, V15.1
-
- Fedora30 5.3.11-200.fc30.x86_64
- #1 SMP x86_64 GNU/Linux GNU gcc (GCC) 9.2.1 20190827 (Red Hat 9.2.1 20190827)
- GNU Fortran (GCC) 9.2.1 20190827 (Red Hat 9.2.1 20190827)
- (cmake and autotools)
-
- Mac OS X 10.11.6, Darwin, Apple clang version 7.3.0 from Xcode 7.3
- 15.6.0, x86-64 gfortran GNU Fortran (GCC) 5.2.0
- (osx1011test) Intel icc/icpc/ifort version 16.0.2
-
- macOS 10.12.6, Darwin, Apple clang LLVM version 8.1.0 from Xcode 8.3
- 16.6.0, x86_64 gfortran GNU Fortran (GCC) 7.1.0
- (kite) Intel icc/icpc/ifort version 17.0.2
-
- Windows 7 x64 Visual Studio 2008
-
-
-Known Problems
-==============
- CMake files do not behave correctly with paths containing spaces.
- Do not use spaces in paths because the required escaping for handling spaces
- results in very complex and fragile build files.
- ADB - 2019/05/07
-
- At present, metadata cache images may not be generated by parallel
- applications. Parallel applications can read files with metadata cache
- images, but since this is a collective operation, a deadlock is possible
- if one or more processes do not participate.
-
- Three tests fail with OpenMPI 3.0.0/GCC-7.2.0-2.29:
- testphdf5 (ecdsetw, selnone, cchunk1, cchunk3, cchunk4, and actualio)
- t_shapesame (sscontig2)
- t_pflush1/fails on exit
- The first two tests fail attempting collective writes.
-
- Parallel builds using OpenMPI 3.03 or later and romio fail several tests
- with collective writes or compression that will not fail when ompio is used
- instead of romio. This can be done by adding "--mca io ompio" to the mpirun
- command. For example, in autotools builds RUNPARALLEL can be set to
- "mpirun --mca io ompio -n 6" provided ompio is installed.
-
- CPP ptable test fails on VS2017 with Intel compiler, JIRA issue: HDFFV-10628.
- This test will pass with VS2015 with Intel compiler.
-
- Older MPI libraries such as OpenMPI 2.0.1 and MPICH 2.1.5 were tested
- while attempting to resolve the Jira issue: HDFFV-10540.
- The known problems of reading or writing > 2GBs when using MPI-2 was
- partially resolved with the MPICH library. The proposed support recognizes
- IO operations > 2GB and if the datatype is not a derived type, the library
- breaks the IO into chunks which can be input or output with the existing
- MPI 2 limitations, i.e. size reporting and function API size/count
- arguments are restricted to be 32 bit integers. For derived types larger
- than 2GB, MPICH 2.1.5 fails while attempting to read or write data.
- OpenMPI in contrast, implements MPI-3 APIs even in the older releases
- and thus does not suffer from the 32 bit size limitation described here.
- OpenMPI releases prior to v3.1.3 appear to have other datatype issues however,
- e.g. within a single parallel test (testphdf5) the subtests (cdsetr, eidsetr)
- report data verification errors before eventually aborting.
- The most recent versions of OpenMPI (v3.1.3 or newer) have evidently
- resolved these issues and parallel HDF5 testing does not currently report
- errors though occasional hangs have been observed.
-
- Known problems in previous releases can be found in the HISTORY*.txt files
- in the HDF5 source. Please report any new problems found to
- help@hdfgroup.org.
-
-
-CMake vs. Autotools installations
-=================================
-While both build systems produce similar results, there are differences.
-Each system produces the same set of folders on linux (only CMake works
-on standard Windows); bin, include, lib and share. Autotools places the
-COPYING and RELEASE.txt file in the root folder, CMake places them in
-the share folder.
-
-The bin folder contains the tools and the build scripts. Additionally, CMake
-creates dynamic versions of the tools with the suffix "-shared". Autotools
-installs one set of tools depending on the "--enable-shared" configuration
-option.
- build scripts
- -------------
- Autotools: h5c++, h5cc, h5fc
- CMake: h5c++, h5cc, h5hlc++, h5hlcc
-
-The include folder holds the header files and the fortran mod files. CMake
-places the fortran mod files into separate shared and static subfolders,
-while Autotools places one set of mod files into the include folder. Because
-CMake produces a tools library, the header files for tools will appear in
-the include folder.
-
-The lib folder contains the library files, and CMake adds the pkgconfig
-subfolder with the hdf5*.pc files used by the bin/build scripts created by
-the CMake build. CMake separates the C interface code from the fortran code by
-creating C-stub libraries for each Fortran library. In addition, only CMake
-installs the tools library. The names of the szip libraries are different
-between the build systems.
-
-The share folder will have the most differences because CMake builds include
-a number of CMake specific files for support of CMake's find_package and support
-for the HDF5 Examples CMake project.
-
-%%%%1.10.5%%%%
-
-HDF5 version 1.10.5 released on 2019-02-25
-================================================================================
-
-
-INTRODUCTION
-
-This document describes the differences between this release and the previous
-HDF5 release. It contains information on the platforms tested and known
-problems in this release. For more details check the HISTORY*.txt files in the
-HDF5 source.
-
-Note that documentation in the links below will be updated at the time of each
-final release.
-
-Links to HDF5 documentation can be found on The HDF5 web page:
-
- https://portal.hdfgroup.org/display/HDF5/HDF5
-
-The official HDF5 releases can be obtained from:
-
- https://www.hdfgroup.org/downloads/hdf5/
-
-Changes from Release to Release and New Features in the HDF5-1.10.x release series
-can be found at:
-
- https://portal.hdfgroup.org/display/HDF5/HDF5+Application+Developer%27s+Guide
-
-If you have any questions or comments, please send them to the HDF Help Desk:
-
- help@hdfgroup.org
-
-
-CONTENTS
-
-- New Features
-- Support for new platforms and languages
-- Bug Fixes since HDF5-1.10.4
-- Supported Platforms
-- Tested Configuration Features Summary
-- More Tested Platforms
-- Known Problems
-- CMake vs. Autotools installations
-
-
-New Features
-============
-
- Configuration:
- -------------
- - Cross compile on mutrino and other Cray XC40 systems.
-
- Added support for CMake options to use CrayLinuxEnvironment, craype-mic-knl
- module for building with craype-haswell module for configuration, and
- batch scripts in bin/batch for use with sbatch or bsub to run tests in
- batch jobs on compute nodes. An instruction file README_HPC describing
- the use of these options was added in release_docs.
-
- (LRK - 2019/02/18, TRILABS-34)
-
- - Rework CMake command files to fix MPI testing.
-
- Added setup fixture to remove any test generated files and added DEPENDS
- to test properties to execute tests in order expected.
-
- (ADB - 2019/02/14, TRILABS-111)
-
- - Disable SZIP or ZLIB options if TGZ files are not available.
-
- Changed the TGZ option for SZip and ZLib to disable the options
- if the source tar.gz files are not found.
-
- (ADB - 2019/02/05, HDFFV-10697)
-
- - Added a new option to enable/disable using pread/pwrite instead of
- read/write in the sec2, log, and core VFDs.
-
- This option is enabled by default when pread/pwrite are detected.
-
- Autotools: --enable-preadwrite
- CMake: HDF5_ENABLE_PREADWRITE
-
- (DER - 2019/02/03, HDFFV-10696)
-
- - Rework CMake versioning for OSX platforms.
-
- Changed the current_version and compatibility_version flags from optional
- with HDF5_BUILD_WITH_INSTALL_NAME to always setting the flags for OSX.
-
- (ADB - 2019/01/22, HDFFV-10685)
-
- - Rework CMake command files to eliminate developer CMP005 warning
-
- Use variables without quotes in if () statements.
-
- (ADB - 2019/01/18, TILABS-105)
-
- - Rework CMake configure files to eliminate developer CMP0075 warning
-
- Renamed varname to HDF5_REQUIRED_LIBRARIES as the contents were not
- required for configuration. Also moved check includes calls to top of
- files.
-
- (ADB - 2019/01/03, HDFFV-10546)
-
- - Keep stderr and stdout separate in tests
-
- Changed test handling of output capture. Tests now keep the stderr
- output separate from the stdout output. It is up to the test to decide
- which output to check against a reference. Also added the option
- to grep for a string in either output.
-
- (ADB - 2018/12/12, HDFFV-10632)
-
- - Incorrectly installed private header files were removed from
- CMake installs.
-
- The CMake build files incorrectly flagged the following header files
- as public and installed them. They are private and will no longer be
- installed.
-
- HDF5 library private package files (H5Xpkg.h)
- H5Edefin.h
- H5Einit.h
- H5Eterm.h
- H5LTparse.h
- h5diff.h
- h5tools_dump.h
- h5tools.h
- h5tools_ref.h
- h5tools_str.h
- h5tools_utils.h
- h5trav.h
-
- (DER - 2018/10/26, HDFFV-10614, 10609)
-
- - Autotools installs now install H5FDwindows.h
-
- This is simply to align the installed header files between the
- autotools and CMake. H5FDwindows.h has no functionality on
- non-Windows systems.
-
- (DER - 2018/10/26, HDFFV-10614)
-
-
- Library:
- --------
- - The sec2, log, and core VFDs can now use pread/pwrite instead of
- read/write.
-
- pread and pwrite do not change the file offset, a feature that was
- requested by a user working with a multi-threaded application.
-
- The option to configure this feature is described above.
-
- (DER - 2019/02/03, HDFFV-10696)
-
- - Add ability to minimize dataset object headers.
-
- Creation of many, very small datasets resulted in extensive file bloat
- due to extra space in the dataset object headers -- this space is
- allocated by default to allow for the insertion of a small number of
- attributes within the object header and not require a continuation
- block, an unnecessary provision in the target use case.
-
- Inform the library to expect no attributes on created datasets, and to
- allocate the least space possible for the object headers.
- NOTE: A continuation block is created if attributes are added to a
- 'minimized' dataset, which can reduce performance.
- NOTE: Some extra space is allocated for attributes essential to the
- correct behavior of the object header (store creation times, e.g.). This
- does not violate the design principle, as the space is calculated and
- allocated as needed at the time of dataset object header creation --
- unused space is not generated.
- New API calls:
- H5Fget_dset_no_attrs_hint
- H5Fset_dset_no_attrs_hint
- H5Pget_dset_no_attrs_hint
- H5Pset_dset_no_attrs_hint
-
- (JOS - 2019/01/04, TRILAB-45)
-
- - Added new chunk query functions
-
- The following public functions were added to discover information about
- the chunks in an HDF5 file.
- herr_t H5Dget_num_chunks(dset_id, fspace_id, *nchunks)
- herr_t H5Dget_chunk_info_by_coord(dset_id, *coord, *filter_mask, *addr, *size)
- herr_t H5Dget_chunk_info(dset_id, fspace_id, index, *coord, *filter_mask, *addr, *size)
-
- (BMR - 2018/11/07, HDFFV-10615)
-
- - Several empty public header files where removed from the distribution
-
- The following files were empty placeholders. They are for internal
- packages that are unlikely to ever have public functionality and have
- thus been removed.
-
- H5Bpublic.h
- H5B2public.h
- H5FSpublic.h
- H5HFpublic.h
- H5HGpublic.h
- H5HLpublic.h
-
- They were only installed in CMake builds.
-
- (DER - 2018/10/26, HDFFV-10614)
-
-
- Parallel Library:
- -----------------
- - Changed the default behavior in parallel when reading the same dataset in its entirety
- (i.e. H5S_ALL dataset selection) which is being read by all the processes collectively.
- The dataset must be contiguous, less than 2GB, and of an atomic datatype.
- The new behavior is the HDF5 library will use an MPI_Bcast to pass the data read from
- the disk by the root process to the remain processes in the MPI communicator associated
- with the HDF5 file.
-
- (MSB - 2019/01/02, HDFFV-10652)
-
- - All MPI-1 API calls have been replaced with MPI-2 equivalents.
-
- This was done to better support OpenMPI, as default builds no longer
- include MPI-1 support (as of OpenMPI 4.0).
-
- (DER - 2018/12/30, HDFFV-10566)
-
- Fortran Library:
- ----------------
- - Added wrappers for dataset object header minimization calls.
- (see the note for TRILAB-45, above)
-
- New API calls:
-
- h5fget_dset_no_attrs_hint_f
- h5fset_dset_no_attrs_hint_f
- h5pget_dset_no_attrs_hint_f
- h5pset_dset_no_attrs_hint_f
-
- (DER - 2019/01/09, TRILAB-45)
-
- - Added new Fortran derived type, c_h5o_info_t, which is interoperable with
- C's h5o_info_t. This is needed for callback functions which
- pass C's h5o_info_t data type definition.
-
- (MSB, 2019/01/08, HDFFV-10443)
-
- - Added new Fortran API, H5gmtime, which converts (C) 'time_t' structure
- to Fortran DATE AND TIME storage format.
-
- (MSB, 2019/01/08, HDFFV-10443)
-
- - Added new Fortran 'fields' optional parameter to: h5ovisit_f, h5oget_info_by_name_f,
- h5oget_info, h5oget_info_by_idx and h5ovisit_by_name_f.
-
- (MSB, 2019/01/08, HDFFV-10443)
-
- C++ Library:
- ------------
- - Added new function to the C++ interface
-
- Added wrapper for H5Ovisit2:
- H5Object::visit()
-
- (BMR - 2019/02/14, HDFFV-10532)
-
-
- Java Library:
- ----------------
- - Rewrote the JNI error handling to be much cleaner
-
- (JTH - 2019/02/12)
-
- - Add new functions to java interface
-
- Added wrappers for:
- H5Fset_libver_bounds
- H5Fget_dset_no_attrs_hint/H5Fset_dset_no_attrs_hint
- H5Pget_dset_no_attrs_hint/H5Pset_dset_no_attrs_hint
-
- (ADB - 2019/01/07, HDFFV-10664)
-
- - Fix java unit tests when Time is a natural number
-
- Time substitution in java/test/junit.sh.in doesn't
- handle the case when Time is a natural number. Fixed
- the regular expression.
-
- (ADB - 2019/01/07, HDFFV-10674)
-
- - Duplicate the data read/write functions of Datasets for Attributes.
-
- Region references could not be displayed for attributes as they could
- for datasets. Datasets had overloaded read and write functions for different
- datatypes that were not available for attributes. After adding similar
- functions, attribute region references work normally.
-
- (ADB - 2018/12/12, HDFVIEW-4)
-
-
- Tools:
- ------
- - The h5repart -family-to-sec2 argument was changed to -family-to-single
-
- In order to better support other single-file VFDs which could work with
- h5repart, the -family-to-sec2 argument was renamed to -family-to-single.
- This is just a name change and the functionality of the argument has not
- changed.
-
- The -family-to-sec2 argument has been kept for backwards-compatibility.
- This argument should be considered deprecated.
-
- (DER - 2018/11/14, HDFFV-10633)
-
-
-Bug Fixes since HDF5-1.10.4 release
-==================================
-
- Library
- -------
- - Fix hangs with collective metadata reads during chunked dataset I/O
-
- In the parallel library, it was discovered that when a particular
- sequence of operations following a pattern of:
-
- "write to chunked dataset" -> "flush file" -> "read from dataset"
-
- occurred with collective metadata reads enabled, hangs could be
- observed due to certain MPI ranks not participating in the collective
- metadata reads.
-
- To fix the issue, collective metadata reads are now disabled during
- chunked dataset raw data I/O.
-
- (JTH - 2019/02/11, HDFFV-10563, HDFFV-10688)
-
- - Performance issue when closing an object
-
- The slow down is due to the search of the "tag_list" to find
- out the "corked" status of an object and "uncork" it if so.
-
- Improve performance by skipping the search of the "tag_list"
- if there are no "corked" objects when closing an object.
-
- (VC - 2019/02/06)
-
- - Uninitialized bytes from a type conversion buffer could be written
- to disk in H5Dwrite calls where type conversion takes place
- and the type conversion buffer was created by the HDF5 library.
-
- When H5Dwrite is called and datatype conversion must be performed,
- the library will create a temporary buffer for type conversion if
- one is not provided by the user via H5Pset_buffer. This internal
- buffer is allocated via malloc and contains uninitialized data. In
- some datatype conversions (float to long double, possibly others),
- some of this uninitialized data could be written to disk.
-
- This was flagged by valgrind in the dtransform test and does not
- appear to be a common occurrence (it is flagged in one test out
- of the entire HDF5 test suite).
-
- Switching to calloc fixed the problem.
-
- (DER - 2019/02/03, HDFFV-10694)
-
- - There was missing protection against division by zero reported to
- The HDF Group as issue #CVE-2018-17434.
-
- Protection against division by zero was added to address the issue
- #CVE-2018-17434.
-
- (BMR - 2019/01/29, HDFFV-10586)
-
- - The issue CVE-2018-17437 was reported to The HDF Group
-
- Although CVE-2018-17437 reported a memory leak, the actual issue
- was invalid read. It was found that the attribute name length
- in an attribute message was corrupted, which caused the buffer
- pointer to be advanced too far and later caused an invalid read.
-
- A check was added to detect when the attribute name or its length
- was corrupted and report the potential of data corruption.
-
- (BMR - 2019/01/29, HDFFV-10588)
-
- - H5Ewalk did not stop when it was supposed to
-
- H5Ewalk was supposed to stop when the callback function stopped
- even though the errors in the stack were not all visited, but it
- did not. This problem is now fixed.
-
- (BMR - 2019/01/29, HDFFV-10684)
-
- - Revert H5Oget_info* and H5Ovisit* functions
-
- In 1.10.3 new H5Oget_info*2 and H5Ovisit*2 functions were
- added for performance. Inadvertently, the original functions;
- H5Oget_info,
- H5Oget_info_by_name,
- H5Oget_info_by_idx,
- H5Ovisit,
- H5Ovisit_by_name
- were versioned to H5Oget_info*1 and H5Ovisit*1. This
- broke the API compatibility for a maintenance release. The
- original functions have been restored.
-
- (ADB - 2019/01/24, HDFFV-10686)
-
- - Fixed a potential invalid memory access and failure that could occur when
- decoding an unknown object header message (from a future version of the
- library).
-
- (NAF - 2019/01/07)
-
- - Deleting attributes in dense storage
-
- The library aborts with "infinite loop closing library" after
- attributes in dense storage are created and then deleted.
-
- When deleting the attribute nodes from the name index v2 B-tree,
- if an attribute is found in the intermediate B-tree nodes,
- which may be merged/redistributed in the process, we need to
- free the dynamically allocated spaces for the intermediate
- decoded attribute.
-
- (VC - 2018/12/26, HDFFV-10659)
-
- - There was missing protection against division by zero reported to
- The HDF Group as issue #CVE-2018-17233.
-
- Protection against division by zero was added to address the issue
- #CVE-2018-17233. In addition, several similar occurrences in the same
- file were fixed as well.
-
- (BMR - 2018/12/23, HDFFV-10577)
-
- - Fixed an issue where the parallel filters tests would fail
- if zlib was not available on the system. Until support can
- be added in the tests for filters beyond gzip/zlib, the tests
- will be skipped if zlib is not available.
-
- (JTH - 2018/12/05)
-
- - A bug was discovered in the parallel library where an application
- would eventually consume all of the available MPI communicators
- when continually writing to a compressed dataset in parallel. This
- was due to internal copies of an HDF5 File Access Property List,
- which each contained a copy of the MPI communicator, not being
- closed at the end of each write operation. This problem was
- exacerbated by larger numbers of processors.
-
- (JTH - 2018/12/05, HDFFV-10629)
-
-
- Fortran
- --------
- - Fixed issue with Fortran not returning h5o_info_t field values
- meta_size%attr%index_size and meta_size%attr%heap_size.
-
- (MSB, 2019/01/08, HDFFV-10443)
-
- - Added symbolic links libhdf5_hl_fortran.so to libhdf5hl_fortran.so and
- libhdf5_hl_fortran.a to libhdf5hl_fortran.a in hdf5/lib directory for
- autotools installs. These were added to match the name of the files
- installed by cmake and the general pattern of hl lib files. We will
- change the names of the installed lib files to the matching name in
- the next major release.
-
- (LRK - 2019/01/04, HDFFV-10596)
-
- - Made Fortran specific subroutines PRIVATE in generic procedures.
-
- Affected generic procedures were functions in H5A, H5D, H5P, H5R and H5T.
-
- (MSB, 2018/12/04, HDFFV-10511)
-
-
- Testing
- -------
- - Fixed a test failure in testpar/t_dset.c caused by
- the test trying to use the parallel filters feature
- on MPI-2 implementations.
-
- (JTH, 2019/2/7)
-
-
-Supported Platforms
-===================
-
- Linux 2.6.32-696.16.1.el6.ppc64 gcc (GCC) 4.4.7 20120313 (Red Hat 4.4.7-18)
- #1 SMP ppc64 GNU/Linux g++ (GCC) 4.4.7 20120313 (Red Hat 4.4.7-18)
- (ostrich) GNU Fortran (GCC) 4.4.7 20120313 (Red Hat 4.4.7-18)
- IBM XL C/C++ V13.1
- IBM XL Fortran V15.1
-
- Linux 3.10.0-327.10.1.el7 GNU C (gcc), Fortran (gfortran), C++ (g++)
- #1 SMP x86_64 GNU/Linux compilers:
- (kituo/moohan) Version 4.8.5 20150623 (Red Hat 4.8.5-4)
- Version 4.9.3, Version 5.2.0
- Intel(R) C (icc), C++ (icpc), Fortran (icc)
- compilers:
- Version 17.0.0.098 Build 20160721
- MPICH 3.1.4 compiled with GCC 4.9.3
-
- SunOS 5.11 32- and 64-bit Sun C 5.12 SunOS_sparc
- (emu) Sun Fortran 95 8.6 SunOS_sparc
- Sun C++ 5.12 SunOS_sparc
-
- Windows 7 Visual Studio 2015 w/ Intel Fortran 16 (cmake)
-
- Windows 7 x64 Visual Studio 2013
- Visual Studio 2015 w/ Intel Fortran 16 (cmake)
- Visual Studio 2015 w/ Intel C, Fortran 2018 (cmake)
- Visual Studio 2015 w/ MSMPI 8 (cmake)
-
- Windows 10 Visual Studio 2015 w/ Intel Fortran 18 (cmake)
-
- Windows 10 x64 Visual Studio 2015 w/ Intel Fortran 18 (cmake)
- Visual Studio 2017 w/ Intel Fortran 18 (cmake)
-
- Mac OS X Yosemite 10.10.5 Apple clang/clang++ version 6.1 from Xcode 7.0
- 64-bit gfortran GNU Fortran (GCC) 4.9.2
- (osx1010dev/osx1010test) Intel icc/icpc/ifort version 15.0.3
-
- Mac OS X El Capitan 10.11.6 Apple clang/clang++ version 7.3.0 from Xcode 7.3
- 64-bit gfortran GNU Fortran (GCC) 5.2.0
- (osx1011dev/osx1011test) Intel icc/icpc/ifort version 16.0.2
-
- MacOS High Sierra 10.13.6 Apple LLVM version 10.0.0 (clang/clang++-1000.10.44.4)
- 64-bit gfortran GNU Fortran (GCC) 8.3.0
-
-
-Tested Configuration Features Summary
-=====================================
-
- In the tables below
- y = tested
- n = not tested in this release
- C = Cluster
- W = Workstation
- x = not working in this release
- dna = does not apply
- ( ) = footnote appears below second table
- <blank> = testing incomplete on this feature or platform
-
-Platform C F90/ F90 C++ zlib SZIP
- parallel F2003 parallel
-Solaris2.11 32-bit n y/y n y y y
-Solaris2.11 64-bit n y/n n y y y
-Windows 7 y y/y n y y y
-Windows 7 x64 y y/y y y y y
-Windows 7 Cygwin n y/n n y y y
-Windows 7 x64 Cygwin n y/n n y y y
-Windows 10 y y/y n y y y
-Windows 10 x64 y y/y n y y y
-Mac OS X Yosemite 10.10.5 64-bit n y/y n y y y
-Mac OS X El Capitan 10.11.6 64-bit n y/y n y y y
-MacOS High Sierra 10.13.6 64-bit n y/y n y y y
-CentOS 7.2 Linux 3.10.0 x86_64 PGI n y/y n y y y
-CentOS 7.2 Linux 3.10.0 x86_64 GNU y y/y y y y y
-CentOS 7.2 Linux 3.10.0 x86_64 Intel n y/y n y y y
-Linux 2.6.32-573.18.1.el6.ppc64 n y/y n y y y
-
-
-Platform Shared Shared Shared Thread-
- C libs F90 libs C++ libs safe
-Solaris2.11 32-bit y y y y
-Solaris2.11 64-bit y y y y
-Windows 7 y y y y
-Windows 7 x64 y y y y
-Windows 7 Cygwin n n n y
-Windows 7 x64 Cygwin n n n y
-Windows 10 y y y y
-Windows 10 x64 y y y y
-Mac OS X Yosemite 10.10.5 64-bit y y y y
-Mac OS X El Capitan 10.11.6 64-bit y y y y
-MacOS High Sierra 10.13.6 64-bit y y y y
-CentOS 7.2 Linux 3.10.0 x86_64 PGI y y y n
-CentOS 7.2 Linux 3.10.0 x86_64 GNU y y y y
-CentOS 7.2 Linux 3.10.0 x86_64 Intel y y y n
-Linux 2.6.32-573.18.1.el6.ppc64 y y y n
-
-Compiler versions for each platform are listed in the preceding
-"Supported Platforms" table.
-
-
-More Tested Platforms
-=====================
-The following configurations are not supported but have been tested for this release.
-
- Linux 2.6.32-573.22.1.el6 GNU C (gcc), Fortran (gfortran), C++ (g++)
- #1 SMP x86_64 GNU/Linux compilers:
- (mayll/platypus) Version 4.4.7 20120313
- Version 4.9.3, 5.3.0, 6.2.0
- PGI C, Fortran, C++ for 64-bit target on
- x86-64;
- Version 17.10-0
- Intel(R) C (icc), C++ (icpc), Fortran (icc)
- compilers:
- Version 17.0.4.196 Build 20170411
- MPICH 3.1.4 compiled with GCC 4.9.3
-
- Linux 3.10.0-327.18.2.el7 GNU C (gcc) and C++ (g++) compilers
- #1 SMP x86_64 GNU/Linux Version 4.8.5 20150623 (Red Hat 4.8.5-4)
- (jelly) with NAG Fortran Compiler Release 6.1(Tozai)
- GCC Version 7.1.0
- MPICH 3.2-GCC-4.9.3
- MPICH 3.2.1-GCC-7.2.0-2.29
- OpenMPI 2.1.5-GCC-7.2.0-2.29
- Intel(R) C (icc) and C++ (icpc) compilers
- Version 17.0.0.098 Build 20160721
- with NAG Fortran Compiler Release 6.1(Tozai)
-
- Linux 3.10.0-327.10.1.el7 MPICH 3.2 compiled with GCC 5.3.0
- #1 SMP x86_64 GNU/Linux
- (moohan)
-
- Fedora 29 4.20.10-200.fc29.x86_64 #1 SMP x86_64 x86_64 x86_64 GNU/Linux
- gcc, g++ (GCC) 8.2.1 20181215
- (Red Hat 8.2.1-6)
- GNU Fortran (GCC) 8.2.1 20181215
- (Red Hat 8.2.1-6)
- (cmake and autotools)
-
- Windows 7 x64 Visual Studio 2008
-
-
-Known Problems
-==============
-
- At present, metadata cache images may not be generated by parallel
- applications. Parallel applications can read files with metadata cache
- images, but since this is a collective operation, a deadlock is possible
- if one or more processes do not participate.
-
- Three tests fail with OpenMPI 3.0.0/GCC-7.2.0-2.29:
- testphdf5 (ecdsetw, selnone, cchunk1, cchunk3, cchunk4, and actualio)
- t_shapesame (sscontig2)
- t_pflush1/fails on exit
- The first two tests fail attempting collective writes.
-
- CPP ptable test fails on VS2017 with Intel compiler, JIRA issue: HDFFV-10628.
- This test will pass with VS2015 with Intel compiler.
-
- Older MPI libraries such as OpenMPI 2.0.1 and MPICH 2.1.5 were tested
- while attempting to resolve the Jira issue: HDFFV-10540.
- The known problems of reading or writing > 2GBs when using MPI-2 was
- partially resolved with the MPICH library. The proposed support recognizes
- IO operations > 2GB and if the datatype is not a derived type, the library
- breaks the IO into chunks which can be input or output with the existing
- MPI 2 limitations, i.e. size reporting and function API size/count
- arguments are restricted to be 32 bit integers. For derived types larger
- than 2GB, MPICH 2.1.5 fails while attempting to read or write data.
- OpenMPI in contrast, implements MPI-3 APIs even in the older releases
- and thus does not suffer from the 32 bit size limitation described here.
- OpenMPI releases prior to v3.1.3 appear to have other datatype issues however,
- e.g. within a single parallel test (testphdf5) the subtests (cdsetr, eidsetr)
- report data verification errors before eventually aborting.
- The most recent versions of OpenMPI (v3.1.3 or newer) have evidently
- resolved these issues and parallel HDF5 testing does not currently report
- errors though occasional hangs have been observed.
-
- Known problems in previous releases can be found in the HISTORY*.txt files
- in the HDF5 source. Please report any new problems found to
- help@hdfgroup.org.
-
-
-CMake vs. Autotools installations
-=================================
-While both build systems produce similar results, there are differences.
-Each system produces the same set of folders on linux (only CMake works
-on standard Windows); bin, include, lib and share. Autotools places the
-COPYING and RELEASE.txt file in the root folder, CMake places them in
-the share folder.
-
-The bin folder contains the tools and the build scripts. Additionally, CMake
-creates dynamic versions of the tools with the suffix "-shared". Autotools
-installs one set of tools depending on the "--enable-shared" configuration
-option.
- build scripts
- -------------
- Autotools: h5c++, h5cc, h5fc
- CMake: h5c++, h5cc, h5hlc++, h5hlcc
-
-The include folder holds the header files and the fortran mod files. CMake
-places the fortran mod files into separate shared and static subfolders,
-while Autotools places one set of mod files into the include folder. Because
-CMake produces a tools library, the header files for tools will appear in
-the include folder.
-
-The lib folder contains the library files, and CMake adds the pkgconfig
-subfolder with the hdf5*.pc files used by the bin/build scripts created by
-the CMake build. CMake separates the C interface code from the fortran code by
-creating C-stub libraries for each Fortran library. In addition, only CMake
-installs the tools library. The names of the szip libraries are different
-between the build systems.
-
-The share folder will have the most differences because CMake builds include
-a number of CMake specific files for support of CMake's find_package and support
-for the HDF5 Examples CMake project.
-
-%%%%1.10.4%%%%
-
-HDF5 version 1.10.4 released on 2018-10-05
-================================================================================
-
-
-INTRODUCTION
-
-This document describes the differences between this release and the previous
-HDF5 release. It contains information on the platforms tested and known
-problems in this release. For more details check the HISTORY*.txt files in the
-HDF5 source.
-
-Note that documentation in the links below will be updated at the time of each
-final release.
-
-Links to HDF5 documentation can be found on The HDF5 web page:
-
- https://portal.hdfgroup.org/display/HDF5/HDF5
-
-The official HDF5 releases can be obtained from:
-
- https://www.hdfgroup.org/downloads/hdf5/
-
-Changes from Release to Release and New Features in the HDF5-1.10.x release series
-can be found at:
-
- https://portal.hdfgroup.org/display/HDF5/HDF5+Application+Developer%27s+Guide
-
-If you have any questions or comments, please send them to the HDF Help Desk:
-
- help@hdfgroup.org
-
-
-CONTENTS
-
-- Bug Fixes since HDF5-1.10.3
-- Supported Platforms
-- Tested Configuration Features Summary
-- More Tested Platforms
-- Known Problems
-- CMake vs. Autotools installations
-
-
-New Features
-============
-
- Configuration:
- -------------
- - Add toolchain and cross-compile support
-
- Added info on using a toolchain file to INSTALL_CMAKE.txt. A
- toolchain file is also used in cross-compiling, which requires
- CMAKE_CROSSCOMPILING_EMULATOR to be set. To help with cross-compiling
- the fortran configure process, the HDF5UseFortran.cmake file macros
- were improved. Fixed a Fortran configure file issue that incorrectly
- used #cmakedefine instead of #define.
-
- (ADB - 2018/10/04, HDFFV-10594)
-
- - Add warning flags for Intel compilers
-
- Identified Intel compiler specific warnings flags that should be used
- instead of GNU flags.
-
- (ADB - 2018/10/04, TRILABS-21)
-
- - Add default rpath to targets
-
- Default rpaths should be set in shared executables and
- libraries to allow the use of loading dependent libraries
- without requiring LD_LIBRARY_PATH to be set. The default
- path should be relative using @rpath on osx and $ORIGIN
- on linux. Windows is not affected.
-
- (ADB - 2018/09/26, HDFFV-10594)
-
- Library:
- --------
- - Allow pre-generated H5Tinit.c and H5make_libsettings.c to be used.
-
- Rather than always running H5detect and generating H5Tinit.c and
- H5make_libsettings.c, supply a location for those files.
-
- (ADB - 2018/09/18, HDFFV-10332)
-
-
-Bug Fixes since HDF5-1.10.3 release
-==================================
-
- Library
- -------
- - Allow H5detect and H5make_libsettings to take a file as an argument.
-
- Rather than only writing to stdout, add a command argument to name
- the file that H5detect and H5make_libsettings will use for output.
- Without an argument, stdout is still used, so backwards compatibility
- is maintained.
-
- (ADB - 2018/09/05, HDFFV-9059)
-
- - A bug was discovered in the parallel library where an application
- would hang if a collective read/write of a chunked dataset occurred
- when collective metadata reads were enabled and some of the ranks
- had no selection in the dataset's dataspace. The ranks which had no
- selection in the dataset's dataspace called H5D__chunk_addrmap() to
- retrieve the lowest chunk address in the dataset. This is because we
- require reads/writes to be performed in strictly non-decreasing order
- of chunk address in the file.
-
- When the chunk index used was a version 1 or 2 B-tree, these
- non-participating ranks would issue a collective MPI_Bcast() call
- that the participating ranks would not issue, causing the hang. Since
- the non-participating ranks are not actually reading/writing anything,
- the H5D__chunk_addrmap() call can be safely removed and the address used
- for the read/write can be set to an arbitrary number (0 was chosen).
-
- (JTH - 2018/08/25, HDFFV-10501)
-
- Java Library:
- ----------------
- - JNI native library dependencies
-
- The build for the hdf5_java native library used the wrong
- hdf5 target library for CMake builds. Correcting the hdf5_java
- library to build with the shared hdf5 library required testing
- paths to change also.
-
- (ADB - 2018/08/31, HDFFV-10568)
-
- - Java iterator callbacks
-
- Change global callback object to a small stack structure in order
- to fix a runtime crash. This crash was discovered when iterating
- through a file with nested group members. The global variable
- visit_callback is overwritten when recursion starts. When recursion
- completes, visit_callback will be pointing to the wrong callback method.
-
- (ADB - 2018/08/15, HDFFV-10536)
-
- - Java HDFLibraryException class
-
- Change parent class from Exception to RuntimeException.
-
- (ADB - 2018/07/30, HDFFV-10534)
-
- - JNI Read and Write
-
- Refactored variable-length functions, H5DreadVL and H5AreadVL,
- to correct dataset and attribute reads. New write functions,
- H5DwriteVL and H5AwriteVL, are under construction.
-
- (ADB - 2018/06/02, HDFFV-10519)
-
-
-Supported Platforms
-===================
-
- Linux 2.6.32-696.16.1.el6.ppc64 gcc (GCC) 4.4.7 20120313 (Red Hat 4.4.7-18)
- #1 SMP ppc64 GNU/Linux g++ (GCC) 4.4.7 20120313 (Red Hat 4.4.7-18)
- (ostrich) GNU Fortran (GCC) 4.4.7 20120313 (Red Hat 4.4.7-18)
- IBM XL C/C++ V13.1
- IBM XL Fortran V15.1
-
- Linux 3.10.0-327.10.1.el7 GNU C (gcc), Fortran (gfortran), C++ (g++)
- #1 SMP x86_64 GNU/Linux compilers:
- (kituo/moohan) Version 4.8.5 20150623 (Red Hat 4.8.5-4)
- Version 4.9.3, Version 5.2.0
- Intel(R) C (icc), C++ (icpc), Fortran (icc)
- compilers:
- Version 17.0.0.098 Build 20160721
- MPICH 3.1.4 compiled with GCC 4.9.3
-
- SunOS 5.11 32- and 64-bit Sun C 5.12 SunOS_sparc
- (emu) Sun Fortran 95 8.6 SunOS_sparc
- Sun C++ 5.12 SunOS_sparc
-
- Windows 7 Visual Studio 2015 w/ Intel Fortran 16 (cmake)
-
- Windows 7 x64 Visual Studio 2012 w/ Intel Fortran 15 (cmake)
- Visual Studio 2013 w/ Intel Fortran 15 (cmake)
- Visual Studio 2015 w/ Intel Fortran 16 (cmake)
- Visual Studio 2015 w/ Intel C, Fortran 2017 (cmake)
- Visual Studio 2015 w/ MSMPI 8 (cmake)
-
- Windows 10 Visual Studio 2015 w/ Intel Fortran 18 (cmake)
-
- Windows 10 x64 Visual Studio 2015 w/ Intel Fortran 18 (cmake)
- Visual Studio 2017 w/ Intel Fortran 18 (cmake)
-
- Mac OS X Yosemite 10.10.5 Apple clang/clang++ version 6.1 from Xcode 7.0
- 64-bit gfortran GNU Fortran (GCC) 4.9.2
- (osx1010dev/osx1010test) Intel icc/icpc/ifort version 15.0.3
-
- Mac OS X El Capitan 10.11.6 Apple clang/clang++ version 7.3.0 from Xcode 7.3
- 64-bit gfortran GNU Fortran (GCC) 5.2.0
- (osx1011dev/osx1011test) Intel icc/icpc/ifort version 16.0.2
-
- Mac OS Sierra 10.12.6 Apple LLVM version 8.1.0 (clang/clang++-802.0.42)
- 64-bit gfortran GNU Fortran (GCC) 7.1.0
- (kite) Intel icc/icpc/ifort version 17.0.2
-
-
-Tested Configuration Features Summary
-=====================================
-
- In the tables below
- y = tested
- n = not tested in this release
- C = Cluster
- W = Workstation
- x = not working in this release
- dna = does not apply
- ( ) = footnote appears below second table
- <blank> = testing incomplete on this feature or platform
-
-Platform C F90/ F90 C++ zlib SZIP
- parallel F2003 parallel
-Solaris2.11 32-bit n y/y n y y y
-Solaris2.11 64-bit n y/n n y y y
-Windows 7 y y/y n y y y
-Windows 7 x64 y y/y y y y y
-Windows 7 Cygwin n y/n n y y y
-Windows 7 x64 Cygwin n y/n n y y y
-Windows 10 y y/y n y y y
-Windows 10 x64 y y/y n y y y
-Mac OS X Mavericks 10.9.5 64-bit n y/y n y y y
-Mac OS X Yosemite 10.10.5 64-bit n y/y n y y y
-Mac OS X El Capitan 10.11.6 64-bit n y/y n y y y
-Mac OS Sierra 10.12.6 64-bit n y/y n y y y
-CentOS 7.2 Linux 3.10.0 x86_64 PGI n y/y n y y y
-CentOS 7.2 Linux 3.10.0 x86_64 GNU y y/y y y y y
-CentOS 7.2 Linux 3.10.0 x86_64 Intel n y/y n y y y
-Linux 2.6.32-573.18.1.el6.ppc64 n y/y n y y y
-
-
-Platform Shared Shared Shared Thread-
- C libs F90 libs C++ libs safe
-Solaris2.11 32-bit y y y y
-Solaris2.11 64-bit y y y y
-Windows 7 y y y y
-Windows 7 x64 y y y y
-Windows 7 Cygwin n n n y
-Windows 7 x64 Cygwin n n n y
-Windows 10 y y y y
-Windows 10 x64 y y y y
-Mac OS X Mavericks 10.9.5 64-bit y n y y
-Mac OS X Yosemite 10.10.5 64-bit y n y y
-Mac OS X El Capitan 10.11.6 64-bit y n y y
-Mac OS Sierra 10.12.6 64-bit y n y y
-CentOS 7.2 Linux 3.10.0 x86_64 PGI y y y n
-CentOS 7.2 Linux 3.10.0 x86_64 GNU y y y y
-CentOS 7.2 Linux 3.10.0 x86_64 Intel y y y n
-Linux 2.6.32-573.18.1.el6.ppc64 y y y n
-
-Compiler versions for each platform are listed in the preceding
-"Supported Platforms" table.
-
-
-More Tested Platforms
-=====================
-The following platforms are not supported but have been tested for this release.
-
- Linux 2.6.32-573.22.1.el6 GNU C (gcc), Fortran (gfortran), C++ (g++)
- #1 SMP x86_64 GNU/Linux compilers:
- (mayll/platypus) Version 4.4.7 20120313
- Version 4.9.3, 5.3.0, 6.2.0
- PGI C, Fortran, C++ for 64-bit target on
- x86-64;
- Version 17.10-0
- Intel(R) C (icc), C++ (icpc), Fortran (icc)
- compilers:
- Version 17.0.4.196 Build 20170411
- MPICH 3.1.4 compiled with GCC 4.9.3
-
- Linux 3.10.0-327.18.2.el7 GNU C (gcc) and C++ (g++) compilers
- #1 SMP x86_64 GNU/Linux Version 4.8.5 20150623 (Red Hat 4.8.5-4)
- (jelly) with NAG Fortran Compiler Release 6.1(Tozai)
- GCC Version 7.1.0
- OpenMPI 3.0.0-GCC-7.2.0-2.29,
- 3.1.0-GCC-7.2.0-2.29
- Intel(R) C (icc) and C++ (icpc) compilers
- Version 17.0.0.098 Build 20160721
- with NAG Fortran Compiler Release 6.1(Tozai)
-
- Linux 3.10.0-327.10.1.el7 MPICH 3.2 compiled with GCC 5.3.0
- #1 SMP x86_64 GNU/Linux
- (moohan)
-
- Linux 2.6.32-573.18.1.el6.ppc64 MPICH mpich 3.1.4 compiled with
- #1 SMP ppc64 GNU/Linux IBM XL C/C++ for Linux, V13.1
- (ostrich) and IBM XL Fortran for Linux, V15.1
-
- Debian 8.4 3.16.0-4-amd64 #1 SMP Debian 3.16.36-1 x86_64 GNU/Linux
- gcc, g++ (Debian 4.9.2-10) 4.9.2
- GNU Fortran (Debian 4.9.2-10) 4.9.2
- (cmake and autotools)
-
- Fedora 24 4.7.2-201.fc24.x86_64 #1 SMP x86_64 x86_64 x86_64 GNU/Linux
- gcc, g++ (GCC) 6.1.1 20160621
- (Red Hat 6.1.1-3)
- GNU Fortran (GCC) 6.1.1 20160621
- (Red Hat 6.1.1-3)
- (cmake and autotools)
-
- Ubuntu 16.04.1 4.4.0-38-generic #57-Ubuntu SMP x86_64 GNU/Linux
- gcc, g++ (Ubuntu 5.4.0-6ubuntu1~16.04.2)
- 5.4.0 20160609
- GNU Fortran (Ubuntu 5.4.0-6ubuntu1~16.04.2)
- 5.4.0 20160609
- (cmake and autotools)
-
-
-Known Problems
-==============
-
- At present, metadata cache images may not be generated by parallel
- applications. Parallel applications can read files with metadata cache
- images, but since this is a collective operation, a deadlock is possible
- if one or more processes do not participate.
-
- Three tests fail with OpenMPI 3.0.0/GCC-7.2.0-2.29:
- testphdf5 (ecdsetw, selnone, cchunk1, cchunk3, cchunk4, and actualio)
- t_shapesame (sscontig2)
- t_pflush1/fails on exit
- The first two tests fail attempting collective writes.
-
- Known problems in previous releases can be found in the HISTORY*.txt files
- in the HDF5 source. Please report any new problems found to
- help@hdfgroup.org.
-
-
-CMake vs. Autotools installations
-=================================
-While both build systems produce similar results, there are differences.
-Each system produces the same set of folders on linux (only CMake works
-on standard Windows); bin, include, lib and share. Autotools places the
-COPYING and RELEASE.txt file in the root folder, CMake places them in
-the share folder.
-
-The bin folder contains the tools and the build scripts. Additionally, CMake
-creates dynamic versions of the tools with the suffix "-shared". Autotools
-installs one set of tools depending on the "--enable-shared" configuration
-option.
- build scripts
- -------------
- Autotools: h5c++, h5cc, h5fc
- CMake: h5c++, h5cc, h5hlc++, h5hlcc
-
-The include folder holds the header files and the fortran mod files. CMake
-places the fortran mod files into separate shared and static subfolders,
-while Autotools places one set of mod files into the include folder. Because
-CMake produces a tools library, the header files for tools will appear in
-the include folder.
-
-The lib folder contains the library files, and CMake adds the pkgconfig
-subfolder with the hdf5*.pc files used by the bin/build scripts created by
-the CMake build. CMake separates the C interface code from the fortran code by
-creating C-stub libraries for each Fortran library. In addition, only CMake
-installs the tools library. The names of the szip libraries are different
-between the build systems.
-
-The share folder will have the most differences because CMake builds include
-a number of CMake specific files for support of CMake's find_package and support
-for the HDF5 Examples CMake project.
-
-%%%%1.10.3%%%%
-
-HDF5 version 1.10.3 released on 2018-08-21
-================================================================================
-
-
-INTRODUCTION
-
-This document describes the differences between this release and the previous
-HDF5 release. It contains information on the platforms tested and known
-problems in this release. For more details check the HISTORY*.txt files in the
-HDF5 source.
-
-Note that documentation in the links below will be updated at the time of each
-final release.
-
-Links to HDF5 documentation can be found on The HDF5 web page:
-
- https://portal.hdfgroup.org/display/HDF5/HDF5
-
-The official HDF5 releases can be obtained from:
-
- https://www.hdfgroup.org/downloads/hdf5/
-
-Changes from Release to Release and New Features in the HDF5-1.10.x release series
-can be found at:
-
- https://portal.hdfgroup.org/display/HDF5/HDF5+Application+Developer%27s+Guide
-
-If you have any questions or comments, please send them to the HDF Help Desk:
-
- help@hdfgroup.org
-
-
-CONTENTS
-
-- New Features
-- Bug Fixes since HDF5-1.10.2
-- Supported Platforms
-- Tested Configuration Features Summary
-- More Tested Platforms
-- Known Problems
-- CMake vs. Autotools installations
-
-
-New Features
-============
-
- Library
- -------
- - Moved the H5DOread/write_chunk() API calls to H5Dread/write_chunk()
-
- The functionality of the direct chunk I/O calls in the high-level
- library has been moved to the H5D package in the main library. This
- will allow using those functions without building the high-level
- library. The parameters and functionality of the H5D calls are
- identical to the H5DO calls.
-
- The original H5DO high-level API calls have been retained, though
- they are now just wrappers for the H5D calls. They are marked as
- deprecated and are only available when the library is built with
- deprecated functions. New code should use the H5D calls for this
- reason.
-
- As a part of this work, the following symbols from H5Dpublic.h are no
- longer used:
-
- H5D_XFER_DIRECT_CHUNK_WRITE_FLAG_NAME
- H5D_XFER_DIRECT_CHUNK_WRITE_FILTERS_NAME
- H5D_XFER_DIRECT_CHUNK_WRITE_OFFSET_NAME
- H5D_XFER_DIRECT_CHUNK_WRITE_DATASIZE_NAME
- H5D_XFER_DIRECT_CHUNK_READ_FLAG_NAME
- H5D_XFER_DIRECT_CHUNK_READ_OFFSET_NAME
- H5D_XFER_DIRECT_CHUNK_READ_FILTERS_NAME
-
- And properties with these names are no longer stored in the dataset
- transfer property lists. The symbols are still defined in H5Dpublic.h,
- but only when the library is built with deprecated symbols.
-
- (DER - 2018/05/04)
-
- Configuration:
- -------------
- - Add missing USE_110_API_DEFAULT option.
-
- Option USE_110_API_DEFAULT sets the default version of
- versioned APIs. The bin/makevers perl script did not set
- the maxidx variable correctly when the 1.10 branch was
- created. This caused the versioning process to always use
- the latest version of any API.
-
- (ADB - 2018/08/17, HDFFV-10552)
-
- - Added configuration checks for the following MPI functions:
-
- MPI_Mprobe - Used for the Parallel Compression feature
- MPI_Imrecv - Used for the Parallel Compression feature
-
- MPI_Get_elements_x - Used for the "big Parallel I/O" feature
- MPI_Type_size_x - Used for the "big Parallel I/O" feature
-
- (JTH - 2018/08/02, HDFFV-10512)
-
- - Added section to the libhdf5.settings file to indicate
- the status of the Parallel Compression and "big Parallel I/O"
- features.
-
- (JTH - 2018/08/02, HDFFV-10512)
-
- - Add option to execute swmr shell scripts from CMake.
-
- Option TEST_SHELL_SCRIPTS redirects processing into a
- separate ShellTests.cmake file for UNIX types. The tests
- execute the shell scripts if a SH program is found.
-
- (ADB - 2018/07/16)
-
-
- C++ Library:
- ------------
- - New wrappers
-
- Added the following items:
-
- + Class DSetAccPropList for the dataset access property list.
-
- + Wrapper for H5Dget_access_plist to class DataSet
- // Gets the access property list of this dataset.
- DSetAccPropList getAccessPlist() const;
-
- + Wrappers for H5Pset_chunk_cache and H5Pget_chunk_cache to class DSetAccPropList
- // Sets the raw data chunk cache parameters.
- void setChunkCache(size_t rdcc_nslots, size_t rdcc_nbytes, double rdcc_w0)
-
- // Retrieves the raw data chunk cache parameters.
- void getChunkCache(size_t &rdcc_nslots, size_t &rdcc_nbytes, double &rdcc_w0)
-
- + New operator!= to class DataType (HDFFV-10472)
- // Determines whether two datatypes are not the same.
- bool operator!=(const DataType& compared_type)
-
- + Wrappers for H5Oget_info2, H5Oget_info_by_name2, and H5Oget_info_by_idx2
- (HDFFV-10458)
-
- // Retrieves information about an HDF5 object.
- void getObjinfo(H5O_info_t& objinfo, unsigned fields = H5O_INFO_BASIC) const;
-
- // Retrieves information about an HDF5 object, given its name.
- void getObjinfo(const char* name, H5O_info_t& objinfo,
- unsigned fields = H5O_INFO_BASIC,
- const LinkAccPropList& lapl = LinkAccPropList::DEFAULT) const;
- void getObjinfo(const H5std_string& name, H5O_info_t& objinfo,
- unsigned fields = H5O_INFO_BASIC,
- const LinkAccPropList& lapl = LinkAccPropList::DEFAULT) const;
-
- // Retrieves information about an HDF5 object, given its index.
- void getObjinfo(const char* grp_name, H5_index_t idx_type,
- H5_iter_order_t order, hsize_t idx, H5O_info_t& objinfo,
- unsigned fields = H5O_INFO_BASIC,
- const LinkAccPropList& lapl = LinkAccPropList::DEFAULT) const;
- void getObjinfo(const H5std_string& grp_name, H5_index_t idx_type,
- H5_iter_order_t order, hsize_t idx, H5O_info_t& objinfo,
- unsigned fields = H5O_INFO_BASIC,
- const LinkAccPropList& lapl = LinkAccPropList::DEFAULT) const;
-
- (BMR - 2018/07/22, HDFFV-10150, HDFFV-10458, HDFFV-1047)
-
-
- Java Library:
- ----------------
- - Java HDFLibraryException class
-
- Change parent class from Exception to RuntimeException.
-
- (ADB - 2018/07/30, HDFFV-10534)
-
- - JNI Read and Write
-
- Refactored variable-length functions, H5DreadVL and H5AreadVL,
- to correct dataset and attribute reads. New write functions,
- H5DwriteVL and H5AwriteVL, are under construction.
-
- (ADB - 2018/06/02, HDFFV-10519)
-
-
-Bug Fixes since HDF5-1.10.2 release
-==================================
-
- Library
- -------
- - Performance issue with H5Oget_info
-
- H5Oget_info family of routines retrieves information for an object such
- as object type, access time, number of attributes, and storage space etc.
- Retrieving all such information regardless is an overkill and causes
- performance issue when doing so for many objects.
-
- Add an additional parameter "fields" to the the H5Oget_info family of routines
- indicating the type of information to be retrieved. The same is done to
- the H5Ovisit family of routines which recursively visits an object
- returning object information in a callback function. Both sets of routines
- are versioned and the corresponding compatibility macros are added.
-
- The version 2 names of the two sets of routines are:
- (1) H5Oget_info2, H5Oget_info_by_idx2, H5Oget_info_by_name2
- (2) H5Ovisit2, H5Ovisit_by_name2
-
- (VC - 2018/08/15, HDFFV-10180)
-
- - Test failure due to metadata size in test/vds.c
-
- The size of metadata from test_api_get_ex_dcpl() in test/vds.c is not as expected
- because the latest format should be used when encoding the layout for VDS.
-
- Set the latest format in a temporary fapl and pass the setting to the routines that
- encode the dataset selection for VDS.
-
- (VC - 2018/08/14 HDFFV-10469)
-
- - Java HDF5LibraryException class
-
- The error minor and major values would be lost after the
- constructor executed.
-
- Created two local class variables to hold the values obtained during
- execution of the constructor. Refactored the class functions to retrieve
- the class values rather then calling the native functions.
- The native functions were renamed and called only during execution
- of the constructor.
- Added error checking to calling class constructors in JNI classes.
-
- (ADB - 2018/08/06, HDFFV-10544)
-
- - Added checks of the defined MPI_VERSION to guard against usage of
- MPI-3 functions in the Parallel Compression and "big Parallel I/O"
- features when HDF5 is built with MPI-2. Previously, the configure
- step would pass but the build itself would fail when it could not
- locate the MPI-3 functions used.
-
- As a result of these new checks, HDF5 can again be built with MPI-2,
- but the Parallel Compression feature will be disabled as it relies
- on the MPI-3 functions used.
-
- (JTH - 2018/08/02, HDFFV-10512)
-
- - User's patches: CVEs
-
- The following patches have been applied:
-
- CVE-2018-11202 - NULL pointer dereference was discovered in
- H5S_hyper_make_spans in H5Shyper.c (HDFFV-10476)
- https://security-tracker.debian.org/tracker/CVE-2018-11202
- https://cve.mitre.org/cgi-bin/cvename.cgi?name=3DCVE-2018-11202
-
- CVE-2018-11203 - A division by zero was discovered in
- H5D__btree_decode_key in H5Dbtree.c (HDFFV-10477)
- https://security-tracker.debian.org/tracker/CVE-2018-11203
- https://cve.mitre.org/cgi-bin/cvename.cgi?name=3DCVE-2018-11203
-
- CVE-2018-11204 - A NULL pointer dereference was discovered in
- H5O__chunk_deserialize in H5Ocache.c (HDFFV-10478)
- https://security-tracker.debian.org/tracker/CVE-2018-11204
- https://cve.mitre.org/cgi-bin/cvename.cgi?name=3DCVE-2018-11204
-
- CVE-2018-11206 - An out of bound read was discovered in
- H5O_fill_new_decode and H5O_fill_old_decode in H5Ofill.c
- (HDFFV-10480)
- https://security-tracker.debian.org/tracker/CVE-2018-11206
- https://cve.mitre.org/cgi-bin/cvename.cgi?name=3DCVE-2018-11206
-
- CVE-2018-11207 - A division by zero was discovered in
- H5D__chunk_init in H5Dchunk.c (HDFFV-10481)
- https://security-tracker.debian.org/tracker/CVE-2018-11207
- https://cve.mitre.org/cgi-bin/cvename.cgi?name=3DCVE-2018-11207
-
- (BMR - 2018/7/22, PR#s: 1134 and 1139,
- HDFFV-10476, HDFFV-10477, HDFFV-10478, HDFFV-10480, HDFFV-10481)
-
- - H5Adelete
-
- H5Adelete failed when deleting the last "large" attribute that
- is stored densely via fractal heap/v2 b-tree.
-
- After removing the attribute, update the ainfo message. If the
- number of attributes goes to zero, remove the message.
-
- (VC - 2018/07/20, HDFFV-9277)
-
- - A bug was discovered in the parallel library which caused partial
- parallel reads of filtered datasets to return incorrect data. The
- library used the incorrect dataspace for each chunk read, causing
- the selection used in each chunk to be wrong.
-
- The bug was not caught during testing because all of the current
- tests which do parallel reads of filtered data read all of the data
- using an H5S_ALL selection. Several tests were added which exercise
- partial parallel reads.
-
- (JTH - 2018/07/16, HDFFV-10467)
-
- - A bug was discovered in the parallel library which caused parallel
- writes of filtered datasets to trigger an assertion failure in the
- file free space manager.
-
- This occurred when the filter used caused chunks to repeatedly shrink
- and grow over the course of several dataset writes. The previous chunk
- information, such as the size of the chunk and the offset in the file,
- was being cached and not updated after each write, causing the next write
- to the chunk to retrieve the incorrect cached information and run into
- issues when reallocating space in the file for the chunk.
-
- (JTH - 2018/07/16, HDFFV-10509)
-
- - A bug was discovered in the parallel library which caused the
- H5D__mpio_array_gatherv() function to allocate too much memory.
-
- When the function is called with the 'allgather' parameter set
- to a non-true value, the function will receive data from all MPI
- ranks and gather it to the single rank specified by the 'root'
- parameter. However, the bug in the function caused memory for
- the received data to be allocated on all MPI ranks, not just the
- singular rank specified as the receiver. In some circumstances,
- this would cause an application to fail due to the large amounts
- of memory being allocated.
-
- (JTH - 2018/07/16, HDFFV-10467)
-
- - Error checks in h5stat and when decoding messages
-
- h5stat exited with seg fault/core dumped when
- errors are encountered in the internal library.
-
- Add error checks and --enable-error-stack option to h5stat.
- Add range checks when decoding messages: old fill value, old
- layout and refcount.
-
- (VC - 2018/07/11, HDFFV-10333)
-
- - If an HDF5 file contains a malformed compound datatype with a
- suitably large offset, the type conversion code can run off
- the end of the type conversion buffer, causing a segmentation
- fault.
-
- This issue was reported to The HDF Group as issue #CVE-2017-17507.
-
- NOTE: The HDF5 C library cannot produce such a file. This condition
- should only occur in a corrupt (or deliberately altered) file
- or a file created by third-party software.
-
- THE HDF GROUP WILL NOT FIX THIS BUG AT THIS TIME
-
- Fixing this problem would involve updating the publicly visible
- H5T_conv_t function pointer typedef and versioning the API calls
- which use it. We normally only modify the public API during
- major releases, so this bug will not be fixed at this time.
-
- (DER - 2018/02/26, HDFFV-10356)
-
-
- Configuration
- -------------
- - Applied patches to address Cywin build issues
-
- There were three issues for Cygwin builds:
- - Shared libs were not built.
- - The -std=c99 flag caused a SIG_SETMASK undeclared error.
- - Undefined errors when buildbing test shared libraries.
-
- Patches to address these issues were received and incorporated in this version.
-
- (LRK - 2018/07/18, HDFFV-10475)
-
- - The --enable-debug/production configure flags are listed as 'deprecated'
- when they should really be listed as 'removed'.
-
- In the autotools overhaul several years ago, we removed these flags and
- implemented a new --enable-build-mode= flag. This was done because we
- changed the semantics of the modes and didn't want users to silently
- be exposed to them. The newer system is also more flexible and us to
- add other modes (like 'clean').
-
- The --enable-debug/production flags are now listed as removed.
-
- (DER - 2018/05/31, HDFFV-10505)
-
- - Moved the location of gcc attribute.
-
- The gcc attribute(no_sanitize), named as the macro HDF_NO_UBSAN,
- was located after the function name. Builds with GCC 7 did not
- indicate any problem, but GCC 8 issued errors. Moved the
- attribute before the function name, as required.
-
- (ADB - 2018/05/22, HDFFV-10473)
-
- - Reworked java test suite into individual JUnit tests.
-
- Testing the whole suite of java unit tests in a single JUnit run
- made it difficult to determine actual failures when tests would fail.
- Running each file set of tests individually, allows individual failures
- to be diagnosed easier. A side benefit is that tests for optional components
- of the library can be disabled if not configured.
-
- (ADB - 2018/05/16, HDFFV-9739)
-
- - Converted CMake global commands ADD_DEFINITIONS and INCLUDE_DIRECTORIES
- to use target_* type commands. This change modernizes the CMake usage
- in the HDF5 library.
-
- In addition, there is the intention to convert to generator expressions,
- where possible. The exception is Fortran FLAGS on Windows Visual Studio.
- The HDF macros TARGET_C_PROPERTIES and TARGET_FORTRAN_PROPERTIES have
- been removed with this change in usage.
-
- The additional language (C++ and Fortran) checks have also been localized
- to only be checked when that language is enabled.
-
- (ADB - 2018/05/08)
-
-
- Performance
- -------------
- - Revamped internal use of DXPLs, improving performance
-
- (QAK - 2018/05/20)
-
-
- Fortran
- --------
- - Fixed issue with h5fget_obj_count_f and using a file id of H5F_OBJ_ALL_F not
- returning the correct count.
-
- (MSB - 2018/5/15, HDFFV-10405)
-
-
- C++ APIs
- --------
- - Adding default arguments to existing functions
-
- Added the following items:
- + Two more property list arguments are added to H5Location::createDataSet:
- const DSetAccPropList& dapl = DSetAccPropList::DEFAULT
- const LinkCreatPropList& lcpl = LinkCreatPropList::DEFAULT
-
- + One more property list argument is added to H5Location::openDataSet:
- const DSetAccPropList& dapl = DSetAccPropList::DEFAULT
-
- (BMR - 2018/07/21, PR# 1146)
-
- - Improvement C++ documentation
-
- Replaced the table in main page of the C++ documentation from mht to htm format
- for portability.
-
- (BMR - 2018/07/17, PR# 1141)
-
-
-Supported Platforms
-===================
-
- Linux 2.6.32-696.16.1.el6.ppc64 gcc (GCC) 4.4.7 20120313 (Red Hat 4.4.7-18)
- #1 SMP ppc64 GNU/Linux g++ (GCC) 4.4.7 20120313 (Red Hat 4.4.7-18)
- (ostrich) GNU Fortran (GCC) 4.4.7 20120313 (Red Hat 4.4.7-18)
- IBM XL C/C++ V13.1
- IBM XL Fortran V15.1
-
- Linux 3.10.0-327.10.1.el7 GNU C (gcc), Fortran (gfortran), C++ (g++)
- #1 SMP x86_64 GNU/Linux compilers:
- (kituo/moohan) Version 4.8.5 20150623 (Red Hat 4.8.5-4)
- Version 4.9.3, Version 5.2.0
- Intel(R) C (icc), C++ (icpc), Fortran (icc)
- compilers:
- Version 17.0.0.098 Build 20160721
- MPICH 3.1.4 compiled with GCC 4.9.3
-
- SunOS 5.11 32- and 64-bit Sun C 5.12 SunOS_sparc
- (emu) Sun Fortran 95 8.6 SunOS_sparc
- Sun C++ 5.12 SunOS_sparc
-
- Windows 7 Visual Studio 2015 w/ Intel Fortran 16 (cmake)
-
- Windows 7 x64 Visual Studio 2012 w/ Intel Fortran 15 (cmake)
- Visual Studio 2013 w/ Intel Fortran 15 (cmake)
- Visual Studio 2015 w/ Intel Fortran 16 (cmake)
- Visual Studio 2015 w/ Intel C, Fortran 2017 (cmake)
- Visual Studio 2015 w/ MSMPI 8 (cmake)
-
- Windows 10 Visual Studio 2015 w/ Intel Fortran 18 (cmake)
-
- Windows 10 x64 Visual Studio 2015 w/ Intel Fortran 18 (cmake)
- Visual Studio 2017 w/ Intel Fortran 18 (cmake)
-
- Mac OS X Yosemite 10.10.5 Apple clang/clang++ version 6.1 from Xcode 7.0
- 64-bit gfortran GNU Fortran (GCC) 4.9.2
- (osx1010dev/osx1010test) Intel icc/icpc/ifort version 15.0.3
-
- Mac OS X El Capitan 10.11.6 Apple clang/clang++ version 7.3.0 from Xcode 7.3
- 64-bit gfortran GNU Fortran (GCC) 5.2.0
- (osx1011dev/osx1011test) Intel icc/icpc/ifort version 16.0.2
-
- Mac OS Sierra 10.12.6 Apple LLVM version 8.1.0 (clang/clang++-802.0.42)
- 64-bit gfortran GNU Fortran (GCC) 7.1.0
- (swallow/kite) Intel icc/icpc/ifort version 17.0.2
-
-Tested Configuration Features Summary
-=====================================
-
- In the tables below
- y = tested
- n = not tested in this release
- C = Cluster
- W = Workstation
- x = not working in this release
- dna = does not apply
- ( ) = footnote appears below second table
- <blank> = testing incomplete on this feature or platform
-
-Platform C F90/ F90 C++ zlib SZIP
- parallel F2003 parallel
-Solaris2.11 32-bit n y/y n y y y
-Solaris2.11 64-bit n y/n n y y y
-Windows 7 y y/y n y y y
-Windows 7 x64 y y/y y y y y
-Windows 7 Cygwin n y/n n y y y
-Windows 7 x64 Cygwin n y/n n y y y
-Windows 10 y y/y n y y y
-Windows 10 x64 y y/y n y y y
-Mac OS X Mavericks 10.9.5 64-bit n y/y n y y y
-Mac OS X Yosemite 10.10.5 64-bit n y/y n y y y
-Mac OS X El Capitan 10.11.6 64-bit n y/y n y y y
-Mac OS Sierra 10.12.6 64-bit n y/y n y y y
-CentOS 7.2 Linux 2.6.32 x86_64 PGI n y/y n y y y
-CentOS 7.2 Linux 2.6.32 x86_64 GNU y y/y y y y y
-CentOS 7.2 Linux 2.6.32 x86_64 Intel n y/y n y y y
-Linux 2.6.32-573.18.1.el6.ppc64 n y/y n y y y
-
-
-Platform Shared Shared Shared Thread-
- C libs F90 libs C++ libs safe
-Solaris2.11 32-bit y y y y
-Solaris2.11 64-bit y y y y
-Windows 7 y y y y
-Windows 7 x64 y y y y
-Windows 7 Cygwin n n n y
-Windows 7 x64 Cygwin n n n y
-Windows 10 y y y y
-Windows 10 x64 y y y y
-Mac OS X Mavericks 10.9.5 64-bit y n y y
-Mac OS X Yosemite 10.10.5 64-bit y n y y
-Mac OS X El Capitan 10.11.6 64-bit y n y y
-Mac OS Sierra 10.12.6 64-bit y n y y
-CentOS 7.2 Linux 2.6.32 x86_64 PGI y y y n
-CentOS 7.2 Linux 2.6.32 x86_64 GNU y y y y
-CentOS 7.2 Linux 2.6.32 x86_64 Intel y y y n
-Linux 2.6.32-573.18.1.el6.ppc64 y y y n
-
-Compiler versions for each platform are listed in the preceding
-"Supported Platforms" table.
-
-
-More Tested Platforms
-=====================
-The following platforms are not supported but have been tested for this release.
-
- Linux 2.6.32-573.22.1.el6 GNU C (gcc), Fortran (gfortran), C++ (g++)
- #1 SMP x86_64 GNU/Linux compilers:
- (mayll/platypus) Version 4.4.7 20120313
- Version 4.9.3, 5.3.0, 6.2.0
- PGI C, Fortran, C++ for 64-bit target on
- x86-64;
- Version 17.10-0
- Intel(R) C (icc), C++ (icpc), Fortran (icc)
- compilers:
- Version 17.0.4.196 Build 20170411
- MPICH 3.1.4 compiled with GCC 4.9.3
-
- Linux 3.10.0-327.18.2.el7 GNU C (gcc) and C++ (g++) compilers
- #1 SMP x86_64 GNU/Linux Version 4.8.5 20150623 (Red Hat 4.8.5-4)
- (jelly) with NAG Fortran Compiler Release 6.1(Tozai)
- GCC Version 7.1.0
- OpenMPI 3.0.0-GCC-7.2.0-2.29,
- 3.1.0-GCC-7.2.0-2.29
- Intel(R) C (icc) and C++ (icpc) compilers
- Version 17.0.0.098 Build 20160721
- with NAG Fortran Compiler Release 6.1(Tozai)
-
- Linux 3.10.0-327.10.1.el7 MPICH 3.2 compiled with GCC 5.3.0
- #1 SMP x86_64 GNU/Linux
- (moohan)
-
- Linux 2.6.32-573.18.1.el6.ppc64 MPICH mpich 3.1.4 compiled with
- #1 SMP ppc64 GNU/Linux IBM XL C/C++ for Linux, V13.1
- (ostrich) and IBM XL Fortran for Linux, V15.1
-
- Debian 8.4 3.16.0-4-amd64 #1 SMP Debian 3.16.36-1 x86_64 GNU/Linux
- gcc, g++ (Debian 4.9.2-10) 4.9.2
- GNU Fortran (Debian 4.9.2-10) 4.9.2
- (cmake and autotools)
-
- Fedora 24 4.7.2-201.fc24.x86_64 #1 SMP x86_64 x86_64 x86_64 GNU/Linux
- gcc, g++ (GCC) 6.1.1 20160621
- (Red Hat 6.1.1-3)
- GNU Fortran (GCC) 6.1.1 20160621
- (Red Hat 6.1.1-3)
- (cmake and autotools)
-
- Ubuntu 16.04.1 4.4.0-38-generic #57-Ubuntu SMP x86_64 GNU/Linux
- gcc, g++ (Ubuntu 5.4.0-6ubuntu1~16.04.2)
- 5.4.0 20160609
- GNU Fortran (Ubuntu 5.4.0-6ubuntu1~16.04.2)
- 5.4.0 20160609
- (cmake and autotools)
-
-
-Known Problems
-==============
-
- At present, metadata cache images may not be generated by parallel
- applications. Parallel applications can read files with metadata cache
- images, but since this is a collective operation, a deadlock is possible
- if one or more processes do not participate.
-
- Three tests fail with OpenMPI 3.0.0/GCC-7.2.0-2.29:
- testphdf5 (ecdsetw, selnone, cchunk1, cchunk3, cchunk4, and actualio)
- t_shapesame (sscontig2)
- t_pflush1/fails on exit
- The first two tests fail attempting collective writes.
-
- Known problems in previous releases can be found in the HISTORY*.txt files
- in the HDF5 source. Please report any new problems found to
- help@hdfgroup.org.
-
-
-CMake vs. Autotools installations
-=================================
-While both build systems produce similar results, there are differences.
-Each system produces the same set of folders on linux (only CMake works
-on standard Windows); bin, include, lib and share. Autotools places the
-COPYING and RELEASE.txt file in the root folder, CMake places them in
-the share folder.
-
-The bin folder contains the tools and the build scripts. Additionally, CMake
-creates dynamic versions of the tools with the suffix "-shared". Autotools
-installs one set of tools depending on the "--enable-shared" configuration
-option.
- build scripts
- -------------
- Autotools: h5c++, h5cc, h5fc
- CMake: h5c++, h5cc, h5hlc++, h5hlcc
-
-The include folder holds the header files and the fortran mod files. CMake
-places the fortran mod files into separate shared and static subfolders,
-while Autotools places one set of mod files into the include folder. Because
-CMake produces a tools library, the header files for tools will appear in
-the include folder.
-
-The lib folder contains the library files, and CMake adds the pkgconfig
-subfolder with the hdf5*.pc files used by the bin/build scripts created by
-the CMake build. CMake separates the C interface code from the fortran code by
-creating C-stub libraries for each Fortran library. In addition, only CMake
-installs the tools library. The names of the szip libraries are different
-between the build systems.
-
-The share folder will have the most differences because CMake builds include
-a number of CMake specific files for support of CMake's find_package and support
-for the HDF5 Examples CMake project.
-
-
-%%%%1.10.2%%%%
-
-HDF5 version 1.10.2 released on 2018-03-29
-================================================================================
-
-
-INTRODUCTION
-
-This document describes the differences between this release and the previous
-HDF5 release. It contains information on the platforms tested and known
-problems in this release. For more details check the HISTORY*.txt files in the
-HDF5 source.
-
-Note that documentation in the links below will be updated at the time of each
-final release.
-
-Links to HDF5 documentation can be found on The HDF5 web page:
-
- https://portal.hdfgroup.org/display/HDF5/HDF5
-
-The official HDF5 releases can be obtained from:
-
- https://www.hdfgroup.org/downloads/hdf5/
-
-Changes from Release to Release and New Features in the HDF5-1.10.x release series
-can be found at:
-
- https://portal.hdfgroup.org/display/HDF5/HDF5+Application+Developer%27s+Guide
-
-If you have any questions or comments, please send them to the HDF Help Desk:
-
- help@hdfgroup.org
-
-
-CONTENTS
-
-- New Features
-- Support for new platforms and languages
-- Bug Fixes since HDF5-1.10.1
-- Supported Platforms
-- Tested Configuration Features Summary
-- More Tested Platforms
-- Known Problems
-
-
-New Features
-============
-
- Configuration and Build Systems:
- --------------------------------
- - CMake builds
- --------------
-
- - Changed minimum CMake required version to 3.10.
-
- This change removed the need to support a copy of the FindMPI.cmake module,
- which has been removed, along with its subfolder in the config/cmake_ext_mod
- location.
-
- (ADB - 2018/03/09)
-
- - Added pkg-config file generation
-
- Added pkg-config file generation for the C, C++, HL, and HL C++ libraries.
- In addition, builds on Linux will create h5cc, h5c++, h5hlcc, and h5hlc++ scripts in the bin
- directory that use the pkg-config files. The scripts can be used to build HDF5 C and C++
- applications (i.e, similar to the compiler scripts produced by the Autotools builds).
-
- (ADB - 2018/03/08, HDFFV-4359)
-
- - Refactored use of CMAKE_BUILD_TYPE for new variable, which understands
- the type of generator in use.
-
- Added new configuration macros to use new HDF_BUILD_TYPE variable. This
- variable is set correctly for the type of generator being used for the build.
-
- (ADB - 2018/01/08, HDFFV-10385, HDFFV-10296)
-
- - Autotools builds
- ------------------
-
- - Removed version-specific gcc/gfortran flags for version 4.0 (inclusive)
- and earlier.
-
- The config/gnu-flags file, which is sourced as a part of the configure
- process, adds version-specific flags for use when building HDF5. Most of
- these flags control warnings and do not affect the final product.
-
- Flags for older versions of the compiler were consolidated into the
- common flags section. Moving these flags simplifies maintenance of
- the file.
-
- The upshot of this is that building with ancient versions of gcc
- (<= 4.0) will possibly no longer work without hand-hacking the file
- to remove the flags not understood by that version of the compiler.
- Nothing should change when building with gcc >= 4.1.
-
- (DER - 2017/05/31, HDFFV-9937)
-
- - -fno-omit-frame-pointer was added when building with debugging symbols
- enabled.
-
- Debugging symbols can be enabled independently of the overall build
- mode in both the autotools and CMake. This allows (limited) debugging
- of optimized code. Since many debuggers rely on the frame pointer,
- we've disabled this optimization when debugging symbols are requested
- (e.g.: via building with --enable-symbols).
-
- (DER - 2017/05/31, HDFFV-10226)
-
-
- Library:
- --------
- - Added an enumerated value to H5F_libver_t for H5Pset_libver_bounds().
-
- Currently, the library defines two values for H5F_libver_t and supports
- only two pairs of (low, high) combinations as derived from these values.
- Thus the bounds setting via H5Pset_libver_bounds() is rather restricted.
-
- Added an enumerated value (H5F_LIBVER_V18) to H5F_libver_t and
- H5Pset_libver_bounds() now supports five pairs of (low, high) combinations
- as derived from these values. This addition provides the user more
- flexibility in setting bounds for object creation.
-
- (VC - 2018/03/14)
-
- - Added prefix option to VDS files.
-
- Currently, VDS source files must be in the active directory to be
- found by the virtual file. Adding the option of a prefix to be set
- on the virtual file, using a data access property list (DAPL),
- allows the source files to locate at an absolute or relative path
- to the virtual file.
- Private utility functions in H5D and H5L packages merged into single
- function in H5F package.
-
- New public APIs:
- herr_t H5Pset_virtual_prefix(hid_t dapl_id, const char* prefix);
- ssize_t H5Pget_virtual_prefix(hid_t dapl_id, char* prefix /*out*/, size_t size);
- The prefix can also be set with an environment variable, HDF5_VDS_PREFIX.
-
- (ADB - 2017/12/12, HDFFV-9724, HDFFV-10361)
-
- - H5FDdriver_query() API call added to the C library.
-
- This new library call allows the user to query a virtual file driver
- (VFD) for the feature flags it supports (listed in H5FDpublic.h).
- This can be useful to determine if a VFD supports SWMR, for example.
-
- Note that some VFDs have feature flags that may only be present
- after a file has been created or opened (e.g.: the core VFD will
- have the H5FD_FEAT_POSIX_COMPAT_HANDLE flag set if the backing
- store is switched on). Since the new API call queries a generic VFD
- unassociated with a file, these flags will never be returned.
-
- (DER - 2017/05/31, HDFFV-10215)
-
- - H5FD_FEAT_DEFAULT_VFD_COMPATIBLE VFD feature flag added to the C library.
-
- This new feature flag indicates that the VFD is compatible with the
- default VFD. VFDs that set this flag create single files that follow
- the canonical HDF5 file format.
-
- (DER - 2017/05/31, HDFFV-10214)
-
- - The H5I_REFERENCE value in the H5I_type_t enum (defined in H5Ipublic.h)
- has been marked as deprecated.
-
- This ID type value is not used in the C library. i.e.: There are no
- hid_t values that are of ID type H5I_REFERENCE.
-
- This enum value will be removed in a future major version of the library.
- The code will remain unchanged in the HDF5 1.10.x releases and branches.
-
- (DER - 2017/04/05, HDFFV-10252)
-
-
- Parallel Library:
- -----------------
- - Enabled compression for parallel applications.
-
- With this release parallel applications can create and write compressed
- datasets (or the datasets with the filters such as Fletcher32 applied).
-
- (EIP - 2018/03/29)
-
- - Addressed slow file close on some Lustre file systems.
-
- Slow file close has been reported on some Lustre file systems.
- While the ultimate cause is not understood fully, the proximate
- cause appears to be long delays in MPI_File_set_size() calls at
- file close and flush.
-
- To minimize this problem pending a definitive diagnosis and fix,
- PHDF5 has been modified to avoid MPI_File_set_size() calls when
- possible. This is done by comparing the library's EOA (End of
- Allocation) with the file systems EOF, and skipping the
- MPI_File_set_size() call if the two match.
-
- (JRM - 2018/03/29)
-
- - Optimized parallel open/location of the HDF5 super-block.
-
- Previous releases of PHDF5 required all parallel ranks to
- search for the HDF5 superblock signature when opening the
- file. As this is accomplished more or less as a synchronous
- operation, a large number of processes can experience a
- slowdown in the file open due to filesystem contention.
-
- As a first step in improving the startup/file-open performance,
- we allow MPI rank 0 of the associated MPI communicator to locate
- the base offset of the super-block and then broadcast that result
- to the remaining ranks in the parallel group. Note that this
- approach is utilized ONLY during file opens which employ the MPIO
- file driver in HDF5 by previously having called H5Pset_fapl_mpio().
-
- HDF5 parallel file operations which do not employ multiple ranks
- e.g. specifying MPI_COMM_SELF (whose MPI_Comm_size == 1)
- as opposed to MPI_COMM_WORLD, will not be affected by this
- optimization. Conversely, parallel file operations on subgroups
- of MPI_COMM_WORLD are allowed to be run in parallel with each
- subgroup operating as an independent collection of processes.
-
- (RAW - 2017/10/10, HDFFV-10294)
-
- - Added large (>2GB) MPI-IO transfers.
-
- Previous releases of PHDF5 would fail when attempting to
- read or write greater than 2GB of data in a single IO operation.
- This issue stems principally from an MPI API whose definitions
- utilize 32 bit integers to describe the number of data elements
- and datatype that MPI should use to effect a data transfer.
- Historically, HDF5 has invoked MPI-IO with the number of
- elements in a contiguous buffer represented as the length
- of that buffer in bytes.
-
- Resolving the issue and thus enabling larger MPI-IO transfers
- is accomplished first, by detecting when a user IO request would
- exceed the 2GB limit as described above. Once a transfer request
- is identified as requiring special handling, PHDF5 now creates a
- derived datatype consisting of a vector of fixed sized blocks
- which is in turn wrapped within a single MPI_Type_struct to
- contain the vector and any remaining data. The newly created
- datatype is then used in place of MPI_BYTE and can be used to
- fulfill the original user request without encountering API
- errors.
-
- (RAW - 2017/09/10, HDFFV-8839)
-
-
- C++ Library:
- ------------
- - The following C++ API wrappers have been added to the C++ Library:
- + H5Lcreate_soft:
- // Creates a soft link from link_name to target_name.
- void link(const char *target_name, const char *link_name,...)
- void link(const H5std_string& target_name,...)
-
- + H5Lcreate_hard:
- // Creates a hard link from new_name to curr_name.
- void link(const char *curr_name, const Group& new_loc,...)
- void link(const H5std_string& curr_name, const Group& new_loc,...)
-
- // Creates a hard link from new_name to curr_name in same location.
- void link(const char *curr_name, const hid_t same_loc,...)
- void link(const H5std_string& curr_name, const hid_t same_loc,...)
-
- Note: previous version of H5Location::link will be deprecated.
-
- + H5Lcopy:
- // Copy an object from a group of file to another.
- void copyLink(const char *src_name, const Group& dst,...)
- void copyLink(const H5std_string& src_name, const Group& dst,...)
-
- // Copy an object from a group of file to the same location.
- void copyLink(const char *src_name, const char *dst_name,...)
- void copyLink(const H5std_string& src_name,...)
-
- + H5Lmove:
- // Rename an object in a group or file to a new location.
- void moveLink(const char* src_name, const Group& dst,...)
- void moveLink(const H5std_string& src_name, const Group& dst,...)
-
- // Rename an object in a group or file to the same location.
- void moveLink(const char* src_name, const char* dst_name,...)
- void moveLink(const H5std_string& src_name,...)
-
- Note: previous version H5Location::move will be deprecated.
-
- + H5Ldelete:
- // Removes the specified link from this location.
- void unlink(const char *link_name,
- const LinkAccPropList& lapl = LinkAccPropList::DEFAULT)
- void unlink(const H5std_string& link_name,
- const LinkAccPropList& lapl = LinkAccPropList::DEFAULT)
-
- Note: additional parameter is added to previous H5Location::unlink.
-
- + H5Tencode and H5Tdecode:
- // Creates a binary object description of this datatype.
- void DataType::encode() - C API H5Tencode()
-
- // Returns the decoded type from the binary object description.
- DataType::decode() - C API H5Tdecode()
- ArrayType::decode() - C API H5Tdecode()
- CompType::decode() - C API H5Tdecode()
- DataType::decode() - C API H5Tdecode()
- EnumType::decode() - C API H5Tdecode()
- FloatType::decode() - C API H5Tdecode()
- IntType::decode() - C API H5Tdecode()
- StrType::decode() - C API H5Tdecode()
- VarLenType::decode() - C API H5Tdecode()
-
- + H5Lget_info:
- // Returns the information of the named link.
- H5L_info_t getLinkInfo(const H5std_string& link_name,...)
-
- (BMR - 2018/03/11, HDFFV-10149)
-
- - Added class LinkCreatPropList for link create property list.
-
- (BMR - 2018/03/11, HDFFV-10149)
-
- - Added overloaded functions H5Location::createGroup to take a link
- creation property list.
- Group createGroup(const char* name, const LinkCreatPropList& lcpl)
- Group createGroup(const H5std_string& name, const LinkCreatPropList& lcpl)
-
- (BMR - 2018/03/11, HDFFV-10149)
-
- - A document is added to the HDF5 C++ API Reference Manual to show the
- mapping from a C API to C++ wrappers. It can be found from the main
- page of the C++ API Reference Manual.
-
- (BMR - 2017/10/17, HDFFV-10151)
-
-
- Java Library:
- ----------------
- - Wrapper added for enabling the error stack.
-
- H5error_off would disable the error stack reporting. In order
- to re-enable the reporting, the error stack info needs to be
- saved so that H5error_on can revert state.
-
- (ADB - 2018/03/13, HDFFV-10412)
-
- - Wrappers were added for the following C APIs:
- H5Pset_evict_on_close
- H5Pget_evict_on_close
- H5Pset_chunk_opts
- H5Pget_chunk_opts
- H5Pset_efile_prefix
- H5Pget_efile_prefix
- H5Pset_virtual_prefix
- H5Pget_virtual_prefix
-
- (ADB - 2017/12/20)
-
- - The H5I_REFERENCE value in the H5I_type_t enum (defined in H5Ipublic.h)
- has been marked as deprecated.
-
- JNI code which refers to this value will be removed in a future
- major version of the library. The code will remain unchanged in the
- 1.10.x releases and branches.
-
- See the C library section, above, for further information.
-
- (HDFFV-10252, DER, 2017/04/05)
-
-
- Tools:
- ------
- - h5diff has a new option to display error stack.
-
- Updated h5diff with the --enable-error-stack argument, which
- enables the display of the hdf5 error stack. This completes the
- improvement to the main tools: h5copy, h5diff, h5dump, h5ls and
- h5repack.
-
- (ADB - 2017/08/30, HDFFV-9774)
-
-
-Support for new platforms, languages and compilers.
-=======================================
- - None
-
-Bug Fixes since HDF5-1.10.1 release
-==================================
-
- Library
- -------
- - The data read after a direct chunk write to a chunked dataset with
- one chunk was incorrect.
-
- The problem was due to the passing of a null dataset pointer to
- the insert callback for the chunk index in the routine
- H5D__chunk_direct_write() in H5Dchunk.c
- The dataset was a single-chunked dataset which will use the
- single chunk index when latest format was enabled on file creation.
- The single chunk index was the only index that used this pointer
- in the insert callback.
-
- Passed the dataset pointer to the insert callback for the chunk
- index in H5D__chunk_direct_write().
-
- (VC - 2018/03/20, HDFFV-10425)
-
- - Added public routine H5DOread_chunk to the high-level C library.
-
- The patch for H5DOwrite_chunk() to write an entire chunk to the file
- directly was contributed by GE Healthcare and integrated by The HDF Group
- developers.
-
- (VC - 2017/05/19, HDFFV-9934)
-
- - Freeing of object header after failed checksum verification.
-
- It was discovered that the object header (in H5Ocache.c) was not released properly
- when the checksum verification failed and a re-load of the object
- header was needed.
-
- Freed the object header that failed the chksum verification only
- after the new object header is reloaded, deserialized and set up.
-
- (VC - 2018/03/14, HDFFV-10209)
-
- - Updated H5Pset_evict_on_close in H5Pfapl.c
-
- Changed the minor error number from H5E_CANTSET to H5E_UNSUPPORTED for
- parallel library.
-
- (ADB - 2018/03/06, HDFFV-10414)
-
- - Fixed the problems with the utility function that could not handle lowercase
- Windows drive letters.
-
- Added call to upper function for drive letter.
-
- (ADB - 2017/12/18, HDFFV-10307)
-
- - Fixed H5Sencode() bug when the number of elements selected was > 2^32.
-
- H5Sencode() incorrectly encodes dataspace selection with number of
- elements exceeding 2^32. When decoding such selection via H5Sdecode(),
- the number of elements in the decoded dataspace is not the same as
- what is encoded. This problem exists for H5S_SEL_HYPER and
- H5S_SEL_POINTS encoding.
-
- The cause of the problem is due to the fact that the library uses 32 bits to
- encode counts and block offsets for the selection.
- The solution is to use the original 32 bit encodings if possible,
- but use a different way to encode selection if more that 32 bits is needed.
- See details in the RFC: H5Sencode/H5Sdecode Format Change i
- https://bitbucket.hdfgroup.org/projects/HDFFV/repos/hdf5doc/browse/RFCs/HDF5_Library/H5SencodeFormatChange.
-
- (VC - 2017/11/28, HDFFV-9947)
-
- - Fixed filter plugin handling in H5PL.c and H5Z.c to not require i availability of
- dependent libraries (e.g., szip or zlib).
-
- It was discovered that the dynamic loading process used by
- filter plugins had issues with library dependencies.
-
- CMake build process changed to use LINK INTERFACE keywords, which
- allowed HDF5 C library to make dependent libraries private. The
- filter plugin libraries no longer require dependent libraries
- (such as szip or zlib) to be available.
-
- (ADB - 2017/11/16, HDFFV-10328)
-
- - Fixed rare object header corruption bug.
-
- In certain cases, such as when converting large attributes to dense
- storage, an error could occur which would either fail an assertion or
- cause file corruption. Fixed and added test.
-
- (NAF - 2017/11/14, HDFFV-10274)
-
- - Updated H5Zfilter_avail in H5Z.c.
-
- The public function checked for plugins, while the private
- function did not.
-
- Modified H5Zfilter_avail and private function, H5Z_filter_avail.
- Moved check for plugin from public to private function. Updated
- H5P__set_filter due to change in H5Z_filter_avail. Updated tests.
-
- (ADB - 2017/10/10, HDFFV-10297, HDFFV-10319)
-
- - h5dump produced SEGFAULT when dumping corrypted file.
-
- The behavior was due to the error in the internal function H5HL_offset_into().
-
- (1) Fixed H5HL_offset_into() to return error when offset exceeds heap data
- block size.
- (2) Fixed other places in the library that call this routine to detect
- error routine.
-
- (VC - 2017/08/30, HDFFV-10216)
-
- - Fixes for paged aggregation feature.
-
- Skip test in test/fheap.c when:
- (1) multi/split drivers and
- (2) persisting free-space or using paged aggregation strategy
-
- (VC, 2017/07/10)
-
- Changes made based on RFC review comments:
- (1) Added maximum value for file space page size
- (2) Dropped check for page end metadata threshold
- (3) Removed "can_shrink" and "shrink" callbacks for small section class
-
- (VC - 2017/06/09)
-
- - Fixed for infinite loop in H5VM_power2up().
-
- The function H5VM_power2up() returns the next power of 2
- for n. When n exceeds 2^63, it overflows and becomes 0 causing
- the infinite looping.
-
- The fix ensures that the function checks for n >= 2^63
- and returns 0.
-
- (VC - 2017/07/10, HDFFV-10217)
-
- - Fixed for H5Ocopy doesn't work with open identifiers.
-
- Changes made so that raw data for dataset objects are copied from
- cached info when possible instead of flushing objects to file and
- read them back in again.
-
- (VC - 2017/07/05, HDFFV-7853)
-
- - An uninitialized struct could cause a memory access error when using
- variable-length or reference types in a compressed, chunked dataset.
-
- A struct containing a callback function pointer and a pointer to some
- associated data was used before initialization. This could cause a
- memory access error and system crash. This could only occur under
- unusual conditions when using variable-lenth and reference types in
- a compressed, chunked dataset.
-
- On recent versions of Visual Studio, when built in debug mode, the
- debug heap will complain and cause a crash if the code in question
- is executed (this will cause the objcopy test to fail).
-
- (DER - 2017/11/21, HDFFV-10330)
-
- - Fixed collective metadata writes on file close.
-
- It was discovered that metadata was being written twice as part of
- the parallel file close behavior, once independently and once
- collectively.
-
- A fix for this error was included as part of the parallel compression
- feature but remained undocumented here.
-
- (RAW - 2017/12/01, HDFFV-10272)
-
- - If an HDF5 file contains a filter pipeline message with a 'number of
- filters' field that exceeds the maximum number of allowed filters,
- the error handling code will attempt to dereference a NULL pointer.
-
- This issue was reported to The HDF Group as issue #CVE-2017-17505.
- https://security-tracker.debian.org/tracker/CVE-2017-17505
- https://cve.mitre.org/cgi-bin/cvename.cgi?name=3DCVE-2017-17505
-
- NOTE: The HDF5 C library cannot produce such a file. This condition
- should only occur in a corrupt (or deliberately altered) file
- or a file created by third-party software.
-
- This problem arose because the error handling code assumed that
- the 'number of filters' field implied that a dynamic array of that
- size had already been created and that the cleanup code should
- iterate over that array and clean up each element's resources. If
- an error occurred before the array has been allocated, this will
- not be true.
-
- This has been changed so that the number of filters is set to
- zero on errors. Additionally, the filter array traversal in the
- error handling code now requires that the filter array not be NULL.
-
- (DER - 2018/02/06, HDFFV-10354)
-
- - If an HDF5 file contains a filter pipeline message which contains
- a 'number of filters' field that exceeds the actual number of
- filters in the message, the HDF5 C library will read off the end of
- the read buffer.
-
- This issue was reported to The HDF Group as issue #CVE-2017-17506.
- https://security-tracker.debian.org/tracker/CVE-2017-17506
- https://cve.mitre.org/cgi-bin/cvename.cgi?name=3DCVE-2017-17506
-
- NOTE: The HDF5 C library cannot produce such a file. This condition
- should only occur in a corrupt (or deliberately altered) file
- or a file created by third-party software.
-
- The problem was fixed by passing the buffer size with the buffer
- and ensuring that the pointer cannot be incremented off the end
- of the buffer. A mismatch between the number of filters declared
- and the actual number of filters will now invoke normal HDF5
- error handling.
-
- (DER - 2018/02/26, HDFFV-10355)
-
- - If an HDF5 file contains a malformed compound datatype with a
- suitably large offset, the type conversion code can run off
- the end of the type conversion buffer, causing a segmentation
- fault.
-
- This issue was reported to The HDF Group as issue #CVE-2017-17507.
- https://security-tracker.debian.org/tracker/CVE-2017-17506
- https://cve.mitre.org/cgi-bin/cvename.cgi?name=3DCVE-2017-17506
-
- NOTE: The HDF5 C library cannot produce such a file. This condition
- should only occur in a corrupt (or deliberately altered) file
- or a file created by third-party software.
-
- THE HDF GROUP WILL NOT FIX THIS BUG AT THIS TIME
-
- Fixing this problem would involve updating the publicly visible
- H5T_conv_t function pointer typedef and versioning the API calls
- which use it. We normally only modify the public API during
- major releases, so this bug will not be fixed at this time.
-
- (DER - 2018/02/26, HDFFV-10356)
-
- - If an HDF5 file contains a malformed compound type which contains
- a member of size zero, a division by zero error will occur while
- processing the type.
-
- This issue was reported to The HDF Group as issue #CVE-2017-17508.
- https://security-tracker.debian.org/tracker/CVE-2017-17508
- https://cve.mitre.org/cgi-bin/cvename.cgi?name=3DCVE-2017-17508
-
- NOTE: The HDF5 C library cannot produce such a file. This condition
- should only occur in a corrupt (or deliberately altered) file
- or a file created by third-party software.
-
- Checking for zero before dividing fixes the problem. Instead of the
- division by zero, the normal HDF5 error handling is invoked.
-
- (DER - 2018/02/26, HDFFV-10357)
-
- - If an HDF5 file contains a malformed symbol table node that declares
- it contains more symbols than it actually contains, the library
- can run off the end of the metadata cache buffer while processing
- the symbol table node.
-
- This issue was reported to The HDF Group as issue #CVE-2017-17509.
- https://security-tracker.debian.org/tracker/CVE-2017-17509
- https://cve.mitre.org/cgi-bin/cvename.cgi?name=3DCVE-2017-17509
-
- NOTE: The HDF5 C library cannot produce such a file. This condition
- should only occur in a corrupt (or deliberately altered) file
- or a file created by third-party software.
-
- Performing bounds checks on the buffer while processing fixes the
- problem. Instead of the segmentation fault, the normal HDF5 error
- handling is invoked.
-
- (DER - 2018/03/12, HDFFV-10358)
-
- - Fixed permissions passed to open(2) on file create.
-
- On Windows, the POSIX permissions passed to open(2) when creating files
- were only incidentally correct. They are now set to the correct value of
- (_S_IREAD | _S_IWRITE).
-
- On other platforms, the permissions were set to a mix of 666, 644, and
- 000. They are now set uniformly to 666.
-
- (DER - 2017/04/28, HDFFV-9877)
-
- - The H5FD_FEAT_POSIX_COMPAT_HANDLE flag is no longer used to determine
- if a virtual file driver (VFD) is compatible with SWMR.
-
- Use of this VFD feature flag was not in line with the documentation in
- the public H5FDpublic.h file. In particular, it was being used as a
- proxy for determining if SWMR I/O is allowed. This is unnecessary as we
- already have a feature flag for this (H5FD_SUPPORTS_SWMR_IO).
-
- (DER - 2017/05/31, HDFFV-10214)
-
-
- Configuration
- -------------
- - CMake changes
-
- - Updated CMake commands configuration.
-
- A number of improvements were made to the CMake commands. Most
- changes simplify usage or eliminate unused constructs. Also,
- some changes support better cross-platform support.
-
- (ADB - 2018/02/01, HDFFV-10398)
-
- - Corrected usage of CMAKE_BUILD_TYPE variable.
-
- The use of the CMAKE_BUILD_TYPE is incorrect for multi-config
- generators (Visual Studio and XCode) and is optional for single
- config generators. Created a new macro to check
- GLOBAL PROPERTY -> GENERATOR_IS_MULTI_CONFIG
- Created two new HDF variable, HDF_BUILD_TYPE and HDF_CFG_BUILD_TYPE.
- Defaults for these variables is "Release".
-
- (ADB - 2018/01/10, HDFFV-10385)
-
- - Added replacement of fortran flags if using static CRT.
-
- Added TARGET_STATIC_CRT_FLAGS call to HDFUseFortran.cmake file in
- config/cmake_ext_mod folder.
-
- (ADB - 2018/01/08, HDFFV-10334)
-
-
- - The hdf5 library used shared szip and zlib, which needlessly required
- applications to link with the same szip and zlib libraries.
-
- Changed the target_link_libraries commands to use the static libs.
- Removed improper link duplication of szip and zlib.
- Adjusted the link dependencies and the link interface values of
- the target_link_libraries commands.
-
- (ADB - 2017/11/14, HDFFV-10329)
-
- - CMake MPI
-
- CMake implementation for MPI was problematic and would create incorrect
- MPI library references in the hdf5 libraries.
-
- Reworked the CMake MPI code to properly create CMake targets. Also merged
- the latest CMake FindMPI.cmake changes to the local copy. This is necessary
- until HDF changes the CMake minimum to 3.9 or greater.
-
- (ADB - 2017/11/02, HDFFV-10321)
-
- - Corrected FORTRAN_HAVE_C_LONG_DOUBLE processing in the autotools.
-
- A bug in the autotools Fortran processing code always set the
- FORTRAN_HAVE_C_LONG_DOUBLE variable to be true regardless of
- whether or not a C long double type was present.
-
- This would cause compilation failures on platforms where a C
- long double type was not available and the Fortran wrappers
- were being built.
-
- (DER - 2017/07/05, HDFFV-10247)
-
- - The deprecated --enable-production and --enable-debug configure options
- failed to emit errors when passed an empty string
- (e.g.: --enable-debug="").
-
- Due to the way we checked for these options being set, it was possible
- to avoid the error message and continue configuration if an empty string
- was passed to the option.
-
- Any use of --enable-production or --enable-debug will now halt the
- configuration step and emit a helpful error message
- (use --enable-build-mode=debug|production instead).
-
- (DER - 2017/07/05, HDFFV-10248)
-
- - CMake
-
- Too many commands for POST_BUILD step caused command line to be
- too big on windows.
-
- Changed foreach of copy command to use a custom command with the
- use of the HDFTEST_COPY_FILE macro.
-
- (ADB - 2017/07/12, HDFFV-10254)
-
- - CMake test execution environment
-
- The parallel HDF5 test: 't_pread' assumed the use of autotools
- and the directory structure associated with that testing approach.
- Modified the test code to check whether the 'h5jam' utility can be
- found in the same directory as the test executable (which is
- preferred directory structure utilized by cmake) and if found
- will invoke the tool directly rather than utilizing a relative path.
-
- (RAW - 2017/11/03, HDFFV-10318)
-
- - Fortran compilation fails for xlf and CMake builds.
-
- Fixed CMake shared library build for H5match_types and modules
-
- (MSB - 2017/12/19, HDFFV-10363)
-
- - Shared libraries fail test on OSX with Fortran enabled with CMake.
-
- Fixed by removing the F77 use of EQUIVALENCE and COMMON, replaced
- using MODULES. Updated CMake.
-
- (MSB - 2017/12/07, HDFFV-10223)
-
- - The bin/trace script now emits an error code on problems and autogen.sh
- will fail if bin/trace fails.
-
- The bin/trace script adds tracing functionality to public HDF5 API calls.
- It is only of interest to developers who modify the HDF5 source code.
- Previously, bin/trace just wrote an error message to stdout when it
- encountered problems, so autogen.sh processing did not halt and a broken
- version of the library could be built. The script will now return an
- error code when it encounters problems, and autogen.sh will fail.
-
- This only affects users who run autogen.sh to rebuild the Autotools files,
- which is not necessary to build HDF5 from source in official releases of the
- library. CMake users are unaffected as bin/trace is not run via CMake
- at this time.
-
- (DER - 2017/04/25, HDFFV-10178)
-
- - FC_BASENAME was changed from gfortran40 to gfortran in a few places.
-
- In the autotools, FC_BASENAME was set to gfortran40 in a few locations
- (config/gnu-fflags and config/freebsd). This was probably a historical
- artifact and did not seem to affect many users.
-
- The value is now correctly set to gfortran.
-
- (DER - 2017/05/26, HDFFV-10249)
-
- - The ar flags were changed to -cr (was: -cru)
-
- The autotools set the flags for ar to -cru by default. The -u flag,
- which allows selective replacement of only the members which have
- changed, raises warnings on some platforms, so the flags are now set to
- -cr via AR_FLAGS in configure.ac. This causes the static library to
- always be completely recreated from the object files on each build.
-
- (DER - 2017/11/15, HDFFV-10428)
-
-
- Fortran
- --------
- - Fixed compilation errors when using Intel 18 Fortran compilers
- (MSB - 2017/11/3, HDFFV-10322)
-
- Tools
- -----
- - h5clear
-
- An enhancement to the tool in setting a file's stored EOA.
-
- It was discovered that a crashed file's stored EOA in the superblock
- was smaller than the actual file's EOF. When the file was reopened
- and closed, the library truncated the file to the stored EOA.
-
- Added an option to the tool in setting the file's stored EOA in the
- superblock to the maximum of (EOA, EOF) + increment.
- An option was also added to print the file's EOA and EOF.
-
- (VC - 2018/03/14, HDFFV-10360)
-
- - h5repack
-
- h5repack changes the chunk parameters when a change of layout is not
- specified and a filter is applied.
-
- HDFFV-10297, HDFFV-10319 reworked code for h5repack and h5diff code
- in the tools library. The check for an existing layout was incorrectly
- placed into an if block and not executed. The check was moved into
- the normal path of the function.
-
- (ADB - 2018/02/21, HDFFV-10412)
-
- - h5dump
-
- The tools library will hide the error stack during file open.
-
- While this is preferable almost always, there are reasons to enable
- display of the error stack when a tool will not open a file. Adding an
- optional argument to the --enable-error-stack will provide this use case.
- As an optional argument it will not affect the operation of the
- --enable-error-stack. h5dump is the only tool to implement this change.
-
- (ADB - 2018/02/15, HDFFV-10384)
-
- - h5dump
-
- h5dump would output an indented blank line in the filters section.
-
- h5dump overused the h5tools_simple_prefix function, which is a
- function intended to account for the data index (x,y,z) option.
- Removed the function call for header information.
-
- (ADB - 2018/01/25, HDFFV-10396)
-
- - h5repack
-
- h5repack incorrectly searched internal object table for name.
-
- h5repack would search the table of objects for a name, if the
- name did not match it tried to determine if the name without a
- leading slash would match. The logic was flawed! The table
- stored names(paths) without a leading slash and did a strstr
- of the table path to the name.
- The assumption was that if there was a difference of one then
- it was a match, however "pressure" would match "/pressure" as
- well as "/pressure1", "/pressure2", etc. Changed logic to remove
- any leading slash and then do a full compare of the name.
-
- (ADB - 2018/01/18, HDFFV-10393)
-
- - h5repack
-
- h5repack failed to handle command line parameters for customer filters.
-
- User defined filter parameter conversions would fail when integers were
- represented on the command line with character string
- larger then 9 characters. Increased local variable array for storing
- the current command line parameter to prevent buffer overflows.
-
- (ADB - 2018/01/17, HDFFV-10392)
-
- - h5diff
-
- h5diff seg faulted if comparing VL strings against fixed strings.
-
- Reworked solution for HDFFV-8625 and HDFFV-8639. Implemented the check
- for string objects of same type in the diff_can_type function by
- adding an if(tclass1 == H5T_STRING) block. This "if block" moves the
- same check that was added for attributes to this function, which is
- used by all object types. This function handles complex type structures.
- Also added a new test file in h5diffgenttest for testing this issue
- and removed the temporary files used in the test scripts.
-
- (ADB - 2018/01/04, HDFFV-8745)
-
- - h5repack
-
- h5repack failed to copy a dataset with existing filter.
-
- Reworked code for h5repack and h5diff code in the tools library. Added
- improved error handling, cleanup of resources and checks of calls.
- Modified H5Zfilter_avail and private function, H5Z_filter_avail.
- Moved check for plugin from public to private function. Updated
- H5P__set_filter due to change in H5Z_filter_avail. Updated tests.
- Note, h5repack output display has changed to clarify the individual
- steps of the repack process. The output indicates if an operation
- applies to all objects. Lines with notation and no information
- have been removed.
-
- (ADB - 2017/10/10, HDFFV-10297, HDFFV-10319)
-
- - h5repack
-
- h5repack always set the User Defined filter flag to H5Z_FLAG_MANDATORY.
-
- Added another parameter to the 'UD=' option to set the flag by default
- to '0' or H5Z_FLAG_MANDATORY, the other choice is '1' or H5Z_FLAG_OPTIONAL.
-
- (ADB - 2017/08/31, HDFFV-10269)
-
- - h5ls
-
- h5ls generated error on stack when it encountered a H5S_NULL
- dataspace.
-
- Adding checks for H5S_NULL before calling H5Sis_simple (located
- in the h5tools_dump_mem function) fixed the issue.
-
- (ADB - 2017/08/17, HDFFV-10188)
-
- - h5repack
-
- Added tests to h5repack.sh.in to verify options added for paged
- aggregation work as expected.
-
- (VC - 2017/08/03)
-
- - h5dump
-
- h5dump segfaulted on output of XML file.
-
- Function that escape'd strings used the full buffer length
- instead of just the length of the replacement string in a
- strncpy call. Using the correct length fixed the issue.
-
- (ADB - 2017/08/01, HDFFV-10256)
-
- - h5diff
-
- h5diff segfaulted on compare of a NULL variable length string.
-
- Improved h5diff compare of strings by adding a check for
- NULL strings and setting the lengths to zero.
-
- (ADB - 2017/07/25, HDFFV-10246)
-
- - h5import
-
- h5import crashed trying to import data from a subset of a dataset.
-
- Improved h5import by adding the SUBSET keyword. h5import understands
- to use the Count times the Block as the size of the dimensions.
- Added INPUT_B_ORDER keyword to old-style configuration files.
- The import from h5dump function expects the binary files to use native
- types (FILE '-b' option) in the binary file.
-
- (ADB - 2017/06/15, HDFFV-10219)
-
- - h5repack
-
- h5repack did not maintain the creation order flag of the root
- group.
-
- Improved h5repack by reading the creation order and applying the
- flag to the new root group. Also added arguments to set the
- order and index direction, which applies to the traversing of the
- original file, on the command line.
-
- (ADB - 2017/05/26, HDFFV-8611)
-
- - h5diff
-
- h5diff failed to account for strpad type and null terminators
- of char strings. Also, h5diff failed to account for string length
- differences and would give a different result depending on file
- order in the command line.
-
- Improved h5diff compare of strings and arrays by adding a check for
- string lengths and if the strpad was null filled.
-
- (ADB - 2017/05/18, HDFFV-9055, HDFFV-10128)
-
- High-Level APIs:
- ------
- - H5DOwrite_chunk() problems when overwriting an existing chunk with
- no filters enabled.
-
- When overwriting chunks and no filters were being used, the library would
- fail (when asserts are enabled, e.g. debug builds) or incorrectly
- insert additional chunks instead of overwriting (when asserts are not
- enabled, e.g. production builds).
-
- This has been fixed and a test was added to the hl/test_dset_opt test.
-
- (DER - 2017/05/11, HDFFV-10187)
-
- C++ APIs
- --------
- - Removal of memory leaks.
-
- A private function was inadvertently called, causing memory leaks. This
- is now fixed.
-
- (BMR - 2018/03/12 - User's reported in email)
-
- Testing
- -------
- - Memory for three variables in testphdf5's coll_write_test was malloced
- but not freed, leaking memory when running the test.
-
- The variables' memory is now freed.
-
- (LRK - 2018/03/12, HDFFV-10397)
-
- - Refactored the testpar/t_bigio.c test to include ALARM macros
-
- Changed the test to include the ALARM_ON and ALARM_OFF macros which
- are intended to prevent nightly test hangs that have been observed
- with this particular parallel test example. The code was also modified to
- simplify status reporting (only from MPI rank 0) and additional
- status checking added.
-
- (RAW - 2017/11/08, HDFFV-10301)
-
-
-Supported Platforms
-===================
-
- Linux 2.6.32-696.16.1.el6.ppc64 gcc (GCC) 4.4.7 20120313 (Red Hat 4.4.7-18)
- #1 SMP ppc64 GNU/Linux g++ (GCC) 4.4.7 20120313 (Red Hat 4.4.7-18)
- (ostrich) GNU Fortran (GCC) 4.4.7 20120313 (Red Hat 4.4.7-18)
- IBM XL C/C++ V13.1
- IBM XL Fortran V15.1
-
- Linux 3.10.0-327.10.1.el7 GNU C (gcc), Fortran (gfortran), C++ (g++)
- #1 SMP x86_64 GNU/Linux compilers:
- (kituo/moohan) Version 4.8.5 20150623 (Red Hat 4.8.5-4)
- Version 4.9.3, Version 5.2.0,
- Intel(R) C (icc), C++ (icpc), Fortran (icc)
- compilers:
- Version 17.0.0.098 Build 20160721
- MPICH 3.1.4 compiled with GCC 4.9.3
-
- SunOS 5.11 32- and 64-bit Sun C 5.12 SunOS_sparc
- (emu) Sun Fortran 95 8.6 SunOS_sparc
- Sun C++ 5.12 SunOS_sparc
-
- Windows 7 Visual Studio 2012 w/ Intel Fortran 15 (cmake)
- Visual Studio 2013 w/ Intel Fortran 15 (cmake)
- Visual Studio 2015 w/ Intel Fortran 16 (cmake)
-
- Windows 7 x64 Visual Studio 2012 w/ Intel Fortran 15 (cmake)
- Visual Studio 2013 w/ Intel Fortran 15 (cmake)
- Visual Studio 2015 w/ Intel Fortran 16 (cmake)
- Visual Studio 2015 w/ Intel C, Fortran 2017 (cmake)
- Visual Studio 2015 w/ MSMPI 8 (cmake)
- Cygwin(CYGWIN_NT-6.1 2.8.0(0.309/5/3)
- gcc and gfortran compilers (GCC 5.4.0)
- (cmake and autotools)
-
- Windows 10 Visual Studio 2015 w/ Intel Fortran 16 (cmake)
- Cygwin(CYGWIN_NT-6.1 2.8.0(0.309/5/3)
- gcc and gfortran compilers (GCC 5.4.0)
- (cmake and autotools)
-
- Windows 10 x64 Visual Studio 2015 w/ Intel Fortran 16 (cmake)
-
- Mac OS X Yosemite 10.10.5 Apple clang/clang++ version 6.1 from Xcode 7.0
- 64-bit gfortran GNU Fortran (GCC) 4.9.2
- (osx1010dev/osx1010test) Intel icc/icpc/ifort version 15.0.3
-
- Mac OS X El Capitan 10.11.6 Apple clang/clang++ version 7.3.0 from Xcode 7.3
- 64-bit gfortran GNU Fortran (GCC) 5.2.0
- (osx1011dev/osx1011test) Intel icc/icpc/ifort version 16.0.2
-
- Mac OS Sierra 10.12.6 Apple LLVM version 8.1.0 (clang/clang++-802.0.42)
- 64-bit gfortran GNU Fortran (GCC) 7.1.0
- (swallow/kite) Intel icc/icpc/ifort version 17.0.2
-
-
-Tested Configuration Features Summary
-=====================================
-
- In the tables below
- y = tested
- n = not tested in this release
- C = Cluster
- W = Workstation
- x = not working in this release
- dna = does not apply
- ( ) = footnote appears below second table
- <blank> = testing incomplete on this feature or platform
-
-Platform C F90/ F90 C++ zlib SZIP
- parallel F2003 parallel
-Solaris2.11 32-bit n y/y n y y y
-Solaris2.11 64-bit n y/n n y y y
-Windows 7 y y/y n y y y
-Windows 7 x64 y y/y y y y y
-Windows 7 Cygwin n y/n n y y y
-Windows 7 x64 Cygwin n y/n n y y y
-Windows 10 y y/y n y y y
-Windows 10 x64 y y/y n y y y
-Mac OS X Mountain Lion 10.8.5 64-bit n y/y n y y y
-Mac OS X Mavericks 10.9.5 64-bit n y/y n y y y
-Mac OS X Yosemite 10.10.5 64-bit n y/y n y y y
-Mac OS X El Capitan 10.11.6 64-bit n y/y n y y y
-CentOS 7.2 Linux 2.6.32 x86_64 PGI n y/y n y y y
-CentOS 7.2 Linux 2.6.32 x86_64 GNU y y/y y y y y
-CentOS 7.2 Linux 2.6.32 x86_64 Intel n y/y n y y y
-Linux 2.6.32-573.18.1.el6.ppc64 n y/y n y y y
-
-
-Platform Shared Shared Shared Thread-
- C libs F90 libs C++ libs safe
-Solaris2.11 32-bit y y y y
-Solaris2.11 64-bit y y y y
-Windows 7 y y y y
-Windows 7 x64 y y y y
-Windows 7 Cygwin n n n y
-Windows 7 x64 Cygwin n n n y
-Windows 10 y y y y
-Windows 10 x64 y y y y
-Mac OS X Mountain Lion 10.8.5 64-bit y n y y
-Mac OS X Mavericks 10.9.5 64-bit y n y y
-Mac OS X Yosemite 10.10.5 64-bit y n y y
-Mac OS X El Capitan 10.11.6 64-bit y n y y
-CentOS 7.2 Linux 2.6.32 x86_64 PGI y y y n
-CentOS 7.2 Linux 2.6.32 x86_64 GNU y y y y
-CentOS 7.2 Linux 2.6.32 x86_64 Intel y y y n
-Linux 2.6.32-573.18.1.el6.ppc64 y y y n
-
-Compiler versions for each platform are listed in the preceding
-"Supported Platforms" table.
-
-
-More Tested Platforms
-=====================
-The following platforms are not supported but have been tested for this release.
-
- Linux 2.6.32-573.22.1.el6 GNU C (gcc), Fortran (gfortran), C++ (g++)
- #1 SMP x86_64 GNU/Linux compilers:
- (mayll/platypus) Version 4.4.7 20120313
- Version 4.9.3, 5.3.0, 6.2.0
- PGI C, Fortran, C++ for 64-bit target on
- x86-64;
- Version 17.10-0
- Intel(R) C (icc), C++ (icpc), Fortran (icc)
- compilers:
- Version 17.0.4.196 Build 20170411
- MPICH 3.1.4 compiled with GCC 4.9.3
-
- Linux 3.10.0-327.18.2.el7 GNU C (gcc) and C++ (g++) compilers
- #1 SMP x86_64 GNU/Linux Version 4.8.5 20150623 (Red Hat 4.8.5-4)
- (jelly) with NAG Fortran Compiler Release 6.1(Tozai)
- GCC Version 7.1.0
- OpenMPI 3.0.0-GCC-7.2.0-2.29
- Intel(R) C (icc) and C++ (icpc) compilers
- Version 17.0.0.098 Build 20160721
- with NAG Fortran Compiler Release 6.1(Tozai)
-
- Linux 3.10.0-327.10.1.el7 MPICH 3.2 compiled with GCC 5.3.0
- #1 SMP x86_64 GNU/Linux
- (moohan)
-
- Linux 2.6.32-573.18.1.el6.ppc64 MPICH mpich 3.1.4 compiled with
- #1 SMP ppc64 GNU/Linux IBM XL C/C++ for Linux, V13.1
- (ostrich) and IBM XL Fortran for Linux, V15.1
-
- Debian 8.4 3.16.0-4-amd64 #1 SMP Debian 3.16.36-1 x86_64 GNU/Linux
- gcc, g++ (Debian 4.9.2-10) 4.9.2
- GNU Fortran (Debian 4.9.2-10) 4.9.2
- (cmake and autotools)
-
- Fedora 24 4.7.2-201.fc24.x86_64 #1 SMP x86_64 x86_64 x86_64 GNU/Linux
- gcc, g++ (GCC) 6.1.1 20160621
- (Red Hat 6.1.1-3)
- GNU Fortran (GCC) 6.1.1 20160621
- (Red Hat 6.1.1-3)
- (cmake and autotools)
-
- Ubuntu 16.04.1 4.4.0-38-generic #57-Ubuntu SMP x86_64 GNU/Linux
- gcc, g++ (Ubuntu 5.4.0-6ubuntu1~16.04.2)
- 5.4.0 20160609
- GNU Fortran (Ubuntu 5.4.0-6ubuntu1~16.04.2)
- 5.4.0 20160609
- (cmake and autotools)
-
-
-Known Problems
-==============
-
- At present, metadata cache images may not be generated by parallel
- applications. Parallel applications can read files with metadata cache
- images, but since this is a collective operation, a deadlock is possible
- if one or more processes do not participate.
-
- Three tests fail with OpenMPI 3.0.0/GCC-7.2.0-2.29:
- testphdf5 (ecdsetw, selnone, cchunk1, cchunk3, cchunk4, and actualio)
- t_shapesame (sscontig2)
- t_pflush1/fails on exit
- The first two tests fail attempting collective writes.
-
- Known problems in previous releases can be found in the HISTORY*.txt files
- in the HDF5 source. Please report any new problems found to
- help@hdfgroup.org.
-
-
-%%%%1.10.1%%%%
-
-HDF5 version 1.10.1 released on 2017-04-27
-================================================================================
-
-INTRODUCTION
-
-This document describes the differences between HDF5-1.10.0-patch1 and
-HDF5 1.10.1, and contains information on the platforms tested and known
-problems in HDF5-1.10.1. For more details check the HISTORY*.txt files
-in the HDF5 source.
-
-Links to HDF5 1.10.1 source code, documentation, and additional materials can
-be found on The HDF5 web page at:
-
- https://support.hdfgroup.org/HDF5/
-
-The HDF5 1.10.1 release can be obtained from:
-
- https://support.hdfgroup.org/HDF5/release/obtain5.html
-
-User documentation for the snapshot can be accessed directly at this location:
-
- https://support.hdfgroup.org/HDF5/doc/
-
-New features in the HDF5-1.10.x release series, including brief general
-descriptions of some new and modified APIs, are described in the "New Features
-in HDF5 Release 1.10" document:
-
- https://support.hdfgroup.org/HDF5/docNewFeatures/index.html
-
-All new and modified APIs are listed in detail in the "HDF5 Software Changes
-from Release to Release" document, in the section "Release 10.1 (current
-release) versus Release 1.10.0
-
- https://support.hdfgroup.org/HDF5/doc/ADGuide/Changes.html
-
-If you have any questions or comments, please send them to the HDF Help Desk:
-
- help@hdfgroup.org
-
-
-CONTENTS
-
-- Major New Features Introduced in HDF5 1.10.1
-- Other New Features and Enhancements
-- Support for New Platforms, Languages, and Compilers
-- Bug Fixes since HDF5-1.10.0-patch1
-- Supported Platforms
-- Tested Configuration Features Summary
-- More Tested Platforms
-- Known Problems
-
-
-Major New Features Introduced in HDF5 1.10.1
-============================================
-
-For links to the RFCs and documentation in this section please view
-https://support.hdfgroup.org/HDF5/docNewFeatures in a web browser.
-
-________________________________________
-Metadata Cache Image
-________________________________________
-
- HDF5 metadata is typically small, and scattered throughout the HDF5 file.
- This can affect performance, particularly on large HPC systems. The
- Metadata Cache Image feature can improve performance by writing the
- metadata cache in a single block on file close, and then populating the
- cache with the contents of this block on file open, thus avoiding the many
- small I/O operations that would otherwise be required on file open and
- close. See the RFC for complete details regarding this feature. Also,
- see the Fine Tuning the Metadata Cache documentation.
-
- At present, metadata cache images may not be generated by parallel
- applications. Parallel applications can read files with metadata cache
- images, but since this is a collective operation, a deadlock is possible
- if one or more processes do not participate.
-
-________________________________________
-Metadata Cache Evict on Close
-________________________________________
-
- The HDF5 library's metadata cache is fairly conservative about holding on
- to HDF5 object metadata (object headers, chunk index structures, etc.),
- which can cause the cache size to grow, resulting in memory pressure on
- an application or system. The "evict on close" property will cause all
- metadata for an object to be evicted from the cache as long as metadata
- is not referenced from any other open object. See the Fine Tuning the
- Metadata Cache documentation for information on the APIs.
-
- At present, evict on close is disabled in parallel builds.
-
-________________________________________
-Paged Aggregation
-________________________________________
-
- The current HDF5 file space allocation accumulates small pieces of metadata
- and raw data in aggregator blocks which are not page aligned and vary
- widely in sizes. The paged aggregation feature was implemented to provide
- efficient paged access of these small pieces of metadata and raw data.
- See the RFC for details. Also, see the File Space Management documentation.
-
-________________________________________
-Page Buffering
-________________________________________
-
- Small and random I/O accesses on parallel file systems result in poor
- performance for applications. Page buffering in conjunction with paged
- aggregation can improve performance by giving an application control of
- minimizing HDF5 I/O requests to a specific granularity and alignment.
- See the RFC for details. Also, see the Page Buffering documentation.
-
- At present, page buffering is disabled in parallel builds.
-
-
-
-Other New Features and Enhancements
-===================================
-
- Library
- -------
- - Added a mechanism for disabling the SWMR file locking scheme.
-
- The file locking calls used in HDF5 1.10.0 (including patch1)
- will fail when the underlying file system does not support file
- locking or where locks have been disabled. To disable all file
- locking operations, an environment variable named
- HDF5_USE_FILE_LOCKING can be set to the five-character string
- 'FALSE'. This does not fundamentally change HDF5 library
- operation (aside from initial file open/create, SWMR is lock-free),
- but users will have to be more careful about opening files
- to avoid problematic access patterns (i.e.: multiple writers)
- that the file locking was designed to prevent.
-
- Additionally, the error message that is emitted when file lock
- operations set errno to ENOSYS (typical when file locking has been
- disabled) has been updated to describe the problem and potential
- resolution better.
-
- (DER, 2016/10/26, HDFFV-9918)
-
- - The return type of H5Pget_driver_info() has been changed from void *
- to const void *.
-
- The pointer returned by this function points to internal library
- memory and should not be freed by the user.
-
- (DER, 2016/11/04, HDFFV-10017)
-
- - The direct I/O VFD has been removed from the list of VFDs that
- support SWMR.
-
- This configuration was never officially tested and several SWMR
- tests fail when this VFD is set.
-
- (DER, 2016/11/03, HDFFV-10169)
-
- Configuration:
- --------------
- - The minimum version of CMake required to build HDF5 is now 3.2.2.
-
- (ADB, 2017/01/10)
-
- - An --enable/disable-developer-warnings option has been added to
- configure.
-
- This disables warnings that do not indicate poor code quality such
- as -Winline and gcc's -Wsuggest-attribute. Developer warnings are
- disabled by default.
-
- (DER, 2017/01/10)
-
- - A bin/restore.sh script was added that reverts autogen.sh processing.
-
- (DER, 2016/11/08)
-
- - CMake: Added NAMESPACE hdf5:: to package configuration files to allow
- projects using installed HDF5 binaries built with CMake to link with
- them without specifying the HDF5 library location via IMPORTED_LOCATION.
-
- (ABD, 2016/10/17, HDFFV-10003)
-
- - CMake: Changed the CTEST_BUILD_CONFIGURATION option to
- CTEST_CONFIGURATION_TYPE as recommended by the CMake documentation.
-
- (ABD, 2016/10/17, HDFFV-9971)
-
-
- Fortran Library:
- ----------------
-
- - The HDF5 Fortran library can now be compiled with the NAG compiler.
-
- (MSB, 2017/2/10, HDFFV-9973)
-
-
- C++ Library:
- ------------
-
- - The following C++ API wrappers have been added to the C++ Library:
-
- // Sets/Gets the strategy and the threshold value that the library
- // will employ in managing file space.
- FileCreatPropList::setFileSpaceStrategy - H5Pset_file_space_strategy
- FileCreatPropList::getFileSpaceStrategy - H5Pget_file_space_strategy
-
- // Sets/Gets the file space page size for paged aggregation.
- FileCreatPropList::setFileSpacePagesize - H5Pset_file_space_page_size
- FileCreatPropList::getFileSpacePagesize - H5Pget_file_space_page_size
-
- // Checks if the given ID is valid.
- IdComponent::isValid - H5Iis_valid
-
- // Sets/Gets the number of soft or user-defined links that can be
- // traversed before a failure occurs.
- LinkAccPropList::setNumLinks - H5Pset_nlinks
- LinkAccPropList::getNumLinks - H5Pget_nlinks
-
- // Returns a copy of the creation property list of a datatype.
- DataType::getCreatePlist - H5Tget_create_plist
-
- // Opens/Closes an object within a group or a file, regardless of object
- // type
- Group::getObjId - H5Oopen
- Group::closeObjId - H5Oclose
-
- // Maps elements of a virtual dataset to elements of the source dataset.
- DSetCreatPropList::setVirtual - H5Pset_virtual
-
- // Gets general information about this file.
- H5File::getFileInfo - H5Fget_info2
-
- // Returns the number of members in a type.
- IdComponent::getNumMembers - H5Inmembers
-
- // Determines if an element type exists.
- IdComponent::typeExists - H5Itype_exists
-
- // Determines if an object exists.
- H5Location::exists - H5Lexists.
-
- // Returns the header version of an HDF5 object.
- H5Object::objVersion - H5Oget_info for version
-
- (BMR, 2017/03/20, HDFFV-10004, HDFFV-10139, HDFFV-10145)
-
- - New exception: ObjHeaderIException for H5O interface.
-
- (BMR, 2017/03/15, HDFFV-10145)
-
- - New class LinkAccPropList for link access property list, to be used by
- wrappers of H5Lexists.
-
- (BMR, 2017/01/04, HDFFV-10145)
-
- - New constructors to open datatypes in ArrayType, CompType, DataType,
- EnumType, FloatType, IntType, StrType, and VarLenType.
-
- (BMR, 2016/12/26, HDFFV-10056)
-
- - New member functions:
-
- DSetCreatPropList::setNbit() to setup N-bit compression for a dataset.
-
- ArrayType::getArrayNDims() const
- ArrayType::getArrayDims() const
- both to replace the non-const versions.
-
- (BMR, 2016/04/25, HDFFV-8623, HDFFV-9725)
-
-
- Tools:
- ------
- - The following options have been added to h5clear:
- -s: clear the status_flags field in the file's superblock
- -m: Remove the metadata cache image from the file
-
- (QAK, 2017/03/22, PR#361)
-
-
- High-Level APIs:
- ---------------
- - Added New Fortran 2003 API for h5tbmake_table_f.
-
- (MSB, 2017/02/10, HDFFV-8486)
-
-
-
-Support for New Platforms, Languages, and Compilers
-===================================================
-
- - Added NAG compiler
-
-
-
-Bug Fixes since HDF5-1.10.0-patch1 release
-==================================
-
- Library
- -------
- - Outdated data structure was used in H5D_CHUNK_DEBUG blocks, causing
- compilation errors when H5D_CHUNK_DEBUG was defined. This is fixed.
-
- (BMR, 2017/04/04, HDFFV-8089)
-
- - SWMR implementation in the HDF5 1.10.0 and 1.10.0-patch1 releases has a
- broken metadata flush dependency that manifested itself with the following
- error at the end of the HDF5 error stack:
-
- H5Dint.c line 846 in H5D__swmr_setup(): dataspace chunk index must be 0
- for SWMR access, chunkno = 1
- major: Dataset
- minor: Bad value
-
- It was also reported at https://github.com/areaDetector/ADCore/issues/203
-
- The flush dependency is fixed in this release.
-
- - Changed the plugins dlopen option from RTLD_NOW to RTLD_LAZY
-
- (ABD, 2016/12/12, PR#201)
-
- - A number of issues were fixed when reading/writing from/to corrupted
- files to ensure that the library fails gracefully in these cases:
-
- * Writing to a corrupted file that has an object message which is
- incorrectly marked as shareable on disk results in a buffer overflow /
- invalid write instead of a clean error message.
-
- * Decoding data from a corrupted file with a dataset encoded with the
- H5Z_NBIT decoding can result in a code execution vulnerability under
- the context of the application using the HDF5 library.
-
- * When decoding an array datatype from a corrupted file, the HDF5 library
- fails to return an error in production if the number of dimensions
- decoded is greater than the maximum rank.
-
- * When decoding an "old style" array datatype from a corrupted file, the
- HDF5 library fails to return an error in production if the number of
- dimensions decoded is greater than the maximum rank.
-
- (NAF, 2016/10/06, HDFFV-9950, HDFFV-9951, HDFFV-9992, HDFFV-9993)
-
- - Fixed an error that would occur when copying an object with an attribute
- which is a compound datatype consisting of a variable length string.
-
- (VC, 2016/08/24, HDFFV-7991)
-
- - H5DOappend will no longer fail if a dataset has no append callback
- registered.
-
- (VC, 2016/08/14, HDFFV-9960)
-
- - Fixed an issue where H5Pset_alignment could result in misaligned blocks
- with some input combinations, causing an assertion failure in debug mode.
-
- (NAF, 2016/08/11, HDFFV-9948)
-
- - Fixed a problem where a plugin compiled into a DLL in the default plugin
- directory could not be found by the HDF5 library at runtime on Windows
- when the HDF5_PLUGIN_PATH environment variable was not set.
-
- (ABD, 2016/08/01, HDFFV-9706)
-
- - Fixed an error that would occur when calling H5Adelete on an attribute
- which is attached to an externally linked object in the target file and
- whose datatype is a committed datatype in the main file.
-
- (VC, 2016/07/06, HDFFV-9940)
-
- - (a) Throw an error instead of assertion when v1 btree level hits the 1
- byte limit.
- (b) Modifications to better handle error recovery when conversion by
- h5format_convert fails.
-
- (VC, 2016/05/29, HDFFV-9434)
-
- - Fixed a memory leak where an array used by the library to track SWMR
- read retries was unfreed.
-
- The leaked memory was small (on the order of a few tens of ints) and
- allocated per-file. The memory was allocated (and lost) only when a
- file was opened for SWMR access.
-
- (DER, 2016/04/27, HDFFV-9786)
-
- - Fixed a memory leak that could occur when opening a file for the first
- time (including creating) and the call fails.
-
- This occurred when the file-driver-specific info was not cleaned up.
- The amount of memory leaked varied with the file driver, but would
- normally be less than 1 kB.
-
- (DER, 2016/12/06, HDFFV-10168)
-
- - Fixed a failure in collective metadata writes.
-
- This failure only appeared when collective metadata writes
- were enabled (via H5Pset_coll_metadata_write()).
-
- (JRM, 2017/04/10, HDFFV-10055)
-
-
- Parallel Library
- ----------------
- - Fixed a bug that could occur when allocating a chunked dataset in parallel
- with an alignment set and an alignment threshold greater than the chunk
- size but less than or equal to the raw data aggregator size.
-
- (NAF, 2016/08/11, HDFFV-9969)
-
-
- Configuration
- -------------
- - Configuration will check for the strtoll and strtoull functions
- before using alternatives
-
- (ABD, 2017/03/17, PR#340)
-
- - CMake uses a Windows pdb directory variable if available and
- will generate both static and shared pdb files.
-
- (ABD, 2017/02/06, HDFFV-9875)
-
- - CMake now builds shared versions of tools.
-
- (ABD, 2017/02/01, HDFFV-10123)
-
- - Makefiles and test scripts have been updated to correctly remove files
- created when running "make check" and to avoid removing any files under
- source control. In-source builds followed by "make clean" and "make
- distclean" should result in the original source files.
- (LRK, 2017/01/17, HDFFV-10099)
-
- - The tools directory has been divided into two separate source and test
- directories. This resolves a build dependency and, as a result,
- 'make check' will no longer fail in the tools directory if 'make' was
- not executed first.
-
- (ABD, 2016/10/27, HDFFV-9719)
-
- - CMake: Fixed a timeout error that would occasionally occur when running
- the virtual file driver tests simultaneously due to test directory
- and file name collisions.
-
- (ABD, 2016/09/19, HDFFV-9431)
-
- - CMake: Fixed a command length overflow error by converting custom
- commands inside CMakeTest.cmake files into regular dependencies and
- targets.
-
- (ABD, 2016/07/12, HDFFV-9939)
-
- - Fixed a problem preventing HDF5 to be built on 32-bit CYGWIN by
- condensing cygwin configuration files into a single file and
- removing outdated compiler settings.
-
- (ABD, 2016/07/12, HDFFV-9946)
-
-
- Fortran
- --------
- - Changed H5S_ALL_F from INTEGER to INTEGER(HID_T)
-
- (MSB, 2016/10/14, HDFFV-9987)
-
-
- Tools
- -----
- - h5diff now correctly ignores strpad in comparing strings.
-
- (ABD, 2017/03/03, HDFFV-10128)
-
- - h5repack now correctly parses the command line filter options.
-
- (ABD, 2017/01/24, HDFFV-10046)
-
- - h5diff now correctly returns an error when it cannot read data due
- to an unavailable filter plugin.
-
- (ADB 2017/01/18, HDFFV-9994 )
-
- - Fixed an error in the compiler wrapper scripts (h5cc, h5fc, et al.)
- in which they would erroneously drop the file argument specified via
- the -o flag when the -o flag was specified before the -c flag on the
- command line, resulting in a failure to compile.
-
- (LRK, 2016/11/04, HDFFV-9938, HDFFV-9530)
-
- - h5repack User Defined (UD) filter parameters were not parsed correctly.
-
- The UD filter parameters were not being parsed correctly. Reworked coding
- section to parse the correct values and verify number of parameters.
-
- (ABD, 2016/10/19, HDFFV-9996, HDFFV-9974, HDFFV-9515, HDFFV-9039)
-
- - h5repack allows the --enable-error-stack option on the command line.
-
- (ADB, 2016/08/08, HDFFV-9775)
-
-
- C++ APIs
- --------
- - The member function H5Location::getNumObjs() is moved to
- class Group because the objects are in a group or a file only,
- and H5Object::getNumAttrs to H5Location to get the number of
- attributes at a given location.
-
- (BMR, 2017/03/17, PR#466)
-
- - Due to the change in the C API, the overloaded functions of
- PropList::setProperty now need const for some arguments. They are
- planned for deprecation and are replaced by new versions with proper
- consts.
-
- (BMR, 2017/03/17, PR#344)
-
- - The high-level API Packet Table (PT) did not write data correctly when
- the datatype is a compound type that has string type as one of the
- members. This problem started in 1.8.15, after the fix of HDFFV-9042
- was applied, which caused the Packet Table to use native type to access
- the data. It should be up to the application to specify whether the
- buffer to be read into memory is in the machine's native architecture.
- Thus, the PT is fixed to not use native type but to make a copy of the
- user's provided datatype during creation or the packet table's datatype
- during opening. If an application wishes to use native type to read the
- data, then the application will request that. However, the Packet Table
- doesn't provide a way to specify memory datatype in this release. This
- feature will be available in future releases.
-
- (BMR, 2016/10/27, HDFFV-9758)
-
- - The obsolete macros H5_NO_NAMESPACE and H5_NO_STD have been removed from
- the HDF5 C++ API library.
-
- (BMR, 2016/10/23, HDFFV-9532)
-
- - The problem where a user-defined function cannot access both, attribute
- and dataset, using only one argument is now fixed.
-
- (BMR, 2016/10/11, HDFFV-9920)
-
- - In-memory array information, ArrayType::rank and
- ArrayType::dimensions, were removed. This is an implementation
- detail and should not affect applications.
-
- (BMR, 2016/04/25, HDFFV-9725)
-
-
- Testing
- -------
- - Fixed a problem that caused tests using SWMR to occasionally fail when
- running "make check" using parallel make.
-
- (LRK, 2016/03/22, PR#338, PR#346, PR#358)
-
-
-Supported Platforms
-===================
-
- Linux 2.6.32-573.18.1.el6.ppc64 gcc (GCC) 4.4.7 20120313 (Red Hat 4.4.7-4)
- #1 SMP ppc64 GNU/Linux g++ (GCC) 4.4.7 20120313 (Red Hat 4.4.7-4)
- (ostrich) GNU Fortran (GCC) 4.4.7 20120313
- (Red Hat 4.4.7-4)
- IBM XL C/C++ V13.1
- IBM XL Fortran V15.1
-
- Linux 3.10.0-327.10.1.el7 GNU C (gcc), Fortran (gfortran), C++ (g++)
- #1 SMP x86_64 GNU/Linux compilers:
- (kituo/moohan) Version 4.8.5 20150623 (Red Hat 4.8.5-4)
- Version 4.9.3, Version 5.2.0
- Intel(R) C (icc), C++ (icpc), Fortran (icc)
- compilers:
- Version 15.0.3.187 Build 20150407
- MPICH 3.1.4 compiled with GCC 4.9.3
-
- SunOS 5.11 32- and 64-bit Sun C 5.12 SunOS_sparc
- (emu) Sun Fortran 95 8.6 SunOS_sparc
- Sun C++ 5.12 SunOS_sparc
-
- Windows 7 Visual Studio 2012 w/ Intel Fortran 15 (cmake)
- Visual Studio 2013 w/ Intel Fortran 15 (cmake)
- Visual Studio 2015 w/ Intel Fortran 16 (cmake)
-
- Windows 7 x64 Visual Studio 2012 w/ Intel Fortran 15 (cmake)
- Visual Studio 2013 w/ Intel Fortran 15 (cmake)
- Visual Studio 2015 w/ Intel Fortran 16 (cmake)
- Visual Studio 2015 w/ MSMPI 8 (cmake)
- Cygwin(CYGWIN_NT-6.1 2.8.0(0.309/5/3)
- gcc and gfortran compilers (GCC 5.4.0)
- (cmake and autotools)
-
- Windows 10 Visual Studio 2015 w/ Intel Fortran 16 (cmake)
- Cygwin(CYGWIN_NT-6.1 2.8.0(0.309/5/3)
- gcc and gfortran compilers (GCC 5.4.0)
- (cmake and autotools)
-
- Windows 10 x64 Visual Studio 2015 w/ Intel Fortran 16 (cmake)
-
- Mac OS X Mt. Lion 10.8.5 Apple clang/clang++ version 5.1 from Xcode 5.1
- 64-bit gfortran GNU Fortran (GCC) 4.8.2
- (swallow/kite) Intel icc/icpc/ifort version 15.0.3
-
- Mac OS X Mavericks 10.9.5 Apple clang/clang++ version 6.0 from Xcode 6.2
- 64-bit gfortran GNU Fortran (GCC) 4.9.2
- (wren/quail) Intel icc/icpc/ifort version 15.0.3
-
- Mac OS X Yosemite 10.10.5 Apple clang/clang++ version 6.1 from Xcode 7.0
- 64-bit gfortran GNU Fortran (GCC) 4.9.2
- (osx1010dev/osx1010test) Intel icc/icpc/ifort version 15.0.3
-
- Mac OS X El Capitan 10.11.6 Apple clang/clang++ version 7.3 from Xcode 7.3
- 64-bit gfortran GNU Fortran (GCC) 5.2.0
- (osx1010dev/osx1010test) Intel icc/icpc/ifort version 16.0.2
-
-
-Tested Configuration Features Summary
-=====================================
-
- In the tables below
- y = tested
- n = not tested in this release
- C = Cluster
- W = Workstation
- x = not working in this release
- dna = does not apply
- ( ) = footnote appears below second table
- <blank> = testing incomplete on this feature or platform
-
-Platform C F90/ F90 C++ zlib SZIP
- parallel F2003 parallel
-Solaris2.11 32-bit n y/y n y y y
-Solaris2.11 64-bit n y/n n y y y
-Windows 7 y y/y n y y y
-Windows 7 x64 y y/y y y y y
-Windows 7 Cygwin n y/n n y y y
-Windows 7 x64 Cygwin n y/n n y y y
-Windows 10 y y/y n y y y
-Windows 10 x64 y y/y n y y y
-Mac OS X Mountain Lion 10.8.5 64-bit n y/y n y y y
-Mac OS X Mavericks 10.9.5 64-bit n y/y n y y y
-Mac OS X Yosemite 10.10.5 64-bit n y/y n y y y
-Mac OS X El Capitan 10.11.6 64-bit n y/y n y y y
-CentOS 7.2 Linux 2.6.32 x86_64 PGI n y/y n y y y
-CentOS 7.2 Linux 2.6.32 x86_64 GNU y y/y y y y y
-CentOS 7.2 Linux 2.6.32 x86_64 Intel n y/y n y y y
-Linux 2.6.32-573.18.1.el6.ppc64 n y/y n y y y
-
-
-Platform Shared Shared Shared Thread-
- C libs F90 libs C++ libs safe
-Solaris2.11 32-bit y y y y
-Solaris2.11 64-bit y y y y
-Windows 7 y y y y
-Windows 7 x64 y y y y
-Windows 7 Cygwin n n n y
-Windows 7 x64 Cygwin n n n y
-Windows 10 y y y y
-Windows 10 x64 y y y y
-Mac OS X Mountain Lion 10.8.5 64-bit y n y y
-Mac OS X Mavericks 10.9.5 64-bit y n y y
-Mac OS X Yosemite 10.10.5 64-bit y n y y
-Mac OS X El Capitan 10.11.6 64-bit y n y y
-CentOS 7.2 Linux 2.6.32 x86_64 PGI y y y n
-CentOS 7.2 Linux 2.6.32 x86_64 GNU y y y y
-CentOS 7.2 Linux 2.6.32 x86_64 Intel y y y n
-Linux 2.6.32-573.18.1.el6.ppc64 y y y n
-
-Compiler versions for each platform are listed in the preceding
-"Supported Platforms" table.
-
-
-More Tested Platforms
-=====================
-
-The following platforms are not supported but have been tested for this release.
-
- Linux 2.6.32-573.22.1.el6 GNU C (gcc), Fortran (gfortran), C++ (g++)
- #1 SMP x86_64 GNU/Linux compilers:
- (mayll/platypus) Version 4.4.7 20120313
- Version 4.8.4
- PGI C, Fortran, C++ for 64-bit target on
- x86-64;
- Version 16.10-0
- Intel(R) C (icc), C++ (icpc), Fortran (icc)
- compilers:
- Version 15.0.3.187 (Build 20150407)
- MPICH 3.1.4 compiled with GCC 4.9.3
-
- Linux 3.10.0-327.18.2.el7 GNU C (gcc) and C++ (g++) compilers
- #1 SMP x86_64 GNU/Linux Version 4.8.5 20150623 (Red Hat 4.8.5-4)
- (jelly) with NAG Fortran Compiler Release 6.1(Tozai)
- Intel(R) C (icc) and C++ (icpc) compilers
- Version 15.0.3.187 (Build 20150407)
- with NAG Fortran Compiler Release 6.1(Tozai)
-
- Linux 2.6.32-573.18.1.el6.ppc64 MPICH mpich 3.1.4 compiled with
- #1 SMP ppc64 GNU/Linux IBM XL C/C++ for Linux, V13.1
- (ostrich) and IBM XL Fortran for Linux, V15.1
-
- Debian 8.4 3.16.0-4-amd64 #1 SMP Debian 3.16.36-1 x86_64 GNU/Linux
- gcc, g++ (Debian 4.9.2-10) 4.9.2
- GNU Fortran (Debian 4.9.2-10) 4.9.2
- (cmake and autotools)
-
- Fedora 24 4.7.2-201.fc24.x86_64 #1 SMP x86_64 x86_64 x86_64 GNU/Linux
- gcc, g++ (GCC) 6.1.1 20160621
- (Red Hat 6.1.1-3)
- GNU Fortran (GCC) 6.1.1 20160621
- (Red Hat 6.1.1-3)
- (cmake and autotools)
-
- Ubuntu 16.04.1 4.4.0-38-generic #57-Ubuntu SMP x86_64 GNU/Linux
- gcc, g++ (Ubuntu 5.4.0-6ubuntu1~16.04.2)
- 5.4.0 20160609
- GNU Fortran (Ubuntu 5.4.0-6ubuntu1~16.04.2)
- 5.4.0 20160609
- (cmake and autotools)
-
-
-Known Problems
-==============
-
- At present, metadata cache images may not be generated by parallel
- applications. Parallel applications can read files with metadata cache
- images, but since this is a collective operation, a deadlock is possible
- if one or more processes do not participate.
-
- Known problems in previous releases can be found in the HISTORY*.txt files
- in the HDF5 source. Please report any new problems found to
- help@hdfgroup.org.
-
-
-%%%%1.10.0-patch1%%%%
-
-
-HDF5 version 1.10.0-patch1 released on 2016-05-23
-================================================================================
-
-INTRODUCTION
-
-This document describes the differences between HDF5-1.8 series and
-HDF5 1.10.0 releases, and contains information on the platforms
-tested.
-
-Links to HDF5 1.10.0 source code can be found on The HDF Group's
-development FTP server at the following location:
-
- https://www.hdfgroup.org/HDF5/release/obtain5110.html
-
-User documentation can be accessed directly at this location:
-
- https://www.hdfgroup.org/HDF5/docNewFeatures/
-
-For more information, see the HDF5 home page:
-
- https://www.hdfgroup.org/HDF5/
-
-If you have any questions or comments, please send them to the HDF
-Help Desk:
-
- help@hdfgroup.org
-
-
-
-CONTENTS
-
-- New Features
-- Issues Addressed in this Release
-- Supported Platforms
-- Tested Configuration Features Summary
-- More Tested Platforms
-- Known Problems and Limitations
-
-
-
-New Features
-============
-This release supports the following features:
-
- Configuration
- -------------
- - API Compatibility with HDF5 1.8 Flag Was Added
-
- The 1.10 version of the HDF5 Library can be configured to operate
- identically to the 1.8 library with the --with-default-api-version=v18
- configure flag. This allows existing code to be compiled with the 1.10
- library without requiring immediate changes to the application source
- code. For additional configuration options and other details, see
- "API Compatibility Macros in HDF5" at
- https://www.hdfgroup.org/HDF5/doc/RM/APICompatMacros.html.
-
- - Autotools Configuration Has Been Extensively Reworked
-
- The autotools configuration options have been updated to allow more
- fine-grained control of the build options and to correct some bugs.
- See configure --help for comprehensive information on each option.
-
- Specific changes:
-
- * --enable-debug and --enable-production are no longer accepted.
- Use --enable-build-mode=(debug | production) instead. These set
- appropriate defaults for symbols, optimizations, and other
- configuration options. These defaults can be overridden by the
- user.
-
- * Extra debug output messages are no longer enabled with
- --enable-debug=<package list>. Use --enable-internal-debug=<pkg list>
- instead.
-
- * A new --enable-symbols option allows symbols to be generated
- independently of the build mode. --disable-symbols can be used
- to strip symbols from the binary.
-
- * A new --enable-asserts option sets/unsets NDEBUG. This is
- independent of the build mode. This also enables some extra
- low-overhead debug checks in the library.
-
- * A new --enable-profiling option sets profiling flags. This is
- independent of the build mode.
-
- * A new --enable-optimization option sets the optimization level.
- This is independent of the build mode.
-
- * Many of these options can take a flags string that will be used
- to build the library. This can be useful for specifying custom
- optimization flags such as -Os and -Ofast.
-
- * gnu C++ and Fortran use configure sub-files that update the
- build flags and turn on warnings. The increase in warnings when
- building these wrapper libraries is due to these flag changes
- and not to a decrease in code quality.
-
- * The option to clear file buffers has been removed. Any buffer that
- will eventually be written to disk will now always be memset
- to zero. This prevents the previous contents of the buffer from
- being written to the disk if the buffer contents are not
- completely overwritten, which has security implications.
-
- - LFS Changes
-
- The way the autotools handle large file support (LFS) has been
- overhauled in this release.
-
- * We assume ftello and fseeko exist
-
- * We no longer explicitly use the *64 I/O functions. Instead, we
- rely on a mapping provided by _FILE_OFFSET_BITS or its equivalent.
-
- * _LARGEFILE(64)_SOURCE is no longer exported via AM_CPPFLAGS.
-
-
-
- Parallel Library
- -----------------
- - Collective Metadata I/O
-
- Calls for HDF5 metadata can result in many small reads and writes.
- On metadata reads, collective metadata I/O can improve performance
- by allowing the library to perform optimizations when reading the
- metadata by having one rank read the data and broadcasting it to
- all other ranks.
-
- Collective metadata I/O improves metadata write performance through
- the construction of an MPI derived datatype that is then written
- collectively in a single call. For more information, see
- https://www.hdfgroup.org/HDF5/docNewFeatures/NewFeaturesCollectiveMetadataIoDocs.html.
-
-
-
- Library
- --------
- - Concurrent Access to HDF5 Files - Single Writer/ Multiple Reader (SWMR)
-
- The Single Writer/ Multiple Reader or SWMR feature enables users to
- read data concurrently while writing it. Communications between the
- processes and file locking are not required. The processes can run
- on the same or on different platforms as long as they share a common
- file system that is POSIX compliant. For more information, see the
- Single-Writer/Multiple-Reader (SWMR) documentation at
- https://www.hdfgroup.org/HDF5/docNewFeatures/NewFeaturesSwmrDocs.html.
-
- - Virtual Dataset (VDS)
-
- The VDS feature enables data to be accessed across HDF5 files
- using standard HDF5 objects such as groups and datasets without
- rewriting or rearranging the data. An HDF5 virtual dataset (VDS)
- is an HDF5 dataset that is composed of source HDF5 datasets in
- a predefined mapping. VDS can be used with the SWMR feature. For
- documentation, check
- https://www.hdfgroup.org/HDF5/docNewFeatures/NewFeaturesVirtualDatasetDocs.html.
-
- - Persistent Free File Space Tracking
-
- Usage patterns when working with an HDF5 file sometimes result in
- wasted space within the file. This can also impair access times
- when working with the resulting files. The new file space management
- feature provides strategies for managing space in a file to improve
- performance in both of these areas. For more information, see
- https://www.hdfgroup.org/HDF5/docNewFeatures/NewFeaturesFileSpaceMgmtDocs.html.
-
- - Version 3 Metadata Cache
-
- The version 3 metadata cache moves management of metadata I/O from
- the clients to the metadata cache proper. This change is essential for
- SWMR and other features that have yet to be released.
-
-
-
- C++ Library
- ------------
- - New Member Function Added to H5::ArrayType
-
- The assignment operator ArrayType::operator= was added because
- ArrayType has pointer data members.
-
- (BMR - 2016/03/07, HDFFV-9562)
-
-
-
- Tools
- ------
- - h5watch
-
- The h5watch tool allows users to output new records appended to
- a dataset under SWMR access as it grows. The functionality is
- similar to the Unix user command "tail" with the follow option,
- which outputs appended data as the file grows. For more
- information, see
- https://www.hdfgroup.org/HDF5/docNewFeatures/NewFeaturesSwmrDocs.html#Tools.
-
- - h5format_convert
-
- The h5format_convert tool allows users to convert the indexing
- type of a chunked dataset made with a 1.10.x version of the HDF5
- Library when the latest file format is used to the 1.8.x version 1 B-tree indexing
- type. For example, datasets created using SWMR access, can be
- converted to be accessed by the HDF5 1.18 library and tools. The
- tool does not rewrite raw data, but it does rewrite HDF5 metadata.
-
-
-
- High-Level APIs
- ----------------
- - H5DOappend
-
- The function appends data to a dataset along a specified dimension.
-
-
- C Packet Table API
- ------------------
- - Replacement of a Public Function with H5PTcreate
-
- The existing function H5PTcreate_fl limits applications so they
- can use the deflate compression only. The public function
- H5PTcreate has been added to replace H5PTcreate_fl. H5PTcreate
- takes a property list identifier to provide flexibility on
- creation properties.
-
- (BMR - 2016/03/04, HDFFV-8623)
-
- - New Public Functions: H5PTget_dataset and H5PTget_type
-
- Two accessor functions have been added. H5PTget_dataset returns
- the identifier of the dataset associated with the packet table,
- and H5PTget_type returns the identifier of the datatype used by
- the packet table.
-
- (BMR, 2016/03/04, HDFFV-8623)
-
- - Regarding #ifdef VLPT_REMOVED
-
- The #ifdef VLPT_REMOVED blocks have been removed from the packet
- table (PT) library source except for the following functions:
- + H5PTis_varlen() has been made available again
- + H5PTfree_vlen_readbuff() is now H5PTfree_vlen_buff()
-
- (BMR - 2016/03/04, HDFFV-442)
-
- C++ Packet Table API
- --------------------
- - New Constructor Added to FL_PacketTable
-
- An overloaded constructor has been added to FL_PacketTable and
- takes a property list identifier to provide flexibility on
- creation properties.
-
- (BMR - 2016/03/08, HDFFV-8623)
-
- - New Public Functions
-
- Two accessor wrappers are added to class PacketTable.
- PacketTable::GetDataset() returns the identifier of the dataset
- associated with the packet table, and PacketTable::GetDatatype()
- returns the identifier of the datatype that the packet table uses.
-
- (BMR - 2016/03/04, HDFFV-8623)
-
- - Member Functions with "char*" as an Argument
-
- Overloaded functions were added to provide the "const char*"
- argument; the existing version will be deprecated in future
- releases.
-
- (BMR - 2016/03/04, HDFFV-8623)
-
- - Regarding #ifdef VLPT_REMOVED
-
- The #ifdef VLPT_REMOVED blocks have been removed from the packet
- table library source code except for the following functions:
- + VL_PacketTable::IsVariableLength() was moved to PacketTable
- + VL_PacketTable::FreeReadBuff() is now PacketTable::FreeBuff()
-
- (BMR - 2016/03/04, HDFFV-442)
-
-
-
- Java Wrapper Library
- --------------------
-
- The Java HDF5 JNI library has been integrated into the HDF5 repository.
- The configure option is "--enable-java", and the CMake option is
- HDF5_BUILD_JAVA:BOOL=ON. The package hierarchy has changed from the
- HDF5 1.8 JNI, which was "ncsa.hdf.hdflib.hdf5", to HDF5 1.10,
- "hdf.hdflib.hdf5".
-
- A number of new APIs were added including some for VDS and SWMR.
-
-
-
- Other Important Changes
- -----------------------
-
- The hid_t type was changed from 32-bit to a 64-bit value.
-
-
-
-Issues Addressed in this Release Since 1.10.0
-=============================================
-
- - h5diff would return from a compare attributes abnormally if one of the datatypes
- was a vlen. This resulted in a memory leak as well as an incorrect report of
- attribute comparison.
-
- Fixed.
- (ADB - 2016/04/26, HDFFV-9784)
-
- - The JUnit-interface test may fail on Solaris platforms. The result of
- a test for verifying the content of the error stack to stdout is
- in a different order on Solaris then other platforms.
-
- This test is skipped on Solaris
- (ADB - 2016/04/21, HDFFV-9734)
-
- - When building HDF5 with Java using CMake and specifying Debug for CMAKE_BUILD_TYPE,
- there was a missing command argument for the tests of the examples.
-
- Fixed.
- (ADB - 2016/04/21, HDFFV-9743)
-
- - Changed h5diff to print a warning when a dataset is virtual, enabling
- the data to be compared. In addition h5repack failed to copy the data
- of a virtual dataset to the new file. Function H5D__get_space_status changed
- to correctly determine the H5D_space_status_t allocation value.
-
- CMake added the Fixed Array indexing tests that were only in the autotools
- test scripts.
-
- Fixed and tests added for vds issues.
- (ADB,NAF - 2016/04/21, HDFFV-9756)
-
- - CMake added the h5format_convert tool and tests that were only in the autotools
- build and test scripts. The autotools test script was reworked to allow CMake
- to execute the test suite in parallel.
-
- Also, h5clear tool and tests were added to the misc folder.
-
- Fixed.
- (ADB - 2016/04/21, HDFFV-9766)
-
- - CMake added the h5watch tool and argument tests that were only in the autotools
- build and test scripts. The POSIX only tests were not added to CMake.
-
- CMake HL tools files were refactored to move the CMake test scripts into each tool folder.
-
- Fixed.
- (ADB - 2016/04/21, HDFFV-9770)
-
- - Configure fails to detect valid real KINDs on FreeBSD 9.3 (i386) with Fortran enabled.
-
- Fixed. Added the exponential option to SELECTED_REAL_KIND to distinguish
- KINDs of same precision
- (MSB - 2016/05/14,HDFFV-9912)
-
-
- - Corrected the f90 H5AWRITE_F integer interface's buf to be INTENT(IN).
- (MSB - 2016/05/14)
-
- - Configure fails in sed command on FreeBSD 9.3 (i386) with Fortran enabled.
-
- Fixed.
- (MSB - 2016/05/14,HDFFV-9912)
-
- - Compile time error in H5f90global.F90 with IBM XL Fortran 14.1.0.13 on BG/Q with Fortran
- enabled.
-
- Fixed.
- (MSB - 2016/05/16,HDFFV-9917)
-
- - A cmake build with Fortran enabled does not install module h5fortkit
-
- Fixed.
- (MSB - 2016/05/23,HDFFV-9923)
-
-
-Issues Addressed in this Release Since alpha1
-=============================================
-
- - H5Pget_virtual_printf_gap, H5Pget_virtual_view, H5Pget_efile_prefix
-
- The correct access property list settings from the
- H5Pget_virtual_printf_gap, H5Pget_virtual_view, and
- H5Pget_efile_prefix function calls could not be retrieved
- using H5Dget_access_plist().
-
- Fixed.
-
- (DER and NAF - 2016/03/14, HDFFV-9716)
-
- - h5dump
-
- When h5dump was provided with the name of a non-existing file or
- when optional arguments were the last option on the command line,
- h5dump would segfault.
-
- Fixed.
-
- (ADB 2016/02/28 HDFFV-9639, HDFFV-9684)
-
- - No Error Message for Corrupt Metadata
-
- The HDF5 Library did not propagate an error when it encountered
- corrupt metadata in an HDF5 file. The issue was fixed for a
- specific file provided by a user. If you still see the problem,
- please contact help@hdfgroup.org
-
- Fixed.
-
- (MC - 2016/02/18, HDFFV-9670)
-
- - Problem Reading Chunked Datasets with a String Datatype Larger
- Than the Chunk Size in Bytes
-
- When the latest file format was used and when a chunked dataset
- was created with a datatype with the size bigger than a chunk
- size, the data could not be read back. The issue was reported
- for chunked datasets with a string datatype and was confirmed
- for other datatypes with the sizes bigger than the chunk size in
- bytes.
-
- Fixed.
-
- (JM - 2016/02/13, HDFFV-9672)
-
- - Control over the Location of External Files
-
- Users were unable to specify the locations of external files.
-
- Two APIs - H5Pget_efile_prefix and H5Pset_efile_prefix - were
- added so that users could specify the locations of external files.
-
- (DER - 2016/02/04, HDFFV-8740)
-
-
-
-Issues Addressed in this Release Since alpha0
-=============================================
- - h5format_convert
-
- The h5format_convert tool did not downgrade the version of the
- superblock.
-
- Fixed. The tool now will downgrade the version of the superblock.
-
- (EIP 2016/01/11)
-
- - Crashes with multiple threads: invalid pointers
-
- It was reported that alpha0 crashed when used with multiple
- threads. The issue exists in the HDF5 Library versions 1.8 and
- 1.9. The problem is related to a shared file pointer used in some
- miscellaneous data structures. The thread-safe library exposed
- paths in the library where a file pointer became invalid.
-
- The alpha1 release contains the fixes for the specific use case
- as described in HDFFV-9643. We will keep working on identifying
- and fixing other paths in the library with similar problems.
-
- (EIP - 2016/01/15, HDFFV-9643)
-
-
-
-Supported Platforms
-===================
-The following platforms are supported and have been tested for this release.
-They are built with the configure process unless specified otherwise.
-
- AIX 6.1 xlc/xlc_r 10.1.0.5
- (NASA G-ADA) xlC/xlC_r 10.1.0.5
- xlf90/xlf90_r 12.1.0.6
-
- Linux 2.6.32-573.22.1.el6 GNU C (gcc), Fortran (gfortran), C++ (g++)
- #1 SMP x86_64 GNU/Linux compilers:
- (mayll/platypus) Version 4.4.7 20120313 (Red Hat 4.4.7-16)
- Version 4.9.3, Version 5.2.0
- PGI C, Fortran, C++ for 64-bit target on
- x86-64;
- Version 15.7-0
- Intel(R) C (icc), C++ (icpc), Fortran (icc)
- compilers:
- Version 15.0.3.187 Build 20150407
- MPICH 3.1.4 compiled with GCC 4.9.3
-
- Linux 2.6.32-573.18.1.el6.ppc64 gcc (GCC) 4.4.7 20120313 (Red Hat 4.4.7-11)
- #1 SMP ppc64 GNU/Linux g++ (GCC) 4.4.7 20120313 (Red Hat 4.4.7-11)
- (ostrich) GNU Fortran (GCC) 4.4.7 20120313 (Red Hat 4.4.7-11)
- IBM XL C/C++ V13.1
- IBM XL Fortran V15.1
-
- Linux 3.10.0-327.10.1.el7 GNU C (gcc), Fortran (gfortran), C++ (g++)
- #1 SMP x86_64 GNU/Linux compilers:
- (kituo/moohan) Version 4.8.5 20150623 (Red Hat 4.8.5-4)
- Version 4.9.3, Version 5.2.0
- Intel(R) C (icc), C++ (icpc), Fortran (icc)
- compilers:
- Version 15.0.3.187 Build 20150407
- MPICH 3.1.4 compiled with GCC 4.9.3
-
- SunOS 5.11 32- and 64-bit Sun C 5.12 SunOS_sparc
- (emu) Sun Fortran 95 8.6 SunOS_sparc
- Sun C++ 5.12 SunOS_sparc
-
- Windows 7 Visual Studio 2012 w/ Intel Fortran 15 (cmake)
- Visual Studio 2013 w/ Intel Fortran 15 (cmake)
- Visual Studio 2015 w/ Intel Fortran 16 (cmake)
- Cygwin(CYGWIN_NT-6.1 2.2.1(0.289/5/3) gcc(4.9.3) compiler and gfortran)
- (cmake and autotools)
-
- Windows 7 x64 Visual Studio 2012 w/ Intel Fortran 15 (cmake)
- Visual Studio 2013 w/ Intel Fortran 15 (cmake)
- Visual Studio 2015 w/ Intel Fortran 16 (cmake)
-
- Windows 8.1 Visual Studio 2012 w/ Intel Fortran 15 (cmake)
- Visual Studio 2013 w/ Intel Fortran 15 (cmake)
-
- Windows 8.1 x64 Visual Studio 2012 w/ Intel Fortran 15 (cmake)
- Visual Studio 2013 w/ Intel Fortran 15 (cmake)
-
- Mac OS X Mt. Lion 10.8.5 Apple clang/clang++ version 5.1 from Xcode 5.1
- 64-bit gfortran GNU Fortran (GCC) 4.8.2
- (swallow/kite) Intel icc/icpc/ifort version 15.0.3
-
- Mac OS X Mavericks 10.9.5 Apple clang/clang++ version 6.0 from Xcode 6.2
- 64-bit gfortran GNU Fortran (GCC) 4.9.2
- (wren/quail) Intel icc/icpc/ifort version 15.0.3
-
- Mac OS X Yosemite 10.10.5 Apple clang/clang++ version 6.0 from Xcode 7.0
- 64-bit gfortran GNU Fortran (GCC) 4.9.2
- (osx1010dev/osx1010test) Intel icc/icpc/ifort version 15.0.3
-
- Mac OS X El Capitan 10.11.4 Apple clang/clang++ version 7.3.0 from Xcode 7.3
- 64-bit gfortran GNU Fortran (GCC) 5.2.0
- (osx1010dev/osx1010test) Intel icc/icpc/ifort version 15.0.3
-
-
-
-Tested Configuration Features Summary
-=====================================
-
- In the tables below
- y = tested
- n = not tested in this release
- C = Cluster
- W = Workstation
- x = not working in this release
- dna = does not apply
- ( ) = footnote appears below second table
- <blank> = testing incomplete on this feature or platform
-
-Platform C F90/ F90 C++ zlib SZIP
- parallel F2003 parallel
-SunOS 5.11 32-bit n y/y n y y y
-SunOS 5.11 64-bit n y/y n y y y
-Windows 7 y y/y n y y y
-Windows 7 x64 y y/y n y y y
-Windows 7 Cygwin n y/y n y y n
-Windows 8.1 n y/y n y y y
-Windows 8.1 x64 n y/y n y y y
-Mac OS X Mountain Lion 10.8.5 64-bit n y/y n y y y
-Mac OS X Mavericks 10.9.5 64-bit n y/y n y y y
-Mac OS X Yosemeti 10.10.5 64-bit n y/y n y y y
-AIX 6.1 32- and 64-bit n y/n n y y y
-CentOS 6.7 Linux 2.6.32 x86_64 GNU y y/y y y y y
-CentOS 6.7 Linux 2.6.32 x86_64 Intel n y/y n y y y
-CentOS 6.7 Linux 2.6.32 x86_64 PGI n y/y n y y y
-CentOS 7.1 Linux 3.10.0 x86_64 GNU y y/y y y y y
-CentOS 7.1 Linux 3.10.0 x86_64 Intel n y/y n y y y
-Linux 2.6.32-431.11.2.el6.ppc64 n y/n n y y y
-
-Platform Shared Shared Shared Thread-
- C libs F90 libs C++ libs safe
-SunOS 5.11 32-bit y y y y
-SunOS 5.11 64-bit y y y y
-Windows 7 y y y y
-Windows 7 x64 y y y y
-Windows 7 Cygwin n n n y
-Windows 8.1 y y y y
-Windows 8.1 x64 y y y y
-Mac OS X Mountain Lion 10.8.5 64-bit y n y y
-Mac OS X Mavericks 10.9.5 64-bit y n y y
-Mac OS X Yosemeti 10.10.5 64-bit y n y y
-AIX 6.1 32- and 64-bit y n n y
-CentOS 6.7 Linux 2.6.32 x86_64 GNU y y y y
-CentOS 6.7 Linux 2.6.32 x86_64 Intel y y y y
-CentOS 6.7 Linux 2.6.32 x86_64 PGI y y y y
-CentOS 7.1 Linux 3.10.0 x86_64 GNU y y y y
-CentOS 7.1 Linux 3.10.0 x86_64 Intel y y y y
-Linux 2.6.32-431.11.2.el6.ppc64 y y y y
-
-Compiler versions for each platform are listed in the preceding
-"Supported Platforms" table.
-
-
-
-More Tested Platforms
-=====================
-The following platforms are not supported but have been tested for this release.
-
- Linux 2.6.18-431.11.2.el6 g95 (GCC 4.0.3 (g95 0.94!)
- #1 SMP x86_64 GNU/Linux
- (platypus)
-
- Windows 7 Visual Studio 2008 (cmake)
-
- Windows 7 x64 Visual Studio 2008 (cmake)
-
- Windows 7 x64 Visual Studio 2010 (cmake) with SWMR using GPFS
-
- Windows 10 Visual Studio 2013 w/ Intel Fortran 15 (cmake)
-
- Windows 10 x64 Visual Studio 2013 w/ Intel Fortran 15 (cmake)
-
- Debian7.5.0 3.2.0-4-amd64 #1 SMP Debian 3.2.51-1 x86_64 GNU/Linux
- gcc (Debian 4.7.2-5) 4.7.2
- GNU Fortran (Debian 4.7.2-5) 4.7.2
- (cmake and autotools)
-
- Fedora20 3.15.3-200.fc20.x86_64 #1 SMP x86_64 x86_64 x86_64 GNU/Linux
- gcc (GCC) 4.8.3 20140624 (Red Hat 4.8.3-1)
- GNU Fortran (GCC) 4.8.3 20140624 (Red Hat 4.8.3-1)
- (cmake and autotools)
-
- SUSE 13.1 3.11.10-17-desktop #1 SMP PREEMPT x86_64 x86_64 x86_64 GNU/Linux
- gcc (SUSE Linux) 4.8.1
- GNU Fortran (SUSE Linux) 4.8.1
- (cmake and autotools)
-
- Ubuntu 14.04 3.13.0-35-generic #62-Ubuntu SMP x86_64 GNU/Linux
- gcc (Ubuntu/Linaro 4.9.1-0ubuntu1) 4.9.1
- GNU Fortran (Ubuntu/Linaro 4.9.1-0ubuntu1) 4.9.1
- (cmake and autotools)
-
- hopper.nersc.gov PrgEnv-gnu/5.2.40
- gcc (GCC) 4.9.2 20141030 (Cray Inc.)
- GNU Fortran (GCC) 4.9.2 20141030 (Cray Inc.)
- g++ (GCC) 4.9.2 20141030 (Cray Inc.)
-
-
-
-Known Problems and Limitations
-==============================
-This section contains the list of known problems and limitations introduced
-in this release of HDF5.
-
-Note: this list is not exhaustive of all known issues discovered in HDF5
-software to date. For a list of significant problems and known workarounds
-identified in past releases, please refer to:
-
-https://www.hdfgroup.org/HDF5/release/known_problems/
-
-The HDF Group also maintains a JIRA issue-tracking database which is used to
-capture all known issues which are too numerous to reasonably list in this
-document. The HDF Group is taking steps to make our JIRA issue database
-open to the public, and this section will refer to that database in a future
-release. In the meantime, please contact help@hdfgroup.org if you come across
-an issue not listed here or at the link above, and we will provide any
-information about known workarounds that we have or add it to our list of
-known issues if it is a new issue.
-
- - The flush/refresh test occasionally fails on OS X platforms. This is
- being investigated but no fix or workaround is available at this time.
- (DER - 2016/03/22, HDFFV-9731)
-
- - The VDS/SWMR test will fail with a segmentation fault if the library
- is built with --enable-using-memchecker. The is due to a VDS shutdown
- procedure freeing a shared resource too early when the memory
- checker changes are built. This problem does not arise when the
- memory checker changes are not used since the internal library free
- lists behave differently. The memory checker configure option should
- normally only be used under special circumstances so this should not
- affect most users. Users should be aware that the --enable-using-memchecker
- + VDS combination may cause a segfault, however, so Valgrind et al. may
- have to be used with an HDF5 library built without the feature if this
- proves to be a problem.
- (DER - 2016/03/21, HDFFV-9732)
-
- - SWMR feature limitations
- The SWMR feature will only work if an HDF5 file under SWMR access resides
- on a file system that obeys POSIX write() ordering semantics. Because of
- this, SWMR will not work on network file systems such as NFS or SMB/Windows
- file shares since those systems do not guarantee write odering. SWMR
- regression tests are likely to fail if run on a network file system. SWMR
- is currently not tested on Windows though it can be tested manually
- (some of the SWMR test programs are built by CMake), and there are no
- obvious reasons for it to not work on NTFS or GPFS.
- (EIP - 2016/03/20, HDFFV-9733)
-
- - VDS feature limitation
- Currently, the path to a VDS source file is interpreted as relative to the
- directory where the executable program runs and not to the HDF5 file with
- the VDS dataset unless a full path to the source file is specified during
- the mapping.
- (EIP - 2016/03/20, HDFFV-9724)
-
- - The H5Lexists API changed behavior in HDF5-1.10 when used with a file handle
- and root group name ("/"):
-
- H5Lexists(fileid, "/")
-
- In HDF5-1.8 it returns false (0) and in HDF5-1.10 it returns true (1).
- The documentation will be updated with information regarding this change.
- (LRK - 2016/03/30, HDFFV-8746)
-
-
-%%%%1.10.0%%%%
-
-HDF5 version 1.10.0 released on 2016-03-30
-================================================================================
-
-
-
-INTRODUCTION
-
-This document describes the differences between HDF5-1.8 series and
-HDF5 1.10.0 releases, and contains information on the platforms
-tested.
-
-Links to HDF5 1.10.0 source code can be found on The HDF Group's
-development FTP server at the following location:
-
- https://www.hdfgroup.org/HDF5/release/obtain5110.html
-
-User documentation can be accessed directly at this location:
-
- https://www.hdfgroup.org/HDF5/docNewFeatures/
-
-For more information, see the HDF5 home page:
-
- https://www.hdfgroup.org/HDF5/
-
-If you have any questions or comments, please send them to the HDF
-Help Desk:
-
- help@hdfgroup.org
-
-
-
-CONTENTS
-
-- New Features
-- Issues Addressed in this Release
-- Supported Platforms
-- Tested Configuration Features Summary
-- More Tested Platforms
-- Known Problems and Limitations
-
-
-
-New Features
-============
-This release supports the following features:
-
- Configuration
- -------------
- - API Compatibility with HDF5 1.8 Flag Was Added
-
- The 1.10 version of the HDF5 Library can be configured to operate
- identically to the 1.8 library with the --with-default-api-version=v18
- configure flag. This allows existing code to be compiled with the 1.10
- library without requiring immediate changes to the application source
- code. For additional configuration options and other details, see
- "API Compatibility Macros in HDF5" at
- https://www.hdfgroup.org/HDF5/doc/RM/APICompatMacros.html.
-
- - Autotools Configuration Has Been Extensively Reworked
-
- The autotools configuration options have been updated to allow more
- fine-grained control of the build options and to correct some bugs.
- See configure --help for comprehensive information on each option.
-
- Specific changes:
-
- * --enable-debug and --enable-production are no longer accepted.
- Use --enable-build-mode=(debug | production) instead. These set
- appropriate defaults for symbols, optimizations, and other
- configuration options. These defaults can be overridden by the
- user.
-
- * Extra debug output messages are no longer enabled with
- --enable-debug=<package list>. Use --enable-internal-debug=<pkg list>
- instead.
-
- * A new --enable-symbols option allows symbols to be generated
- independently of the build mode. --disable-symbols can be used
- to strip symbols from the binary.
-
- * A new --enable-asserts option sets/unsets NDEBUG. This is
- independent of the build mode. This also enables some extra
- low-overhead debug checks in the library.
-
- * A new --enable-profiling option sets profiling flags. This is
- independent of the build mode.
-
- * A new --enable-optimization option sets the optimization level.
- This is independent of the build mode.
-
- * Many of these options can take a flags string that will be used
- to build the library. This can be useful for specifying custom
- optimization flags such as -Os and -Ofast.
-
- * gnu C++ and Fortran use configure sub-files that update the
- build flags and turn on warnings. The increase in warnings when
- building these wrapper libraries is due to these flag changes
- and not to a decrease in code quality.
-
- * The option to clear file buffers has been removed. Any buffer that
- will eventually be written to disk will now always be memset
- to zero. This prevents the previous contents of the buffer from
- being written to the disk if the buffer contents are not
- completely overwritten, which has security implications.
-
- - LFS Changes
-
- The way the autotools handle large file support (LFS) has been
- overhauled in this release.
-
- * We assume ftello and fseeko exist
-
- * We no longer explicitly use the *64 I/O functions. Instead, we
- rely on a mapping provided by _FILE_OFFSET_BITS or its equivalent.
-
- * _LARGEFILE(64)_SOURCE is no longer exported via AM_CPPFLAGS.
-
-
-
- Parallel Library
- -----------------
- - Collective Metadata I/O
-
- Calls for HDF5 metadata can result in many small reads and writes.
- On metadata reads, collective metadata I/O can improve performance
- by allowing the library to perform optimizations when reading the
- metadata by having one rank read the data and broadcasting it to
- all other ranks.
-
- Collective metadata I/O improves metadata write performance through
- the construction of an MPI derived datatype that is then written
- collectively in a single call. For more information, see
- https://www.hdfgroup.org/HDF5/docNewFeatures/NewFeaturesCollectiveMetadataIoDocs.html.
-
-
-
- Library
- --------
- - Concurrent Access to HDF5 Files - Single Writer/ Multiple Reader (SWMR)
-
- The Single Writer/ Multiple Reader or SWMR feature enables users to
- read data concurrently while writing it. Communications between the
- processes and file locking are not required. The processes can run
- on the same or on different platforms as long as they share a common
- file system that is POSIX compliant. For more information, see the
- Single-Writer/Multiple-Reader (SWMR) documentation at
- https://www.hdfgroup.org/HDF5/docNewFeatures/NewFeaturesSwmrDocs.html.
-
- - Virtual Dataset (VDS)
-
- The VDS feature enables data to be accessed across HDF5 files
- using standard HDF5 objects such as groups and datasets without
- rewriting or rearranging the data. An HDF5 virtual dataset (VDS)
- is an HDF5 dataset that is composed of source HDF5 datasets in
- a predefined mapping. VDS can be used with the SWMR feature. For
- documentation, check
- https://www.hdfgroup.org/HDF5/docNewFeatures/NewFeaturesVirtualDatasetDocs.html.
-
- - Persistent Free File Space Tracking
-
- Usage patterns when working with an HDF5 file sometimes result in
- wasted space within the file. This can also impair access times
- when working with the resulting files. The new file space management
- feature provides strategies for managing space in a file to improve
- performance in both of these areas. For more information, see
- https://www.hdfgroup.org/HDF5/docNewFeatures/NewFeaturesFileSpaceMgmtDocs.html.
-
- - Version 3 Metadata Cache
-
- The version 3 metadata cache moves management of metadata I/O from
- the clients to the metadata cache proper. This change is essential for
- SWMR and other features that have yet to be released.
-
-
-
- C++ Library
- ------------
- - New Member Function Added to H5::ArrayType
-
- The assignment operator ArrayType::operator= was added because
- ArrayType has pointer data members.
-
- (BMR - 2016/03/07, HDFFV-9562)
-
-
-
- Tools
- ------
- - h5watch
-
- The h5watch tool allows users to output new records appended to
- a dataset under SWMR access as it grows. The functionality is
- similar to the Unix user command "tail" with the follow option,
- which outputs appended data as the file grows. For more
- information, see
- https://www.hdfgroup.org/HDF5/docNewFeatures/NewFeaturesSwmrDocs.html#Tools.
-
- - h5format_convert
-
- The h5format_convert tool allows users to convert the indexing
- type of a chunked dataset made with a 1.10.x version of the HDF5
- Library when the latest file format is used to the 1.8.x version 1 B-tree indexing
- type. For example, datasets created using SWMR access, can be
- converted to be accessed by the HDF5 1.18 library and tools. The
- tool does not rewrite raw data, but it does rewrite HDF5 metadata.
-
-
-
- High-Level APIs
- ----------------
- - H5DOappend
-
- The function appends data to a dataset along a specified dimension.
-
-
- C Packet Table API
- ------------------
- - Replacement of a Public Function with H5PTcreate
-
- The existing function H5PTcreate_fl limits applications so they
- can use the deflate compression only. The public function
- H5PTcreate has been added to replace H5PTcreate_fl. H5PTcreate
- takes a property list identifier to provide flexibility on
- creation properties.
-
- (BMR - 2016/03/04, HDFFV-8623)
-
- - New Public Functions: H5PTget_dataset and H5PTget_type
-
- Two accessor functions have been added. H5PTget_dataset returns
- the identifier of the dataset associated with the packet table,
- and H5PTget_type returns the identifier of the datatype used by
- the packet table.
-
- (BMR, 2016/03/04, HDFFV-8623)
-
- - Regarding #ifdef VLPT_REMOVED
-
- The #ifdef VLPT_REMOVED blocks have been removed from the packet
- table (PT) library source except for the following functions:
- + H5PTis_varlen() has been made available again
- + H5PTfree_vlen_readbuff() is now H5PTfree_vlen_buff()
-
- (BMR - 2016/03/04, HDFFV-442)
-
- C++ Packet Table API
- --------------------
- - New Constructor Added to FL_PacketTable
-
- An overloaded constructor has been added to FL_PacketTable and
- takes a property list identifier to provide flexibility on
- creation properties.
-
- (BMR - 2016/03/08, HDFFV-8623)
-
- - New Public Functions
-
- Two accessor wrappers are added to class PacketTable.
- PacketTable::GetDataset() returns the identifier of the dataset
- associated with the packet table, and PacketTable::GetDatatype()
- returns the identifier of the datatype that the packet table uses.
-
- (BMR - 2016/03/04, HDFFV-8623)
-
- - Member Functions with "char*" as an Argument
-
- Overloaded functions were added to provide the "const char*"
- argument; the existing version will be deprecated in future
- releases.
-
- (BMR - 2016/03/04, HDFFV-8623)
-
- - Regarding #ifdef VLPT_REMOVED
-
- The #ifdef VLPT_REMOVED blocks have been removed from the packet
- table library source code except for the following functions:
- + VL_PacketTable::IsVariableLength() was moved to PacketTable
- + VL_PacketTable::FreeReadBuff() is now PacketTable::FreeBuff()
-
- (BMR - 2016/03/04, HDFFV-442)
-
-
-
- Java Wrapper Library
- --------------------
-
- The Java HDF5 JNI library has been integrated into the HDF5 repository.
- The configure option is "--enable-java", and the CMake option is
- HDF5_BUILD_JAVA:BOOL=ON. The package hierarchy has changed from the
- HDF5 1.8 JNI, which was "ncsa.hdf.hdflib.hdf5", to HDF5 1.10,
- "hdf.hdflib.hdf5".
-
- A number of new APIs were added including some for VDS and SWMR.
-
-
-
- Other Important Changes
- -----------------------
-
- The hid_t type was changed from 32-bit to a 64-bit value.
-
-
-
-Issues Addressed in this Release Since alpha1
-=============================================
-
- - H5Pget_virtual_printf_gap, H5Pget_virtual_view, H5Pget_efile_prefix
-
- The correct access property list settings from the
- H5Pget_virtual_printf_gap, H5Pget_virtual_view, and
- H5Pget_efile_prefix function calls could not be retrieved
- using H5Dget_access_plist().
-
- Fixed.
-
- (DER and NAF - 2016/03/14, HDFFV-9716)
-
- - h5dump
-
- When h5dump was provided with the name of a non-existing file or
- when optional arguments were the last option on the command line,
- h5dump would segfault.
-
- Fixed.
-
- (ADB 2016/02/28 HDFFV-9639, HDFFV-9684)
-
- - No Error Message for Corrupt Metadata
-
- The HDF5 Library did not propagate an error when it encountered
- corrupt metadata in an HDF5 file. The issue was fixed for a
- specific file provided by a user. If you still see the problem,
- please contact help@hdfgroup.org
-
- Fixed.
-
- (MC - 2016/02/18, HDFFV-9670)
-
- - Problem Reading Chunked Datasets with a String Datatype Larger
- Than the Chunk Size in Bytes
-
- When the latest file format was used and when a chunked dataset
- was created with a datatype with the size bigger than a chunk
- size, the data could not be read back. The issue was reported
- for chunked datasets with a string datatype and was confirmed
- for other datatypes with the sizes bigger than the chunk size in
- bytes.
-
- Fixed.
-
- (JM - 2016/02/13, HDFFV-9672)
-
- - Control over the Location of External Files
-
- Users were unable to specify the locations of external files.
-
- Two APIs - H5Pget_efile_prefix and H5Pset_efile_prefix - were
- added so that users could specify the locations of external files.
-
- (DER - 2016/02/04, HDFFV-8740)
-
-
-
-Issues Addressed in this Release Since alpha0
-=============================================
- - h5format_convert
-
- The h5format_convert tool did not downgrade the version of the
- superblock.
-
- Fixed. The tool now will downgrade the version of the superblock.
-
- (EIP 2016/01/11)
-
- - Crashes with multiple threads: invalid pointers
-
- It was reported that alpha0 crashed when used with multiple
- threads. The issue exists in the HDF5 Library versions 1.8 and
- 1.9. The problem is related to a shared file pointer used in some
- miscellaneous data structures. The thread-safe library exposed
- paths in the library where a file pointer became invalid.
-
- The alpha1 release contains the fixes for the specific use case
- as described in HDFFV-9643. We will keep working on identifying
- and fixing other paths in the library with similar problems.
-
- (EIP - 2016/01/15, HDFFV-9643)
-
-
-
-Supported Platforms
-===================
-The following platforms are supported and have been tested for this release.
-They are built with the configure process unless specified otherwise.
-
- AIX 6.1 xlc/xlc_r 10.1.0.5
- (NASA G-ADA) xlC/xlC_r 10.1.0.5
- xlf90/xlf90_r 12.1.0.6
-
- Linux 2.6.32-573.18.1.el6 GNU C (gcc), Fortran (gfortran), C++ (g++)
- #1 SMP x86_64 GNU/Linux compilers:
- (mayll/platypus) Version 4.4.7 20120313 (Red Hat 4.4.7-16)
- Version 4.9.3, Version 5.2.0
- PGI C, Fortran, C++ for 64-bit target on
- x86-64;
- Version 15.7-0
- Intel(R) C (icc), C++ (icpc), Fortran (icc)
- compilers:
- Version 15.0.3.187 Build 20150407
- MPICH 3.1.4 compiled with GCC 4.9.3
-
- Linux 2.6.32-504.8.1.el6.ppc64 gcc (GCC) 4.4.7 20120313 (Red Hat 4.4.7-11)
- #1 SMP ppc64 GNU/Linux g++ (GCC) 4.4.7 20120313 (Red Hat 4.4.7-11)
- (ostrich) GNU Fortran (GCC) 4.4.7 20120313 (Red Hat 4.4.7-11)
- IBM XL C/C++ V13.1
- IBM XL Fortran V15.1
-
- Linux 3.10.0-327.10.1.el7 GNU C (gcc), Fortran (gfortran), C++ (g++)
- #1 SMP x86_64 GNU/Linux compilers:
- (kituo/moohan) Version 4.8.5 20150623 (Red Hat 4.8.5-4)
- Version 4.9.3, Version 5.2.0
- Intel(R) C (icc), C++ (icpc), Fortran (icc)
- compilers:
- Version 15.0.3.187 Build 20150407
- MPICH 3.1.4 compiled with GCC 4.9.3
-
- SunOS 5.11 32- and 64-bit Sun C 5.12 SunOS_sparc
- (emu) Sun Fortran 95 8.6 SunOS_sparc
- Sun C++ 5.12 SunOS_sparc
-
- Windows 7 Visual Studio 2012 w/ Intel Fortran 15 (cmake)
- Visual Studio 2013 w/ Intel Fortran 15 (cmake)
- Visual Studio 2015 w/ Intel Fortran 16 (cmake)
- Cygwin(CYGWIN_NT-6.1 2.2.1(0.289/5/3) gcc(4.9.3) compiler and gfortran)
- (cmake and autotools)
-
- Windows 7 x64 Visual Studio 2012 w/ Intel Fortran 15 (cmake)
- Visual Studio 2013 w/ Intel Fortran 15 (cmake)
- Visual Studio 2015 w/ Intel Fortran 16 (cmake)
-
- Windows 8.1 Visual Studio 2012 w/ Intel Fortran 15 (cmake)
- Visual Studio 2013 w/ Intel Fortran 15 (cmake)
-
- Windows 8.1 x64 Visual Studio 2012 w/ Intel Fortran 15 (cmake)
- Visual Studio 2013 w/ Intel Fortran 15 (cmake)
-
- Mac OS X Mt. Lion 10.8.5 Apple clang/clang++ version 5.1 from Xcode 5.1
- 64-bit gfortran GNU Fortran (GCC) 4.8.2
- (swallow/kite) Intel icc/icpc/ifort version 15.0.3
-
- Mac OS X Mavericks 10.9.5 Apple clang/clang++ version 6.0 from Xcode 6.2.0
- 64-bit gfortran GNU Fortran (GCC) 4.9.2
- (wren/quail) Intel icc/icpc/ifort version 15.0.3
-
- Mac OS X Yosemite 10.10.5 Apple clang/clang++ version 6.0 from Xcode 7.0.0
- 64-bit gfortran GNU Fortran (GCC) 4.9.2
- (osx1010dev/osx1010test) Intel icc/icpc/ifort version 15.0.3
-
- Mac OS X El Capitan 10.11.3 Apple clang/clang++ version 7.0.2 from Xcode 7.0.2
- 64-bit gfortran GNU Fortran (GCC) 5.2.0
- (osx1010dev/osx1010test) Intel icc/icpc/ifort version 15.0.3
-
-
-
-Tested Configuration Features Summary
-=====================================
-
- In the tables below
- y = tested
- n = not tested in this release
- C = Cluster
- W = Workstation
- x = not working in this release
- dna = does not apply
- ( ) = footnote appears below second table
- <blank> = testing incomplete on this feature or platform
-
-Platform C F90/ F90 C++ zlib SZIP
- parallel F2003 parallel
-SunOS 5.11 32-bit n y/y n y y y
-SunOS 5.11 64-bit n y/y n y y y
-Windows 7 y y/y n y y y
-Windows 7 x64 y y/y n y y y
-Windows 7 Cygwin n y/y n y y n
-Windows 8.1 n y/y n y y y
-Windows 8.1 x64 n y/y n y y y
-Mac OS X Mountain Lion 10.8.5 64-bit n y/y n y y y
-Mac OS X Mavericks 10.9.5 64-bit n y/y n y y y
-Mac OS X Yosemeti 10.10.5 64-bit n y/y n y y y
-AIX 6.1 32- and 64-bit n y/n n y y y
-CentOS 6.7 Linux 2.6.32 x86_64 GNU y y/y y y y y
-CentOS 6.7 Linux 2.6.32 x86_64 Intel n y/y n y y y
-CentOS 6.7 Linux 2.6.32 x86_64 PGI n y/y n y y y
-CentOS 7.1 Linux 3.10.0 x86_64 GNU y y/y y y y y
-CentOS 7.1 Linux 3.10.0 x86_64 Intel n y/y n y y y
-Linux 2.6.32-431.11.2.el6.ppc64 n y/n n y y y
-
-Platform Shared Shared Shared Thread-
- C libs F90 libs C++ libs safe
-SunOS 5.11 32-bit y y y y
-SunOS 5.11 64-bit y y y y
-Windows 7 y y y y
-Windows 7 x64 y y y y
-Windows 7 Cygwin n n n y
-Windows 8.1 y y y y
-Windows 8.1 x64 y y y y
-Mac OS X Mountain Lion 10.8.5 64-bit y n y y
-Mac OS X Mavericks 10.9.5 64-bit y n y y
-Mac OS X Yosemeti 10.10.5 64-bit y n y y
-AIX 6.1 32- and 64-bit y n n y
-CentOS 6.7 Linux 2.6.32 x86_64 GNU y y y y
-CentOS 6.7 Linux 2.6.32 x86_64 Intel y y y y
-CentOS 6.7 Linux 2.6.32 x86_64 PGI y y y y
-CentOS 7.1 Linux 3.10.0 x86_64 GNU y y y y
-CentOS 7.1 Linux 3.10.0 x86_64 Intel y y y y
-Linux 2.6.32-431.11.2.el6.ppc64 y y y y
-
-Compiler versions for each platform are listed in the preceding
-"Supported Platforms" table.
-
-
-
-More Tested Platforms
-=====================
-The following platforms are not supported but have been tested for this release.
-
- Linux 2.6.18-431.11.2.el6 g95 (GCC 4.0.3 (g95 0.94!)
- #1 SMP x86_64 GNU/Linux
- (platypus)
-
- Windows 7 Visual Studio 2008 (cmake)
-
- Windows 7 x64 Visual Studio 2008 (cmake)
-
- Windows 7 x64 Visual Studio 2010 (cmake) with SWMR using GPFS
-
- Windows 10 Visual Studio 2013 w/ Intel Fortran 15 (cmake)
-
- Windows 10 x64 Visual Studio 2013 w/ Intel Fortran 15 (cmake)
-
- Debian7.5.0 3.2.0-4-amd64 #1 SMP Debian 3.2.51-1 x86_64 GNU/Linux
- gcc (Debian 4.7.2-5) 4.7.2
- GNU Fortran (Debian 4.7.2-5) 4.7.2
- (cmake and autotools)
-
- Fedora20 3.15.3-200.fc20.x86_64 #1 SMP x86_64 x86_64 x86_64 GNU/Linux
- gcc (GCC) 4.8.3 20140624 (Red Hat 4.8.3-1)
- GNU Fortran (GCC) 4.8.3 20140624 (Red Hat 4.8.3-1)
- (cmake and autotools)
-
- SUSE 13.1 3.11.10-17-desktop #1 SMP PREEMPT x86_64 x86_64 x86_64 GNU/Linux
- gcc (SUSE Linux) 4.8.1
- GNU Fortran (SUSE Linux) 4.8.1
- (cmake and autotools)
-
- Ubuntu 14.04 3.13.0-35-generic #62-Ubuntu SMP x86_64 GNU/Linux
- gcc (Ubuntu/Linaro 4.9.1-0ubuntu1) 4.9.1
- GNU Fortran (Ubuntu/Linaro 4.9.1-0ubuntu1) 4.9.1
- (cmake and autotools)
-
- hopper.nersc.gov PrgEnv-gnu/5.2.40
- gcc (GCC) 4.9.2 20141030 (Cray Inc.)
- GNU Fortran (GCC) 4.9.2 20141030 (Cray Inc.)
- g++ (GCC) 4.9.2 20141030 (Cray Inc.)
-
-
-
-Known Problems and Limitations
-==============================
-This section contains the list of known problems and limitations introduced
-in this release of HDF5.
-
-Note: this list is not exhaustive of all known issues discovered in HDF5
-software to date. For a list of significant problems and known workarounds
-identified in past releases, please refer to:
-
-https://www.hdfgroup.org/HDF5/release/known_problems/
-
-The HDF Group also maintains a JIRA issue-tracking database which is used to
-capture all known issues which are too numerous to reasonably list in this
-document. The HDF Group is taking steps to make our JIRA issue database
-open to the public, and this section will refer to that database in a future
-release. In the meantime, please contact help@hdfgroup.org if you come across
-an issue not listed here or at the link above, and we will provide any
-information about known workarounds that we have or add it to our list of
-known issues if it is a new issue.
-
- - The JUnit-interface test may fail on Solaris platforms. The result of
- a test for verifying the content of the error stack to stdout is
- in a different order on Solaris then other platforms. Use make -i option
- to test beyond the java/test folder.
- (ADB - 2016/03/22, HDFFV-9734)
-
- - The flush/refresh test occasionally fails on OS X platforms. This is
- being investigated but no fix or workaround is available at this time.
- (DER - 2016/03/22, HDFFV-9731)
-
- - The VDS/SWMR test will fail with a segmentation fault if the library
- is built with --enable-using-memchecker. The is due to a VDS shutdown
- procedure freeing a shared resource too early when the memory
- checker changes are built. This problem does not arise when the
- memory checker changes are not used since the internal library free
- lists behave differently. The memory checker configure option should
- normally only be used under special circumstances so this should not
- affect most users. Users should be aware that the --enable-using-memchecker
- + VDS combination may cause a segfault, however, so Valgrind et al. may
- have to be used with an HDF5 library built without the feature if this
- proves to be a problem.
- (DER - 2016/03/21, HDFFV-9732)
-
- - SWMR feature limitations
- The SWMR feature will only work if an HDF5 file under SWMR access resides
- on a file system that obeys POSIX write() ordering semantics. Because of
- this, SWMR will not work on network file systems such as NFS or SMB/Windows
- file shares since those systems do not guarantee write odering. SWMR
- regression tests are likely to fail if run on a network file system. SWMR
- is currently not tested on Windows though it can be tested manually
- (some of the SWMR test programs are built by CMake), and there are no
- obvious reasons for it to not work on NTFS or GPFS.
- (EIP - 2016/03/20, HDFFV-9733)
-
- - VDS feature limitation
- Currently, the path to a VDS source file is interpreted as relative to the
- directory where the executable program runs and not to the HDF5 file with
- the VDS dataset unless a full path to the source file is specified during
- the mapping.
- (EIP - 2016/03/20, HDFFV-9724)
-
- - When building HDF5 with Java using CMake and specifying Debug for CMAKE_BUILD_TYPE,
- there is a missing command argument for the tests of the examples.
-
- This error can be avoided by not building Java with Debug, HDF5_BUILD_JAVA:BOOL=OFF,
- or not building Examples, HDF5_BUILD_EXAMPLES:BOOL=OFF.
- (LRK - 2016/03/30, HDFFV-9743)
-
- - The H5Lexists API changed behavior in HDF5-1.10 when used with a file handle
- and root group name ("/"):
-
- H5Lexists(fileid, "/")
-
- In HDF5-1.8 it returns false (0) and in HDF5-1.10 it returns true (1).
- The documentation will be updated with information regarding this change.
- (LRK - 2016/03/30, HDFFV-8746)
-
diff --git a/release_docs/HISTORY-1_12.txt b/release_docs/HISTORY-1_12.txt
deleted file mode 100644
index 6d0c1e2..0000000
--- a/release_docs/HISTORY-1_12.txt
+++ /dev/null
@@ -1,628 +0,0 @@
-HDF5 History
-============
-
-This file contains development history of the HDF5 1.12 branch
-
-01. Release Information for hdf5-1.12.0
-
-[Search on the string '%%%%' for section breaks of each release.]
-
-%%%%1.12.0%%%%
-
-HDF5 version 1.12.0 released on 2020-02-28
-================================================================================
-
-
-INTRODUCTION
-
-This document describes the new features introduced in the HDF5 1.12.0 release.
-It contains information on the platforms tested and known problems in this
-release. For more details check the HISTORY*.txt files in the HDF5 source.
-
-Note that documentation in the links below will be updated at the time of the
-release.
-
-Links to HDF5 documentation can be found on The HDF5 web page:
-
- https://portal.hdfgroup.org/display/HDF5/HDF5
-
-The official HDF5 releases can be obtained from:
-
- https://www.hdfgroup.org/downloads/hdf5/
-
-More information about the new features can be found at:
-
- https://portal.hdfgroup.org/display/HDF5/New+Features+in+HDF5+Release+1.12
-
-If you have any questions or comments, please send them to the HDF Help Desk:
-
- help@hdfgroup.org
-
-
-CONTENTS
-
-- New Features
-- Support for new platforms and languages
-- Bug Fixes since HDF5-1.12.0-alpha1
-- Major Bug Fixes since HDF5-1.10.0
-- Supported Platforms
-- Tested Configuration Features Summary
-- More Tested Platforms
-- Known Problems
-- CMake vs. Autotools installations
-
-
-New Features
-============
-
- Configuration:
- -------------
- - Added test script for file size compare
-
- If CMake minimum version is at least 3.14, the fileCompareTest.cmake
- script will compare file sizes.
-
- (ADB - 2020/02/24, HDFFV-11036)
-
- - Update CMake minimum version to 3.12
-
- Updated CMake minimum version to 3.12 and added version checks
- for Windows features.
-
- (ADB - 2020/02/05, TRILABS-142)
-
- - Fixed CMake include properties for Fortran libraries
-
- Corrected the library properties for Fortran to use the
- correct path for the Fortran module files.
-
- (ADB - 2020/02/04, HDFFV-11012)
-
- - Added common warnings files for gnu and intel
-
- Added warnings files to use one common set of flags
- during configure for both autotools and CMake build
- systems. The initial implementation only affects a
- general set of flags for gnu and intel compilers.
-
- (ADB - 2020/01/17)
-
- - Added new options to CMake for control of testing
-
- Added CMake options (default ON);
- HDF5_TEST_SERIAL AND/OR HDF5_TEST_PARALLEL
- combined with:
- HDF5_TEST_TOOLS
- HDF5_TEST_EXAMPLES
- HDF5_TEST_SWMR
- HDF5_TEST_FORTRAN
- HDF5_TEST_CPP
- HDF5_TEST_JAVA
-
- (ADB - 2020/01/15, HDFFV-11001)
-
- - Added Clang sanitizers to CMake for analyzer support if compiler is clang.
-
- Added CMake code and files to execute the Clang sanitizers if
- HDF5_ENABLE_SANITIZERS is enabled and the USE_SANITIZER option
- is set to one of the following:
- Address
- Memory
- MemoryWithOrigins
- Undefined
- Thread
- Leak
- 'Address;Undefined'
-
- (ADB - 2019/12/12, TRILAB-135)
-
- - Update CMake for VS2019 support
-
- CMake added support for VS2019 in version 3.15. Changes to the CMake
- generator setting required changes to scripts. Also updated version
- references in CMake files as necessary.
-
- (ADB - 2019/11/18, HDFFV-10962)
-
-
- Library:
- --------
- - Refactored public exposure of haddr_t type in favor of "object tokens"
-
- To better accommodate HDF5 VOL connectors where "object addresses in a file"
- may not make much sense, the following changes were made to the library:
-
- * Introduced new H5O_token_t "object token" type, which represents a
- unique and permanent identifier for referencing an HDF5 object within
- a container; these "object tokens" are meant to replace object addresses.
- Along with the new type, a new H5Oopen_by_token API call was introduced
- to open an object by a token, similar to how object addresses were
- previously used with H5Oopen_by_addr.
-
- * Introduced new H5Lget_info2, H5Lget_info_by_idx2, H5Literate2, H5Literate_by_name2,
- H5Lvisit2 and H5Lvisit_by_name2 API calls, along with their associated H5L_info2_t
- struct and H5L_iterate2_t callback function, which work with the newly-introduced
- object tokens, instead of object addresses. The original functions have been
- renamed to version 1 functions and are deprecated in favor of the new version 2
- functions. The H5L_info_t and H5L_iterate_t types have been renamed to version 1
- types and are now deprecated in favor of their version 2 counterparts. For each of
- the functions and types, compatibility macros take place of the original symbols.
-
- * Introduced new H5Oget_info3, H5Oget_info_by_name3, H5Oget_info_by_idx3,
- H5Ovisit3 and H5Ovisit_by_name3 API calls, along with their associated H5O_info2_t
- struct and H5O_iterate2_t callback function, which work with the newly-introduced
- object tokens, instead of object addresses. The version 2 functions are now
- deprecated in favor of the version 3 functions. The H5O_info_t and H5O_iterate_t
- types have been renamed to version 1 types and are now deprecated in favor of their
- version 2 counterparts. For each, compatibility macros take place of the original
- symbols.
-
- * Introduced new H5Oget_native_info, H5Oget_native_info_by_name and
- H5Oget_native_info_by_idx API calls, along with their associated H5O_native_info_t
- struct, which are used to retrieve the native HDF5 file format-specific information
- about an object. This information (such as object header info and B-tree/heap info)
- has been removed from the new H5O_info2_t struct so that the more generic
- H5Oget_info(_by_name/_by_idx)3 routines will not try to retrieve it for non-native
- VOL connectors.
-
- * Added new H5Otoken_cmp, H5Otoken_to_str and H5Otoken_from_str routines to compare
- two object tokens, convert an object token into a nicely-readable string format and
- to convert an object token string back into a real object token, respectively.
-
- (DER, QAK, JTH - 2020/01/16)
-
- - Virtual Object Layer (VOL)
-
- In this major HDF5 release we introduce HDF5 Virtual Object Layer (VOL).
- VOL is an abstraction layer within the HDF5 library that enables different
- methods for accessing data and objects that conform to the HDF5 data model.
- The VOL layer intercepts all HDF5 API calls that potentially modify data
- on disk and forwards those calls to a plugin "object driver". The data on
- disk can be a different format than the HDF5 format. For more information
- about VOL we refer the reader to the following documents (under review):
-
- VOL HDF5 APIs
- https://portal.hdfgroup.org/display/HDF5/Virtual+Object++Layer
-
- VOL Documentation
- https://bitbucket.hdfgroup.org/projects/HDFFV/repos/hdf5doc/browse/RFCs/HDF5/VOL
-
- Repository with VOL plugins
- https://bitbucket.hdfgroup.org/projects/HDF5VOL
-
- - Enhancements to HDF5 References
-
- HDF5 references were extended to support attributes, and object and dataset
- selections that reside in another HDF5 file. For more information including
- a list of new APIs, see
-
- https://portal.hdfgroup.org/display/HDF5/Update+to+References
-
- - Add new public function H5Sselect_adjust.
-
- This function shifts a dataspace selection by a specified logical offset
- within the dataspace extent. This can be useful for VOL developers to
- implement chunked datasets.
-
- (NAF - 2019/11/18)
-
- - Add new public function H5Sselect_project_intersection.
-
- This function computes the intersection between two dataspace selections
- and projects that intersection into a third selection. This can be useful
- for VOL developers to implement chunked or virtual datasets.
-
- (NAF - 2019/11/13, ID-148)
-
- - Add new public function H5VLget_file_type.
-
- This function returns a datatype equivalent to the supplied datatype but
- with the location set to be in the file. This datatype can then be used
- with H5Tconvert to convert data between file and in-memory representation.
- This funcition is intended for use only by VOL connector developers.
-
- (NAF - 2019/11/08, ID-127)
-
- - New S3 and HDFS Virtual File Drivers (VFDs)
-
- This release has two new VFDs. The S3 VFD allows accessing HDF5 files on
- AWS S3 buckets. HDFS VFD allows accessing HDF5 files stored on Apache HDFS.
- See https://portal.hdfgroup.org/display/HDF5/Virtual+File+Drivers+-+S3+and+HDFS
- for information on enabling those drivers and using those APIs.
-
- Below are specific instructions for enabling S3 VFD on Windows:
-
- Fix windows requirements and java tests. Windows requires CMake 3.13.
- - Install openssl library (with dev files);
- from "Shining Light Productions". msi package preferred.
- - PATH should have been updated with the installation dir.
- - set ENV variable OPENSSL_ROOT_DIR to the installation dir.
- - set ENV variable OPENSSL_CONF to the cfg file, likely %OPENSSL_ROOT_DIR%\bin\openssl.cfg
- - Install libcurl library (with dev files);
- - download the latest released version using git: https://github.com/curl/curl.git
- - Open a Visual Studio Command prompt
- - change to the libcurl root folder
- - run the "buildconf.bat" batch file
- - change to the winbuild directory
- - nmake /f Makefile.vc mode=dll MACHINE=x64
- - copy libcurl-vc-x64-release-dll-ipv6-sspi-winssl dir to C:\curl (installation dir)
- - set ENV variable CURL_ROOT to C:\curl (installation dir)
- - update PATH ENV variable to %CURL_ROOT%\bin (installation bin dir).
- - the aws credentials file should be in %USERPROFILE%\.aws folder
- - set the ENV variable HDF5_ROS3_TEST_BUCKET_URL to the s3 url for the
- s3 bucket containing the HDF5 files to be accessed.
-
- FORTRAN Library:
- ----------------
- - Added new Fortran parameters:
-
- H5F_LIBVER_ERROR_F
- H5F_LIBVER_NBOUNDS_F
- H5F_LIBVER_V18_F
- H5F_LIBVER_V110_F
- H5F_LIBVER_V112_F
-
- - Added new Fortran API: h5pget_libver_bounds_f
-
- (MSB - 2020/02/11, HDFFV-11018)
-
- Java Library:
- ----------------
- - Added ability to test java library with VOLs.
-
- Created new CMake script that combines the java and vol test scripts.
-
- (ADB - 2020/02/03, HDFFV-10996)
-
- - Tests fail for non-English locale.
-
- In the JUnit tests with a non-English locale, only the part before
- the decimal comma is replaced by XXXX and this leads to a comparison
- error. Changed the regex for the Time substitution.
-
- (ADB - 2020/01/09, HDFFV-10995)
-
-
- Tools:
- ------
- - h5diff was updated to use the new reference APIs.
-
- h5diff uses the new reference APIs to compare references.
- Attribute references can also be compared.
-
- (ADB - 2019/12/19, HDFFV-10980)
-
- - h5dump and h5ls were updated to use the new reference APIs.
-
- The tools library now use the new reference APIs to inspect a
- file. Also the DDL spec was updated to reflect the format
- changes produced with the new APIs. The export API and support
- functions in the JNI were updated to match.
-
-
- Other improvements and changes:
-
- - Hyperslab selection code was reworked to improve performance, getting more
- than 10x speedup in some cases.
-
- - The HDF5 Library was enhanced to open files with Unicode names on Windows.
-
- - Deprecated H5Dvlen_reclaim() and replaced it with H5Treclaim().
- This routine is meant to be used when resources are internally allocated
- when reading data, i.e. when using either vlen or new reference types.
- This is applicable to both attribute and dataset reads.
-
- - h5repack was fixed to repack datasets with external storage
- to other types of storage.
-
-
-Support for new platforms, languages and compilers.
-=======================================
- - Added spectrum-mpi with clang, gcc and xl compilers on Linux 3.10.0
- - Added OpenMPI 3.1 and 4.0 with clang, gcc and Intel compilers on Linux 3.10.0
- - Added cray-mpich/PrgEnv with gcc and Intel compilers on Linux 4.14.180
- - Added spectrum mpi with clang, gcc and xl compilers on Linux 4.14.0
-
-
-Bug Fixes since HDF5-1.12.0-alpha1 release
-==========================================
- Library
- -------
- - Improved performance when creating a large number of small datasets by
- retrieving default property values from the API context instead of doing
- skip list searches.
-
- (CJH - 2019/12/10, HDFFV-10658)
-
- - Fixed user-created data access properties not existing in the property list
- returned by H5Dget_access_plist. Thanks to Steven Varga for submitting a
- reproducer and a patch.
-
- (CJH - 2019/12/09, HDFFV-10934)
-
- - Fixed an assertion failure in the parallel library when collectively
- filling chunks. As it is required that chunks be written in
- monotonically non-decreasing order of offset in the file, this assertion
- was being triggered when the list of chunk file space allocations being
- passed to the collective chunk filling routine was not sorted according
- to this particular requirement.
-
- The addition of a sort of the out of order chunks trades a bit of
- performance for the elimination of this assertion and of any complaints
- from MPI implementations about the file offsets used being out of order.
-
- (JTH - 2019/10/07, HDFFV-10792)
-
- FORTRAN library:
- ----------------
-
- - Corrected INTERFACE INTENT(IN) to INTENT(OUT) for buf_size in h5fget_file_image_f.
-
- (MSB - 2020/2/18, HDFFV-11029)
-
- Java Library:
- ----------------
- - Added ability to test java library with VOLs.
-
- Created new CMake script that combines the java and vol test scripts.
-
- (ADB - 2020/02/03, HDFFV-10996)
-
- - Tests fail for non-English locale.
-
- In the JUnit tests with a non-English locale, only the part before
- the decimal comma is replaced by XXXX and this leads to a comparison
- error. Changed the regex for the Time substitution.
-
- (ADB - 2020/01/09, HDFFV-10995)
-
- Tools:
- ------
- - h5repack was fixed to repack the reference attributes properly.
- The code line that checks if the update of reference inside a compound
- datatype is misplaced outside the code block loop that carries out the
- check. In consequence, the next attribute that is not the reference
- type was repacked again as the reference type and caused the failure of
- repacking. The fix is to move the corresponding code line to the correct
- code block.
-
- (KY -2020/02/10, HDFFV-11014)
-
- - h5diff was updated to use the new reference APIs.
-
- h5diff uses the new reference APIs to compare references.
- Attribute references can also be compared.
-
- (ADB - 2019/12/19, HDFFV-10980)
-
- - h5dump and h5ls were updated to use the new reference APIs.
-
- The tools library now use the new reference APIs to inspect a
- file. Also the DDL spec was updated to reflect the format
- changes produced with the new APIs. The export API and support
- functions in the JNI were updated to match.
-
- (ADB - 2019/12/06, HDFFV-10876 and HDFFV-10877)
-
-
-Major Bug Fixes since HDF5-1.10.0 release
-=========================================
-
- - For major bug fixes please see HISTORY-1_10_0-1_12_0.txt file
-
-
-Supported Platforms
-===================
-
- Linux 2.6.32-696.16.1.el6.ppc64 gcc (GCC) 4.4.7 20120313 (Red Hat 4.4.7-18)
- #1 SMP ppc64 GNU/Linux g++ (GCC) 4.4.7 20120313 (Red Hat 4.4.7-18)
- (ostrich) GNU Fortran (GCC) 4.4.7 20120313 (Red Hat 4.4.7-18)
- IBM XL C/C++ V13.1
- IBM XL Fortran V15.1
-
- Linux 3.10.0-327.10.1.el7 GNU C (gcc), Fortran (gfortran), C++ (g++)
- #1 SMP x86_64 GNU/Linux compilers:
- (kituo/moohan) Version 4.8.5 20150623 (Red Hat 4.8.5-4)
- Version 4.9.3, 5.2.0, 7.1.0
- Intel(R) C (icc), C++ (icpc), Fortran (icc)
- compilers:
- Version 17.0.0.098 Build 20160721
- MPICH 3.1.4
-
- Linux-3.10.0- spectrum-mpi/rolling-release with cmake>3.10 and
- 862.14.4.1chaos.ch6.ppc64le clang/3.9,8.0
- #1 SMP ppc64le GNU/Linux gcc/7.3
- (ray) xl/2016,2019
-
- Linux 3.10.0- openmpi/3.1,4.0 with cmake>3.10 and
- 957.12.2.1chaos.ch6.x86_64 clang 5.0
- #1 SMP x86_64 GNU/Linux gcc/7.3,8.2
- (serrano) intel/17.0,18.0/19.0
-
- Linux 3.10.0- openmpi/3.1/4.0 with cmake>3.10 and
- 1062.1.1.1chaos.ch6.x86_64 clang/3.9,5.0,8.0
- #1 SMP x86_64 GNU/Linux gcc/7.3,8.1,8.2
- (chama,quartz) intel/16.0,18.0,19.0
-
- Linux 4.4.180-94.100-default cray-mpich/7.7.6 with PrgEnv-*/6.0.5, cmake>3.10 and
- #1 SMP x86_64 GNU/Linux gcc/7.2.0,8.2.0
- (mutrino) intel/17.0,18.0
-
- Linux 4.14.0- spectrum-mpi/rolling-release with cmake>3.10 and
- 49.18.1.bl6.ppc64le clang/6.0,8.0
- #1 SMP ppc64le GNU/Linux gcc/7.3
- (lassen) xl/2019
-
- SunOS 5.11 32- and 64-bit Sun C 5.12 SunOS_sparc
- (emu) Sun Fortran 95 8.6 SunOS_sparc
- Sun C++ 5.12 SunOS_sparc
-
- Windows 7 x64 Visual Studio 2015 w/ Intel C, Fortran 2018 (cmake)
- Visual Studio 2015 w/ MSMPI 10 (cmake)
-
- Windows 10 x64 Visual Studio 2015 w/ Intel Fortran 18 (cmake)
- Visual Studio 2017 w/ Intel Fortran 19 (cmake)
- Visual Studio 2019 w/ Intel Fortran 19 (cmake)
-
- macOS 10.13.6 High Sierra Apple LLVM version 10.0.0 (clang/clang++-1000.10.44.4)
- 64-bit gfortran GNU Fortran (GCC) 6.3.0
- (bear) Intel icc/icpc/ifort version 19.0.4
-
- macOS 10.14.6 Mohave Apple LLVM version 10.0.1 (clang/clang++-1001.0.46.4)
- 64-bit gfortran GNU Fortran (GCC) 6.3.0
- (bobcat) Intel icc/icpc/ifort version 19.0.4
-
-
-Tested Configuration Features Summary
-=====================================
-
- In the tables below
- y = tested
- n = not tested in this release
- C = Cluster
- W = Workstation
- x = not working in this release
- dna = does not apply
- ( ) = footnote appears below second table
- <blank> = testing incomplete on this feature or platform
-
-Platform C F90/ F90 C++ zlib SZIP
- parallel F2003 parallel
-SunOS 5.11 32-bit n y/y n y y y
-SunOS 5.11 64-bit n y/n n y y y
-Windows 7 y y/y n y y y
-Windows 7 x64 y y/y y y y y
-Windows 7 Cygwin n y/n n y y y
-Windows 7 x64 Cygwin n y/n n y y y
-Windows 10 y y/y n y y y
-Windows 10 x64 y y/y n y y y
-macOS 10.13.6 64-bit n y/y n y y ?
-macOS 10.14.6 64-bit n y/y n y y ?
-CentOS 6.7 Linux 2.6.18 x86_64 GNU n y/y n y y y
-CentOS 6.7 Linux 2.6.18 x86_64 Intel n y/y n y y y
-CentOS 6.7 Linux 2.6.32 x86_64 PGI n y/y n y y y
-CentOS 7.2 Linux 2.6.32 x86_64 GNU y y/y y y y y
-CentOS 7.2 Linux 2.6.32 x86_64 Intel n y/y n y y y
-Linux 2.6.32-573.18.1.el6.ppc64 n y/n n y y y
-
-
-Platform Shared Shared Shared Thread-
- C libs F90 libs C++ libs safe
-SunOS 5.11 32-bit y y y y
-SunOS 5.11 64-bit y y y y
-Windows 7 y y y y
-Windows 7 x64 y y y y
-Windows 7 Cygwin n n n y
-Windows 7 x64 Cygwin n n n y
-Windows 10 y y y y
-Windows 10 x64 y y y y
-macOS 10.13.6 64-bit y n y y
-macOS 10.14.6 64-bit y n y y
-CentOS 6.7 Linux 2.6.18 x86_64 GNU y y y y
-CentOS 6.7 Linux 2.6.18 x86_64 Intel y y y n
-CentOS 6.7 Linux 2.6.32 x86_64 PGI y y y n
-CentOS 7.2 Linux 2.6.32 x86_64 GNU y y y n
-CentOS 7.2 Linux 2.6.32 x86_64 Intel y y y n
-Linux 2.6.32-573.18.1.el6.ppc64 y y y n
-
-Compiler versions for each platform are listed in the preceding
-"Supported Platforms" table.
-
-
-More Tested Platforms
-=====================
-The following platforms are not supported but have been tested for this release.
-
- Linux 2.6.32-573.22.1.el6 GNU C (gcc), Fortran (gfortran), C++ (g++)
- #1 SMP x86_64 GNU/Linux compilers:
- (mayll/platypus) Version 4.4.7 20120313
- Version 4.9.3, 5.3.0, 6.2.0
- PGI C, Fortran, C++ for 64-bit target on
- x86-64;
- Version 17.10-0
- Intel(R) C (icc), C++ (icpc), Fortran (icc)
- compilers:
- Version 17.0.4.196 Build 20170411
- MPICH 3.1.4 compiled with GCC 4.9.3
-
- Linux 3.10.0-327.18.2.el7 GNU C (gcc) and C++ (g++) compilers
- #1 SMP x86_64 GNU/Linux Version 4.8.5 20150623 (Red Hat 4.8.5-4)
- (jelly) with NAG Fortran Compiler Release 6.1(Tozai)
- GCC Version 7.1.0
- OpenMPI 3.0.0-GCC-7.2.0-2.29
- Intel(R) C (icc) and C++ (icpc) compilers
- Version 17.0.0.098 Build 20160721
- with NAG Fortran Compiler Release 6.1(Tozai)
- PGI C (pgcc), C++ (pgc++), Fortran (pgf90)
- compilers:
- Version 18.4, 19.4
- MPICH 3.3
- OpenMPI 2.1.5, 3.1.3, 4.0.0
-
- Fedora30 5.3.11-200.fc30.x86_64
- #1 SMP x86_64 GNU/Linux GNU gcc (GCC) 9.2.1 20190827 (Red Hat 9.2.1 20190827)
- GNU Fortran (GCC) 9.2.1 20190827 (Red Hat 9.2.1 20190827)
- (cmake and autotools)
-
- Mac OS X El Capitan 10.11.6 Apple LLVM version 7.3.0 (clang/clang++-703.0.29)
- 64-bit gfortran GNU Fortran (GCC) 5.2.0
- (osx1011dev/osx1011test) Intel icc/icpc/ifort version 16.0.2
-
- macOS 10.12.6 Sierra Apple LLVM version 9.0.0 (clang/clang++-900.0.39.2)
- 64-bit gfortran GNU Fortran (GCC) 7.4.0
- (kite) Intel icc/icpc/ifort version 17.0.8
-
-
-Known Problems
-==============
- CMake files do not behave correctly with paths containing spaces.
- Do not use spaces in paths because the required escaping for handling spaces
- results in very complex and fragile build files.
- ADB - 2019/05/07
-
- At present, metadata cache images may not be generated by parallel
- applications. Parallel applications can read files with metadata cache
- images, but since this is a collective operation, a deadlock is possible
- if one or more processes do not participate.
-
- Known problems in previous releases can be found in the HISTORY*.txt files
- in the HDF5 source, and in the HDF5 Jira database, available at
- https://jira.hdfgroup.org/. Please register at https://www.hdfgroup.org to
- create a free account for accessing the Jira database. Please report any
- new problems found to help@hdfgroup.org.
-
-
-CMake vs. Autotools installations
-=================================
-While both build systems produce similar results, there are differences.
-Each system produces the same set of folders on linux (only CMake works
-on standard Windows); bin, include, lib and share. Autotools places the
-COPYING and RELEASE.txt file in the root folder, CMake places them in
-the share folder.
-
-The bin folder contains the tools and the build scripts. Additionally, CMake
-creates dynamic versions of the tools with the suffix "-shared". Autotools
-installs one set of tools depending on the "--enable-shared" configuration
-option.
- build scripts
- -------------
- Autotools: h5c++, h5cc, h5fc
- CMake: h5c++, h5cc, h5hlc++, h5hlcc
-
-The include folder holds the header files and the fortran mod files. CMake
-places the fortran mod files into separate shared and static subfolders,
-while Autotools places one set of mod files into the include folder. Because
-CMake produces a tools library, the header files for tools will appear in
-the include folder.
-
-The lib folder contains the library files, and CMake adds the pkgconfig
-subfolder with the hdf5*.pc files used by the bin/build scripts created by
-the CMake build. CMake separates the C interface code from the fortran code by
-creating C-stub libraries for each Fortran library. In addition, only CMake
-installs the tools library. The names of the szip libraries are different
-between the build systems.
-
-The share folder will have the most differences because CMake builds include
-a number of CMake specific files for support of CMake's find_package and support
-for the HDF5 Examples CMake project.
-
diff --git a/release_docs/HISTORY-1_13.txt b/release_docs/HISTORY-1_12_0-1_14_0.txt
index 73b7feb..11ca947 100644
--- a/release_docs/HISTORY-1_13.txt
+++ b/release_docs/HISTORY-1_12_0-1_14_0.txt
@@ -4,6 +4,7 @@ HDF5 History
This file contains development history of the HDF5 1.13 releases from
the develop branch
+05. Release Information for hdf5-1.14.0
04. Release Information for hdf5-1.13.3
03. Release Information for hdf5-1.13.2
02. Release Information for hdf5-1.13.1
@@ -11,6 +12,758 @@ the develop branch
[Search on the string '%%%%' for section breaks of each release.]
+%%%%1.14.0%%%%
+
+HDF5 version 1.14.0 released on 2022-12-28
+
+*** NOTE ***
+
+This file reflects the 1.13.x experimental release history. In the 1.14.0
+release, we consolidated the experimental release notes into a single
+section.
+
+*** NOTE ****
+
+================================================================================
+
+
+INTRODUCTION
+============
+
+This document describes the differences between this release and the previous
+HDF5 release. It contains information on the platforms tested and known
+problems in this release. For more details check the HISTORY*.txt files in the
+HDF5 source.
+
+Note that documentation in the links below will be updated at the time of each
+final release.
+
+Links to HDF5 documentation can be found on The HDF5 web page:
+
+ https://portal.hdfgroup.org/display/HDF5/HDF5
+
+The official HDF5 releases can be obtained from:
+
+ https://www.hdfgroup.org/downloads/hdf5/
+
+Changes from Release to Release and New Features in the HDF5-1.13.x release series
+can be found at:
+
+ https://portal.hdfgroup.org/display/HDF5/Release+Specific+Information
+
+If you have any questions or comments, please send them to the HDF Help Desk:
+
+ help@hdfgroup.org
+
+
+CONTENTS
+========
+
+- New Features
+- Support for new platforms and languages
+- Bug Fixes since HDF5-1.13.3
+- Platforms Tested
+- Known Problems
+- CMake vs. Autotools installations
+
+
+New Features
+============
+
+ Configuration:
+ -------------
+ - Added new option to build libaec and zlib inline with CMake.
+
+ Using the CMake FetchContent module, the external filters can populate
+ content at configure time via any method supported by the ExternalProject
+ module. Whereas ExternalProject_Add() downloads at build time, the
+ FetchContent module makes content available immediately, allowing the
+ configure step to use the content in commands like add_subdirectory(),
+ include() or file() operations.
+
+ The HDF options (and defaults) for using this are:
+ BUILD_SZIP_WITH_FETCHCONTENT:BOOL=OFF
+ LIBAEC_USE_LOCALCONTENT:BOOL=OFF
+ BUILD_ZLIB_WITH_FETCHCONTENT:BOOL=OFF
+ ZLIB_USE_LOCALCONTENT:BOOL=OFF
+
+ The CMake variables to control the path and file names:
+ LIBAEC_TGZ_ORIGPATH:STRING
+ LIBAEC_TGZ_ORIGNAME:STRING
+ ZLIB_TGZ_ORIGPATH:STRING
+ ZLIB_TGZ_ORIGNAME:STRING
+
+ See the CMakeFilters.cmake and config/cmake/cacheinit.cmake files for usage.
+
+ (ADB - 2023/02/21)
+
+ - Removal of MPE support
+
+ The ability to build with MPE instrumentation has been removed along with
+ the following configure options:
+
+ Autotools:
+ --with-mpe=
+
+ CMake has never supported building with MPE support.
+
+ (DER - 2022/11/08)
+
+ - Removal of dmalloc support
+
+ The ability to build with dmalloc support has been removed along with
+ the following configure options:
+
+ Autotools:
+ --with-dmalloc=
+
+ CMake:
+ HDF5_ENABLE_USING_DMALLOC
+
+ (DER - 2022/11/08)
+
+ - Removal of memory allocation sanity checks configure options
+
+ With the removal of the memory allocation sanity checks feature, the
+ following configure options are no longer necessary and have been
+ removed:
+
+ Autotools:
+ --enable-memory-alloc-sanity-check
+
+ CMake:
+ HDF5_MEMORY_ALLOC_SANITY_CHECK
+ HDF5_ENABLE_MEMORY_STATS
+
+ (DER - 2022/11/03)
+
+ Library:
+ --------
+ - Added a Subfiling VFD configuration file prefix environment variable
+
+ The Subfiling VFD now checks for values set in a new environment
+ variable "H5FD_SUBFILING_CONFIG_FILE_PREFIX" to determine if the
+ application has specified a pathname prefix to apply to the file
+ path for its configuration file. For example, this can be useful
+ for cases where the application wishes to write subfiles to a
+ machine's node-local storage while placing the subfiling configuration
+ file on a file system readable by all machine nodes.
+
+ (JTH - 2023/02/22)
+
+ - Overhauled the Virtual Object Layer (VOL)
+
+ The virtual object layer (VOL) was added in HDF5 1.12.0 but the initial
+ implementation required API-breaking changes to better support optional
+ operations and pass-through VOL connectors. The original VOL API is
+ now considered deprecated and VOL users and connector authors should
+ target the 1.14 VOL API.
+
+ The specific changes are too extensive to document in a release note, so
+ VOL users and connector authors should consult the updated VOL connector
+ author's guide and the 1.12-1.14 VOL migration guide.
+
+ (DER - 2022/12/28)
+
+ - H5VLquery_optional() signature change
+
+ The last parameter of this API call has changed from a pointer to hbool_t
+ to a pointer to uint64_t. Due to the changes in how optional operations
+ are handled in the 1.14 VOL API, we cannot make the old API call work
+ with the new scheme, so there is no API compatibility macro for it.
+
+ (DER - 2022/12/28)
+
+ - H5I_free_t callback signature change
+
+ In order to support asynchronous operations and future IDs, the signature
+ of the H5I_free_t callback has been modified to take a second 'request'
+ parameter. Due to the nature of the internal library changes, no API
+ compatibility macro is available for this change.
+
+ (DER - 2022/12/28)
+
+ - Fix for CVE-2019-8396
+
+ Malformed HDF5 files may have truncated content which does not match
+ the expected size. When H5O__pline_decode() attempts to decode these it
+ may read past the end of the allocated space leading to heap overflows
+ as bounds checking is incomplete.
+
+ The fix ensures each element is within bounds before reading.
+
+ (2022/11/09 - HDFFV-10712, CVE-2019-8396, GitHub #2209)
+
+ - Removal of memory allocation sanity checks feature
+
+ This feature added heap canaries and statistics tracking for internal
+ library memory operations. Unfortunately, the heap canaries caused
+ problems when library memory operations were mixed with standard C
+ library memory operations (such as in the filter pipeline, where
+ buffers may have to be reallocated). Since any platform with a C
+ compiler also usually has much more sophisticated memory sanity
+ checking tools than the HDF5 library provided (e.g., valgrind), we
+ have decided to to remove the feature entirely.
+
+ In addition to the configure changes described above, this also removes
+ the following from the public API:
+ H5get_alloc_stats()
+ H5_alloc_stats_t
+
+ (DER - 2022/11/03)
+
+ Parallel Library:
+ -----------------
+ -
+
+
+ Fortran Library:
+ ----------------
+ -
+
+
+ C++ Library:
+ ------------
+ -
+
+
+ Java Library:
+ -------------
+ -
+
+
+ Tools:
+ ------
+ -
+
+
+ High-Level APIs:
+ ----------------
+ -
+
+
+ C Packet Table API:
+ -------------------
+ -
+
+
+ Internal header file:
+ ---------------------
+ -
+
+
+ Documentation:
+ --------------
+ - Ported the existing VOL Connector Author Guide document to doxygen.
+
+ Added new dox file, VOLConnGuide.dox.
+
+ (ADB - 2022/12/20)
+
+
+Support for new platforms, languages and compilers
+==================================================
+ -
+
+Bug Fixes since HDF5-1.13.3 release
+===================================
+ Library
+ -------
+ - Fixed issues in the Subfiling VFD when using the SELECT_IOC_EVERY_NTH_RANK
+ or SELECT_IOC_TOTAL I/O concentrator selection strategies
+
+ Multiple bugs involving these I/O concentrator selection strategies
+ were fixed, including:
+
+ * A bug that caused the selection strategy to be altered when
+ criteria for the strategy was specified in the
+ H5FD_SUBFILING_IOC_SELECTION_CRITERIA environment variable as
+ a single value, rather than in the old and undocumented
+ 'integer:integer' format
+ * Two bugs which caused a request for 'N' I/O concentrators to
+ result in 'N - 1' I/O concentrators being assigned, which also
+ lead to issues if only 1 I/O concentrator was requested
+
+ Also added a regression test for these two I/O concentrator selection
+ strategies to prevent future issues.
+
+ (JTH - 2023/03/15)
+
+ - Fix CVE-2021-37501 / GHSA-rfgw-5vq3-wrjf
+
+ Check for overflow when calculating on-disk attribute data size.
+
+ A bogus hdf5 file may contain dataspace messages with sizes
+ which lead to the on-disk data sizes to exceed what is addressable.
+ When calculating the size, make sure, the multiplication does not
+ overflow.
+ The test case was crafted in a way that the overflow caused the
+ size to be 0.
+
+ (EFE - 2023/02/11 GH-2458)
+
+ - Fixed an issue with collective metadata writes of global heap data
+
+ New test failures in parallel netCDF started occurring with debug
+ builds of HDF5 due to an assertion failure and this was reported in
+ GitHub issue #2433. The assertion failure began happening after the
+ collective metadata write pathway in the library was updated to use
+ vector I/O so that parallel-enabled HDF5 Virtual File Drivers (other
+ than the existing MPI I/O VFD) can support collective metadata writes.
+
+ The assertion failure was fixed by updating collective metadata writes
+ to treat global heap metadata as raw data, as done elsewhere in the
+ library.
+
+ (JTH - 2023/02/16, GH #2433)
+
+ - Seg fault on file close
+
+ h5debug fails at file close with core dump on a file that has an
+ illegal file size in its cache image. In H5F_dest(), the library
+ performs all the closing operations for the file and keeps track of
+ the error encountered when reading the file cache image.
+ At the end of the routine, it frees the file's file structure and
+ returns error. Due to the error return, the file object is not removed
+ from the ID node table. This eventually causes assertion failure in
+ H5VL__native_file_close() when the library finally exits and tries to
+ access that file object in the table for closing.
+
+ The closing routine, H5F_dest(), will not free the file structure if
+ there is error, keeping a valid file structure in the ID node table.
+ It will be freed later in H5VL__native_file_close() when the
+ library exits and terminates the file package.
+
+ (VC - 2022/12/14, HDFFV-11052, CVE-2020-10812)
+
+ - Fix CVE-2018-13867 / GHSA-j8jr-chrh-qfrf
+
+ Validate location (offset) of the accumulated metadata when comparing.
+
+ Initially, the accumulated metadata location is initialized to HADDR_UNDEF
+ - the highest available address. Bogus input files may provide a location
+ or size matching this value. Comparing this address against such bogus
+ values may provide false positives. Thus make sure, the value has been
+ initialized or fail the comparison early and let other parts of the
+ code deal with the bogus address/size.
+ Note: To avoid unnecessary checks, it is assumed that if the 'dirty'
+ member in the same structure is true the location is valid.
+
+ (EFE - 2022/10/10 GH-2230)
+
+ - Fix CVE-2018-16438 / GHSA-9xmm-cpf8-rgmx
+
+ Make sure info block for external links has at least 3 bytes.
+
+ According to the specification, the information block for external links
+ contains 1 byte of version/flag information and two 0 terminated strings
+ for the object linked to and the full path.
+ Although not very useful, the minimum string length for each (with
+ terminating 0) would be one byte.
+ Checking this helps to avoid SEGVs triggered by bogus files.
+
+ (EFE - 2022/10/09 GH-2233)
+
+ - CVE-2021-46244 / GHSA-vrxh-5gxg-rmhm
+
+ Compound datatypes may not have members of size 0
+
+ A member size of 0 may lead to an FPE later on as reported in
+ CVE-2021-46244. To avoid this, check for this as soon as the
+ member is decoded.
+
+ (EFE - 2022/10/05 GEH-2242)
+
+
+ - Fix CVE-2021-45830 / GHSA-5h2h-fjjr-x9m2
+
+ Make H5O__fsinfo_decode() more resilient to out-of-bound reads.
+
+ When decoding a file space info message in H5O__fsinfo_decode() make
+ sure each element to be decoded is still within the message. Malformed
+ hdf5 files may have trunkated content which does not match the
+ expected size. Checking this will prevent attempting to decode
+ unrelated data and heap overflows. So far, only free space manager
+ address data was checked before decoding.
+
+ (EFE - 2022/10/05 GH-2228)
+
+ - Fix CVE-2021-46242 / GHSA-x9pw-hh7v-wjpf
+
+ When evicting driver info block, NULL the corresponding entry.
+
+ Since H5C_expunge_entry() called (from H5AC_expunge_entry()) sets the flag
+ H5C__FLUSH_INVALIDATE_FLAG, the driver info block will be freed. NULLing
+ the pointer in f->shared->drvinfo will prevent use-after-free when it is
+ used in other functions (like H5F__dest()) - as other places will check
+ whether the pointer is initialized before using its value.
+
+ (EFE - 2022/09/29 GH-2254)
+
+ - Fix CVE-2021-45833 / GHSA-x57p-jwp6-4v79
+
+ Report error if dimensions of chunked storage in data layout < 2
+
+ For Data Layout Messages version 1 & 2 the specification state
+ that the value stored in the data field is 1 greater than the
+ number of dimensions in the dataspace. For version 3 this is
+ not explicitly stated but the implementation suggests it to be
+ the case.
+ Thus the set value needs to be at least 2. For dimensionality
+ < 2 an out-of-bounds access occurs.
+
+ (EFE - 2022/09/28 GH-2240)
+
+ - Fix CVE-2018-14031 / GHSA-2xc7-724c-r36j
+
+ Parent of enum datatype message must have the same size as the
+ enum datatype message itself.
+ Functions accessing the enumeration values use the size of the
+ enumeration datatype to determine the size of each element and
+ how much data to copy.
+ Thus the size of the enumeration and its parent need to match.
+ Check in H5O_dtype_decode_helper() to avoid unpleasant surprises
+ later.
+
+ (EFE - 2022/09/28 GH-2236)
+
+ - Fix CVE-2018-17439 / GHSA-vcxv-vp43-rch7
+
+ H5IMget_image_info(): Make sure to not exceed local array size
+
+ Malformed hdf5 files may provide more dimensions than the array dim[] in
+ H5IMget_image_info() is able to hold. Check number of elements first by calling
+ H5Sget_simple_extent_dims() with NULL for both 'dims' and 'maxdims' arguments.
+ This will cause the function to return only the number of dimensions.
+ The fix addresses a stack overflow on write.
+
+ (EFE - 2022/09/27 HDFFV-10589, GH-2226)
+
+
+ Java Library
+ ------------
+ -
+
+
+ Configuration
+ -------------
+ - Correct the CMake generated pkg-config file
+
+ The pkg-config file generated by CMake had the order and placement of the
+ libraries wrong. Also added support for debug library names.
+
+ Changed the order of Libs.private libraries so that dependencies come after
+ dependents. Did not move the compression libraries into Requires.private
+ because there was not a way to determine if the compression libraries had
+ supported pkconfig files. Still recommend that the CMake config file method
+ be used for building projects with CMake.
+
+ (ADB - 2023/02/16 GH-1546,GH-2259)
+
+ - Remove Javadoc generation
+
+ The use of doxygen now supersedes the requirement to build javadocs. We do not
+ have the resources to continue to support two documentation methods and have
+ chosen doxygen as our standard.
+
+ (ADB - 2022/12/19)
+
+ - Change the default for building the high-level tools
+
+ The gif2hdf5 and hdf2gif high-level tools are deprecated and will be removed
+ in a future release. The default build setting for them have been changed from enabled
+ to disabled. A user can enable the build of these tools if needed.
+ autotools: --enable-hlgiftools
+ cmake: HDF5_BUILD_HL_GIF_TOOLS=ON
+
+ (ADB - 2022/12/16)
+
+ - Change the settings of the *pc files to use the correct format
+
+ The pkg-config files generated by CMake uses incorrect syntax for the 'Requires'
+ settings. Changing the set to use 'lib-name = version' instead 'lib-name-version'
+ fixes the issue
+
+ (ADB - 2022/12/06 HDFFV-11355)
+
+ - Move MPI libraries link from PRIVATE to PUBLIC
+
+ The install dependencies were not including the need for MPI libraries when
+ an application or library was built with the C library. Also updated the
+ CMake target link command to use the newer style MPI::MPI_C link variable.
+
+ (ADB - 2022/10/27)
+
+
+ Tools
+ -----
+ - Fix h5repack to only print output when verbose option is selected
+
+ When timing option was added to h5repack, the check for verbose was
+ incorrectly implemented.
+
+ (ADB - 2022/12/02, GH #2270)
+
+
+ Performance
+ -------------
+ -
+
+
+ Fortran API
+ -----------
+ -
+
+ High-Level Library
+ ------------------
+ -
+
+
+ Fortran High-Level APIs
+ -----------------------
+ -
+
+
+ Documentation
+ -------------
+ -
+
+
+ F90 APIs
+ --------
+ -
+
+
+ C++ APIs
+ --------
+ -
+
+
+ Testing
+ -------
+ -
+
+
+Platforms Tested
+===================
+
+ Linux 5.16.14-200.fc35 GNU gcc (GCC) 11.2.1 20220127 (Red Hat 11.2.1-9)
+ #1 SMP x86_64 GNU/Linux GNU Fortran (GCC) 11.2.1 20220127 (Red Hat 11.2.1-9)
+ Fedora35 clang version 13.0.0 (Fedora 13.0.0-3.fc35)
+ (cmake and autotools)
+
+ Linux 5.11.0-34-generic GNU gcc (GCC) 9.3.0-17ubuntu1
+ #36-Ubuntu SMP x86_64 GNU/Linux GNU Fortran (GCC) 9.3.0-17ubuntu1
+ Ubuntu 20.04 Ubuntu clang version 10.0.0-4
+ (cmake and autotools)
+
+ Linux 5.3.18-150300-cray_shasta_c cray-mpich/8.1.16
+ #1 SMP x86_64 GNU/Linux Cray clang 14.0.0
+ (crusher) GCC 11.2.0
+ (cmake)
+
+ Linux 4.14.0-115.35.1.1chaos openmpi 4.0.5
+ #1 SMP aarch64 GNU/Linux GCC 9.2.0 (ARM-build-5)
+ (stria) GCC 7.2.0 (Spack GCC)
+ (cmake)
+
+ Linux 4.14.0-115.35.1.3chaos spectrum-mpi/rolling-release
+ #1 SMP ppc64le GNU/Linux clang 12.0.1
+ (vortex) GCC 8.3.1
+ XL 16.1.1
+ (cmake)
+
+ Linux-4.14.0-115.21.2 spectrum-mpi/rolling-release
+ #1 SMP ppc64le GNU/Linux clang 12.0.1, 14.0.5
+ (lassen) GCC 8.3.1
+ XL 16.1.1.2, 2021,09.22, 2022.08.05
+ (cmake)
+
+ Linux-4.12.14-197.99-default cray-mpich/7.7.14
+ #1 SMP x86_64 GNU/Linux cce 12.0.3
+ (theta) GCC 11.2.0
+ llvm 9.0
+ Intel 19.1.2
+
+ Linux 3.10.0-1160.36.2.el7.ppc64 gcc (GCC) 4.8.5 20150623 (Red Hat 4.8.5-39)
+ #1 SMP ppc64be GNU/Linux g++ (GCC) 4.8.5 20150623 (Red Hat 4.8.5-39)
+ Power8 (echidna) GNU Fortran (GCC) 4.8.5 20150623 (Red Hat 4.8.5-39)
+
+ Linux 3.10.0-1160.24.1.el7 GNU C (gcc), Fortran (gfortran), C++ (g++)
+ #1 SMP x86_64 GNU/Linux compilers:
+ Centos7 Version 4.8.5 20150623 (Red Hat 4.8.5-4)
+ (jelly/kituo/moohan) Version 4.9.3, Version 5.3.0, Version 6.3.0,
+ Version 7.2.0, Version 8.3.0, Version 9.1.0
+ Intel(R) C (icc), C++ (icpc), Fortran (icc)
+ compilers:
+ Version 17.0.0.098 Build 20160721
+ GNU C (gcc) and C++ (g++) 4.8.5 compilers
+ with NAG Fortran Compiler Release 6.1(Tozai)
+ Intel(R) C (icc) and C++ (icpc) 17.0.0.098 compilers
+ with NAG Fortran Compiler Release 6.1(Tozai)
+ MPICH 3.1.4 compiled with GCC 4.9.3
+ MPICH 3.3 compiled with GCC 7.2.0
+ OpenMPI 2.1.6 compiled with icc 18.0.1
+ OpenMPI 3.1.3 and 4.0.0 compiled with GCC 7.2.0
+ PGI C, Fortran, C++ for 64-bit target on
+ x86_64;
+ Version 19.10-0
+ (autotools and cmake)
+
+ Linux-3.10.0-1160.0.0.1chaos openmpi-4.1.2
+ #1 SMP x86_64 GNU/Linux clang 6.0.0, 11.0.1
+ (quartz) GCC 7.3.0, 8.1.0
+ Intel 19.0.4, 2022.2, oneapi.2022.2
+
+ Linux-3.10.0-1160.71.1.1chaos openmpi/4.1
+ #1 SMP x86_64 GNU/Linux GCC 7.2.0
+ (skybridge) Intel/19.1
+ (cmake)
+
+ Linux-3.10.0-1160.66.1.1chaos openmpi/4.1
+ #1 SMP x86_64 GNU/Linux GCC 7.2.0
+ (attaway) Intel/19.1
+ (cmake)
+
+ Linux-3.10.0-1160.59.1.1chaos openmpi/4.1
+ #1 SMP x86_64 GNU/Linux Intel/19.1
+ (chama) (cmake)
+
+ macOS Apple M1 11.6 Apple clang version 12.0.5 (clang-1205.0.22.11)
+ Darwin 20.6.0 arm64 gfortran GNU Fortran (Homebrew GCC 11.2.0) 11.1.0
+ (macmini-m1) Intel icc/icpc/ifort version 2021.3.0 202106092021.3.0 20210609
+
+ macOS Big Sur 11.3.1 Apple clang version 12.0.5 (clang-1205.0.22.9)
+ Darwin 20.4.0 x86_64 gfortran GNU Fortran (Homebrew GCC 10.2.0_3) 10.2.0
+ (bigsur-1) Intel icc/icpc/ifort version 2021.2.0 20210228
+
+ macOS High Sierra 10.13.6 Apple LLVM version 10.0.0 (clang-1000.10.44.4)
+ 64-bit gfortran GNU Fortran (GCC) 6.3.0
+ (bear) Intel icc/icpc/ifort version 19.0.4.233 20190416
+
+ macOS Sierra 10.12.6 Apple LLVM version 9.0.0 (clang-900.39.2)
+ 64-bit gfortran GNU Fortran (GCC) 7.4.0
+ (kite) Intel icc/icpc/ifort version 17.0.2
+
+ Mac OS X El Capitan 10.11.6 Apple clang version 7.3.0 from Xcode 7.3
+ 64-bit gfortran GNU Fortran (GCC) 5.2.0
+ (osx1011test) Intel icc/icpc/ifort version 16.0.2
+
+
+ Linux 2.6.32-573.22.1.el6 GNU C (gcc), Fortran (gfortran), C++ (g++)
+ #1 SMP x86_64 GNU/Linux compilers:
+ Centos6 Version 4.4.7 20120313
+ (platypus) Version 4.9.3, 5.3.0, 6.2.0
+ MPICH 3.1.4 compiled with GCC 4.9.3
+ PGI C, Fortran, C++ for 64-bit target on
+ x86_64;
+ Version 19.10-0
+
+ Windows 10 x64 Visual Studio 2015 w/ Intel C/C++/Fortran 18 (cmake)
+ Visual Studio 2017 w/ Intel C/C++/Fortran 19 (cmake)
+ Visual Studio 2019 w/ clang 12.0.0
+ with MSVC-like command-line (C/C++ only - cmake)
+ Visual Studio 2019 w/ Intel C/C++/Fortran oneAPI 2022 (cmake)
+ Visual Studio 2022 w/ clang 15.0.1
+ with MSVC-like command-line (C/C++ only - cmake)
+ Visual Studio 2022 w/ Intel C/C++/Fortran oneAPI 2022 (cmake)
+ Visual Studio 2019 w/ MSMPI 10.1 (C only - cmake)
+
+
+Known Problems
+==============
+
+ ************************************************************
+ * _ *
+ * (_) *
+ * __ ____ _ _ __ _ __ _ _ __ __ _ *
+ * \ \ /\ / / _` | '__| '_ \| | '_ \ / _` | *
+ * \ V V / (_| | | | | | | | | | | (_| | *
+ * \_/\_/ \__,_|_| |_| |_|_|_| |_|\__, | *
+ * __/ | *
+ * |___/ *
+ * *
+ * Please refrain from running any program (including *
+ * HDF5 tests) which uses the subfiling VFD on Perlmutter *
+ * at the National Energy Research Scientific Computing *
+ * Center, NERSC. *
+ * Doing so may cause a system disruption due to subfiling *
+ * crashing Lustre. The sytem's Lustre bug is expected *
+ * to be resolved by 2023. *
+ * *
+ ************************************************************
+
+ CMake files do not behave correctly with paths containing spaces.
+ Do not use spaces in paths because the required escaping for handling spaces
+ results in very complex and fragile build files.
+ ADB - 2019/05/07
+
+ At present, metadata cache images may not be generated by parallel
+ applications. Parallel applications can read files with metadata cache
+ images, but since this is a collective operation, a deadlock is possible
+ if one or more processes do not participate.
+
+ CPP ptable test fails on both VS2017 and VS2019 with Intel compiler, JIRA
+ issue: HDFFV-10628. This test will pass with VS2015 with Intel compiler.
+
+ The subsetting option in ph5diff currently will fail and should be avoided.
+ The subsetting option works correctly in serial h5diff.
+
+ Several tests currently fail on certain platforms:
+ MPI_TEST-t_bigio fails with spectrum-mpi on ppc64le platforms.
+
+ MPI_TEST-t_subfiling_vfd and MPI_TEST_EXAMPLES-ph5_subfiling fail with
+ cray-mpich on theta and with XL compilers on ppc64le platforms.
+
+ MPI_TEST_testphdf5_tldsc fails with cray-mpich 7.7 on cori and theta.
+
+ Known problems in previous releases can be found in the HISTORY*.txt files
+ in the HDF5 source. Please report any new problems found to
+ help@hdfgroup.org.
+
+
+CMake vs. Autotools installations
+=================================
+While both build systems produce similar results, there are differences.
+Each system produces the same set of folders on linux (only CMake works
+on standard Windows); bin, include, lib and share. Autotools places the
+COPYING and RELEASE.txt file in the root folder, CMake places them in
+the share folder.
+
+The bin folder contains the tools and the build scripts. Additionally, CMake
+creates dynamic versions of the tools with the suffix "-shared". Autotools
+installs one set of tools depending on the "--enable-shared" configuration
+option.
+ build scripts
+ -------------
+ Autotools: h5c++, h5cc, h5fc
+ CMake: h5c++, h5cc, h5hlc++, h5hlcc
+
+The include folder holds the header files and the fortran mod files. CMake
+places the fortran mod files into separate shared and static subfolders,
+while Autotools places one set of mod files into the include folder. Because
+CMake produces a tools library, the header files for tools will appear in
+the include folder.
+
+The lib folder contains the library files, and CMake adds the pkgconfig
+subfolder with the hdf5*.pc files used by the bin/build scripts created by
+the CMake build. CMake separates the C interface code from the fortran code by
+creating C-stub libraries for each Fortran library. In addition, only CMake
+installs the tools library. The names of the szip libraries are different
+between the build systems.
+
+The share folder will have the most differences because CMake builds include
+a number of CMake specific files for support of CMake's find_package and support
+for the HDF5 Examples CMake project.
+
+The issues with the gif tool are:
+ HDFFV-10592 CVE-2018-17433
+ HDFFV-10593 CVE-2018-17436
+ HDFFV-11048 CVE-2020-10809
+These CVE issues have not yet been addressed and are avoided by not building
+the gif tool by default. Enable building the High-Level tools with these options:
+ autotools: --enable-hltools
+ cmake: HDF5_BUILD_HL_TOOLS=ON
%%%%1.13.3%%%%
diff --git a/release_docs/HISTORY-1_8.txt b/release_docs/HISTORY-1_8.txt
deleted file mode 100644
index 461e0be..0000000
--- a/release_docs/HISTORY-1_8.txt
+++ /dev/null
@@ -1,14439 +0,0 @@
-HDF5 History
-============
-
-This file contains development history of HDF5 1.8 branch
-
-23. Release Information for hdf5-1.8.21
-22. Release Information for hdf5-1.8.20
-21. Release Information for hdf5-1.8.19
-20. Release Information for hdf5-1.8.18
-19. Release Information for hdf5-1.8.17
-18. Release Information for hdf5-1.8.16
-17. Release Information for hdf5-1.8.15
-16. Release Information for hdf5-1.8.14
-15. Release Information for hdf5-1.8.13
-14. Release Information for hdf5-1.8.12
-13. Release Information for hdf5-1.8.11
-12. Release Information for hdf5-1.8.10-patch1
-11. Release Information for hdf5-1.8.10
-10. Release Information for hdf5-1.8.9
-09. Release Information for hdf5-1.8.8
-08. Release Information for hdf5-1.8.7
-07. Release Information for hdf5-1.8.6
-06. Release Information for hdf5-1.8.5
-05. Release Information for hdf5-1.8.4
-04. Release Information for hdf5-1.8.3
-03. Release Information for hdf5-1.8.2
-02. Release Information for hdf5-1.8.1
-01. Release Information for hdf5-1.8.0
-
-[Search on the string '%%%%' for section breaks of each release.]
-
-%%%%1.8.21%%%%
-
-
-HDF5 version 1.8.21 released on 2018-06-04
-================================================================================
-
-INTRODUCTION
-============
-
-This document describes the differences between HDF5-1.8.20 and
-HDF5-1.8.21, and contains information on the platforms tested and
-known problems in HDF5-1.8.21.
-For more details, see the files HISTORY-1_0-1_8_0_rc3.txt
-and HISTORY-1_8.txt in the release_docs/ directory of the HDF5 source.
-
-Links to the HDF5 1.8.21 source code, documentation, and additional materials
-can be found on the HDF5 web page at:
-
- https://support.hdfgroup.org/HDF5/
-
-The HDF5 1.8.21 release can be obtained from:
-
- https://support.hdfgroup.org/HDF5/release/obtain518.html
-
-User documentation for 1.8.21 can be accessed directly at this location:
-
- https://support.hdfgroup.org/HDF5/doc1.8/
-
-New features in the HDF5-1.8.x release series, including brief general
-descriptions of some new and modified APIs, are described in the "What's New
-in 1.8.0?" document:
-
- https://support.hdfgroup.org/HDF5/doc/ADGuide/WhatsNew180.html
-
-All new and modified APIs are listed in detail in the "HDF5 Software Changes
-from Release to Release" document, in the section "Release 1.8.21 (current
-release) versus Release 1.8.20
-
- https://support.hdfgroup.org/HDF5/doc1.8/ADGuide/Changes.html
-
-If you have any questions or comments, please send them to the HDF Help Desk:
-
- help@hdfgroup.org
-
-
-CONTENTS
-========
-
-- New Features
-- Support for New Platforms, Languages, and Compilers
-- Bug Fixes since HDF5-1.8.20
-- Supported Platforms
-- Supported Configuration Features Summary
-- More Tested Platforms
-- Known Problems
-
-
-New Features
-============
-
- Configuration
- -------------
- - CMake
-
- Change minimum version to 3.10.
-
- This change removes the need to support a copy of the FindMPI.cmake module,
- which has been removed, along with its subfolder in the config/cmake_ext_mod
- location.
-
- (ADB - 2018/03/09)
-
- - CMake
-
- Add pkg-config file generation
-
- Added pkg-config file generation for the C, C++, HL, and HL C++ libraries.
- In addition, builds on linux will create h5cXXX scripts that use the pkg-config
- files. This is a limited implementation of a script like autotools h5cc.
-
- (ADB - 2018/03/08, HDFFV-4359)
-
- - CMake
-
- Refactor use of CMAKE_BUILD_TYPE for new variable, which understands
- the type of generator in use.
-
- Added new configuration macros to use new HDF_BUILD_TYPE variable. This
- variable is set correctly for the type of generator being used for the build.
-
- (ADB - 2018/01/08, HDFFV-10385, HDFFV-10296)
-
- C++ API
- -------
- - The following C++ API wrappers have been added to class H5Location
- + H5Lcreate_soft:
- // Creates a soft link from link_name to target_name.
- void link(const char *target_name, const char *link_name,...)
- void link(const H5std_string& target_name,...)
-
- + H5Lcreate_hard:
- // Creates a hard link from new_name to curr_name.
- void link(const char *curr_name, const Group& new_loc,...)
- void link(const H5std_string& curr_name, const Group& new_loc,...)
-
- // Creates a hard link from new_name to curr_name in the same location.
- void link(const char *curr_name, const hid_t same_loc,...)
- void link(const H5std_string& curr_name, const hid_t same_loc,...)
-
- Note: previous version CommonFG::link will be deprecated.
-
- + H5Lcopy:
- // Copy an object from a group of file to another.
- void copyLink(const char *src_name, const Group& dst,...)
- void copyLink(const H5std_string& src_name, const Group& dst,...)
-
- // Copy an object from a group of file to the same location.
- void copyLink(const char *src_name, const char *dst_name,...)
- void copyLink(const H5std_string& src_name,...)
-
- + H5Lmove:
- // Rename an object in a group or file to a new location.
- void moveLink(const char* src_name, const Group& dst,...)
- void moveLink(const H5std_string& src_name, const Group& dst,...)
-
- // Rename an object in a group or file to the same location.
- void moveLink(const char* src_name, const char* dst_name,...)
- void moveLink(const H5std_string& src_name,...)
-
- Note: previous version CommonFG::move will be deprecated.
-
- + H5Ldelete:
- // Removes the specified link from this location.
- void unlink(const char *link_name,
- const LinkAccPropList& lapl = LinkAccPropList::DEFAULT)
- void unlink(const H5std_string& link_name,
- const LinkAccPropList& lapl = LinkAccPropList::DEFAULT)
-
- Note: An additional parameter is added to CommonFG::unlink and it
- is moved to H5Location.
-
- (BMR - 2018/05/11 - HDFFV-10445)
-
- - New property list subclasses
-
- Property list subclasses StrCreatPropList, LinkCreatPropList, and
- AttrCreatPropList are added for the C property list classes
- H5P_STRING_CREATE, H5P_LINK_CREATE, and H5P_ATTRIBUTE_CREATE.
-
- (BMR - 2018/05/11 - HDFFV-10445)
-
- - Another argument, LinkCreatPropList& lcpl, is added to the following
- functions for the use of link creation property list.
- Group createGroup(const char* name, size_t size_hint = 0,
- const LinkCreatPropList& lcpl = LinkCreatPropList::DEFAULT)
- Group createGroup(const H5std_string& name, size_t size_hint = 0,
- const LinkCreatPropList& lcpl = LinkCreatPropList::DEFAULT)
-
- (BMR - 2018/05/11 - HDFFV-10445)
-
-
-
-Support for New Platforms, Languages, and Compilers
-===================================================
-
- - Added support for Visual Studio 2017 w/ Intel Fortran 18 on Windows 10 x64.
-
-
-Bug Fixes since HDF5-1.8.20
-===========================
-
- - If an HDF5 file contains a filter pipeline message with a 'number of
- filters' field that exceeds the maximum number of allowed filters,
- the error handling code will attempt to dereference a NULL pointer.
-
- This issue was reported to The HDF Group as issue #CVE-2017-17505.
-
- NOTE: The HDF5 C library cannot produce such a file. This condition
- should only occur in a corrupt (or deliberately altered) file
- or a file created by third-party software.
-
- This problem arose because the error handling code assumed that
- the 'number of filters' field implied that a dynamic array of that
- size had already been created and that the cleanup code should
- iterate over that array and clean up each element's resources. If
- an error occurred before the array has been allocated, this will
- not be true.
-
- This has been changed so that the number of filters is set to
- zero on errors. Additionally, the filter array traversal in the
- error handling code now requires that the filter array not be NULL.
-
- (DER - 2018/02/06, HDFFV-10354)
-
- - If an HDF5 file contains a filter pipeline message which contains
- a 'number of filters' field that exceeds the actual number of
- filters in the message, the HDF5 C library will read off the end of
- the read buffer.
-
- This issue was reported to The HDF Group as issue #CVE-2017-17506.
-
- NOTE: The HDF5 C library cannot produce such a file. This condition
- should only occur in a corrupt (or deliberately altered) file
- or a file created by third-party software.
-
- The problem was fixed by passing the buffer size with the buffer
- and ensuring that the pointer cannot be incremented off the end
- of the buffer. A mismatch between the number of filters declared
- and the actual number of filters will now invoke normal HDF5
- error handling.
-
- (DER - 2018/02/26, HDFFV-10355)
-
- - If an HDF5 file contains a malformed compound datatype with a
- suitably large offset, the type conversion code can run off
- the end of the type conversion buffer, causing a segmentation
- fault.
-
- This issue was reported to The HDF Group as issue #CVE-2017-17507.
-
- NOTE: The HDF5 C library cannot produce such a file. This condition
- should only occur in a corrupt (or deliberately altered) file
- or a file created by third-party software.
-
- THE HDF GROUP WILL NOT FIX THIS BUG AT THIS TIME
-
- Fixing this problem would involve updating the publicly visible
- H5T_conv_t function pointer typedef and versioning the API calls
- which use it. We normally only modify the public API during
- major releases, so this bug will not be fixed at this time.
-
- (DER - 2018/02/26, HDFFV-10356)
-
- - If an HDF5 file contains a malformed compound type which contains
- a member of size zero, a division by zero error will occur while
- processing the type.
-
- This issue was reported to The HDF Group as issue #CVE-2017-17508.
-
- NOTE: The HDF5 C library cannot produce such a file. This condition
- should only occur in a corrupt (or deliberately altered) file
- or a file created by third-party software.
-
- Checking for zero before dividing fixes the problem. Instead of the
- division by zero, the normal HDF5 error handling is invoked.
-
- (DER - 2018/02/26, HDFFV-10357)
-
- - If an HDF5 file contains a malformed symbol table node that declares
- it contains more symbols than it actually contains, the library
- can run off the end of the metadata cache buffer while processing
- the symbol table node.
-
- This issue was reported to The HDF Group as issue #CVE-2017-17509.
-
- NOTE: The HDF5 C library cannot produce such a file. This condition
- should only occur in a corrupt (or deliberately altered) file
- or a file created by third-party software.
-
- Performing bounds checks on the buffer while processing fixes the
- problem. Instead of the segmentation fault, the normal HDF5 error
- handling is invoked.
-
- (DER - 2018/03/12, HDFFV-10358)
-
-
- Configuration
- -------------
- - Library
-
- Moved the location of gcc attribute.
-
- The gcc attribute(no_sanitize), named as the macro HDF_NO_UBSAN,
- was located after the function name. Builds with GCC 7 did not
- indicate any problem, but GCC 8 issued errors. Moved the
- attribute before the function name, as required.
-
- (ADB 2018/05/22, HDFFV-10473)
-
- - CMake
-
- Update CMake commands configuration.
-
- A number of improvements were made to the CMake commands. Most
- changes simplify usage or eliminate unused constructs. Also,
- some changes support better cross-platform support.
-
- (ADB - 2018/02/01, HDFFV-10398)
-
- - CMake
-
- Correct usage of CMAKE_BUILD_TYPE variable.
-
- The use of the CMAKE_BUILD_TYPE is incorrect for multi-config
- generators (Visual Studio and XCode) and is optional for single
- config generators. Created a new macro to check
- GLOBAL PROPERTY -> GENERATOR_IS_MULTI_CONFIG
- Created two new HDF variable, HDF_BUILD_TYPE and HDF_CFG_BUILD_TYPE.
- Defaults for these variables is "Release".
-
- (ADB - 2018/01/10, HDFFV-10385)
-
- - CMake
-
- Add replacement of fortran flags if using static CRT.
-
- Added TARGET_STATIC_CRT_FLAGS call to HDFUseFortran.cmake file in
- config/cmake_ext_mod folder.
-
- (ADB - 2018/01/08, HDFFV-10334)
-
-
- Library
- -------
- - Utility function can not handle lowercase Windows drive letters
-
- Added call to toupper function for drive letter.
-
- (ADB - 2017/12/18, HDFFV-10307)
-
-
- Tools
- -----
- - h5repack
-
- h5repack changes the chunk parameters when a change of layout is not
- specified and a filter is applied.
-
- HDFFV-10297, HDFFV-10319 reworked code for h5repack and h5diff code
- in the tools library. The check for an existing layout was incorrectly
- placed into an if block and not executed. The check was moved into
- the normal path of the function.
-
- (ADB - 2018/02/21, HDFFV-10412)
-
- - h5dump
-
- the tools library will hide the error stack during file open.
-
- While this is preferable almost always, there are reasons to enable
- display of the error stack when a tool will not open a file. Adding an
- optional argument to the --enable-error-stack will provide this use case.
- As an optional argument it will not affect the operation of the
- --enable-error-stack. h5dump is the only tool to implement this change.
-
- (ADB - 2018/02/15, HDFFV-10384)
-
- - h5dump
-
- h5dump would output an indented blank line in the filters section.
-
- h5dump overused the h5tools_simple_prefix function, which is a
- function intended to account for the data index (x,y,z) option.
- Removed the function call for header information.
-
- (ADB - 2018/01/25, HDFFV-10396)
-
- - h5repack
-
- h5repack incorrectly searched internal object table for name.
-
- h5repack would search the table of objects for a name, if the
- name did not match it tried to determine if the name without a
- leading slash would match. The logic was flawed! The table
- stored names(paths) without a leading slash and did a strstr
- of the table path to the name.
- The assumption was that if there was a difference of one then
- it was a match, however "pressure" would match "/pressure" as
- well as "/pressure1", "/pressure2", etc. Changed logic to remove
- any leading slash and then do a full compare of the name.
-
- (ADB - 2018/01/18, HDFFV-10393)
-
- - h5repack
-
- h5repack failed to handle command line parameters for customer filters.
-
- User defined filter parameter conversions would fail when integers
- were represented on the command line with character strings
- larger than 9 characters. Increased local variable array for storing
- the current command line parameter to prevent buffer overflows.
-
- (ADB - 2018/01/17, HDFFV-10392)
-
- - h5diff
-
- h5diff seg faulted if comparing VL strings against fixed strings.
-
- Reworked solution for HDFFV-8625 and HDFFV-8639. Implemented the check
- for string objects of same type in the diff_can_type function by
- adding an if(tclass1 == H5T_STRING) block. This "if block" moves the
- same check that was added for attributes to this function, which is
- used by all object types. This function handles complex type structures.
- Also added a new test file in h5diffgentest for testing this issue
- and removed the temporary files used in the test scripts.
-
- (ADB - 2018/01/04, HDFFV-8745)
-
-
- C++ API
- -------
- - Removal of memory leaks
-
- A private function was inadvertently called, causing memory leaks. This
- is now fixed.
-
- (BMR - 2018/04/12 - User reported in email)
-
- - Changes in exception classes
-
- Some exception classes are reorganized to reflect the HDF5 object
- hierarchy and allow customization.
- DataSetIException -> LocationException -> Exception
- DataTypeIException -> LocationException -> Exception
- GroupIException -> LocationException -> Exception
- AttributeIException -> LocationException -> Exception
- FileIException -> GroupIException -> LocationException -> Exception
- Member functions in H5Location and H5Object now throw specific exceptions
- associated with the invoking objects.
-
- (BMR - 2018/05/11)
-
- - H5Location::closeObjId is made static
- (BMR - 2018/05/11)
-
- - H5A wrappers in H5Location are removed as they have been in H5Object.
- (BMR - 2018/05/11)
-
-
-Supported Platforms
-===================
-The following platforms are supported and have been tested for this release.
-They are built with the configure process unless specified otherwise.
-
- Linux 2.6.32-573.22.1.el6 GNU C (gcc), Fortran (gfortran), C++ (g++)
- #1 SMP x86_64 GNU/Linux compilers:
- (platypus/mayll) Version 4.4.7 20120313
- Versions 4.9.3, 5.3.0, 6.2.0
- PGI C, Fortran, C++ for 64-bit target on
- x86-64;
- Version 17.10-0
- Intel(R) C (icc), C++ (icpc), Fortran (icc)
- compilers:
- Version 17.0.4.196 Build 20160721
- MPICH 3.1.4 compiled with GCC 4.9.3
- OpenMPI 2.0.1 compiled with GCC 4.9.3
-
- Linux 2.6.32-573.18.1.el6 gcc (GCC) 4.4.7 20120313 (Red Hat 4.4.7-16)
- #1 SMP ppc64 GNU/Linux g++ (GCC) 4.4.7 20120313 (Red Hat 4.4.7-16)
- (ostrich) GNU Fortran (GCC) 4.4.7 20120313 (Red Hat 4.4.7-16)
- IBM XL C/C++ V13.1
- IBM XL Fortran V15.1
-
- Linux 3.10.0-327.10.1.el7 GNU C (gcc), Fortran (gfortran), C++ (g++)
- #1 SMP x86_64 GNU/Linux compilers:
- (kituo/moohan/jelly Version 4.8.5 20150623 (Red Hat 4.8.5-4)
- Versions 4.9.3, 5.3.0, 6.2.0
- Intel(R) C (icc), C++ (icpc), Fortran (icc)
- compilers:
- Version 17.0.4.196 Build 20170411
- MPICH 3.1.4 compiled with GCC 4.9.3
- NAG Fortran Compiler Release 6.1(Tozai) Build 6116
-
- SunOS 5.11 32- and 64-bit Sun C 5.12 SunOS_sparc
- (emu) Sun Fortran 95 8.6 SunOS_sparc
- Sun C++ 5.12 SunOS_sparc
-
- Windows 7 Visual Studio 2015 w/ Intel Fortran 16 (cmake)
-
- Windows 7 x64 Visual Studio 2012 w/ Intel Fortran 15 (cmake)
- Visual Studio 2013 w/ Intel Fortran 15 (cmake)
- Visual Studio 2015 w/ Intel Fortran 16 (cmake)
- Visual Studio 2015 w/ Intel C, Fortran 2017 (cmake)
- Visual Studio 2015 w/ MSMPI 8 (cmake)
-
- Windows 10 Visual Studio 2015 w/ Intel Fortran 16 (cmake)
-
- Windows 10 x64 Visual Studio 2015 w/ Intel Fortran 16 (cmake)
- Visual Studio 2017 w/ Intel Fortran 18 (cmake)
-
- Mac OS X Mavericks 10.9.5 Apple LLVM version 6.0 (clang-600.0.57)
- 64-bit gfortran GNU Fortran (GCC) 4.9.2
- (wren/quail) Intel icc/icpc/ifort version 15.0.3
-
- Mac OS X Yosemite 10.10.5 Apple LLVM version 6.1 (clang-602.0.53)
- 64-bit gfortran GNU Fortran (GCC) 4.9.2
- (osx1010dev/osx1010test) Intel icc/icpc/ifort version 15.0.3
-
- Mac OS X El Capitan 10.11.6 Apple LLVM version 7.3.0 (clang-703.0.29)
- 64-bit gfortran GNU Fortran (GCC) 5.2.0
- (VM osx1011dev/osx1011test) Intel icc/icpc/ifort version 16.0.2
-
- Mac OS Sierra 10.12.6 Apple LLVM version 8.1 (clang-802.0.42)
- 64-bit gfortran GNU Fortran (GCC) 7.1.0
- (kite) Intel icc/icpc/ifort version 17.0.2
-
-
-Tested Configuration Features Summary
-=====================================
-
- In the tables below
- y = tested
- n = not tested in this release
- C = Cluster
- W = Workstation
- x = not working in this release
- dna = does not apply
- ( ) = footnote appears below second table
- <blank> = testing incomplete on this feature or platform
-
-Platform C F90/ F90 C++ zlib SZIP
- parallel F2003 parallel
-SunOS 5.11 32-bit n y/y n y y y
-SunOS 5.11 64-bit n y/y n y y y
-Windows 7 y y/y n y y y
-Windows 7 x64 y y/y n y y y
-Windows 7 Cygwin n y/n n y y y
-Windows 7 x64 Cygwin n y/n n y y y
-Windows 10 y y/y n y y y
-Windows 10 x64 y y/y n y y y
-Mac OS X Yosemite 10.10.5 64-bit n y/y n y y y
-Mac OS X El Capitan 10.11.6 64-bit n y/y n y y y
-Mac OS Sierra 10.12.6 64-bit n y/y n y y y
-AIX 6.1 32- and 64-bit n y/n n y y y
-CentOS 6.7 Linux 2.6.32 x86_64 GNU y y/y y y y y
-CentOS 6.7 Linux 2.6.32 x86_64 Intel n y/y n y y y
-CentOS 6.7 Linux 2.6.32 x86_64 PGI n y/y n y y y
-CentOS 7.1 Linux 3.10.0 x86_64 GNU y y/y y y y y
-CentOS 7.1 Linux 3.10.0 x86_64 Intel n y/y n y y y
-Linux 2.6.32-573.18.1.el6.ppc64 n y/n n y y y
-
-Platform Shared Shared Shared Thread-
- C libs F90 libs C++ libs safe
-SunOS 5.11 32-bit y y y y
-SunOS 5.11 64-bit y y y y
-Windows 7 y y y y
-Windows 7 x64 y y y y
-Windows 7 Cygwin n n n y
-Windows 7 x64 Cygwin n n n y
-Windows 10 y y y y
-Windows 10 x64 y y y y
-Mac OS X Yosemite 10.10.5 64-bit y n y y
-Mac OS X El Capitan 10.11.6 64-bit y n y y
-Mac OS Sierra 10.12.6 64-bit y n y y
-AIX 6.1 32- and 64-bit y n n y
-CentOS 6.7 Linux 2.6.32 x86_64 GNU y y y y
-CentOS 6.7 Linux 2.6.32 x86_64 Intel y y y y
-CentOS 6.7 Linux 2.6.32 x86_64 PGI y y y y
-CentOS 7.1 Linux 3.10.0 x86_64 GNU y y y y
-CentOS 7.1 Linux 3.10.0 x86_64 Intel y y y y
-Linux 2.6.32-573.18.1.el6.ppc64 y y y y
-
-Compiler versions for each platform are listed in the preceding
-"Supported Platforms" table.
-
-
-More Tested Platforms
-=====================
-The following platforms are not supported but have been tested for this release.
-
- Linux 2.6.32-573.22.1.el6 g95 (GCC 4.0.3 (g95 0.94!)
- #1 SMP x86_64 GNU/Linux
- (mayll)
-
- Debian8.4.0 3.16.0-4-amd64 #1 SMP Debian 3.16.36-1 x86_64 GNU/Linux
- gcc (Debian 4.9.2-10) 4.9.2
- GNU Fortran (Debian 4.9.2-10) 4.9.2
- (cmake and autotools)
-
- Fedora24 4.7.2-201.fc24.x86_64 #1 SMP x86_64 x86_64 x86_64 GNU/Linux
- gcc (GCC) 6.1.1 20160621 (Red Hat 6.1.1-3)
- GNU Fortran (GCC) 6.1.1 20160621 (Red Hat 6.1.1-3)
- (cmake and autotools)
-
- CentOS 7.2 3.10.0-327.28.2.el7.x86_64 #1 SMP x86_64 x86_64 x86_64 GNU/Linux
- gcc (GCC) 4.8.5 20150623 (Red Hat 4.8.5-4)
- GNU Fortran (GCC) 4.8.5 20150623 (Red Hat 4.8.5-4)
- (cmake and autotools)
-
- Ubuntu 16.04 4.4.0-38-generic #62-Ubuntu SMP x86_64 GNU/Linux
- gcc (Ubuntu 5.4.0-6ubuntu1~16.04.2) 5.4.0
- GNU Fortran (Ubuntu 5.4.0-6ubuntu1~16.04.2) 5.4.0
- (cmake and autotools)
-
-
-Known Problems
-==============
-
- The dynamically loaded plugin test libraries require undefined references
- to HDF5 functions to be resolved at runtime in order to function properly.
- With autotools on CYGWIN this results in build errors, and we have not
- found a solution that satisfies both. Therefore the dynamically loaded
- plugin tests have been disabled on CYGWIN.
-
- Mac OS X 10.13 added additional subdirectory structure in .libs for shared
- libraries. Consequently "make check" will fail testing java and dynamically
- loaded plugin test libraries attempting to copy files from the previous
- locations in .libs directories. This will be addressed in the next release
- when support for the Mac OS X 10.13 platform is added.
-
- Known problems in previous releases can be found in the HISTORY*.txt files
- in the HDF5 source. Please report any new problems found to
- help@hdfgroup.org.
-
-
-%%%%1.8.20%%%%
-
-
-HDF5 version 1.8.20 released on 2017-11-28
-================================================================================
-
-INTRODUCTION
-============
-
-This document describes the differences between HDF5-1.8.19 and
-HDF5-1.8.20, and contains information on the platforms tested and
-known problems in HDF5-1.8.20.
-For more details, see the files HISTORY-1_0-1_8_0_rc3.txt
-and HISTORY-1_8.txt in the release_docs/ directory of the HDF5 source.
-
-Links to the HDF5 1.8.20 source code, documentation, and additional materials
-can be found on the HDF5 web page at:
-
- https://support.hdfgroup.org/HDF5/
-
-The HDF5 1.8.20 release can be obtained from:
-
- https://support.hdfgroup.org/HDF5/release/obtain518.html
-
-User documentation for 1.8.20 can be accessed directly at this location:
-
- https://support.hdfgroup.org/HDF5/doc1.8/
-
-New features in the HDF5-1.8.x release series, including brief general
-descriptions of some new and modified APIs, are described in the "What's New
-in 1.8.0?" document:
-
- https://support.hdfgroup.org/HDF5/doc/ADGuide/WhatsNew180.html
-
-All new and modified APIs are listed in detail in the "HDF5 Software Changes
-from Release to Release" document, in the section "Release 1.8.20 (current
-release) versus Release 1.8.19
-
- https://support.hdfgroup.org/HDF5/doc1.8/ADGuide/Changes.html
-
-If you have any questions or comments, please send them to the HDF Help Desk:
-
- help@hdfgroup.org
-
-
-CONTENTS
-========
-
-- New Features
-- Support for New Platforms, Languages, and Compilers
-- Bug Fixes since HDF5-1.8.20
-- Supported Platforms
-- Supported Configuration Features Summary
-- More Tested Platforms
-- Known Problems
-
-
-New Features
-============
-
- Tools
- -----
- - h5diff
-
- h5diff has new option enable-error-stack.
-
- Updated h5diff with the --enable-error-stack argument, which
- enables the display of the hdf5 error stack. This completes the
- improvement to the main tools; h5copy, h5diff, h5dump, h5ls and
- h5repack.
-
- (ADB - 2017/08/30, HDFFV-9774)
-
-
- C++ API
- -------
- - The following C++ API wrappers have been added to the C++ Library:
-
- // Creates a binary object description of this datatype.
- void DataType::encode() - C API H5Tencode()
-
- // Returns the decoded type from the binary object description.
- DataType::decode() - C API H5Tdecode()
- ArrayType::decode() - C API H5Tdecode()
- CompType::decode() - C API H5Tdecode()
- DataType::decode() - C API H5Tdecode()
- EnumType::decode() - C API H5Tdecode()
- FloatType::decode() - C API H5Tdecode()
- IntType::decode() - C API H5Tdecode()
- StrType::decode() - C API H5Tdecode()
- VarLenType::decode() - C API H5Tdecode()
-
- // Three overloaded functions to retrieve information about an object
- H5Location::getObjectInfo() - H5Oget_info()/H5Oget_info_by_name()
-
- (BMR - 2017/10/17, HDFFV-10175)
-
- - New constructors to open existing datatypes added in ArrayType,
- CompType, DataType, EnumType, FloatType, IntType, StrType, and
- VarLenType.
-
- (BMR - 2017/10/17, HDFFV-10175)
-
- - A document is added to the HDF5 C++ API Reference Manual to show the
- mapping from a C API to C++ wrappers. It can be found from the main
- page of the C++ API Reference Manual.
-
- (BMR - 2017/10/17, HDFFV-10151)
-
-
- High-Level APIs
- ---------------
- - H5DOread_chunk
-
- Users wanted to read compressed data directly from a file without any
- processing by the HDF5 data transfer pipeline, just as they were able
- to write it directly to a file with H5DOwrite_chunk.
-
- New API function, corresponding to existing function H5DOwrite_chunk.
- H5DOread_chunk reads a raw data chunk directly from a chunked dataset
- in the file into the application buffer, bypassing the library’s internal
- data transfer pipeline, including filters.
-
- (VC - 2017/05/02, HDFFV-9934)
-
-
-Support for New Platforms, Languages, and Compilers
-===================================================
-
- - Added NAG compiler
-
-
-Bug Fixes since HDF5-1.8.19
-===========================
-
- Configuration
- -------------
- - cmake
-
- The hdf5 library used shared szip and zlib, which needlessly required
- applications to link with the same szip and zlib libraries.
-
- Changed the target_link_libraries commands to use the static libs.
- Removed improper link duplication of szip and zlib.
- Adjusted the link dependencies and the link interface values of
- the target_link_libraries commands.
-
- (ADB - 2017/11/14, HDFFV-10329)
-
- - cmake MPI
-
- CMake implementation for MPI was problematic and would create incorrect
- MPI library references in the hdf5 libraries.
-
- Reworked the CMake MPI code to properly create CMake targets.Also merged
- the latest CMake FindMPI.cmake changes to the local copy. This is necessary
- until HDF changes the CMake minimum to 3.9 or greater.
-
- (ADB - 2017/11/02, HDFFV-10321)
-
-
- - Fixed Fortran linker flags when using the NAG Fortran compiler (autotools).
-
- (HDFFV-10037, MSB, 2017/10/21)
-
- - cmake
-
- Too many commands for POST_BUILD step caused command line to be
- too big on windows.
-
- Changed foreach of copy command to use a custom command with the
- use of the HDFTEST_COPY_FILE macro.
-
- (ADB - 2017/07/12, HDFFV-10254)
-
-
- Library
- -------
- - filter plugin handling in H5PL.c and H5Z.c
-
- It was discovered that the dynamic loading process used by
- filter plugins had issues with library dependencies.
-
- CMake build process changed to use LINK INTERFACE keywords, which
- allowed HDF5 C library to make dependent libraries private. The
- filter plugin libraries no longer require dependent libraries
- (such as szip or zlib) to be available.
- (ADB - 2017/11/16, HDFFV-10328)
-
- - Fix rare object header corruption bug
-
- In certain cases, such as when converting large attributes to dense
- storage, an error could occur which would either fail an assertion or
- cause file corruption. Fixed and added test.
-
- (NAF - 2017/11/14, HDFFV-10274)
-
- - H5Zfilter_avail in H5Z.c
-
- The public function checked for plugins, while the private
- function did not.
-
- Modified H5Zfilter_avail and private function, H5Z_filter_avail.
- Moved check for plugin from public to private function. Updated
- H5P__set_filter due to change in H5Z_filter_avail. Updated tests.
-
- (ADB - 2017/10/10, HDFFV-10297, HDFFV-10319)
-
- - Fix H5Sencode bug when num points selected is >2^32
-
- Modified to fail if the 32 bit limit is exceeded when encoding either
- offsets or counts in the selection.
-
- (HDFFV-10323, VC, 2017/09/07)
-
- - Fix H5HL_offset_into()
-
- (1) Fix H5HL_offset_into() to return error when offset exceeds heap data
- block size.
- (2) Fix other places in the library that call this routine to detect
- error routine.
-
- (HDFFV-10216, VC, 2017/09/05)
-
-
- Tools
- -----
- - h5repack
-
- h5repack failed to copy a dataset with existing filter.
-
- Reworked code for h5repack and h5diff code in tools library. Added
- improved error handling, cleanup of resources and checks of calls.
- Modified H5Zfilter_avail and private function, H5Z_filter_avail.
- Moved check for plugin from public to private function. Updated
- H5P__set_filter due to change in H5Z_filter_avail. Updated tests.
- Note, h5repack output display has changed to clarify the individual
- steps of the repack process. The output indicates if an operation
- applies to all objects. Lines with notation and no information
- have been removed.
-
- (ADB - 2017/10/10, HDFFV-10297, HDFFV-10319)
-
- - h5repack
-
- h5repack always set the User Defined filter flag to H5Z_FLAG_MANDATORY.
-
- Added another parameter to the 'UD=' option to set the flag by default
- to '0' or H5Z_FLAG_MANDATORY, the other choice is '1' or H5Z_FLAG_OPTIONAL.
-
- (ADB - 2017/08/31, HDFFV-10269)
-
- - h5ls
-
- h5ls generated error on stack when it encountered a H5S_NULL
- dataspace.
-
- Adding checks for H5S_NULL before calling H5Sis_simple (located
- in the h5tools_dump_mem function) fixed the issue.
-
- (ADB - 2017/08/17, HDFFV-10188)
-
- - h5dump
-
- h5dump segfaulted on output of XML file.
-
- Function that escape'd strings used the full buffer length
- instead of just the length of the replacement string in a
- strncpy call. Using the correct length fixed the issue.
-
- (ADB - 2017/08/01, HDFFV-10256)
-
- - h5diff
-
- h5diff segfaulted on compare of a NULL variable length string.
-
- Improved h5diff compare of strings by adding a check for
- NULL strings and setting the lengths to zero.
-
- (ADB - 2017/07/25, HDFFV-10246)
-
- - h5import
-
- h5import crashed trying to import data from a subset of a dataset.
-
- Improved h5import by adding the SUBSET keyword. h5import understands
- to use the Count times the Block as the size of the dimensions.
- Added INPUT_B_ORDER keyword to old-style configuration files.
- The import from h5dump function expects the binary files to use native
- types (FILE '-b' option) in the binary file.
-
- (ADB - 2017/06/15, HDFFV-10219)
-
-
- C++ API
- -------
- - Marked the following functions deprecated because they were moved to
- class H5Object:
- H5Location::createAttribute()
- H5Location::openAttribute()
- H5Location::attrExists()
- H5Location::removeAttr()
- H5Location::renameAttr()
- H5Location::getNumAttrs()
-
- (BMR - 2017/10/17)
-
-
-Supported Platforms
-===================
-The following platforms are supported and have been tested for this release.
-They are built with the configure process unless specified otherwise.
-
- Linux 2.6.32-573.22.1.el6 GNU C (gcc), Fortran (gfortran), C++ (g++)
- #1 SMP x86_64 GNU/Linux compilers:
- (platypus/mayll) Version 4.4.7 20120313
- Versions 4.9.3, 5.3.0, 6.2.0
- PGI C, Fortran, C++ for 64-bit target on
- x86-64;
- Version 16.10-0
- Intel(R) C (icc), C++ (icpc), Fortran (icc)
- compilers:
- Version 17.0.0.196 Build 20160721
- MPICH 3.1.4 compiled with GCC 4.9.3
- OpenMPI 2.0.1 compiled with GCC 4.9.3
-
- Linux 2.6.32-573.18.1.el6 gcc (GCC) 4.4.7 20120313 (Red Hat 4.4.7-16)
- #1 SMP ppc64 GNU/Linux g++ (GCC) 4.4.7 20120313 (Red Hat 4.4.7-16)
- (ostrich) GNU Fortran (GCC) 4.4.7 20120313 (Red Hat 4.4.7-16)
- IBM XL C/C++ V13.1
- IBM XL Fortran V15.1
-
- Linux 3.10.0-327.10.1.el7 GNU C (gcc), Fortran (gfortran), C++ (g++)
- #1 SMP x86_64 GNU/Linux compilers:
- (kituo/moohan/jelly Version 4.8.5 20150623 (Red Hat 4.8.5-4)
- Versions 4.9.3, 5.3.0, 6.2.0
- Intel(R) C (icc), C++ (icpc), Fortran (icc)
- compilers:
- Version 17.0.4.196 Build 20170411
- MPICH 3.1.4 compiled with GCC 4.9.3
- NAG Fortran Compiler Release 6.1(Tozai) Build 6116
-
- SunOS 5.11 32- and 64-bit Sun C 5.12 SunOS_sparc
- (emu) Sun Fortran 95 8.6 SunOS_sparc
- Sun C++ 5.12 SunOS_sparc
-
- Windows 7 Visual Studio 2012 w/ Intel Fortran 15 (cmake)
- Visual Studio 2013 w/ Intel Fortran 15 (cmake)
- Visual Studio 2015 w/ Intel Fortran 16 (cmake)
-
- Windows 7 x64 Visual Studio 2012 w/ Intel Fortran 15 (cmake)
- Visual Studio 2013 w/ Intel Fortran 15 (cmake)
- Visual Studio 2015 w/ Intel Fortran 16 (cmake)
- Visual Studio 2015 w/ Intel C, Fortran 2017 (cmake)
- Visual Studio 2015 w/ MSMPI 8 (cmake)
- Cygwin(CYGWIN_NT-6.1 2.8.0(0.309/5/3)
- gcc and gfortran compilers (GCC 5.4.0)
- (cmake and autotools)
-
- Windows 10 Visual Studio 2015 w/ Intel Fortran 16 (cmake)
- Cygwin(CYGWIN_NT-6.1 2.8.0(0.309/5/3)
- gcc and gfortran compilers (GCC 5.4.0)
- (cmake and autotools)
-
- Windows 10 x64 Visual Studio 2015 w/ Intel Fortran 16 (cmake)
-
- Mac OS X Mavericks 10.9.5 Apple LLVM version 6.0 (clang-600.0.57)
- 64-bit gfortran GNU Fortran (GCC) 4.9.2
- (wren/quail) Intel icc/icpc/ifort version 15.0.3
-
- Mac OS X Yosemite 10.10.5 Apple LLVM version 6.1 (clang-602.0.53)
- 64-bit gfortran GNU Fortran (GCC) 4.9.2
- (osx1010dev/osx1010test) Intel icc/icpc/ifort version 15.0.3
-
- Mac OS X El Capitan 10.11.6 Apple LLVM version 7.3.0 (clang-703.0.29)
- 64-bit gfortran GNU Fortran (GCC) 5.2.0
- (VM osx1011dev/osx1011test) Intel icc/icpc/ifort version 16.0.2
-
- Mac OS Sierra 10.12.6 Apple LLVM version 8.1 (clang-802.0.42)
- 64-bit gfortran GNU Fortran (GCC) 7.1.0
- (kite) Intel icc/icpc/ifort version 17.0.2
-
-Tested Configuration Features Summary
-=====================================
-
- In the tables below
- y = tested
- n = not tested in this release
- C = Cluster
- W = Workstation
- x = not working in this release
- dna = does not apply
- ( ) = footnote appears below second table
- <blank> = testing incomplete on this feature or platform
-
-Platform C F90/ F90 C++ zlib SZIP
- parallel F2003 parallel
-SunOS 5.11 32-bit n y/y n y y y
-SunOS 5.11 64-bit n y/y n y y y
-Windows 7 y y/y n y y y
-Windows 7 x64 y y/y n y y y
-Windows 7 Cygwin n y/n n y y y
-Windows 7 x64 Cygwin n y/n n y y y
-Windows 10 y y/y n y y y
-Windows 10 x64 y y/y n y y y
-Mac OS X Mavericks 10.9.5 64-bit n y/y n y y y
-Mac OS X Yosemite 10.10.5 64-bit n y/y n y y y
-Mac OS X El Capitan 10.11.6 64-bit n y/y n y y y
-Mac OS Sierra 10.12.6 64-bit n y/y n y y y
-AIX 6.1 32- and 64-bit n y/n n y y y
-CentOS 6.7 Linux 2.6.32 x86_64 GNU y y/y y y y y
-CentOS 6.7 Linux 2.6.32 x86_64 Intel n y/y n y y y
-CentOS 6.7 Linux 2.6.32 x86_64 PGI n y/y n y y y
-CentOS 7.1 Linux 3.10.0 x86_64 GNU y y/y y y y y
-CentOS 7.1 Linux 3.10.0 x86_64 Intel n y/y n y y y
-Linux 2.6.32-431.11.2.el6.ppc64 n y/n n y y y
-
-Platform Shared Shared Shared Thread-
- C libs F90 libs C++ libs safe
-SunOS 5.11 32-bit y y y y
-SunOS 5.11 64-bit y y y y
-Windows 7 y y y y
-Windows 7 x64 y y y y
-Windows 7 Cygwin n n n y
-Windows 7 x64 Cygwin n n n y
-Windows 10 y y y y
-Windows 10 x64 y y y y
-Mac OS X Mavericks 10.9.5 64-bit y n y y
-Mac OS X Yosemite 10.10.5 64-bit y n y y
-Mac OS X El Capitan 10.11.6 64-bit y n y y
-Mac OS Sierra 10.12.6 64-bit y n y y
-AIX 6.1 32- and 64-bit y n n y
-CentOS 6.7 Linux 2.6.32 x86_64 GNU y y y y
-CentOS 6.7 Linux 2.6.32 x86_64 Intel y y y y
-CentOS 6.7 Linux 2.6.32 x86_64 PGI y y y y
-CentOS 7.1 Linux 3.10.0 x86_64 GNU y y y y
-CentOS 7.1 Linux 3.10.0 x86_64 Intel y y y y
-Linux 2.6.32-431.11.2.el6.ppc64 y y y y
-
-Compiler versions for each platform are listed in the preceding
-"Supported Platforms" table.
-
-
-More Tested Platforms
-=====================
-The following platforms are not supported but have been tested for this release.
-
- Linux 2.6.32-573.22.1.el6 g95 (GCC 4.0.3 (g95 0.94!)
- #1 SMP x86_64 GNU/Linux
- (mayll)
-
- Debian8.4.0 3.16.0-4-amd64 #1 SMP Debian 3.16.36-1 x86_64 GNU/Linux
- gcc (Debian 4.9.2-10) 4.9.2
- GNU Fortran (Debian 4.9.2-10) 4.9.2
- (cmake and autotools)
-
- Fedora24 4.7.2-201.fc24.x86_64 #1 SMP x86_64 x86_64 x86_64 GNU/Linux
- gcc (GCC) 6.1.1 20160621 (Red Hat 6.1.1-3)
- GNU Fortran (GCC) 6.1.1 20160621 (Red Hat 6.1.1-3)
- (cmake and autotools)
-
- CentOS 7.2 3.10.0-327.28.2.el7.x86_64 #1 SMP x86_64 x86_64 x86_64 GNU/Linux
- gcc (GCC) 4.8.5 20150623 (Red Hat 4.8.5-4)
- GNU Fortran (GCC) 4.8.5 20150623 (Red Hat 4.8.5-4)
- (cmake and autotools)
-
- Ubuntu 16.04 4.4.0-38-generic #62-Ubuntu SMP x86_64 GNU/Linux
- gcc (Ubuntu 5.4.0-6ubuntu1~16.04.2) 5.4.0
- GNU Fortran (Ubuntu 5.4.0-6ubuntu1~16.04.2) 5.4.0
- (cmake and autotools)
-
-
-Known Problems
-==============
-
- The dynamically loaded plugin test libraries require undefined references
- to HDF5 functions to be resolved at runtime in order to function properly.
- With autotools on CYGWIN this results in build errors, and we have not
- found a solution that satisfies both. Therefore the dynamically loaded
- plugin tests have been disabled on CYGWIN.
-
- Mac OS X 10.13 added additional subdirectory structure in .libs for shared
- libraries. Consequently "make check" will fail testing java and dynamically
- loaded plugin test libraries attempting to copy files from the previous
- locations in .libs directories. This will be addressed in the next release
- when support for the Mac OS X 10.13 platform is added.
-
- Known problems in previous releases can be found in the HISTORY*.txt files
- in the HDF5 source. Please report any new problems found to
- help@hdfgroup.org.
-
-
-%%%%1.8.19%%%%
-
-
-HDF5 version 1.8.19 released on 2017-06-15
-================================================================================
-
-INTRODUCTION
-============
-
-This document describes the differences between HDF5-1.8.18 and
-HDF5-1.8.19, and contains information on the platforms tested and
-known problems in HDF5-1.8.19.
-For more details, see the files HISTORY-1_0-1_8_0_rc3.txt
-and HISTORY-1_8.txt in the release_docs/ directory of the HDF5 source.
-
-Links to the HDF5 1.8.19 source code, documentation, and additional materials
-can be found on the HDF5 web page at:
-
- https://support.hdfgroup.org/HDF5/
-
-The HDF5 1.8.19 release can be obtained from:
-
- https://support.hdfgroup.org/HDF5/release/obtain518.html
-
-User documentation for 1.8.19 can be accessed directly at this location:
-
- https://support.hdfgroup.org/HDF5/doc1.8/
-
-New features in the HDF5-1.8.x release series, including brief general
-descriptions of some new and modified APIs, are described in the "What's New
-in 1.8.0?" document:
-
- https://support.hdfgroup.org/HDF5/doc/ADGuide/WhatsNew180.html
-
-All new and modified APIs are listed in detail in the "HDF5 Software Changes
-from Release to Release" document, in the section "Release 1.8.19 (current
-release) versus Release 1.8.18
-
- https://support.hdfgroup.org/HDF5/doc1.8/ADGuide/Changes.html
-
-If you have any questions or comments, please send them to the HDF Help Desk:
-
- help@hdfgroup.org
-
-
-CONTENTS
-========
-
-- New Features
-- Support for New Platforms, Languages, and Compilers
-- Bug Fixes since HDF5-1.8.19
-- Supported Platforms
-- Supported Configuration Features Summary
-- More Tested Platforms
-- Known Problems
-
-
-New Features
-============
-
- Configuration
- --------------
- - CMake in the Tools
-
- User-defined filters on Windows require that tools be built
- with shared libraries.
-
- CMake command code added to build tools with
- shared libraries as well as with static libraries.
-
- (ADB - 2017/02/07, HDFFV-10123)
-
-
- Library
- -------
- - H5PL package
-
- Users would like to be able to set the plugin path programmatically
- instead of through the environment variable.
-
- H5PL package obtained new APIs for manipulating the entries of
- the plugin path table. The new APIs are;
- H5PLappend - Insert a plugin path at the end of the list.
- H5PLprepend - Insert a plugin path at the beginning of the list.
- H5PLreplace - Replace the path at the specified index.
- H5PLinsert - Insert a plugin path at the specified index, moving
- other paths after the index.
- H5PLremove - Remove the plugin path at the specified index and
- compacting the list.
- H5PLget - Query the plugin path at the specified index.
- H5PLsize - Query the size of the current list of plugin paths.
-
- (ADB - 2017/04/04, HDFFV-10143)
-
- - H5Dget_chunk_storage_size
-
- The storage size of a chunk in the file is needed to determine the size
- of the buffer to be allocated for reading a chunk directly from a file.
-
- New API function gets the size in bytes currently allocated within a
- file for a raw data chunk in a dataset. This function was added to get
- the chunk size in support of the implementation of H5DOread_chunks, but
- may also be useful for other purposes.
-
- (VC - 2017/05/02, HDFFV-9934)
-
- C++ API
- -------
- - The following C++ API wrappers have been added to the C++ Library:
- // Determines if a name exists.
- H5Location::nameExists() - C API H5Lexists()
-
- // Checks if an ID is valid.
- IdComponent::isValid() - C API H5Iis_valid()
-
- // Sets the number of soft or user-defined links that can be
- // traversed before a failure occurs.
- LinkAccPropList::setNumLinks() - C API H5Pset_nlinks()
-
- // Gets the number of soft or user-defined link traversals allowed
- LinkAccPropList::getNumLinks() - C API H5Pget_nlinks()
-
- // Returns a copy of the creation property list of a datatype.
- DataType::getCreatePlist() - C API H5Tget_create_plist()
-
- // Opens an object within a location, regardless its type.
- H5Location::openObjId() - C API H5Oopen()
- H5Location::openObjId() - C API H5Oopen()
-
- // Closes an object opened by openObjId().
- H5Location::closeObjId() - C API H5Oclose()
-
- // Gets general information about a file.
- H5File::getFileInfo() - C API H5Fget_info()
-
- // Returns the header version of an HDF5 object.
- H5Object::objVersion() - C API H5Oget_info()
-
- (BMR, 2017/05/13, HDFFV-10004, HDFFV-10156)
-
- - New class LinkAccPropList is added for link access property list
-
- (BMR, 2017/05/13, HDFFV-10156)
-
- High-Level APIs
- ---------------
- - H5DOread_chunk
-
- Users wanted to read compressed data directly from a file without any
- processing by the HDF5 data transfer pipeline, just as they were able
- to write it directly to a file with H5DOwrite_chunk.
-
- New API function, corresponding to existing function H5DOwrite_chunk.
- H5DOread_chunk reads a raw data chunk directly from a chunked dataset
- in the file into the application buffer, bypassing the library’s internal
- data transfer pipeline, including filters.
-
- (VC - 2017/05/02, HDFFV-9934)
-
-
-Support for New Platforms, Languages, and Compilers
-===================================================
-
- - Added OpenMPI 2.0.1 compiled with GCC 4.9.3
-
-
-Bug Fixes since HDF5-1.8.18
-===========================
-
- Configuration
- -------------
- - Support for Fortran shared libraries on OS X with autotools now
- works. Cmake builds still disables Fortran shared libraries on OS X.
- (MSB - 2017/04/30, HDFFV-2772)
-
-
- Library
- -------
- - bitfield datatypes
-
- bitfield datatypes did not fully support endianness of the data.
-
- Improved the endianness of bitfield datatypes by adding missing functional
- code. This code used integer types as a template.
-
- (ADB - 2017/05/12, HDFFV-10186)
-
- - Newly created datasets with H5D_COMPACT layout failed to open after
- several H5Dopen/H5Dclose cycles.
-
- The layout "dirty" flag for a compact dataset is now properly reset
- before flushing the message.
-
- (VC - 2017/05/11, HDFFV-10051)
- - Missing #ifdef __cplusplus macros were added to the generated H5Epubgen.h file.
-
- (DER - 2017/04/25, HDFFV-9638)
-
-
- Tools
- -----
- - h5repack
-
- h5repack did not maintain the creation order flag of the root
- group.
-
- Improved h5repack by reading the creation order and applying the
- flag to the new root group. Also added arguments to set the
- order and index direction, which applies to the traversing of the
- original file, on the command line.
-
- (ADB - 2017/05/26, HDFFV-8611)
-
- - h5diff
-
- h5diff failed to account for strpad type and null terminators
- of char strings. Also, h5diff failed to account for string length
- differences and would give a different result depending on file
- order in the command line.
-
- Improved h5diff compare of strings and arrays by adding a check for
- string lengths and if the strpad was null filled.
-
- (ADB - 2017/05/18, HDFFV-9055, HDFFV-10128)
-
- - h5diff
-
- h5diff help text about epsilon comparison was confusing.
-
- Changed h5diff help text to indicate that the 'a' refers to the
- datapoint in file1 and 'b' refers to the datapoint value in file2.
-
- (ADB - 2017/05/16, HDFFV-9995)
-
- - h5diff
-
- h5diff did not report user-defined filter data differences correctly.
-
- Improved h5diff compare of user-defined filter data by reporting an
- error if the user-defined filter plugin cannot be found.
-
- (ADB - 2017/01/18, HDFFV-9994)
- C++ API
- -------
- - The class hierarchy is revised to better reflect the HDF5 model.
- Class H5File is now derived from class Group instead of H5Location.
- Class Attribute is now derived from H5Location instead of IdComponent.
- Wrappers of H5A APIs in H5Location are now duplicated in H5Object,
- the original wrappers in H5Location will be deprecated in future
- releases.
-
- (BMR - 2017/05/15, HDFFV-10156)
-
-
-
-Supported Platforms
-===================
-The following platforms are supported and have been tested for this release.
-They are built with the configure process unless specified otherwise.
-
- Linux 2.6.32-573.22.1.el6 GNU C (gcc), Fortran (gfortran), C++ (g++)
- #1 SMP x86_64 GNU/Linux compilers:
- (platypus/mayll) Version 4.4.7 20120313
- Versions 4.9.3, 5.2.0, 6.2.0
- PGI C, Fortran, C++ for 64-bit target on
- x86-64;
- Version 16.10-0
- Intel(R) C (icc), C++ (icpc), Fortran (icc)
- compilers:
- Version 17.0.0.098 Build 20160721
- MPICH 3.1.4 compiled with GCC 4.9.3
- OpenMPI 2.0.1 compiled with GCC 4.9.3
-
- Linux 2.6.32-573.18.1.el6 gcc (GCC) 4.4.7 20120313 (Red Hat 4.4.7-16)
- #1 SMP ppc64 GNU/Linux g++ (GCC) 4.4.7 20120313 (Red Hat 4.4.7-16)
- (ostrich) GNU Fortran (GCC) 4.4.7 20120313 (Red Hat 4.4.7-16)
- IBM XL C/C++ V13.1
- IBM XL Fortran V15.1
-
- Linux 3.10.0-327.10.1.el7 GNU C (gcc), Fortran (gfortran), C++ (g++)
- #1 SMP x86_64 GNU/Linux compilers:
- (kituo/moohan) Version 4.8.5 20150623 (Red Hat 4.8.5-4)
- Versions 4.9.3, 5.3.0, 6.2.0
- Intel(R) C (icc), C++ (icpc), Fortran (icc)
- compilers:
- Version 17.0.4.196 Build 20170411
- MPICH 3.1.4 compiled with GCC 4.9.3
-
- SunOS 5.11 32- and 64-bit Sun C 5.12 SunOS_sparc
- (emu) Sun Fortran 95 8.6 SunOS_sparc
- Sun C++ 5.12 SunOS_sparc
- Windows 7 Visual Studio 2012 w/ Intel Fortran 15 (cmake)
- Visual Studio 2013 w/ Intel Fortran 15 (cmake)
- Visual Studio 2015 w/ Intel Fortran 16 (cmake)
-
- Windows 7 x64 Visual Studio 2012 w/ Intel Fortran 15 (cmake)
- Visual Studio 2013 w/ Intel Fortran 15 (cmake)
- Visual Studio 2015 w/ Intel Fortran 16 (cmake)
- Visual Studio 2015 w/ Intel C, Fortran 2017 (cmake)
- Visual Studio 2015 w/ MSMPI 8 (cmake)
- Cygwin(CYGWIN_NT-6.1 2.8.0(0.309/5/3)
- gcc and gfortran compilers (GCC 5.4.0)
- (cmake and autotools)
-
- Windows 10 Visual Studio 2015 w/ Intel Fortran 16 (cmake)
- Cygwin(CYGWIN_NT-6.1 2.8.0(0.309/5/3)
- gcc and gfortran compilers (GCC 5.4.0)
- (cmake and autotools)
-
- Windows 10 x64 Visual Studio 2015 w/ Intel Fortran 16 (cmake)
-
- Mac OS X Mt. Lion 10.8.5 Apple LLVM version 5.1 (clang-503.0.40)
- 64-bit gfortran GNU Fortran (GCC) 4.8.2
- (swallow/kite) Intel icc/icpc/ifort version 15.0.3
-
- Mac OS X Mavericks 10.9.5 Apple LLVM version 6.0 (clang-600.0.57)
- 64-bit gfortran GNU Fortran (GCC) 4.9.2
- (wren/quail) Intel icc/icpc/ifort version 15.0.3
-
- Mac OS X Yosemite 10.10.5 Apple LLVM version 6.1 (clang-602.0.53)
- 64-bit gfortran GNU Fortran (GCC) 4.9.2
- (osx1010dev/osx1010test) Intel icc/icpc/ifort version 15.0.3
-
- Mac OS X El Capitan 10.11.4 Apple LLVM version 7.3.0 (clang-703.0.29)
- 64-bit gfortran GNU Fortran (GCC) 5.2.0
- (VM osx1011dev/osx1011test) Intel icc/icpc/ifort version 16.0.2
-
-
-Tested Configuration Features Summary
-=====================================
-
- In the tables below
- y = tested
- n = not tested in this release
- C = Cluster
- W = Workstation
- x = not working in this release
- dna = does not apply
- ( ) = footnote appears below second table
- <blank> = testing incomplete on this feature or platform
-Platform C F90/ F90 C++ zlib SZIP
- parallel F2003 parallel
-SunOS 5.11 32-bit n y/y n y y y
-SunOS 5.11 64-bit n y/y n y y y
-Windows 7 y y/y n y y y
-Windows 7 x64 y y/y n y y y
-Windows 7 Cygwin n y/n n y y y
-Windows 7 x64 Cygwin n y/n n y y y
-Windows 10 y y/y n y y y
-Windows 10 x64 y y/y n y y y
-Mac OS X Mountain Lion 10.8.5 64-bit n y/y n y y y
-Mac OS X Mavericks 10.9.5 64-bit n y/y n y y y
-Mac OS X Yosemite 10.10.5 64-bit n y/y n y y y
-AIX 6.1 32- and 64-bit n y/n n y y y
-CentOS 6.7 Linux 2.6.32 x86_64 GNU y y/y y y y y
-CentOS 6.7 Linux 2.6.32 x86_64 Intel n y/y n y y y
-CentOS 6.7 Linux 2.6.32 x86_64 PGI n y/y n y y y
-CentOS 7.1 Linux 3.10.0 x86_64 GNU y y/y y y y y
-CentOS 7.1 Linux 3.10.0 x86_64 Intel n y/y n y y y
-Linux 2.6.32-431.11.2.el6.ppc64 n y/n n y y y
-
-Platform Shared Shared Shared Thread-
- C libs F90 libs C++ libs safe
-SunOS 5.11 32-bit y y y y
-SunOS 5.11 64-bit y y y y
-Windows 7 y y y y
-Windows 7 x64 y y y y
-Windows 7 Cygwin n n n y
-Windows 7 x64 Cygwin n n n y
-Windows 10 y y y y
-Windows 10 x64 y y y y
-Mac OS X Mountain Lion 10.8.5 64-bit y n y y
-Mac OS X Mavericks 10.9.5 64-bit y n y y
-Mac OS X Yosemite 10.10.5 64-bit y n y y
-AIX 6.1 32- and 64-bit y n n y
-CentOS 6.7 Linux 2.6.32 x86_64 GNU y y y y
-CentOS 6.7 Linux 2.6.32 x86_64 Intel y y y y
-CentOS 6.7 Linux 2.6.32 x86_64 PGI y y y y
-CentOS 7.1 Linux 3.10.0 x86_64 GNU y y y y
-CentOS 7.1 Linux 3.10.0 x86_64 Intel y y y y
-Linux 2.6.32-431.11.2.el6.ppc64 y y y y
-
-Compiler versions for each platform are listed in the preceding
-"Supported Platforms" table.
-
-
-More Tested Platforms
-=====================
-The following platforms are not supported but have been tested for this release.
-
- Linux 2.6.32-573.22.1.el6 g95 (GCC 4.0.3 (g95 0.94!)
- #1 SMP x86_64 GNU/Linux
- (mayll)
-
- Debian8.4.0 3.16.0-4-amd64 #1 SMP Debian 3.16.36-1 x86_64 GNU/Linux
- gcc (Debian 4.9.2-10) 4.9.2
- GNU Fortran (Debian 4.9.2-10) 4.9.2
- (cmake and autotools)
-
- Fedora24 4.7.2-201.fc24.x86_64 #1 SMP x86_64 x86_64 x86_64 GNU/Linux
- gcc (GCC) 6.1.1 20160621 (Red Hat 6.1.1-3)
- GNU Fortran (GCC) 6.1.1 20160621 (Red Hat 6.1.1-3)
- (cmake and autotools)
-
- CentOS 7.2 3.10.0-327.28.2.el7.x86_64 #1 SMP x86_64 x86_64 x86_64 GNU/Linux
- gcc (GCC) 4.8.5 20150623 (Red Hat 4.8.5-4)
- GNU Fortran (GCC) 4.8.5 20150623 (Red Hat 4.8.5-4)
- (cmake and autotools)
-
- Ubuntu 16.04 4.4.0-38-generic #62-Ubuntu SMP x86_64 GNU/Linux
- gcc (Ubuntu 5.4.0-6ubuntu1~16.04.2) 5.4.0
- GNU Fortran (Ubuntu 5.4.0-6ubuntu1~16.04.2) 5.4.0
- (cmake and autotools)
-
-
-Known Problems
-==============
-
- The dynamically loaded plugin test libraries require undefined references
- to HDF5 functions to be resolved at runtime in order to function properly.
- With autotools on CYGWIN this results in build errors, and we have not
- found a solution that satisfies both. Therefore the dynamically loaded
- plugin tests have been disabled on CYGWIN.
-
- Known problems in previous releases can be found in the HISTORY*.txt files
- in the HDF5 source. Please report any new problems found to
- help@hdfgroup.org.
-
-
-%%%%1.8.18%%%%
-
-
-HDF5 version 1.8.18 released on 2016-11-14
-================================================================================
-
-INTRODUCTION
-============
-
-This document describes the differences between HDF5-1.8.17 and
-HDF5-1.8.18, and contains information on the platforms tested and
-known problems in HDF5-1.8.18.
-For more details, see the files HISTORY-1_0-1_8_0_rc3.txt
-and HISTORY-1_8.txt in the release_docs/ directory of the HDF5 source.
-
-Links to the HDF5 1.8.18 source code, documentation, and additional materials
-can be found on the HDF5 web page at:
-
- https://support.hdfgroup.org/HDF5/
-
-The HDF5 1.8.18 release can be obtained from:
-
- https://support.hdfgroup.org/HDF5/release/obtain518.html
-
-User documentation for 1.8.18 can be accessed directly at this location:
-
- https://support.hdfgroup.org/HDF5/doc1.8/
-
-New features in the HDF5-1.8.x release series, including brief general
-descriptions of some new and modified APIs, are described in the "What's New
-in 1.8.0?" document:
-
- https://support.hdfgroup.org/HDF5/doc/ADGuide/WhatsNew180.html
-
-All new and modified APIs are listed in detail in the "HDF5 Software Changes
-from Release to Release" document, in the section "Release 1.8.18 (current
-release) versus Release 1.8.17
-
- https://support.hdfgroup.org/HDF5/doc1.8/ADGuide/Changes.html
-
-If you have any questions or comments, please send them to the HDF Help Desk:
-
- help@hdfgroup.org
-
-
-CONTENTS
-========
-
-- New Features
-- Support for New Platforms, Languages, and Compilers
-- Bug Fixes since HDF5-1.8.17
-- Supported Platforms
-- Supported Configuration Features Summary
-- More Tested Platforms
-- Known Problems
-
-
-New Features
-============
-
- Configuration
- -------------
-
- - CMake: Added NAMESPACE hdf5:: to package configuration files to allow
- projects using installed HDF5 binaries built with CMake to link with
- them without specifying the HDF5 library location via IMPORTED_LOCATION.
-
- (ADB, 2016/10/17, HDFFV-10003)
-
-
- - CMake: Changed the CTEST_BUILD_CONFIGURATION option to
- CTEST_CONFIGURATION_TYPE as recommended by the CMake documentation.
-
- (ADB, 2016/10/17, HDFFV-9971)
-
- - CMake: Added support for GIT
-
- (ADB, 2016/07/12)
-
-
- Library
- -------
- - None
-
-
- Parallel Library
- ----------------
- - None
-
-
- Tools
- -----
- - None
-
-
- High-Level APIs
- ---------------
- - None
-
-
- Fortran API
- -----------
- - None
-
-
- C++ API
- -------
- - None
-
-
-Support for New Platforms, Languages, and Compilers
-===================================================
-
-
-
-Bug Fixes since HDF5-1.8.17
-===========================
-
- Configuration
- -------------
-
- - Fixed a problem preventing HDF5 to be built on 32-bit CYGWIN by
- condensing cygwin configuration files into a single file and
- removing outdated compiler settings.
-
- (ABD, 2016/07/12, HDFFV-9946)
-
-
- - CMake: Fixed a command length overflow error by converting custom
- commands inside CMakeTest.cmake files into regular dependencies and
- targets.
-
- (ABD, 2016/07/12, HDFFV-9939)
-
-
- - CMake: Fixed a timeout error that would occasionally occur when running
- the virtual file driver tests simultaneously due to test directory and file
- name collisions.
-
- (ABD, 2016/09/19, HDFFV-9431)
-
-
- Library
- -------
-
- - Fixed a memory leak that would occur when the library allocated memory
- for an external file prefix (H5Pset_efile_prefix) and failed to free it.
-
- (DER, 2016/04/29)
-
-
- - Fixed an error that would occur when calling H5Adelete on an attribute
- which is attached to an externally linked object in the target file and
- whose datatype is a committed datatype in the main file.
-
- (VC, 2016-07-04, HDFFV-9940)
-
-
- - Fixed a problem where a plugin compiled into a DLL in the default plugin
- directory could not be found by the HDF5 library at runtime on Windows
- when the HDF5_PLUGIN_PATH environment variable was not set.
-
- (ABD, 2016/08/01, HDFFV-9706)
-
-
- - Fixed an issue where H5Pset_alignment could result in misaligned blocks
- with some input combinations, causing an assertion failure in debug mode.
-
- (NAF, 2016/08/11, HDFFV-9948)
-
-
- - A number of issues were fixed when reading/writing from/to corrupted
- files to ensure that the library fails gracefully in these cases:
-
- * Writing to a corrupted file that has an object message which is
- incorrectly marked as shareable on disk results in a buffer overflow /
- invalid write instead of a clean error message.
-
- * Decoding data from a corrupted file with a dataset encoded with the
- H5Z_NBIT decoding can result in a code execution vulnerability under
- the context of the application using the HDF5 library.
-
- * When decoding an array datatype from a corrupted file, the HDF5 library
- fails to return an error in production if the number of dimensions
- decoded is greater than the maximum rank.
-
- * When decoding an "old style" array datatype from a corrupted file, the
- HDF5 library fails to return an error in production if the number of
- dimensions decoded is greater than the maximum rank.
-
- (NAF, 2016/10/06, HDFFV-9950, HDFFV-9951, HDFFV-9992, HDFFV-9993)
-
-
- - Fixed an error that would occur when copying an object with an attribute
- which is a compound datatype consisting of a variable length string.
-
- (VC, 2016-10-17, HDFFV-7991)
-
-
- Parallel Library
- ----------------
-
- - Fixed a bug that could occur when allocating a chunked dataset in parallel
- with an alignment set and an alignment threshold greater than the chunk
- size but less than or equal to the raw data aggregator size.
-
- (NAF, 2016/08/11, HDFFV-9969)
-
-
- Performance
- -------------
- - None
-
-
- Tools
- -----
-
- - Fixed an error in the compiler wrapper scripts (h5cc, h5fc, et al.)
- in which they would erroneously drop the file argument specified via
- the -o flag when the -o flag was specified before the -c flag on the
- command line, resulting in a failure to compile.
-
- (LRK, 2016/06/08, HDFFV-9938, HDFFV-9530)
-
-
- - h5repack User Defined (UD) filter parameters were not parsed correctly.
-
- The UD filter parameters were not being parsed correctly. Reworked coding
- section to parse the correct values and verify number of parameters.
-
- (ADB, 2016/10/19, HDFFV-9996, HDFFV-9974, HDFFV-9515, HDFFV-9039)
-
-
- Fortran API
- -----------
-
- - Fortran library fails to compile and fails tests with NAG compiler.
-
- * Removed the non-standard assumption that KIND=SIZEOF, in the HDF5
- configure programs.
- * Removed Fortran 66 character/integer conversions from tests.
- * Removed the use of C_SIZEOF in the test programs
- * Changed to using STORAGE_SIZE in the test programs if available. Otherwise,
- uses C_SIZEOF or SIZEOF.
-
- (MSB, 2016/9/22, HDFFV-9973)
-
-
- - Fortran segfaults for F03 tests with NAG compiler
-
- * Removed INTENT(OUT) from 'fillvalue' in F2003 interface
- for H5Pget_fill_value_f.
-
- (MSB, 2016/9/22, HDFFV-9980)
-
-
- C++ API
- -------
-
- - The macro H5_NO_NAMESPACE is deprecated from the HDF5 C++ API library.
- In future releases, the macros H5_NO_STD and OLD_HEADER_FILENAME may
- also be removed.
-
- (BMR, 2016/10/27, HDFFV-9532)
-
-
- High-Level APIs:
- ---------------
-
- - The high-level API Packet Table (PT) did not write data correctly when
- the datatype is a compound type that has string type as one of the
- members. This problem started in 1.8.15, after the fix of HDFFV-9042
- was applied, which caused the Packet Table to use native type to access
- the data. It should be up to the application to specify whether the
- buffer to be read into memory in the machine’s native architecture.
- Thus, the PT is fixed to not use native type but to make a copy of the
- user's provided datatype during creation or the packet table's datatype
- during opening. If an application wishes to use native type to read the
- data, then the application will request that. However, the Packet Table
- doesn't provide a way to specify memory datatype in this release. This
- feature will be available in future releases, HDFFV-10023.
-
- (BMR, 2016/10/27, HDFFV-9758)
-
-
- Fortran High-Level APIs:
- ------------------------
- - None
-
-
- Testing
- -------
- - None
-
-
-Supported Platforms
-===================
-The following platforms are supported and have been tested for this release.
-They are built with the configure process unless specified otherwise.
-
- Linux 2.6.32-573.22.1.el6 GNU C (gcc), Fortran (gfortran), C++ (g++)
- #1 SMP x86_64 GNU/Linux compilers:
- (platypus/mayll) Version 4.4.7 20120313
- Versions 4.8.4, 4.9.3, 5.2.0
- PGI C, Fortran, C++ for 64-bit target on
- x86-64;
- Version 15.7-0
- Intel(R) C (icc), C++ (icpc), Fortran (icc)
- compilers:
- Version 15.0.3.187 Build 20150407
- MPICH 3.1.4 compiled with GCC 4.9.3
-
- Linux 2.6.32-573.18.1.el6 gcc (GCC) 4.4.7 20120313 (Red Hat 4.4.7-16)
- #1 SMP ppc64 GNU/Linux g++ (GCC) 4.4.7 20120313 (Red Hat 4.4.7-16)
- (ostrich) GNU Fortran (GCC) 4.4.7 20120313 (Red Hat 4.4.7-16)
- IBM XL C/C++ V13.1
- IBM XL Fortran V15.1
-
- Linux 3.10.0-327.10.1.el7 GNU C (gcc), Fortran (gfortran), C++ (g++)
- #1 SMP x86_64 GNU/Linux compilers:
- (kituo/moohan) Version 4.8.5 20150623 (Red Hat 4.8.5-4)
- Versions 4.9.3, 5.2.0
- Intel(R) C (icc), C++ (icpc), Fortran (icc)
- compilers:
- Version 15.0.3.187 Build 20150407
- MPICH 3.1.4 compiled with GCC 4.9.3
-
- SunOS 5.11 32- and 64-bit Sun C 5.12 SunOS_sparc
- (emu) Sun Fortran 95 8.6 SunOS_sparc
- Sun C++ 5.12 SunOS_sparc
-
- Windows 7 Visual Studio 2012 w/ Intel Fortran 15 (cmake)
- Visual Studio 2013 w/ Intel Fortran 15 (cmake)
- Visual Studio 2015 w/ Intel Fortran 16 (cmake)
- Cygwin(CYGWIN_NT-6.1 2.2.1(0.289/5/3) gcc(4.9.3) compiler and gfortran)
- (cmake and autotools)
-
- Windows 7 x64 Visual Studio 2012 w/ Intel Fortran 15 (cmake)
- Visual Studio 2013 w/ Intel Fortran 15 (cmake)
- Visual Studio 2015 w/ Intel Fortran 16 (cmake)
-
- Windows 10 Visual Studio 2015 w/ Intel Fortran 16 (cmake)
-
- Windows 10 x64 Visual Studio 2015 w/ Intel Fortran 16 (cmake)
-
- Mac OS X Mt. Lion 10.8.5 Apple LLVM version 5.1 (clang-503.0.40)
- 64-bit gfortran GNU Fortran (GCC) 4.8.2
- (swallow/kite) Intel icc/icpc/ifort version 15.0.3
-
- Mac OS X Mavericks 10.9.5 Apple LLVM version 6.0 (clang-600.0.57)
- 64-bit gfortran GNU Fortran (GCC) 4.9.2
- (wren/quail) Intel icc/icpc/ifort version 15.0.3
-
- Mac OS X Yosemite 10.10.5 Apple LLVM version 6.1 (clang-602.0.53)
- 64-bit gfortran GNU Fortran (GCC) 4.9.2
- (osx1010dev/osx1010test) Intel icc/icpc/ifort version 15.0.3
-
- Mac OS X El Capitan 10.11.4 Apple LLVM version 7.3.0 (clang-703.0.29)
- 64-bit gfortran GNU Fortran (GCC) 5.2.0
- (VM osx1011dev/osx1011test) Intel icc/icpc/ifort version 16.0.2
-
-
-Tested Configuration Features Summary
-=====================================
-
- In the tables below
- y = tested
- n = not tested in this release
- C = Cluster
- W = Workstation
- x = not working in this release
- dna = does not apply
- ( ) = footnote appears below second table
- <blank> = testing incomplete on this feature or platform
-
-Platform C F90/ F90 C++ zlib SZIP
- parallel F2003 parallel
-SunOS 5.11 32-bit n y/y n y y y
-SunOS 5.11 64-bit n y/y n y y y
-Windows 7 y y/y n y y y
-Windows 7 x64 y y/y n y y y
-Windows 7 Cygwin n y/y n y y n
-Windows 10 n y/y n y y y
-Windows 10 x64 n y/y n y y y
-Mac OS X Mountain Lion 10.8.5 64-bit n y/y n y y y
-Mac OS X Mavericks 10.9.5 64-bit n y/y n y y y
-Mac OS X Yosemite 10.10.5 64-bit n y/y n y y y
-AIX 6.1 32- and 64-bit n y/n n y y y
-CentOS 6.7 Linux 2.6.32 x86_64 GNU y y/y y y y y
-CentOS 6.7 Linux 2.6.32 x86_64 Intel n y/y n y y y
-CentOS 6.7 Linux 2.6.32 x86_64 PGI n y/y n y y y
-CentOS 7.1 Linux 3.10.0 x86_64 GNU y y/y y y y y
-CentOS 7.1 Linux 3.10.0 x86_64 Intel n y/y n y y y
-Linux 2.6.32-431.11.2.el6.ppc64 n y/n n y y y
-
-Platform Shared Shared Shared Thread-
- C libs F90 libs C++ libs safe
-SunOS 5.11 32-bit y y y y
-SunOS 5.11 64-bit y y y y
-Windows 7 y y y y
-Windows 7 x64 y y y y
-Windows 7 Cygwin n n n y
-Windows 10 y y y y
-Windows 10 x64 y y y y
-Mac OS X Mountain Lion 10.8.5 64-bit y n y y
-Mac OS X Mavericks 10.9.5 64-bit y n y y
-Mac OS X Yosemite 10.10.5 64-bit y n y y
-AIX 6.1 32- and 64-bit y n n y
-CentOS 6.7 Linux 2.6.32 x86_64 GNU y y y y
-CentOS 6.7 Linux 2.6.32 x86_64 Intel y y y y
-CentOS 6.7 Linux 2.6.32 x86_64 PGI y y y y
-CentOS 7.1 Linux 3.10.0 x86_64 GNU y y y y
-CentOS 7.1 Linux 3.10.0 x86_64 Intel y y y y
-Linux 2.6.32-431.11.2.el6.ppc64 y y y y
-
-Compiler versions for each platform are listed in the preceding
-"Supported Platforms" table.
-
-
-More Tested Platforms
-=====================
-The following platforms are not supported but have been tested for this release.
-
- Linux 2.6.32-573.22.1.el6 g95 (GCC 4.0.3 (g95 0.94!)
- #1 SMP x86_64 GNU/Linux
- (platypus)
-
- Debian8.4.0 3.16.0-4-amd64 #1 SMP Debian 3.16.36-1 x86_64 GNU/Linux
- gcc (Debian 4.9.2-10) 4.9.2
- GNU Fortran (Debian 4.9.2-10) 4.9.2
- (cmake and autotools)
-
- Fedora24 4.7.2-201.fc24.x86_64 #1 SMP x86_64 x86_64 x86_64 GNU/Linux
- gcc (GCC) 6.1.1 20160621 (Red Hat 6.1.1-3)
- GNU Fortran (GCC) 6.1.1 20160621 (Red Hat 6.1.1-3)
- (cmake and autotools)
-
- CentOS 7.2 3.10.0-327.28.2.el7.x86_64 #1 SMP x86_64 x86_64 x86_64 GNU/Linux
- gcc (GCC) 4.8.5 20150623 (Red Hat 4.8.5-4)
- GNU Fortran (GCC) 4.8.5 20150623 (Red Hat 4.8.5-4)
- (cmake and autotools)
-
- Ubuntu 16.04 4.4.0-38-generic #62-Ubuntu SMP x86_64 GNU/Linux
- gcc (Ubuntu 5.4.0-6ubuntu1~16.04.2) 5.4.0
- GNU Fortran (Ubuntu 5.4.0-6ubuntu1~16.04.2) 5.4.0
- (cmake and autotools)
-
-
-Known Problems
-==============
-* On windows platforms in debug configurations, the VFD flush1 tests will fail
- with the split and multi VFD drivers. These tests will display a modal debug
- dialog which must be answered or wait for the test timeout to expire.
- (ADB - 2014/06/23 - HDFFV-8851)
-
-* CLANG compiler with the options -fcatch-undefined-behavior and -ftrapv
- catches some undefined behavior in the alignment algorithm of the macro DETECT_I
- in H5detect.c (Issue 8147). Since the algorithm is trying to detect the alignment
- of integers, ideally the flag -fcatch-undefined-behavior shouldn't to be used for
- H5detect.c. In the future, we can separate flags for H5detect.c from the rest of
- the library. (SLU - 2013/10/16)
-
-* Make provided by Solaris fails in "make check". Solaris users should use
- gmake to build and install the HDF5 software. (AKC - 2013/10/08 - HDFFV-8534)
-
-* The C++ and FORTRAN bindings are not currently working on FreeBSD with the
- native release 8.2 compilers (4.2.1), but are working with gcc 4.6 from the
- ports (and probably gcc releases after that).
- (QAK - 2012/10/19)
-
-* The following h5dump test case fails in BG/P machines (and potentially other
- machines that use a command script to launch executables):
-
- h5dump --no-compact-subset -d "AHFINDERDIRECT::ah_centroid_t[0] it=0 tl=0"
- tno-subset.h5
-
- This is due to the embedded spaces in the dataset name being interpreted
- by the command script launcher as meta-characters, thus passing three
- arguments to h5dump's -d flag. The command passes if run by hand, just
- not via the test script.
- (AKC - 2012/05/03)
-
-* The STDIO VFD does not work on some architectures, possibly due to 32/64
- bit or large file issues. The basic STDIO VFD test is known to fail on
- 64-bit SunOS 5.10 on SPARC when built with -m64 and 32-bit OS X/Darwin
- 10.7.0. The STDIO VFD test has been disabled while we investigate and
- a fix should appear in a future release.
- (DER - 2011/10/14 - HDFFV-8235)
-
-* h5diff can report inconsistent results when comparing datasets of enum type
- that contain invalid values. This is due to how enum types are handled in
- the library and will be addressed in a future release.
- (DER - 2011/10/14 - HDFFV-7527)
-
-* The links test can fail under the stdio VFD due to some issues with external
- links. This will be investigated and fixed in a future release.
- (DER - 2011/10/14 - HDFFV-7768)
-
-* After the shared library support was fixed for some bugs, it was discovered
- that "make prefix=XXX install" no longer works for shared libraries. It
- still works correctly for static libraries. Therefore, if you want to
- install the HDF5 shared libraries in a location such as /usr/local/hdf5,
- you need to specify the location via the --prefix option during configure
- time. E.g, ./configure --prefix=/usr/local/hdf5 ...
- (AKC - 2011/05/07 - HDFFV-7583)
-
-* The parallel test, t_shapesame, in testpar/, may run for a long time and may
- be terminated by the alarm signal. If that happens, one can increase the
- alarm seconds (default is 1200 seconds = 20 minutes) by setting the
- environment variable, $HDF5_ALARM_SECONDS, to a larger value such as 3600
- (60 minutes). Note that the t_shapesame test may fail in some systems
- (see the "While working on the 1.8.6 release..." problem below). If
- it does, it will waste more time if $HDF5_ALARM_SECONDS is set
- to a larger value.
- (AKC - 2011/05/07)
-
-* Shared Fortran libraries are not quite working on AIX. While they are
- generated when --enable-shared is specified, the fortran and hl/fortran
- tests fail. the issue. HL and C++ shared libraries should now be
- working as intended, however.
- (MAM - 2011/04/20)
-
-* While working on the 1.8.6 release of HDF5, a bug was discovered that can
- occur when reading from a dataset in parallel shortly after it has been
- written to collectively. The issue was exposed by a new test in the parallel
- HDF5 test suite, but had existed before that. We believe the problem lies with
- certain MPI implementations and/or file systems.
-
- We have provided a pure MPI test program, as well as a standalone HDF5
- program, that can be used to determine if this is an issue on your system.
- They should be run across multiple nodes with a varying number of processes.
- These programs can be found at:
- http://www.hdfgroup.org/ftp/HDF5/examples/known_problems/
- (NAF - 2011/01/19)
-
-* All the VFL drivers aren't backward compatible. In H5FDpublic.h, the
- structure H5FD_class_t changed in 1.8. There is new parameter added to
- get_eoa and set_eoa callback functions. A new callback function
- get_type_map was added in. The public function H5FDrealloc was taken
- out in 1.8. The problem only happens when users define their own driver
- for 1.6 and try to plug in 1.8 library. Because there's only one user
- complaining about it, we (Elena, Quincey, and I) decided to leave it as
- it is (see bug report #1279). Quincey will make a plan for 1.10.
- (SLU - 2010/02/02)
-
-* The --enable-static-exec configure flag will only statically link libraries
- if the static version of that library is present. If only the shared version
- of a library exists (i.e., most system libraries on Solaris, AIX, and Mac,
- for example, only have shared versions), the flag should still result in a
- successful compilation, but note that the installed executables will not be
- fully static. Thus, the only guarantee on these systems is that the
- executable is statically linked with just the HDF5 library.
- (MAM - 2009/11/04)
-
-* A dataset created or rewritten with a v1.6.3 library or after cannot be read
- with the v1.6.2 library or before when the Fletcher32 EDC filter is enabled.
- There was a bug in the calculation of the Fletcher32 checksum in the
- library before v1.6.3; the checksum value was not consistent between big-
- endian and little-endian systems. This bug was fixed in Release 1.6.3.
- However, after fixing the bug, the checksum value was no longer the same as
- before on little-endian system. Library releases after 1.6.4 can still read
- datasets created or rewritten with an HDF5 library of v1.6.2 or before.
- (SLU - 2005/06/30)
-
-
-%%%%1.8.17%%%%
-
-
-HDF5 version 1.8.17 released on 2016-05-10
-================================================================================
-
-INTRODUCTION
-============
-
-This document describes the differences between HDF5-1.8.16 and
-HDF5-1.8.17-*, and contains information on the platforms tested and
-known problems in HDF5-1.8.17-*.
-For more details, see the files HISTORY-1_0-1_8_0_rc3.txt
-and HISTORY-1_8.txt in the release_docs/ directory of the HDF5 source.
-
-Links to the HDF5 1.8.17 source code, documentation, and additional materials
-can be found on the HDF5 web page at:
-
- http://www.hdfgroup.org/products/hdf5/
-
-The HDF5 1.8.17 release can be obtained from:
-
- http://www.hdfgroup.org/HDF5/release/obtain5.html
-
-User documentation for 1.8.17 can be accessed directly at this location:
-
- http://www.hdfgroup.org/HDF5/doc/
-
-New features in the HDF5-1.8.x release series, including brief general
-descriptions of some new and modified APIs, are described in the "What's New
-in 1.8.0?" document:
-
- http://www.hdfgroup.org/HDF5/doc/ADGuide/WhatsNew180.html
-
-All new and modified APIs are listed in detail in the "HDF5 Software Changes
-from Release to Release" document, in the section "Release 1.8.17 (current
-release) versus Release 1.8.16
-
- http://www.hdfgroup.org/HDF5/doc/ADGuide/Changes.html
-
-If you have any questions or comments, please send them to the HDF Help Desk:
-
- help@hdfgroup.org
-
-
-
-CONTENTS
-========
-
-- New Features
-- Support for New Platforms, Languages, and Compilers
-- Bug Fixes since HDF5-1.8.16
-- Supported Platforms
-- Supported Configuration Features Summary
-- More Tested Platforms
-- Known Problems
-
-
-
-New Features
-============
-
- Configuration
- -------------
- - Cmakehdf5: Added Ability to Run Multiple Make Commands
-
- Added option --njobs to specify up to how many jobs to launch during
- build (cmake) and testing (ctest).
-
- (AKC - 2015/12/13, HDFFV-9612)
-
- - Cmakehdf5: Added Szip Support and Verbose Option
-
- Added --with-szlib to support the Szip library; and
- --enable/disable-verbose to display all CMake process output.
-
- (AKC - 2015/11/16, HDFFV-8932 and DAILYTEST-195)
-
- - CMake minimum is now 3.1.0. (ADB - 2015/11/14)
-
- - Large File System (LFS) Support has Changed in the Autotools
-
- We assume that fseeko and ftello exist.
-
- The *64 I/O functions and types are no longer explicitly used.
- We now rely on a mapping provided by _FILE_OFFSET_BITS (or its
- equivalent).
-
- _LARGEFILE(64)_SOURCE is no longer exposed via AM_CPPFLAGS.
-
- (DER - 2016/03/29, HDFFV-9626 and HDFFV-9541)
-
-
-
- Library
- -------
- - New API Calls for Searching for External Dataset Storage
-
- API calls that determine the search path for dataset external
- storage were added. H5Pset/get_efile_prefix() API calls were added
- to the library. These functions give control over the search path
- for dataset external storage that has been configured with
- H5Pset_external().
-
- Additionally, the HDF5_EXTFILE_PREFIX environment variable can be
- used to control the search path.
-
- (DER - 2016/04/20, HDFFV-8740)
-
-
-
- Parallel Library
- ----------------
- - None
-
-
-
- Tools
- -----
- - None
-
-
-
- High-Level APIs
- ---------------
-
- C Packet Table API
- ------------------
- - Replacement of a Public Function with H5PTcreate
-
- The existing function H5PTcreate_fl limits applications so they
- can use the deflate compression only. The public function
- H5PTcreate has been added to replace H5PTcreate_fl. H5PTcreate
- takes a property list identifier to provide flexibility on
- creation properties. This also removes the following warning:
- "deprecated conversion from string constant to "char*"
- [-Wwrite-strings]".
-
- (BMR - 2016/04/25, HDFFV-9708, HDFFV-8615)
-
- - New Public Functions: H5PTget_dataset and H5PTget_type
-
- Two accessor functions have been added. H5PTget_dataset returns
- the identifier of the dataset associated with the packet table,
- and H5PTget_type returns the identifier of the datatype used by
- the packet table.
-
- (BMR - 2016/04/25, HDFFV-8623 patch 3)
-
- - Regarding #ifdef VLPT_REMOVED
-
- The #ifdef VLPT_REMOVED blocks have been removed from the packet
- table (PT) library source except for the following functions:
- + H5PTis_varlen() has been made available again
- + H5PTfree_vlen_readbuff() is now H5PTfree_vlen_buff()
-
- (BMR - 2016/04/25, HDFFV-442)
-
- C++ Packet Table API
- --------------------
- - New Constructor in FL_PacketTable
-
- An overloaded constructor has been added to FL_PacketTable and
- takes a property list identifier to provide flexibility on
- creation properties such as compression.
-
- FL_PacketTable(hid_t fileID, const char* name, hid_t dtypeID,
- hsize_t chunkSize = 0, hid_t plistID = H5P_DEFAULT)
-
- (BMR - 2016/04/25, HDFFV-8623 patch 5)
-
- - New Member Functions in PacketTable
-
- Two accessor wrappers were added to class PacketTable.
-
- PacketTable::GetDataset() returns the identifier of the dataset
- associated with the packet table, and PacketTable::GetDatatype()
- returns the identifier of the datatype that the packet table uses.
-
- (BMR - 2016/04/25, HDFFV-8623 patch 4)
-
- - New Member Functions with "char*" as an Argument
-
- Overloaded functions were added to provide the "const char*"
- argument; the existing version will be deprecated in future
- releases. This also removes the following warning:
- "deprecated conversion from string constant to "char*"
- [-Wwrite-strings]".
-
- (BMR - 2016/04/25, HDFFV-8623 patch 1, HDFFV-8615)
-
- - Regarding #ifdef VLPT_REMOVED
-
- The #ifdef VLPT_REMOVED blocks have been removed from the packet
- table library source code except for the following functions:
- + VL_PacketTable::IsVariableLength() was moved to PacketTable
- + VL_PacketTable::FreeReadBuff() is now PacketTable::FreeBuff()
-
- (BMR - 2016/04/25, HDFFV-442)
-
-
-
- Fortran API
- -----------
- - None
-
-
-
- C++ API
- -------
- - New Member Function in DSetCreatPropList
-
- DSetCreatPropList::setNbit() was added to setup N-bit compression for
- a dataset.
-
- (BMR - 2016/04/25, HDFFV-8623 patch 7)
-
- - New Overloaded "const" Member Functions in ArrayType
-
- The two following functions were added:
- ArrayType::getArrayNDims() const
- ArrayType::getArrayDims() const
- to provide const version, and the non-const version was marked
- deprecated. In-memory array information, ArrayType::rank and
- ArrayType::dimensions, were removed. This is an implementation
- detail and should not affect applications.
-
- (BMR, 2016/04/25, HDFFV-9725)
-
- - New member function added
-
- The assignment operator ArrayType::operator= is added because ArrayType
- has pointer data members.
-
- (BMR, 2016/03/07, HDFFV-9562)
-
-
-Support for New Platforms, Languages, and Compilers
-===================================================
- - Mac OS X El Capitan 10.11.4 with compilers Apple clang/clang++
- version 7.3.0 from Xcode 7.3, gfortran GNU Fortran (GCC) 5.2.0
- and Intel icc/icpc/ifort version 16.0.2
-
-
-
-Bug Fixes since HDF5-1.8.16
-===========================
-
- Configuration
- -------------
- - Updated Linux Language Level Flags to Match the Autotools. Removed
- Linux-specific Flags from OS X.
-
- An addition to the flags simply being out of sync with the Autotools,
- the Linux flags were used on OS X builds which led to symbols not being
- found. Although this was non-fatal and compilation continued (implicit
- definitions were used by the compiler and the symbols resolved at link
- time), a large number of warnings were raised.
-
- Linux changes:
-
- * CHANGED: _POSIX_C_SOURCE (from 199605 to 200112L)
- * ADDED: _GNU_SOURCE
- * REMOVED: _BSD_SOURCE
- * REMOVED: _DEFAULT_SOURCE
-
- (DER - 2015/12/08, HDFFV-9627)
-
- - The --enable-clear-file-buffers configure Option was Non-functional
- so the Feature was Always Enabled (its default value).
-
- Regardless of the configure flag, the setting was always enabled when
- the Autotools were used to configure HDF5. This was due to the "no"
- option being processed after the "*" option in configure.ac so "*"
- matched first. CMake was unaffected.
-
- The option now works correctly.
-
- NOTE that builders are always advised to leave this option enabled.
- When disabled, buffers that are written to disk may contain the
- memory's previous contents, which may include secure information.
- The performance overhead of the feature (a single memset call per
- allocation) is minimal.
-
- (DER - 2016/02/03, HDFFV-9676)
-
- - Added a patch to remove '"'s from arguments for MPI compilers that
- were causing errors compiling H5lib_settings.c with SGI MPT.
-
- (LRK - 2016/04/20, HDFFV-9439)
-
- Library
- -------
- - Fixed shared file pointer problem which caused a crash when running a
- program provided by a user.
-
- (VC - 2016/04/01, HDFFV-9469)
-
- - Fixed some format string warnings that prevent compiling with
- -Werror=format-security on gcc.
-
- These only appeared in error messages and would not cause problems
- under normal operation.
-
- (DER - 2016/01/13, HDFFV-9640)
-
- - Fixed a library segmentation fault when accessing a corrupted
- file provided by a user.
-
- (MSC - 2016/02/19, HDFFV-9670)
-
-
-
- Parallel Library
- ----------------
- - None
-
-
-
- Performance
- -------------
- - None
-
-
-
- Tools
- -----
- - h5dump: Sub-setting Fixed for Dimensions Greater than Two
-
- When a dataset has more than two dimensions, sub-setting would
- incorrectly calculate the data that needed to be displayed.
- Added in block and stride calculations that account for dimensions
- greater than two. NOTE: lines that have line breaks inserted
- because of display length calculations may have index info that
- is incorrect until the next dimension break.
-
- (ADB - 2016/03/07, HDFFV-9698)
-
- - h5dump: Issue with Argument Segmentation Fault
-
- When an argument with an optional value was at the end of the command
- line with a value, h5dump would crash. Reworked check for remaining
- arguments.
-
- (ADB - 2016/03/07, HDFFV-9570, HDFFV-9684)
-
- - h5dump: Issue with Default Fill Value
-
- Added all default cases of fill value to the display of fill value.
-
- (ADB -, 2016/03/07, HDFFV-9241)
-
- - h5dump: Clarified Help
-
- Clarified usage of -O F option in h5dump utility help.
-
- (ADB - 2016/03/07, HDFFV-9066)
-
- - h5dump: Issue with Double Free Fault
-
- Added a check for filename not null before calling free().
-
- (ADB - 2016/01/27, HDFFV-9639)
-
- - VS2015 Release Changed how Timezone was Handled
-
- Created a function, HDget_timezone, in H5system.c. Replaced
- timezone variable usage with function call.
-
- (ADB - 2015/11/02, HDFFV-9550)
-
-
-
- Fortran API
- -----------
- - None
-
-
-
- C++ API
- -------
- - Removal of Obsolete Methods
-
- The overloaded methods which had parameters that should be const
- but were not have been removed.
-
- (BMR - 2016/01/13, HDFFV-9789)
-
-
-
- High-Level APIs:
- ---------------
- - Fixed Memory Leak in Packet Table API
-
- Applied user's patch to fix memory leak in the creation of a
- packet table.
-
- (BMR - 2016/04/25, HDFFV-9700)
-
-
-
- Fortran High-Level APIs:
- ------------------------
- - None
-
-
-
- Testing
- -------
- - None
-
-
-
-Supported Platforms
-===================
-The following platforms are supported and have been tested for this release.
-They are built with the configure process unless specified otherwise.
-
- AIX 6.1 xlc/xlc_r 10.1.0.5
- (NASA G-ADA) xlC/xlC_r 10.1.0.5
- xlf90/xlf90_r 12.1.0.6
-
- Linux 2.6.32-573.22.1.el6 GNU C (gcc), Fortran (gfortran), C++ (g++)
- #1 SMP x86_64 GNU/Linux compilers:
- (platypus) Version 4.4.7 20120313
- Version 4.9.3, Version 5.2.0
- PGI C, Fortran, C++ for 64-bit target on
- x86-64;
- Version 15.7-0
- Intel(R) C (icc), C++ (icpc), Fortran (icc)
- compilers:
- Version 15.0.3.187 Build 20150407
- MPICH 3.1.4 compiled with GCC 4.9.3
-
- Linux 2.6.32-504.8.1.el6.ppc64 gcc (GCC) 4.4.7 20120313 (Red Hat 4.4.7-16)
- #1 SMP ppc64 GNU/Linux g++ (GCC) 4.4.7 20120313 (Red Hat 4.4.7-16)
- (ostrich) GNU Fortran (GCC) 4.4.7 20120313 (Red Hat 4.4.7-16)
- IBM XL C/C++ V13.1
- IBM XL Fortran V15.1
-
- Linux 3.10.0-229.14.1.el7 GNU C (gcc), Fortran (gfortran), C++ (g++)
- #1 SMP x86_64 GNU/Linux compilers:
- (kituo/moohan) Version 4.8.5 20150623 (Red Hat 4.8.5-4)
- Version 5.2.0
- Intel(R) C (icc), C++ (icpc), Fortran (icc)
- compilers:
- Version 15.0.3.187 Build 20150407
- MPICH 3.1.4 compiled with GCC 4.9.3
-
- SunOS 5.11 32- and 64-bit Sun C 5.12 SunOS_sparc
- (emu) Sun Fortran 95 8.6 SunOS_sparc
- Sun C++ 5.12 SunOS_sparc
-
- Windows 7 Visual Studio 2012 w/ Intel Fortran 15 (cmake)
- Visual Studio 2013 w/ Intel Fortran 15 (cmake)
- Visual Studio 2015 (cmake)
- Cygwin(CYGWIN_NT-6.1 2.2.1(0.289/5/3) gcc(4.9.3) compiler and gfortran)
- (cmake and autotools)
-
- Windows 7 x64 Visual Studio 2012 w/ Intel Fortran 15 (cmake)
- Visual Studio 2013 w/ Intel Fortran 15 (cmake)
- Visual Studio 2015 (cmake)
-
- Windows 8.1 Visual Studio 2012 w/ Intel Fortran 15 (cmake)
- Visual Studio 2013 w/ Intel Fortran 15 (cmake)
-
- Windows 8.1 x64 Visual Studio 2012 w/ Intel Fortran 15 (cmake)
- Visual Studio 2013 w/ Intel Fortran 15 (cmake)
-
- Mac OS X Mt. Lion 10.8.5 Apple clang/clang++ version 5.1 from Xcode 5.1
- 64-bit gfortran GNU Fortran (GCC) 4.8.2
- (swallow/kite) Intel icc/icpc/ifort version 15.0.3
-
- Mac OS X Mavericks 10.9.5 Apple clang/clang++ version 6.0 from Xcode 6.2
- 64-bit gfortran GNU Fortran (GCC) 4.9.2
- (wren/quail) Intel icc/icpc/ifort version 15.0.3
-
- Mac OS X Yosemite 10.10.5 Apple clang/clang++ version 6.1 from Xcode 7.0
- 64-bit gfortran GNU Fortran (GCC) 4.9.2
- (osx1010dev/osx1010test) Intel icc/icpc/ifort version 15.0.3
-
- Mac OS X El Capitan 10.11.4 Apple clang/clang++ version 7.3.0 from Xcode 7.3
- 64-bit gfortran GNU Fortran (GCC) 5.2.0
- (osx1011dev/ox1011test) Intel icc/icpc/ifort version 16.0.2
-
-
-Tested Configuration Features Summary
-=====================================
-
- In the tables below
- y = tested
- n = not tested in this release
- C = Cluster
- W = Workstation
- x = not working in this release
- dna = does not apply
- ( ) = footnote appears below second table
- <blank> = testing incomplete on this feature or platform
-
-Platform C F90/ F90 C++ zlib SZIP
- parallel F2003 parallel
-SunOS 5.11 32-bit n y/y n y y y
-SunOS 5.11 64-bit n y/y n y y y
-Windows 7 y y/y n y y y
-Windows 7 x64 y y/y n y y y
-Windows 7 Cygwin n y/y n y y n
-Windows 8.1 n y/y n y y y
-Windows 8.1 x64 n y/y n y y y
-Mac OS X Mountain Lion 10.8.5 64-bit n y/y n y y y
-Mac OS X Mavericks 10.9.5 64-bit n y/y n y y y
-Mac OS X Yosemeti 10.10.5 64-bit n y/y n y y y
-AIX 6.1 32- and 64-bit n y/n n y y y
-CentOS 6.7 Linux 2.6.32 x86_64 GNU y y/y y y y y
-CentOS 6.7 Linux 2.6.32 x86_64 Intel n y/y n y y y
-CentOS 6.7 Linux 2.6.32 x86_64 PGI n y/y n y y y
-CentOS 7.1 Linux 3.10.0 x86_64 GNU y y/y y y y y
-CentOS 7.1 Linux 3.10.0 x86_64 Intel n y/y n y y y
-Linux 2.6.32-431.11.2.el6.ppc64 n y/n n y y y
-
-Platform Shared Shared Shared Thread-
- C libs F90 libs C++ libs safe
-SunOS 5.11 32-bit y y y y
-SunOS 5.11 64-bit y y y y
-Windows 7 y y y y
-Windows 7 x64 y y y y
-Windows 7 Cygwin n n n y
-Windows 8.1 y y y y
-Windows 8.1 x64 y y y y
-Mac OS X Mountain Lion 10.8.5 64-bit y n y y
-Mac OS X Mavericks 10.9.5 64-bit y n y y
-Mac OS X Yosemeti 10.10.5 64-bit y n y y
-AIX 6.1 32- and 64-bit y n n y
-CentOS 6.7 Linux 2.6.32 x86_64 GNU y y y y
-CentOS 6.7 Linux 2.6.32 x86_64 Intel y y y y
-CentOS 6.7 Linux 2.6.32 x86_64 PGI y y y y
-CentOS 7.1 Linux 3.10.0 x86_64 GNU y y y y
-CentOS 7.1 Linux 3.10.0 x86_64 Intel y y y y
-Linux 2.6.32-431.11.2.el6.ppc64 y y y y
-
-Compiler versions for each platform are listed in the preceding
-"Supported Platforms" table.
-
-
-More Tested Platforms
-=====================
-The following platforms are not supported but have been tested for this release.
-
- Linux 2.6.18-431.11.2.el6 g95 (GCC 4.0.3 (g95 0.94!)
- #1 SMP x86_64 GNU/Linux
- (platypus)
-
- Windows 7 Visual Studio 2008 (cmake)
-
- Windows 7 x64 Visual Studio 2008 (cmake)
-
- Windows 10 Visual Studio 2013 w/ Intel Fortran 15 (cmake)
-
- Windows 10 x64 Visual Studio 2013 w/ Intel Fortran 15 (cmake)
-
- Debian7.5.0 3.2.0-4-amd64 #1 SMP Debian 3.2.51-1 x86_64 GNU/Linux
- gcc (Debian 4.7.2-5) 4.7.2
- GNU Fortran (Debian 4.7.2-5) 4.7.2
- (cmake and autotools)
-
- Fedora20 3.15.3-200.fc20.x86_64 #1 SMP x86_64 x86_64 x86_64 GNU/Linux
- gcc (GCC) 4.8.3 20140624 (Red Hat 4.8.3-1)
- GNU Fortran (GCC) 4.8.3 20140624 (Red Hat 4.8.3-1)
- (cmake and autotools)
-
- SUSE 13.1 3.11.10-17-desktop #1 SMP PREEMPT x86_64 x86_64 x86_64 GNU/Linux
- gcc (SUSE Linux) 4.8.1
- GNU Fortran (SUSE Linux) 4.8.1
- (cmake and autotools)
-
- Ubuntu 14.04 3.13.0-35-generic #62-Ubuntu SMP x86_64 GNU/Linux
- gcc (Ubuntu/Linaro 4.9.1-0ubuntu1) 4.9.1
- GNU Fortran (Ubuntu/Linaro 4.9.1-0ubuntu1) 4.9.1
- (cmake and autotools)
-
- hopper.nersc.gov PrgEnv-gnu/5.2.40
- gcc (GCC) 4.9.2 20141030 (Cray Inc.)
- GNU Fortran (GCC) 4.9.2 20141030 (Cray Inc.)
- g++ (GCC) 4.9.2 20141030 (Cray Inc.)
-
-
-Known Problems
-==============
-* On windows platforms in debug configurations, the VFD flush1 tests will fail
- with the split and multi VFD drivers. These tests will display a modal debug
- dialog which must be answered or wait for the test timeout to expire.
- (ADB - 2014/06/23 - HDFFV-8851)
-
-* CLANG compiler with the options -fcatch-undefined-behavior and -ftrapv
- catches some undefined behavior in the alignment algorithm of the macro DETECT_I
- in H5detect.c (Issue 8147). Since the algorithm is trying to detect the alignment
- of integers, ideally the flag -fcatch-undefined-behavior shouldn't to be used for
- H5detect.c. In the future, we can separate flags for H5detect.c from the rest of
- the library. (SLU - 2013/10/16)
-
-* Make provided by Solaris fails in "make check". Solaris users should use
- gmake to build and install the HDF5 software. (AKC - 2013/10/08 - HDFFV-8534)
-
-* The C++ and FORTRAN bindings are not currently working on FreeBSD with the
- native release 8.2 compilers (4.2.1), but are working with gcc 4.6 from the
- ports (and probably gcc releases after that).
- (QAK - 2012/10/19)
-
-* The following h5dump test case fails in BG/P machines (and potentially other
- machines that use a command script to launch executables):
-
- h5dump --no-compact-subset -d "AHFINDERDIRECT::ah_centroid_t[0] it=0 tl=0"
- tno-subset.h5
-
- This is due to the embedded spaces in the dataset name being interpreted
- by the command script launcher as meta-characters, thus passing three
- arguments to h5dump's -d flag. The command passes if run by hand, just
- not via the test script.
- (AKC - 2012/05/03)
-
-* The STDIO VFD does not work on some architectures, possibly due to 32/64
- bit or large file issues. The basic STDIO VFD test is known to fail on
- 64-bit SunOS 5.10 on SPARC when built with -m64 and 32-bit OS X/Darwin
- 10.7.0. The STDIO VFD test has been disabled while we investigate and
- a fix should appear in a future release.
- (DER - 2011/10/14 - HDFFV-8235)
-
-* h5diff can report inconsistent results when comparing datasets of enum type
- that contain invalid values. This is due to how enum types are handled in
- the library and will be addressed in a future release.
- (DER - 2011/10/14 - HDFFV-7527)
-
-* The links test can fail under the stdio VFD due to some issues with external
- links. This will be investigated and fixed in a future release.
- (DER - 2011/10/14 - HDFFV-7768)
-
-* After the shared library support was fixed for some bugs, it was discovered
- that "make prefix=XXX install" no longer works for shared libraries. It
- still works correctly for static libraries. Therefore, if you want to
- install the HDF5 shared libraries in a location such as /usr/local/hdf5,
- you need to specify the location via the --prefix option during configure
- time. E.g, ./configure --prefix=/usr/local/hdf5 ...
- (AKC - 2011/05/07 - HDFFV-7583)
-
-* The parallel test, t_shapesame, in testpar/, may run for a long time and may
- be terminated by the alarm signal. If that happens, one can increase the
- alarm seconds (default is 1200 seconds = 20 minutes) by setting the
- environment variable, $HDF5_ALARM_SECONDS, to a larger value such as 3600
- (60 minutes). Note that the t_shapesame test may fail in some systems
- (see the "While working on the 1.8.6 release..." problem below). If
- it does, it will waste more time if $HDF5_ALARM_SECONDS is set
- to a larger value.
- (AKC - 2011/05/07)
-
-* Shared Fortran libraries are not quite working on AIX. While they are
- generated when --enable-shared is specified, the fortran and hl/fortran
- tests fail. the issue. HL and C++ shared libraries should now be
- working as intended, however.
- (MAM - 2011/04/20)
-
-* While working on the 1.8.6 release of HDF5, a bug was discovered that can
- occur when reading from a dataset in parallel shortly after it has been
- written to collectively. The issue was exposed by a new test in the parallel
- HDF5 test suite, but had existed before that. We believe the problem lies with
- certain MPI implementations and/or file systems.
-
- We have provided a pure MPI test program, as well as a standalone HDF5
- program, that can be used to determine if this is an issue on your system.
- They should be run across multiple nodes with a varying number of processes.
- These programs can be found at:
- http://www.hdfgroup.org/ftp/HDF5/examples/known_problems/
- (NAF - 2011/01/19)
-
-* All the VFL drivers aren't backward compatible. In H5FDpublic.h, the
- structure H5FD_class_t changed in 1.8. There is new parameter added to
- get_eoa and set_eoa callback functions. A new callback function
- get_type_map was added in. The public function H5FDrealloc was taken
- out in 1.8. The problem only happens when users define their own driver
- for 1.6 and try to plug in 1.8 library. Because there's only one user
- complaining about it, we (Elena, Quincey, and I) decided to leave it as
- it is (see bug report #1279). Quincey will make a plan for 1.10.
- (SLU - 2010/02/02)
-
-* The --enable-static-exec configure flag will only statically link libraries
- if the static version of that library is present. If only the shared version
- of a library exists (i.e., most system libraries on Solaris, AIX, and Mac,
- for example, only have shared versions), the flag should still result in a
- successful compilation, but note that the installed executables will not be
- fully static. Thus, the only guarantee on these systems is that the
- executable is statically linked with just the HDF5 library.
- (MAM - 2009/11/04)
-
-* A dataset created or rewritten with a v1.6.3 library or after cannot be read
- with the v1.6.2 library or before when the Fletcher32 EDC filter is enabled.
- There was a bug in the calculation of the Fletcher32 checksum in the
- library before v1.6.3; the checksum value was not consistent between big-
- endian and little-endian systems. This bug was fixed in Release 1.6.3.
- However, after fixing the bug, the checksum value was no longer the same as
- before on little-endian system. Library releases after 1.6.4 can still read
- datasets created or rewritten with an HDF5 library of v1.6.2 or before.
- (SLU - 2005/06/30)
-
-
-%%%%1.8.16%%%%
-
-
-HDF5 version 1.8.16 released on 2015-11-10
-================================================================================
-
-INTRODUCTION
-============
-
-This document describes the differences between HDF5-1.8.15 and
-HDF5-1.8.16, and contains information on the platforms tested and
-known problems in HDF5-1.8.16.
-For more details, see the files HISTORY-1_0-1_8_0_rc3.txt
-and HISTORY-1_8.txt in the release_docs/ directory of the HDF5 source.
-
-Links to the HDF5 1.8.16 source code, documentation, and additional materials
-can be found on the HDF5 web page at:
-
- http://www.hdfgroup.org/products/hdf5/
-
-The HDF5 1.8.16 release can be obtained from:
-
- http://www.hdfgroup.org/HDF5/release/obtain5.html
-
-User documentation for 1.8.16 can be accessed directly at this location:
-
- http://www.hdfgroup.org/HDF5/doc/
-
-New features in the HDF5-1.8.x release series, including brief general
-descriptions of some new and modified APIs, are described in the "What's New
-in 1.8.0?" document:
-
- http://www.hdfgroup.org/HDF5/doc/ADGuide/WhatsNew180.html
-
-All new and modified APIs are listed in detail in the "HDF5 Software Changes
-from Release to Release" document, in the section "Release 1.8.16 (current
-release) versus Release 1.8.15":
-
- http://www.hdfgroup.org/HDF5/doc/ADGuide/Changes.html
-
-If you have any questions or comments, please send them to the HDF Help Desk:
-
- help@hdfgroup.org
-
-
-CONTENTS
-========
-
-- New Features
-- Support for New Platforms, Languages, and Compilers
-- Bug Fixes since HDF5-1.8.15
-- Supported Platforms
-- Supported Configuration Features Summary
-- More Tested Platforms
-- Known Problems
-
-New Features
-============
-
- Configuration and Build
- -------------
- - The thread-safety + high-level library combination has been marked
- as "unsupported" in the Autotools
-
- The global lock used by the thread-safety feature has never been
- raised to the high-level library level, making it possible that
- the library state could change if a context switch were to occur in
- a high-level library call. Because of this, the combination of
- thread-safety and high-level library is officially unsupported by
- The HDF Group.
-
- In the past, although this combination has never been supported, this
- was not enforced by the build systems. These changes will cause an
- Autotools configure step to fail if --enable-threadsafe and
- --enable-hl are combined unless additional options are specified.
- Since the high-level library is built by default, this means that
- these extra configuration options will need to be used any time
- --enable-threadsafe is selected.
-
- To build with --enable-threadsafe, either:
-
- 1) Use --disable-hl to disable the high-level library (recommended)
-
- 2) Use --enable-unsupported to build the high-level library with
- the thread-safety feature.
-
- (DER - 2015/09/10 HDFFV-8719)
-
- - Using CMake now builds both static and shared libraries.
-
- The CMake files have been updated to build both static and shared
- libraries, with tools only built statically. The packaging of the
- libraries and tools will include cmake-config files that allows
- projects to choose either shared or static (default) libraries
- to be found with the find_package command using the COMPONENTS
- keyword and a list of components. The imported libraries will
- include any interface specific settings and dependent libraries.
-
- The default setting for BUILD_SHARED_LIBS has changed from OFF
- to ON, which builds both static and shared libraries. The static
- libraries are always built because of tools requirements.
-
- (ADB - 2015/08/24 HDFFV-5881)
-
- - Inline functions now correctly annotated with Autotools builds.
-
- The method used to detect the appropriate inline markup scheme was
- nonfunctional in Autotools builds. The Autotools have been modified
- to correctly detect the compiler's inline markup symbol and apply it
- to the source. Note that only a very small number of internal
- functions are marked inline so this was not a very big change or
- likely to significantly affect performance.
-
- As a part of this change, the H5_inline symbol no longer appears in
- H5pubconf.h.
-
- (DER - 2015/08/13 HDFFV-9119, HDFFV-9421)
-
- - Removed obsolete/unmaintained files from config/
-
- Several files were removed from the config directory. These files
- represent old operating systems, were no longer necessary, and/or
- were no longer maintained. configure.ac was updated to reflect the
- removed files.
-
- Removed:
-
- craynv
- dec-flags
- hpux11.23
- ia64-linux-gnu
- nec-superux14.1
- sv1-cray
- x86_64-redstorm-linux-gnu
- powerpc-ibm-aix5.x
-
- As a part of this work, a few lines that deal with locating the
- sys/fpu.h header on SGI machines and some OSF/1 configure lines
- were also removed. The Solaris config was also renamed to not have
- a version number since the version number was ignored by configure
- as it applies to all Solaris versions.
-
- (DER - 2015/09/04 HDFFV-9116)
-
- - Removed the FP_TO_INTEGER_OVERFLOW_WORKS macro/defines from the library
-
- This was for working around bugs in the Cray X1 compiler, which is no
- longer supported.
-
- (DER - 2015/09/09 HDFFV-9191)
-
- - Removed the H5_SW_ULONG_TO_FP_BOTTOM_BIT_WORKS and
- H5_FP_TO_ULLONG_BOTTOM_BIT_WORKS symbols and associated code.
-
- H5_SW_ULONG_TO_FP_BOTTOM_BIT_WORKS was a work-around on old 64-bit
- SGI and Solaris systems.
-
- H5_FP_TO_ULLONG_BOTTOM_BIT_WORKS was a work-around for old PGI
- compilers on Linux.
-
- Neither of these were used in any current library code and only appeared
- in the dt_arith test.
-
- (DER - 2015/09/09 HDFFV-9187)
-
- - Removed CONVERT_DENORMAL_FLOAT symbol and associated code from the
- library.
-
- This was only set in configure files for Cray and NEC computers. These
- config files no longer exist so there is no effect on currently
- supported platforms.
-
- (DER - 2015/09/09 HDFFV-9188)
-
- - Removed _BSD_SOURCE and _DEFAULT_SOURCE from configure.ac
-
- These are old BSD-compatibility symbols that are no longer needed by
- the library.
-
- (DER - 2015/09/10 HDFFV-9079)
-
- - Removed HW_FP_TO_LLONG_NOT_WORKS symbol and associated code from the
- library.
-
- This was part of a work-around for the VS.NET 2003 compiler, which is
- no longer supported.
-
- (DER - 2015/09/10 HDFFV-9189)
-
- - Removed the BAD_LOG2_CODE_GENERATED symbol and associated code from the
- library.
-
- This was an IRIX work-around.
-
- (DER - 2015/09/11 HDFFV-9195)
-
- - Decoupled shared object version numbers for wrapper libraries from the
- shared object version number for the HDF5 library. These will be
- maintained on an individual basis according to the interface changes
- specific to these wrapper libraries.
-
- For HDF5 1.8.16 the shared object version numbers were changed from
- 10.0.1 to 10.1.0 for the HDF5 library due to added APIs. For the C++
- wrapper library they were changed from 10.0.1 to 11.0.0 due to changes
- in existing APIs. For all other wrapper libraries the versions were
- changed from 10.0.1 to 10.0.2 because while the APIs had no changes
- there have been changes in code that did not result in changes to their
- interfaces.
-
- (LRK - 2015/10/28)
-
- Library
- -------
-
- - H5F_ACC_DEBUG flag for H5Fopen/create: functionality removed
-
- The symbol was used to emit some extra debugging information
- for HDF Group developers in the multi VFD. The underlying
- functionality has been removed due to disuse. The symbol
- remains defined since it was visible in H5Fpublic.h but it
- has been set to zero and has no effect anywhere in the library.
-
- (DER - 2015-05-02, HDFFV-1074)
-
- - New public API call: H5is_library_threadsafe()
-
- This API call indicates if the library was built with thread-
- safety enabled.
-
- (DER - 2015-09-01, HDFFV-9496)
-
- Parallel Library
- ----------------
- - None
-
- Tools
- -----
- - None
-
- High-Level APIs
- ---------------
- - None
-
- Fortran API
- -----------
- - None
-
-
- C++ API
- -------
- - Class H5::ObjCreatPropList is added for the object creation property
- list class.
-
- Class H5::ObjCreatPropList is derived from H5::PropList and is a
- baseclass of H5::DSetCreatPropList. Additional property list classes
- will be derived from H5::ObjCreatPropList when they are added to the
- library in future releases.
-
- (BMR, 2015/10/13, Part of HDFFV-9169)
-
- - New Wrappers for C Functions H5P[s/g]et_attr_phase_change and
- H5P[s/g]et_attr_creation_order.
-
- Wrappers were added to class H5::ObjCreatPropList for the C Functions
- H5Pset_attr_phase_change: H5::ObjCreatPropList::setAttrPhaseChange
- H5Pget_attr_phase_change: H5::ObjCreatPropList::getAttrPhaseChange
- H5Pset_attr_creation_order: H5::ObjCreatPropList::setAttrCrtOrder
- H5Pget_attr_creation_order: H5::ObjCreatPropList::getAttrCrtOrder
-
- (BMR, 2015/10/13, Part of HDFFV-9167 and HDFFV-9169)
-
-
-Support for New Platforms, Languages, and Compilers
-===================================================
- - Added VS2015 with Intel Fortran 16 to supported Windows 7 platforms
-
-
-Bug Fixes since HDF5-1.8.15
-===========================
-
- Configuration
- -------------
-
- - CMake test for long long printf format improved
-
- The CMake configuration test for determining the printf format string
- for printing a long long integer was fixed. The test would crash
- when executed with VS2015.
-
- (ADB - 2015-10-21 HDFFV-9488)
-
- Library
- -------
- - VS2015 removed global variable timezone
-
- The usage of the global variable timezone was modified for VS2015 by
- adding an alias to Windows builds.
-
- (ADB - 2015-10-23 HDFFV-9550)
-
- - Fix potential error in H5Iclear_type
-
- If the ID type's close callback could close another ID of the same type,
- H5Iclear_type could occasionally run into problems due to the inner
- workings of the skip list package. This could potentially cause an
- error on library shutdown without calling H5Iclear_type directly. This
- issue has been fixed.
-
- (NAF - 2015-08-12)
-
- - Fix uninitialized memory in dataspace selection code
-
- When creating a dataspace with H5Screate and setting the extent with
- H5Sextent_copy, the selection offset was not initialized, potentially
- causing invalid I/O. There may be other cases where this happened.
- Modified the library to always initialize the offset.
-
- (NAF - 2015-09-08)
-
- - Truncate file in H5Fflush() if EOA != EOF to avoid file
- corruption in certain scenarios
-
- In the following scenario, the resulting HDF5 file would be
- incorrectly corrupted because the truncate operation
- was at some point wrongly moved out of the flush operation:
- - Create a new file with a single dataset.
- - Write parts of the dataset (make sure that some values at
- the end of the dataset are not initialized).
- - Flush the file.
- - Crash the program.
- - Try to open the file with h5dump or h5debug, but the
- resulting file is corrupted.
-
- (MSC - 2015-06-15 HDFFV-9418)
-
-
- Parallel Library
- ----------------
- -
- (XYZ - YYYY/MM/DD HDFFV-####)
-
- Performance
- -------------
- - None
-
- Tools
- -----
- - VS2015 changed the default format for printing of exponents
-
- VS2015 default format for exponents changed with the elimination
- of the leading '0'. CMake now tests for the VS2015 compiler and
- adjusts which reference files are used by tests.
-
- (ADB - 2015-10-23 HDFFV-9550)
-
- - Fixed h5repack with user-defined filters
-
- h5repack would throw a buffer overrun exception on Windows when
- parsing a user-defined filter ID of 5 digits. A local variable in
- the parse routine was not of sufficient size.
-
- (ADB - 2015/09/01 HDFFV-9515)
-
- Fortran API
- ------------
- - None
-
-
- C++ API
- ------
- - Removed memory leaks
-
- The static global constant objects were changed to constant references
- referencing dynamically allocated objects. This ensures that the clean-up
- process in the C++ library occurs before the termination of the C library
- and prevents memory leaks because the previous global constants were not
- properly deleted before the C library termination.
-
- (BMR, 2015/10/13, HDFFV-9529)
-
- - Fixed the problem about identifiers being closed prematurely.
-
- The C++ library needs to increment the ID's reference counter when it is
- duplicated in the form of C++ objects, but not when the ID is obtained
- from a C function. With this approach, both problems, prematurely
- closing ID's and memory leaks due to ID's not being closed, should be
- eliminated.
-
- (BMR, 2015/10/15, HDFFV-7947)
-
-
- High-Level APIs:
- ------
- - None
-
-
- Fortran High-Level APIs:
- ------------------------
- - None
-
-
- Testing
- -------
- - None
-
-
-Supported Platforms
-===================
-The following platforms are supported and have been tested for this release.
-They are built with the configure process unless specified otherwise.
-
- AIX 6.1 xlc/xlc_r 10.1.0.5
- (NASA G-ADA) xlC/xlC_r 10.1.0.5
- xlf90/xlf90_r 12.1.0.6
-
- Linux 2.6.32-573.3.1.el6 GNU C (gcc), Fortran (gfortran), C++ (g++)
- #1 SMP x86_64 GNU/Linux compilers:
- (platypus) Version 4.4.7 20120313
- Version 4.8.4, Version 5.2.0
- PGI C, Fortran, C++ for 64-bit target on
- x86-64;
- Version 15.7-0
- Intel(R) C (icc), C++ (icpc), Fortran (icc)
- compilers:
- Version 15.0.3.187 Build 20150407
- MPICH 3.1.4 compiled with GCC 4.9.3
-
- Linux 2.6.32-504.8.1.el6.ppc64 gcc (GCC) 4.4.7 20120313 (Red Hat 4.4.7-11)
- #1 SMP ppc64 GNU/Linux g++ (GCC) 4.4.7 20120313 (Red Hat 4.4.7-11)
- (ostrich) GNU Fortran (GCC) 4.4.7 20120313 (Red Hat 4.4.7-11)
- IBM XL C/C++ V13.1
- IBM XL Fortran V15.1
-
- Linux 3.10.0-229.14.1.el7 GNU C (gcc), Fortran (gfortran), C++ (g++)
- #1 SMP x86_64 GNU/Linux compilers:
- (kituo/moohan) Version 4.8.3 20140911 (Red Hat 4.8.3-9)
- Version 5.2.0
- Intel(R) C (icc), C++ (icpc), Fortran (icc)
- compilers:
- Version 15.0.3.187 Build 20150407
- MPICH 3.1.4 compiled with GCC 4.9.3
-
- SunOS 5.11 32- and 64-bit Sun C 5.12 SunOS_sparc
- (emu) Sun Fortran 95 8.6 SunOS_sparc
- Sun C++ 5.12 SunOS_sparc
-
- Windows 7 Visual Studio 2012 w/ Intel Fortran 15 (cmake)
- Visual Studio 2013 w/ Intel Fortran 15 (cmake)
- Visual Studio 2015 w/ Intel Fortran 16 (cmake)
- Cygwin(CYGWIN_NT-6.1 2.2.1(0.289/5/3) gcc(4.9.3) compiler and gfortran)
- (cmake and autotools)
-
- Windows 7 x64 Visual Studio 2012 w/ Intel Fortran 15 (cmake)
- Visual Studio 2013 w/ Intel Fortran 15 (cmake)
- Visual Studio 2015 w/ Intel Fortran 16 (cmake)
-
- Windows 8.1 Visual Studio 2012 w/ Intel Fortran 15 (cmake)
- Visual Studio 2013 w/ Intel Fortran 15 (cmake)
-
- Windows 8.1 x64 Visual Studio 2012 w/ Intel Fortran 15 (cmake)
- Visual Studio 2013 w/ Intel Fortran 15 (cmake)
-
- Mac OS X Mt. Lion 10.8.5 Apple clang/clang++ version 5.1 from Xcode 5.1
- 64-bit gfortran GNU Fortran (GCC) 4.8.2
- (swallow/kite) Intel icc/icpc/ifort version 15.0.3
-
- Mac OS X Mavericks 10.9.5 Apple clang/clang++ version 6.0 from Xcode 6.2.0
- 64-bit gfortran GNU Fortran (GCC) 4.9.2
- (wren/quail) Intel icc/icpc/ifort version 15.0.3
-
- Mac OS X Yosemite 10.10.5 Apple clang/clang++ version 6.0 from Xcode 7.0.0
- 64-bit gfortran GNU Fortran (GCC) 4.9.2
- (osx1010dev/osx1010test) Intel icc/icpc/ifort version 15.0.3
-
-Tested Configuration Features Summary
-=====================================
-
- In the tables below
- y = tested
- n = not tested in this release
- C = Cluster
- W = Workstation
- x = not working in this release
- dna = does not apply
- ( ) = footnote appears below second table
- <blank> = testing incomplete on this feature or platform
-
-Platform C F90/ F90 C++ zlib SZIP
- parallel F2003 parallel
-SunOS 5.11 32-bit n y/y n y y y
-SunOS 5.11 64-bit n y/y n y y y
-Windows 7 y y/y n y y y
-Windows 7 x64 y y/y n y y y
-Windows 7 Cygwin n y/y n y y n
-Windows 8.1 n y/y n y y y
-Windows 8.1 x64 n y/y n y y y
-Mac OS X Mountain Lion 10.8.5 64-bit n y/y n y y y
-Mac OS X Mavericks 10.9.5 64-bit n y/y n y y y
-Mac OS X Yosemeti 10.10.5 64-bit n y/y n y y y
-AIX 6.1 32- and 64-bit n y/n n y y y
-CentOS 6.7 Linux 2.6.32 x86_64 GNU y y/y y y y y
-CentOS 6.7 Linux 2.6.32 x86_64 Intel n y/y n y y y
-CentOS 6.7 Linux 2.6.32 x86_64 PGI n y/y n y y y
-CentOS 7.1 Linux 3.10.0 x86_64 GNU y y/y y y y y
-CentOS 7.1 Linux 3.10.0 x86_64 Intel n y/y n y y y
-Linux 2.6.32-431.11.2.el6.ppc64 n y/n n y y y
-
-Platform Shared Shared Shared Thread-
- C libs F90 libs C++ libs safe
-SunOS 5.11 32-bit y y y y
-SunOS 5.11 64-bit y y y y
-Windows 7 y y y y
-Windows 7 x64 y y y y
-Windows 7 Cygwin n n n y
-Windows 8.1 y y y y
-Windows 8.1 x64 y y y y
-Mac OS X Mountain Lion 10.8.5 64-bit y n y y
-Mac OS X Mavericks 10.9.5 64-bit y n y y
-Mac OS X Yosemeti 10.10.5 64-bit y n y y
-AIX 6.1 32- and 64-bit y n n y
-CentOS 6.7 Linux 2.6.32 x86_64 GNU y y y y
-CentOS 6.7 Linux 2.6.32 x86_64 Intel y y y y
-CentOS 6.7 Linux 2.6.32 x86_64 PGI y y y y
-CentOS 7.1 Linux 3.10.0 x86_64 GNU y y y y
-CentOS 7.1 Linux 3.10.0 x86_64 Intel y y y y
-Linux 2.6.32-431.11.2.el6.ppc64 y y y y
-
-Compiler versions for each platform are listed in the preceding
-"Supported Platforms" table.
-
-
-More Tested Platforms
-=====================
-The following platforms are not supported but have been tested for this release.
-
- Linux 2.6.18-431.11.2.el6 g95 (GCC 4.0.3 (g95 0.94!)
- #1 SMP x86_64 GNU/Linux
- (platypus)
-
- Mac OS X El Capitan 10.11 Apple clang/clang++ version 7.0.0 from Xcode 7.0.1
- 64-bit gfortran GNU Fortran (GCC) 5.2.0
- (VM)
-
- Windows 7 Visual Studio 2008 (cmake)
-
- Windows 7 x64 Visual Studio 2008 (cmake)
-
- Windows 10 Visual Studio 2013 w/ Intel Fortran 15 (cmake)
-
- Windows 10 x64 Visual Studio 2013 w/ Intel Fortran 15 (cmake)
-
- Debian7.5.0 3.2.0-4-amd64 #1 SMP Debian 3.2.51-1 x86_64 GNU/Linux
- gcc (Debian 4.7.2-5) 4.7.2
- GNU Fortran (Debian 4.7.2-5) 4.7.2
- (cmake and autotools)
-
- Fedora20 3.15.3-200.fc20.x86_64 #1 SMP x86_64 x86_64 x86_64 GNU/Linux
- gcc (GCC) 4.8.3 20140624 (Red Hat 4.8.3-1)
- GNU Fortran (GCC) 4.8.3 20140624 (Red Hat 4.8.3-1)
- (cmake and autotools)
-
- SUSE 13.1 3.11.10-17-desktop #1 SMP PREEMPT x86_64 x86_64 x86_64 GNU/Linux
- gcc (SUSE Linux) 4.8.1
- GNU Fortran (SUSE Linux) 4.8.1
- (cmake and autotools)
-
- Ubuntu 14.04 3.13.0-35-generic #62-Ubuntu SMP x86_64 GNU/Linux
- gcc (Ubuntu/Linaro 4.9.1-0ubuntu1) 4.9.1
- GNU Fortran (Ubuntu/Linaro 4.9.1-0ubuntu1) 4.9.1
- (cmake and autotools)
-
- hopper.nersc.gov PrgEnv-gnu/5.2.40
- gcc (GCC) 4.9.2 20141030 (Cray Inc.)
- GNU Fortran (GCC) 4.9.2 20141030 (Cray Inc.)
- g++ (GCC) 4.9.2 20141030 (Cray Inc.)
-
-
-Known Problems
-==============
-* On Windows platforms in debug configurations, the VFD flush1 tests will fail
- with the split and multi VFD drivers. These tests will display a modal debug
- dialog which must be answered or wait for the test timeout to expire.
- (ADB - 2014/06/23 - HDFFV-8851)
-
-* CLANG compiler with the options -fcatch-undefined-behavior and -ftrapv
- catches some undefined behavior in the alignment algorithm of the macro DETECT_I
- in H5detect.c (Issue 8147). Since the algorithm is trying to detect the alignment
- of integers, ideally the flag -fcatch-undefined-behavior shouldn't to be used for
- H5detect.c. In the future, we can separate flags for H5detect.c from the rest of
- the library. (SLU - 2013/10/16)
-
-* Make provided by Solaris fails in "make check". Solaris users should use
- gmake to build and install the HDF5 software. (AKC - 2013/10/08 - HDFFV-8534)
-
-* The C++ and FORTRAN bindings are not currently working on FreeBSD with the
- native release 8.2 compilers (4.2.1), but are working with gcc 4.6 from the
- ports (and probably gcc releases after that).
- (QAK - 2012/10/19)
-
-* The following h5dump test case fails in BG/P machines (and potentially other
- machines that use a command script to launch executables):
-
- h5dump --no-compact-subset -d "AHFINDERDIRECT::ah_centroid_t[0] it=0 tl=0"
- tno-subset.h5
-
- This is due to the embedded spaces in the dataset name being interpreted
- by the command script launcher as meta-characters, thus passing three
- arguments to h5dump's -d flag. The command passes if run by hand, just
- not via the test script.
- (AKC - 2012/05/03)
-
-* The STDIO VFD does not work on some architectures, possibly due to 32/64
- bit or large file issues. The basic STDIO VFD test is known to fail on
- 64-bit SunOS 5.10 on SPARC when built with -m64 and 32-bit OS X/Darwin
- 10.7.0. The STDIO VFD test has been disabled while we investigate and
- a fix should appear in a future release.
- (DER - 2011/10/14 - HDFFV-8235)
-
-* h5diff can report inconsistent results when comparing datasets of enum type
- that contain invalid values. This is due to how enum types are handled in
- the library and will be addressed in a future release.
- (DER - 2011/10/14 - HDFFV-7527)
-
-* The links test can fail under the stdio VFD due to some issues with external
- links. This will be investigated and fixed in a future release.
- (DER - 2011/10/14 - HDFFV-7768)
-
-* After the shared library support was fixed for some bugs, it was discovered
- that "make prefix=XXX install" no longer works for shared libraries. It
- still works correctly for static libraries. Therefore, if you want to
- install the HDF5 shared libraries in a location such as /usr/local/hdf5,
- you need to specify the location via the --prefix option during configure
- time. E.g, ./configure --prefix=/usr/local/hdf5 ...
- (AKC - 2011/05/07 - HDFFV-7583)
-
-* The parallel test, t_shapesame, in testpar/, may run for a long time and may
- be terminated by the alarm signal. If that happens, one can increase the
- alarm seconds (default is 1200 seconds = 20 minutes) by setting the
- environment variable, $HDF5_ALARM_SECONDS, to a larger value such as 3600
- (60 minutes). Note that the t_shapesame test may fail in some systems
- (see the "While working on the 1.8.6 release..." problem below). If
- it does, it will waste more time if $HDF5_ALARM_SECONDS is set
- to a larger value.
- (AKC - 2011/05/07)
-
-* Shared Fortran libraries are not quite working on AIX. While they are
- generated when --enable-shared is specified, the Fortran and HL/Fortran
- tests fail. HL and C++ shared libraries should now be working as intended,
- however.
- (MAM - 2011/04/20)
-
-* While working on the 1.8.6 release of HDF5, a bug was discovered that can
- occur when reading from a dataset in parallel shortly after it has been
- written to collectively. The issue was exposed by a new test in the parallel
- HDF5 test suite, but had existed before that. We believe the problem lies with
- certain MPI implementations and/or file systems.
-
- We have provided a pure MPI test program, as well as a standalone HDF5
- program, that can be used to determine if this is an issue on your system.
- They should be run across multiple nodes with a varying number of processes.
- These programs can be found at:
- http://www.hdfgroup.org/ftp/HDF5/examples/known_problems/
- (NAF - 2011/01/19)
-
-* All of the VFL drivers aren't backward compatible. In H5FDpublic.h, the
- structure H5FD_class_t changed in 1.8. There is new parameter added to
- get_eoa and set_eoa callback functions. A new callback function
- get_type_map was added in. The public function H5FDrealloc was taken
- out in 1.8. The problem only happens when users define their own driver
- for 1.6 and try to plug in 1.8 library. Because there's only one user
- complaining about it, we (Elena, Quincey, and I) decided to leave it as
- it is (see bug report #1279). Quincey will make a plan for 1.10.
- (SLU - 2010/02/02)
-
-* The --enable-static-exec configure flag will only statically link libraries
- if the static version of that library is present. If only the shared version
- of a library exists (i.e., most system libraries on Solaris, AIX, and Mac,
- for example, only have shared versions), the flag should still result in a
- successful compilation, but note that the installed executables will not be
- fully static. Thus, the only guarantee on these systems is that the
- executable is statically linked with just the HDF5 library.
- (MAM - 2009/11/04)
-
-* A dataset created or rewritten with a v1.6.3 library or after cannot be read
- with the v1.6.2 library or before when the Fletcher32 EDC filter is enabled.
- There was a bug in the calculation of the Fletcher32 checksum in the
- library before v1.6.3; the checksum value was not consistent between big-
- endian and little-endian systems. This bug was fixed in Release 1.6.3.
- However, after fixing the bug, the checksum value was no longer the same as
- before on little-endian systems. Library releases after 1.6.4 can still read
- datasets created or rewritten with an HDF5 library of v1.6.2 or before.
- (SLU - 2005/06/30)
-
-
-%%%%1.8.15%%%%
-
-
-HDF5 version 1.8.15 released on 2015-05-04
-================================================================================
-
-INTRODUCTION
-============
-
-This document describes the differences between HDF5-1.8.14 and
-HDF5-1.8.15, and contains information on the platforms tested and
-known problems in HDF5-1.8.15.
-
-Links to the HDF5 source code, documentation, and additional materials
-can be found on the HDF5 web page at:
-
- http://www.hdfgroup.org/products/hdf5/
-
-The HDF5 release can be obtained from:
-
- http://www.hdfgroup.org/HDF5/release/obtain5.html
-
-User documentation for HDF5 can be accessed directly at this location:
-
- http://www.hdfgroup.org/HDF5/doc/
-
-All new and modified APIs are listed in detail in the "HDF5 Software Changes
-from Release to Release" document at this location:
-
- http://www.hdfgroup.org/HDF5/doc/ADGuide/Changes.html
-
-If you have any questions or comments, please send them to the HDF Help Desk:
-
- help@hdfgroup.org
-
-
-CONTENTS
-========
-
-- New Features
-- Support for New Platforms, Languages, and Compilers
-- Bug Fixes since HDF5-1.8.14
-- Supported Platforms
-- Supported Configuration Features Summary
-- More Tested Platforms
-- Known Problems
-
-
-New Features
-============
-
- Configuration
- -------------
- - CMake
-
- Improvements made to the CMake build system.
-
- The default options were changed to align with the Autotools configure
- defaults. CMake configure files now support components when packaged
- with CPack. Windows CPack supports WiX packaging, and will look for
- WiX and NSIS in the standard locations.
-
- The CMake minimum has been changed to 3.1.
-
- (ADB - 2015/04/01 HDFFV-8074, 8968, 9006)
-
- - cmakehdf5 for Cmake building.
- Added configure options to support the building of Fortran or CXX API,
- to enable/disable testings. Use "cmakehdf5 --help" for details.
- (AKC - 2014/12/09 HDFFV-8932)
-
- - Building Shared and Parallel Made Explicit
-
- When --enable-parallel is specified, configure used to disable
- shared by default.
-
- Removed the restriction for building shared when parallel is
- enabled. --disable-shared has to be used explicitly if user
- wishes to disable shared libraries.
-
- (MSC - 2015/02/19 HDFFV-9069)
-
- - Inferring Parallel Compilers
-
- configure was trying to infer if a compiler is a parallel
- compiler with MPI support and enable parallel even if the user
- did not explicitly enable parallel. This should not happen.
-
- Disabled inferring parallel compilers to enable parallel HDF5
- build. --enable-parallel has to be used explicitly to build
- parallel HDF5 regardless of the compiler type being used.
-
- (MSC - 2015/02/19 HDFFV-9068)
-
- - Large File Support Configuration Option
-
- Removed the option to enable or disable large file support. It will
- always be enabled.
-
- (MSC - 2015/02/19 HDFFV-9097)
-
- - Removed Configuration Feature
-
- When configure detected that the CodeWarrior compiler was being used it
- would define a symbol that caused a test in test/tfile.c to be skipped
- due to a broken CodeWarrior open() command.
-
- Since this only masks the problem instead of fixing it and we don't
- support CodeWarrior anyway, this functionality was removed.
-
- (DER - 2015/02/21, HDFFV-9080)
-
- - VMS Build/Test Files Have Been Removed
-
- HDF5 no longer supports VMS, and the files were getting out of date.
- Since we have no access to a VMS machine, there is no way for us to
- maintain them.
-
- A Subversion tag was created at:
-
- https://svn.hdfgroup.uiuc.edu/tags/vms_last_support_1_8
-
- immediately before removing the files.
-
- (DER - 2015-02-26, HDFFV-9147)
-
- - Removal of --with-default-vfd configure Option
-
- In theory, this option was intended to allow setting a default
- VFD that would be used by the library. In practice, the feature
- only accepted the POSIX (SEC2) VFD (already the default) and
- the stdio VFD (a demo VFD not intended for production use). The
- inability to pass key VFD parameters at configure time limits the
- full implementation of this feature, so it was retired.
-
- (DER - 2015-02-26, HDFFV-9081)
-
- - Direct VFD configure Behavior
-
- The configure options for Linux now allow the Direct VFD to build
- without passing additional compiler options/defines like _GNU_SOURCE.
- Passing --enable-direct-vfd is now all that is needed to enable
- the feature.
-
- The Direct VFD is now disabled by default since it is intended for
- specialized audiences. It was previously enabled by default, but the
- configure script did not set correct POSIX levels, etc. making this
- a moot point.
-
- Note that the Direct VFD can only be configured on Linux when
- the O_DIRECT flag to open()/create() and posix_memalign() function
- are available. This is unchanged from previous behavior.
-
- (DER - 2015-02-26, HDFFV-9057, 7567, 9088, 7566)
-
- - _POSIX_C_SOURCE, _GNU_SOURCE, and _BSD_SOURCE No Longer Exported
- to h5cc and Other Compiler Wrappers
-
- The _POSIX_C_SOURCE, _GNU_SOURCE, and _BSD_SOURCE definitions are
- not required for using API functions and may conflict with user
- code requirements.
-
- (DER - 2015-03-08, HDFFV-9152)
-
- - Removed the --enable-filters Option from configure
-
- This option allowed the user to disable selected internal filters,
- presumably to make the library smaller. It has been removed since
- it saved little space (the internal filters are small with respect
- to the overall library size) and was not generally extendible to
- the library at large due to the large number of #ifdefs that would
- be required.
-
- Note that this features applied to internal filters such as shuffle
- and n-bit and not external filters like gzip or Szip. Those are still
- enabled or disabled via their own configure options.
-
- (DER - 2015-03-08, HDFFV-9086)
-
- - Removed Obsolete Time Functionality from configure and the C Library
-
- The library contained some residual functionality from obsolete
- time zone handling code. This has been removed, and the configure
- checks for the time functions have been cleaned up.
-
- * Lumped all the time functionality together in configure.ac.
- This was previously more spread out due to Solaris issues
- with the ordering of certain checks.
-
- * Removed processing that handles __tm_gmtoff members of struct
- tm. (libc-4)
-
- * Removed BSDgettimeofday(). (IRIX 5.3)
-
- * Removed timezone struct handling in gettimeofday() (considered
- harmful).
-
- Note that the HDF5 Library stores timestamps in a platform-independent
- manner, so old files can still be read. This only affects converting
- system time to HDF5 timestamps.
-
- The library currently uses the tm_gmtoff member of the tm struct
- (preferred, if available) or the timezone global variable to
- construct HDF5 timestamps.
-
- (DER - 2015-03-09, HDFFV-9083 and 9085)
-
- - Added -D_DEFAULT_SOURCE to CPPFLAGS on Linux Systems
-
- This is the replacement for -D_BSD_SOURCE in versions of glibc since 2.19.
- Since both are defined, it should work for all versions of glibc. Defining
- both suppresses the warning about defining _BSD_SOURCE.
-
- (NAF - 2015-04-02, HDFFV-9079)
-
- Library
- -------
- - Added Memory Allocation Functions that Use the Library's Allocator
-
- HDF5 filters may need to allocate or resize the buffer that is passed
- to them from the library. If the filter has been compiled separately
- from the library, it and the library may use different memory
- allocation libraries for the (re)allocation and free calls. This can
- cause heap corruption and crashes. This is particularly a problem on
- Windows since each C run-time library is implemented as a separate
- shared library, but can also show up on POSIX systems when debug or
- high-performance allocation libraries are in use.
-
- Two new functions (H5allocate_memory() and H5resize_memory()) were
- added to the HDF5 C library. These functions have the same semantics as
- malloc/calloc and realloc, respectively. Their primary purpose is to
- allow filter authors to allocate or resize memory using the same
- memory allocation library as the HDF5 library. Filter authors are
- highly encouraged to use these new functions in place of malloc,
- calloc, and realloc. They should also use the H5free_memory() call when
- freeing memory.
-
- Note that the filters provided with the library (zlib, szip, etc.) do
- not experience the problems that these new functions are intended to
- fix. This work only applies to third-party filters that are compiled
- separately from the library.
-
- (DER - 2015-04-01, HDFFV-9100)
-
- - H5Pset_istore_k and H5Pset_sym_k
-
- These two functions didn't check the value of the input parameter "ik".
- When 2*ik exceeded 2 bytes of storage, data was lost in the file;
- for example, some chunks would be overwritten.
-
- Added validation of "ik" to not exceed the max v1 btree entries (2 bytes)
- to these two routines.
-
- (VC - 2015-03-24, HDFFV-9173)
-
- - Added Functions to Control the Value of H5PL_no_plugin_g without
- Using an Environment Variable
-
- Sometimes it is necessary for an application to disable the use of
- dynamically loaded plugin libraries without requiring the library to
- be built with plugin support disabled or to set an environment
- variable to disable plugin support globally.
-
- Two new functions (H5PLset_loading_state() and H5PLget_loading_state())
- were added to the HDF5 C Library. These functions require a parameter
- that indicates which type of dynamically loaded plugin is enabled or
- disabled.
-
- (ADB - 2015-03-17, HDFFV-8520)
-
- Parallel Library
- ----------------
- - MPI_Finalize and HDF5 Library Shutdown
-
- Calling HDF5 routines after MPI_Finalize has been closed should
- not be done, since those routines might call MPI functions that
- would not be possible to do after finalizing the MPI library.
-
- Attached an attribute destroy callback to MPI_COMM_SELF that
- shuts down the HDF5 library when MPI_COMM_SELF is destroyed,
- in other words, on MPI_Finalize. This should fix several issues
- that users see when they forget to close HDF5 objects before
- calling MPI_Finalize().
-
- (MSC - 2015/02/25, HDFFV-883)
-
- Tools
- -----
- - None
-
- High-Level APIs
- ---------------
- - None
-
- Fortran API
- -----------
- - Added Global Variables
-
- These new global variables are equivalent to the C definitions
- without the '_F':
-
- H5G_UDLINK_F
- H5G_SAME_LOC_F
- H5O_TYPE_UNKNOWN_F
- H5O_TYPE_GROUP_F
- H5O_TYPE_DATASET_F
- H5O_NAMED_DATATYPE_F
- H5O_TYPE_NTYPES_F
-
- (MSB - 2015/02/03, HDFFV-9040)
-
-
- C++ API
- -------
- - New Wrappers for C Functions H5P[s/g]et_libver_bounds
-
- Wrappers were added to class H5::FileAccPropList for the
- C Functions H5Pget_libver_bounds and H5Pset_libver_bounds.
-
- (BMR, 2015/04/06, Part of HDFFV-9167)
-
- - New Wrappers to Get the Object Header's Version
-
- The following wrappers are added to class H5::CommonFG
- Returns the object header version of an object in a file or group,
- given the object's name.
-
- unsigned childObjVersion(const char* objname) const;
- unsigned childObjVersion(const H5std_string& objname) const;
-
- (BMR, 2015/04/06)
-
- - New DataType Constructor
-
- Added a DataType constructor that takes a PredType object, and this
- constructor will invoke H5Tcopy to generate another datatype id
- from a predefined datatype.
-
- (BMR, 2015/04/06)
-
-
-Support for New Platforms, Languages, and Compilers
-===================================================
- - Support for Linux 3.10.0-123.20.1.el7 added (LK - 2015/04/01)
- - Support for Mac OS X Yosemite 10.10 added (AKC - 2015/03/04, HDFFV-9007)
- - Support for AIX 6.1 added and AIX 5.3 is retired. (AKC - 2015/01/09)
-
-Bug Fixes since HDF5-1.8.14
-===========================
-
- Configuration
- -------------
- - Make uninstall generated "test: argument expected".
- The error is due to $EXAMPLETOPDIR is used without setting a value first.
-
- Fixed by assign it with the proper value.
-
- (AKC - 2015/04/29, HDFFV-9298)
-
- - Windows Installer Incorrect Display of PATH Environment Variable
-
- In the Windows installer, the dialog box where the user can elect to
- add the product's bin path to the %PATH% environment variable displayed
- an incorrect path. This path was missing the C:\Program Files part
- and used the POSIX file separator '/' before the bin (<path>/bin,
- instead of <path>\bin).
-
- The dialog box text was changed to simply say that the product's bin
- path would be added instead of explicitly displaying the path.
- This is in line with most installers. The reason for not fixing the
- displayed path instead is that it is difficult to pass the correct
- path from CPack to the NSIS installer for display.
-
- Note that this was never a code issue - it was just a display
- problem. The installer always did the right thing when updating the
- environment variable.
-
- (DER - 2014/11/14, HDFFV-9016)
-
- Library
- -------
- - Incorrect Usage of List in CMake COMPILE_DEFINITIONS set_property
-
- The CMake command set_property with COMPILE_DEFINITIONS property
- needs a quoted semi-colon separated list of values. CMake will
- transform the list to a series of -D{value} for the compile.
-
- (ADB - 2014/12/09, HDFV-9041)
-
- - Fixed Compile Errors on Windows w/ Visual Studio and CMake When
- UNICODE is Defined
-
- The HDF5 Library could not be built on Windows with Visual Studio when
- UNICODE was defined. This was due to the incorrect use of the TEXT()
- macro and some Win32 API functions that take TCHAR parameters. The faulty
- code was a part of the filter plugin functionality. This was a
- compile-time error that only affected users who build HDF5 from source
- and define UNICODE, usually when HDF5 is being built as a part of a
- larger product. There were no run-time effects.
-
- These errors caused no problems when UNICODE was not defined. HDF5 is
- normally not built with UNICODE defined and the binaries were
- unaffected.
-
- The fix was to remove the TEXT() macro and explicitly use the
- 'A' form of the Win32 API calls, which expect char strings instead of
- wchar_t strings.
-
- Note that HDF5 currently does not support Unicode file paths on Windows.
-
- (DER - 2015/02/22, HDFFV-8927)
-
- - Addition of Error Tracing Functionality to Several C API Calls
-
- A bug in a text processing script caused API calls that return a
- pointer to not receive error tracing macros/functionality.
-
- The bug has been corrected and error tracing functionality has been
- added to the affected API calls. These functions will now correctly
- print trace information when library errors are encountered.
-
- (DER - 2015/02/26, HDFFV-9141)
-
- - H5Rdereference Now Checks for HADDR_UNDEF or Uninitialized References
-
- When passed HADDR_UNDEF or uninitialized references, the previous
- behavior of H5Rdereference was to continue to process the reference
- as a valid address.
-
- H5Rdereference was changed to return immediately (with an error
- message) if the references are HADDR_UNDEF or uninitialized.
-
- (MSB - 2015/3/10, HDFFV-7959)
-
- - Fixed Bugs in H5Sextent_copy
-
- H5Sextent_copy would not free the previous extent, resulting in a memory
- leak. Also, H5Sextent_copy would not update the number of elements
- selected if the selection was "all", causing various problems. These
- issues have been fixed.
-
- (NAF - 2015/04/02)
-
-
- Parallel Library
- ----------------
- - Fixed a Potential Memory Error
-
- Fixed a potential memory error when performing parallel I/O on a
- dataset with a single chunk, and at least one process has nothing
- to do.
-
- (NAF - 2015/02/16)
-
- - Parallel Test Problem Fixed
-
- Fixed problem with parallel tests where they failed beyond a
- certain number of ranks. All tests should work for any arbitrary
- number of ranks.
-
- (MSC - 2014/11/06, HDFFV-1027,8962,8963)
-
- - MPE Support
-
- Enabling MPE was causing HDF5 build to fail. Support for it was
- dropped at some point in time.
-
- Fixed problem with enabling MPE. Users should use the community
- maintained MPE on github (http://git.mpich.org/mpe.git/).
-
- (MSC - 2015/02/20, HDFFV-9135)
-
- Performance
- -------------
- - None
-
- Tools
- -----
- - h5repack crashed on enumerated 8-bit type.
-
- Previous version 1.8.14 introduced an error that caused the reading
- of enumerated 8-bit type nested in compound type to fail.
-
- Fixed library code responsible for reading the particular type.
- (AKC - 2015.03/31, HDFFV-8667)
-
- - h52gif crashed non-8bit images.
-
- h52gif crashed if instructed to convert images other than 8bit images.
-
- h52gif could handle only 8bit images. Added code to detect non-8bit
- images and flag them as failure. Update tool document page to reflect
- the limit.
- (AKC - 2015/03/31, HDFFV-8957)
-
- - perform/benchpar.c retired.
-
- benchpar.c has not been built for a long time and its original purpose
- is not needed any more.
- (AKC - 2014/12/19, HDFFV-8156)
-
- - Source perform/ directory moved to tools/perform.
- The perform directory is moved to tools/perform for easier maintenance.
- (AKC - 2014/12/17, HDFFV-9046)
-
- Fortran API
- ------------
- - Fortran Fails with --enable-fortran2003 and Intel 15.x Compilers
-
- Added BIND(C) to the offending APIs.
-
- The Fortran Library (--enable-fortran2003) now works using Intel 15.x
- without the need for any additional compilers flags.
-
- (MSB - 2015/1/26, HDFFV-9049)
-
- - h5tenum_insert_f Does Not Work with Default 8 Byte Integers
- (xlf compiler)
-
- In the Fortran 90 API, 'value' is no longer cast into the C int type.
- Therefore, if h5tenum_insert_f is passed an 8 byte integer (via -i8)
- then 'value' is written as the same type as the default Fortran
- integer type (which can be 8 bytes).
-
- A new Fortran 2003 API was added which is more in line with the C
- API and users are strongly encouraged to use the Fortran 2003 API
- instead of the Fortran 90 API.
-
- SUBROUTINE h5tenum_insert_f(type_id, name, value, hdferr)
- INTEGER(HID_T) , INTENT(IN) :: type_id
- CHARACTER(LEN=*), INTENT(IN) :: name
- TYPE(C_PTR) , INTENT(IN) :: value
- INTEGER, INTENT(OUT) :: hdferr
-
- (MSB - 2015/2/19, HDFFV-8908)
-
- - Some Fortran APIs Never Returned the Error State
-
- Some Fortran APIs never returned the error state: they
- would always return a positive number. The APIs include
- the following:
-
- h5fget_file_image_f
- h5lget_name_by_idx_f
- h5oget_comment_by_name_f
-
- They were corrected to return a negative number as described in
- the Reference Manual if an error occurred.
-
- (MSB - 2015/3/19, HDF5-239)
-
- - Fixed h5pget_class_f
-
- h5pget_class_f never correlated the class identifier to the property
- list class name as indicated in the HDF5 Reference Manual; it instead
- returned a property list class identifier as an INTEGER. The INTEGER
- needed to be of type INTEGER(HID_T) to be correct.
-
- The h5pget_class_f API was changed to return an INTEGER(HID_T)
- property list class identifier instead of an INTEGER. This mimics the
- intended behavior of the C API.
-
- (MSB - 2015/3/16, HDFFV5-9162)
-
- C++ API
- ------
- - Combined Two H5File::getObjCount Overloaded Methods
-
- The following two methods
-
- ssize_t getObjCount(unsigned types) const;
- ssize_t getObjCount() const;
-
- were combined into one:
-
- ssize_t getObjCount(unsigned types = H5F_OBJ_ALL) const;
-
- (BMR - 2015/04/06)
-
- - Many Warnings Were Removed
-
- Many warnings such as conversion, unused variables, missing base
- class initialization, and initializing base classes in wrong order
- were removed.
-
- (BMR, 2015/04/06)
-
- - Functionality Deprecation
-
- The following two constructors of classes AbstractDs, IdComponent,
- H5Location, and H5Object are no longer appropriate after the data member
- "id" had been moved from IdComponent to the sub-classes in previous
- releases.
-
- <Classname>(const hid_t h5_id);
- <Classname>(const <Classname>& original);
-
- The copy constructors were no-op and removed in 1.8.15. The other
- constructors will be removed from 1.10 release, and then from 1.8.17
- if their removal does not cause any problems.
-
- (BMR, 2015-04-06)
-
-
- High-Level APIs:
- ------
- - Suppress Warnings from Flex/Bison-generated Code
-
- Warning suppression #pragmas, etc. have been added to H5LTparse.c and
- H5LTanalyze.c. We have no control over this code since it's created by
- a generator.
-
- (DER - 2015/03/08 - HDFFV-9149)
-
- - Changed hdf5_hl.h to Include the HDF5 Main Library "hdf5.h"
-
- User's no longer need to include both hdf5_hl.h and hdf5.h
-
- (MSB - 2015/2/14, HDFFV-8685)
-
-
- - H5PTcreate_fl Does Not Convert to Memory Datatype
-
- H5PTcreate_fl now converts to the table's native memory datatype
- to fix the problem of handling BE and LE packet tables.
-
- (MSB - 2015/2/26 - HDFFV-9042)
-
- - Fix for H5LT Attribute Functions
-
- H5LT attribute functions fail to create attributes whose name
- is a substring of an existing attribute.
-
- H5LT attribute functions can now create attributes whose name
- is a substring of an existing attribute.
-
- (MSB - 2015/2/24, HDFFV-9132)
-
-
- Fortran High-Level APIs:
- ------------------------
-
- - Internal Library Fix for Missing Argument Declaration
-
- In Interface block for h5tbmake_table_c, "max_char_size_field_names"
- is listed as an input, but in the argument definitions it is
- "INTEGER :: max_char_size". This caused no known problems with the
- Fortran HL API.
-
- Fixed missing argument definition.
-
- (MSB - 2015/2/18, HDFFV-8559)
-
-
- Testing
- -------
- - None
-
-
-Supported Platforms
-===================
-The following platforms are supported and have been tested for this release.
-They are built with the configure process unless specified otherwise.
-
- AIX 6.1 xlc/xlc_r 10.1.0.5
- (NASA G-ADA) xlC/xlC_r 10.1.0.5
- xlf90/xlf90_r 12.1.0.6
-
- Linux 2.6.18-308.13.1.el5PAE GNU C (gcc), Fortran (gfortran), C++ (g++)
- #1 SMP i686 i686 i386 compilers for 32-bit applications;
- (jam) Version 4.1.2 20080704 (Red Hat 4.1.2-55)
- Version 4.8.4, 4.9.2
- PGI C, Fortran, C++ Compilers for 32-bit
- applications;
- Version 14.10-0
- Intel(R) C, C++, Fortran Compiler for 32-bit
- applications;
- Version 15.0.1.133 (Build 20141023)
-
- Linux 2.6.18-371.6.1.el5 GNU C (gcc), Fortran (gfortran), C++ (g++)
- #1 SMP x86_64 GNU/Linux compilers for 64-bit applications;
- (koala) Version 4.1.2 20080704 (Red Hat 4.1.2-55)
- Version 4.8.4, 4.9.2
- Intel(R) C, C++, Fortran Compilers for
- applications running on Intel(R) 64;
- Version 15.0.1.133 Build 20141023
-
- Linux 2.6.32-431.11.2.el6 GNU C (gcc), Fortran (gfortran), C++ (g++)
- #1 SMP x86_64 GNU/Linux compilers:
- (platypus) Version 4.4.7 20120313
- Version 4.8.2, Version 4.9.2
- PGI C, Fortran, C++ for 64-bit target on
- x86-64;
- Version 14.10-0
- Intel(R) C (icc), C++ (icpc), Fortran (icc)
- compilers:
- Version 15.0.1.133 Build 20141023
-
- Linux 3.10.0-123.20.1.el7 GNU C (gcc), Fortran (gfortran), C++ (g++)
- #1 SMP x86_64 GNU/Linux compilers:
- (moohan) Version 4.8.2 20140120 (Red Hat 4.8.2-16)
- Intel(R) C Intel(R) 64 Compiler XE for
- applications running on Intel(R) 64,
- Version 15.0.1.133 Build 20141023
-
- Linux 2.6.32-431.29.2.el6.ppc64 gcc (GCC) 4.4.7 20120313 (Red Hat 4.4.7-4)
- #1 SMP ppc64 GNU/Linux g++ (GCC) 4.4.7 20120313 (Red Hat 4.4.7-4)
- (ostrich) GNU Fortran (GCC) 4.4.7 20120313 (Red Hat 4.4.7-4)
- IBM XL C/C++ V13.1
- IBM XL Fortran V15.1
-
- SunOS 5.11 32- and 64-bit Sun C 5.12 SunOS_sparc
- (emu) Sun Fortran 95 8.6 SunOS_sparc
- Sun C++ 5.12 SunOS_sparc
-
- Windows 7 Visual Studio 2008 (cmake)
- Visual Studio 2010 w/ Intel Fortran 14 (cmake)
- Visual Studio 2012 w/ Intel Fortran 15 (cmake)
- Visual Studio 2013 w/ Intel Fortran 15 (cmake)
- Cygwin(CYGWIN_NT-6.1 1.7.34(0.285/5/3) gcc(4.9.2) compiler and gfortran)
- (cmake and autotools)
-
- Windows 7 x64 Visual Studio 2008 (cmake)
- Visual Studio 2010 w/ Intel Fortran 14 (cmake)
- Visual Studio 2012 w/ Intel Fortran 15 (cmake)
- Visual Studio 2013 w/ Intel Fortran 15 (cmake)
-
- Windows 8.1 Visual Studio 2012 w/ Intel Fortran 15 (cmake)
- Visual Studio 2013 w/ Intel Fortran 15 (cmake)
-
- Windows 8.1 x64 Visual Studio 2012 w/ Intel Fortran 15 (cmake)
- Visual Studio 2013 w/ Intel Fortran 15 (cmake)
-
- Mac OS X Mt. Lion 10.8.5 Apple clang/clang++ version 5.1 from Xcode 5.1
- 64-bit gfortran GNU Fortran (GCC) 4.8.2
- (swallow/kite) Intel icc/icpc/ifort version 14.0.2
-
- Mac OS X Mavericks 10.9.5 Apple clang/clang++ version 6.0 from Xcode 6.1.1
- 64-bit gfortran GNU Fortran (GCC) 4.8.2
- (wren/quail) Intel icc/icpc/ifort version 14.0.2
-
- Mac OS X Yosemite 10.10.2 Apple clang/clang++ version 6.0 from Xcode 6.1.1
- 64-bit gfortran GNU Fortran (GCC) 4.9.2
- (osx1010dev/osx1010test) Intel icc/icpc/ifort version 15.0.1
-
-
-Tested Configuration Features Summary
-=====================================
-
- In the tables below
- y = tested
- n = not tested in this release
- C = Cluster
- W = Workstation
- x = not working in this release
- dna = does not apply
- ( ) = footnote appears below second table
- <blank> = testing incomplete on this feature or platform
-
-Platform C F90/ F90 C++ zlib SZIP
- parallel F2003 parallel
-SunOS 5.11 32-bit n y/y n y y y
-SunOS 5.11 64-bit n y/y n y y y
-Windows 7 y y/y n y y y
-Windows 7 x64 y y/y n y y y
-Windows 7 Cygwin n y/y n y y n
-Windows 8.1 n y/y n y y y
-Windows 8.1 x64 n y/y n y y y
-Mac OS X Mountain Lion 10.8.5 64-bit n y/y n y y y
-Mac OS X Mavericks 10.9.5 64-bit n y/y n y y y
-Mac OS X Yosemeti 10.10.2 64-bit n y/y n y y y
-AIX 6.1 32- and 64-bit n y/n n y y y
-CentOS 5.9 Linux 2.6.18-308 i686 GNU y y/y y y y y
-CentOS 5.9 Linux 2.6.18-308 i686 Intel n y/y n y y y
-CentOS 5.9 Linux 2.6.18-308 i686 PGI n y/y n y y y
-CentOS 5.9 Linux 2.6.18 x86_64 GNU n y/y n y y y
-CentOS 5.9 Linux 2.6.18 x86_64 Intel n y/y n y y y
-CentOS 6.4 Linux 2.6.32 x86_64 GNU y y/y y y y y
-CentOS 6.4 Linux 2.6.32 x86_64 Intel n y/y n y y y
-CentOS 6.4 Linux 2.6.32 x86_64 PGI n y/y n y y y
-CentOS 7.0 Linux 3.10.0 x86_64 GNU y y/y y y y y
-CentOS 7.0 Linux 3.10.0 x86_64 Intel n y/y n y y y
-Linux 2.6.32-431.11.2.el6.ppc64 n y/n n y y y
-
-Platform Shared Shared Shared Thread-
- C libs F90 libs C++ libs safe
-SunOS 5.11 32-bit y y y y
-SunOS 5.11 64-bit y y y y
-Windows 7 y y y y
-Windows 7 x64 y y y y
-Windows 7 Cygwin n n n y
-Windows 8.1 y y y y
-Windows 8.1 x64 y y y y
-Mac OS X Mountain Lion 10.8.5 64-bit y n y y
-Mac OS X Mavericks 10.9.5 64-bit y n y y
-Mac OS X Yosemeti 10.10.2 64-bit y n y y
-AIX 6.1 32- and 64-bit y n n y
-CentOS 5.9 Linux 2.6.18-308 i686 GNU y y y y
-CentOS 5.9 Linux 2.6.18-308 i686 Intel y y y n
-CentOS 5.9 Linux 2.6.18-308 i686 PGI y y y n
-CentOS 5.9 Linux 2.6.18 x86_64 GNU y y y y
-CentOS 5.9 Linux 2.6.18 x86_64 Intel y y y n
-CentOS 6.4 Linux 2.6.32 x86_64 GNU y y y n
-CentOS 6.4 Linux 2.6.32 x86_64 Intel y y y n
-CentOS 6.4 Linux 2.6.32 x86_64 PGI y y y n
-CentOS 7.0 Linux 3.10.0 x86_64 GNU y y y n
-CentOS 7.0 Linux 3.10.0 x86_64 Intel y y y n
-Linux 2.6.32-431.11.2.el6.ppc64 y y y n
-
-Compiler versions for each platform are listed in the preceding
-"Supported Platforms" table.
-
-
-More Tested Platforms
-=====================
-The following platforms are not supported but have been tested for this release.
-
- Linux 2.6.18-308.13.1.el5PAE MPICH mpich 3.1.3 compiled with
- #1 SMP i686 i686 i386 gcc 4.9.2 and gfortran 4.9.2
- (jam) g95 (GCC 4.0.3 (g95 0.94!)
-
- Linux 2.6.18-431.11.2.el6 MPICH mpich 3.1.3 compiled with
- #1 SMP x86_64 GNU/Linux gcc 4.9.2 and gfortran 4.9.2
- (platypus) g95 (GCC 4.0.3 (g95 0.94!)
-
- FreeBSD 8.2-STABLE i386 gcc 4.5.4 [FreeBSD] 20110526
- (loyalty) gcc 4.6.1 20110527
- g++ 4.6.1 20110527
- gfortran 4.6.1 20110527
-
- FreeBSD 8.2-STABLE amd64 gcc 4.5.4 [FreeBSD] 20110526
- (freedom) gcc 4.6.1 20110527
- g++ 4.6.1 20110527
- gfortran 4.6.1 20110527
-
- Debian7.5.0 3.2.0-4-amd64 #1 SMP Debian 3.2.51-1 x86_64 GNU/Linux
- gcc (Debian 4.7.2-5) 4.7.2
- GNU Fortran (Debian 4.7.2-5) 4.7.2
- (cmake and autotools)
-
- Fedora20 3.15.3-200.fc20.x86_64 #1 SMP x86_64 x86_64 x86_64 GNU/Linux
- gcc (GCC) 4.8.3 20140624 (Red Hat 4.8.3-1)
- GNU Fortran (GCC) 4.8.3 20140624 (Red Hat 4.8.3-1)
- (cmake and autotools)
-
- SUSE 13.1 3.11.10-17-desktop #1 SMP PREEMPT x86_64 x86_64 x86_64 GNU/Linux
- gcc (SUSE Linux) 4.8.1
- GNU Fortran (SUSE Linux) 4.8.1
- (cmake and autotools)
-
- Ubuntu 14.04 3.13.0-35-generic #62-Ubuntu SMP x86_64 GNU/Linux
- gcc (Ubuntu/Linaro 4.9.1-0ubuntu1) 4.9.1
- GNU Fortran (Ubuntu/Linaro 4.9.1-0ubuntu1) 4.9.1
- (cmake and autotools)
-
- hopper.nersc.gov PrgEnv-gnu/5.2.40
- gcc (GCC) 4.9.2 20141030 (Cray Inc.)
- GNU Fortran (GCC) 4.9.2 20141030 (Cray Inc.)
- g++ (GCC) 4.9.2 20141030 (Cray Inc.)
-
-
-Known Problems
-==============
-* On Windows platforms in debug configurations, the VFD flush1 tests will fail
- with the split and multi VFD drivers. These tests will display a modal debug
- dialog which must be answered or wait for the test timeout to expire.
- (ADB - 2014/06/23 - HDFFV-8851)
-
-* CLANG compiler with the options -fcatch-undefined-behavior and -ftrapv
- catches some undefined behavior in the alignment algorithm of the macro DETECT_I
- in H5detect.c (Issue 8147). Since the algorithm is trying to detect the alignment
- of integers, ideally the flag -fcatch-undefined-behavior shouldn't to be used for
- H5detect.c. In the future, we can separate flags for H5detect.c from the rest of
- the library. (SLU - 2013/10/16)
-
-* Make provided by Solaris fails in "make check". Solaris users should use
- gmake to build and install the HDF5 software. (AKC - 2013/10/08 - HDFFV-8534)
-
-* The C++ and FORTRAN bindings are not currently working on FreeBSD with the
- native release 8.2 compilers (4.2.1), but are working with gcc 4.6 from the
- ports (and probably gcc releases after that).
- (QAK - 2012/10/19)
-
-* The following h5dump test case fails in BG/P machines (and potentially other
- machines that use a command script to launch executables):
-
- h5dump --no-compact-subset -d "AHFINDERDIRECT::ah_centroid_t[0] it=0 tl=0"
- tno-subset.h5
-
- This is due to the embedded spaces in the dataset name being interpreted
- by the command script launcher as meta-characters, thus passing three
- arguments to h5dump's -d flag. The command passes if run by hand, just
- not via the test script.
- (AKC - 2012/05/03)
-
-* The STDIO VFD does not work on some architectures, possibly due to 32/64
- bit or large file issues. The basic STDIO VFD test is known to fail on
- 64-bit SunOS 5.10 on SPARC when built with -m64 and 32-bit OS X/Darwin
- 10.7.0. The STDIO VFD test has been disabled while we investigate and
- a fix should appear in a future release.
- (DER - 2011/10/14 - HDFFV-8235)
-
-* h5diff can report inconsistent results when comparing datasets of enum type
- that contain invalid values. This is due to how enum types are handled in
- the library and will be addressed in a future release.
- (DER - 2011/10/14 - HDFFV-7527)
-
-* The links test can fail under the stdio VFD due to some issues with external
- links. This will be investigated and fixed in a future release.
- (DER - 2011/10/14 - HDFFV-7768)
-
-* After the shared library support was fixed for some bugs, it was discovered
- that "make prefix=XXX install" no longer works for shared libraries. It
- still works correctly for static libraries. Therefore, if you want to
- install the HDF5 shared libraries in a location such as /usr/local/hdf5,
- you need to specify the location via the --prefix option during configure
- time. E.g, ./configure --prefix=/usr/local/hdf5 ...
- (AKC - 2011/05/07 - HDFFV-7583)
-
-* The parallel test, t_shapesame, in testpar/, may run for a long time and may
- be terminated by the alarm signal. If that happens, one can increase the
- alarm seconds (default is 1200 seconds = 20 minutes) by setting the
- environment variable, $HDF5_ALARM_SECONDS, to a larger value such as 3600
- (60 minutes). Note that the t_shapesame test may fail in some systems
- (see the "While working on the 1.8.6 release..." problem below). If
- it does, it will waste more time if $HDF5_ALARM_SECONDS is set
- to a larger value.
- (AKC - 2011/05/07)
-
-* Shared Fortran libraries are not quite working on AIX. While they are
- generated when --enable-shared is specified, the fortran and hl/fortran
- tests fail. the issue. HL and C++ shared libraries should now be
- working as intended, however.
- (MAM - 2011/04/20)
-
-* While working on the 1.8.6 release of HDF5, a bug was discovered that can
- occur when reading from a dataset in parallel shortly after it has been
- written to collectively. The issue was exposed by a new test in the parallel
- HDF5 test suite, but had existed before that. We believe the problem lies with
- certain MPI implementations and/or file systems.
-
- We have provided a pure MPI test program, as well as a standalone HDF5
- program, that can be used to determine if this is an issue on your system.
- They should be run across multiple nodes with a varying number of processes.
- These programs can be found at:
- http://www.hdfgroup.org/ftp/HDF5/examples/known_problems/
- (NAF - 2011/01/19)
-
-* All the VFL drivers aren't backward compatible. In H5FDpublic.h, the
- structure H5FD_class_t changed in 1.8. There is new parameter added to
- get_eoa and set_eoa callback functions. A new callback function
- get_type_map was added in. The public function H5FDrealloc was taken
- out in 1.8. The problem only happens when users define their own driver
- for 1.6 and try to plug in 1.8 library. Because there's only one user
- complaining about it, we (Elena, Quincey, and I) decided to leave it as
- it is (see bug report #1279). Quincey will make a plan for 1.10.
- (SLU - 2010/02/02)
-
-* The --enable-static-exec configure flag will only statically link libraries
- if the static version of that library is present. If only the shared version
- of a library exists (i.e., most system libraries on Solaris, AIX, and Mac,
- for example, only have shared versions), the flag should still result in a
- successful compilation, but note that the installed executables will not be
- fully static. Thus, the only guarantee on these systems is that the
- executable is statically linked with just the HDF5 library.
- (MAM - 2009/11/04)
-
-* A dataset created or rewritten with a v1.6.3 library or after cannot be read
- with the v1.6.2 library or before when the Fletcher32 EDC filter is enabled.
- There was a bug in the calculation of the Fletcher32 checksum in the
- library before v1.6.3; the checksum value was not consistent between big-
- endian and little-endian systems. This bug was fixed in Release 1.6.3.
- However, after fixing the bug, the checksum value was no longer the same as
- before on little-endian system. Library releases after 1.6.4 can still read
- datasets created or rewritten with an HDF5 library of v1.6.2 or before.
- (SLU - 2005/06/30)
-
-
-%%%%1.8.14%%%%
-
-
-HDF5 version 1.8.14 released on 2014-11-12
-================================================================================
-
-INTRODUCTION
-============
-
-This document describes the differences between HDF5-1.8.13 and
-HDF5-1.8.14, and contains information on the platforms tested and
-known problems in HDF5-1.8.14.
-
-All new and modified APIs are listed in the "HDF5 Software Changes
-from Release to Release" document along with details about previous
-releases at:
-
- http://www.hdfgroup.org/HDF5/doc/ADGuide/Changes.html
-
-Links to the HDF5 1.8.14 source code, documentation, and additional materials
-can be found on the HDF5 web page at:
-
- http://www.hdfgroup.org/products/hdf5/
-
-The HDF5 1.8.14 release can be obtained from:
-
- http://www.hdfgroup.org/HDF5/release/obtain5.html
-
-User documentation for 1.8.14 can be accessed directly at this location:
-
- http://www.hdfgroup.org/HDF5/doc/
-
-If you have any questions or comments, please send them to the HDF Help Desk:
-
- help@hdfgroup.org
-
-
-CONTENTS
-========
-
-- New Features
-- Support for New Platforms, Languages, and Compilers
-- Bug Fixes since HDF5-1.8.13
-- Supported Platforms
-- Supported Configuration Features Summary
-- More Tested Platforms
-- Known Problems
-
-
-New Features
-============
-
- Configuration
- -------------
- - bin/cmakehdf5 configures, builds and installs C, C++, Fortran and High
- level API's. (It used to build the C API only).
- (AKC 2014/10/17 HDFFV-8932).
-
- Library
- -------
- - None
-
- Parallel Library
- ----------------
- - Chunk Fill Writes Changed to Collective
-
- Slow performance in chunk fill writes. Chunk fills
- in the past were written independently by rank 0 one block
- at a time.
-
- Optimized the chunk fill write algorithm so that all
- chunk fill values will be written collectively in a single MPI-IO
- call. This should show a great performance improvement when
- creating chunked datasets in parallel when the chunk dimensions
- are fairly small.
-
- (MSC - 2014/08/22, HDFFV-8878)
-
- Tools
- -----
- - None
-
- High-level APIs
- ---------------
- - None
-
- Fortran API
- -----------
- - None
-
- C++ API
- -------
- - Initialization of Object IDs
-
- The data member "id" in classes that represent HDF5 objects were
- initialized to 0, which caused problem for some users.
-
- Replaced 0 with H5I_INVALID_HID to initialize these "id"s. For the
- PropList class, H5P_DEFAULT is used instead of H5I_INVALID_HID.
-
- (BMR - 2014/09/30, HDFFV-4259)
-
-
-
-Support for New Platforms, Languages, and Compilers
-===================================================
- - None
-
-Bug Fixes since HDF5-1.8.13
-===========================
-
- Configuration
- -------------
- - CMake and SVN URLs
-
- The SVN URLs will be different when the HDF Group domain name changes.
-
- Removed the SVN URL references in the cacheinit.cmake and release_docs files.
-
- (ADB - 2014/10/27, HDFFV-8953)
-
- - CMake Packaging
-
- A Fortran module was not generated if the compiler was not F2003
- compliant.
-
- Removed the module name from the package list of Fortran modules because
- that module was never generated. This was only an issue for Fortran
- compilers that are not F2003 compatible.
-
- (ADB - 2014/10/16, HDFFV-8932)
-
- - Shared Library Interface Version Number (soname)
-
- In order to increase the maintainability of HDF5, an architectural
- change was made which required the renaming of several public symbols in
- H5Ppublic.h.
-
- The shared library interface version number ("soname") has been increased
- on account of these changes. For a full list of the changed symbols, see
- the interface compatibility report, which is available as a link off of
- the 'HDF5 Software Changes from Release to Release' document:
-
- http://www.hdfgroup.org/HDF5/doc/ADGuide/Changes.html
-
- (AKC - 2014/10/03, HDFFV-8937)
-
- - Configure Settings for Mac OSX Need Defaults for PROD_XXX, DEBUG_XXX,
- and PROFILE_XXX
-
- The configure setting files for Mac OSX (config/apple) did not
- have the default settings of PROD_XXX, DEBUG_XXX, PROFILE_XXX.
-
- Added the default settings. Mac platforms now builds library with
- "-O3" optimization when the default clang compiler is used.
-
- (AKC - 2014/10/01, HDFFV-8933)
-
- - CMake ConfigureChecks
-
- Two include files were missing from two C tests.
-
- Propagated the configure test changes to H5_LDOUBLE_TO_INTEGER_WORKS_TEST
- and H5_ULLONG_TO_LDOUBLE_PRECISION_TEST to ConfigureChecks.cmake (added
- stdlib.h and string.h in the HDFTests.c file).
-
- (ADB - 2014/09/02 HDFFV-8845)
-
- - CMake Parallel Test Missing
-
- The source file was removed in the previous release but the parallel
- test t_posix_compliant was not.
-
- Removed the t_posix_compliant parallel test from the library.
-
- (ADB - 2014/8/14 HDFFV-8880)
-
- - Autotools Reconfigure. Bison. Flex.
-
- The Bison and Flex files were out of date.
-
- Bison was upgraded to 2.7, and Flex was upgraded to 2.5.37. The
- bin/reconfigure script now will execute Bison and Flex and update
- the hl/src files.
-
- (ADB - 2014/06/16 HDFFV-8709)
-
- - Autotools Reconfigure. m4.
-
- The m4 macro processor was out of date.
-
- Reconfigured Autotools with m4 upgraded to 1.4.17.
-
- (ADB - 2014/06/12 HDFFV-8743)
-
- - Autotools: Modified configure to add an entry at the beginning of AM_LDFLAGS
- for the hdf5 install directory. Without this entry the relink commands
- invoked by "make install" to create libraries dependent on libhdf5.so added
- a dependency on the first libhdf5.so found in any directory in AM_LDFLAGS
- regardless of its version. (LRK - 2014/10/17 HDFFV-8944)
-
- - Changed Autotools Build Behavior. Fortran High-level Library.
-
- The Fortran high-level (HL) library did not compile if the default
- size of a REAL is DOUBLE PRECISION; the build would fail during
- compilation.
-
- Configure now checks to see if REAL is DOUBLE PRECISION, Fortran is
- enabled, and HL library is enabled. If this is true, then configure
- will stop with an error message.
-
- (MSB - 2014/8/11, HDFFV-8883/HDFFV-889)
-
-
-
- Library
- -------
- - Fixed Identifier Management Code
-
- Opening an object returns an identifier; closing the object should
- free up the identifier. A problem was found where the identifiers
- were not being freed up correctly.
-
- Fixed the problem so that identifiers that have been used can be
- used again after their object has been closed.
-
- (QAK - 2014/10/16, HDFFV-8930)
-
- - Removal of DllMain() from Static Windows Builds
-
- A DllMain() function was added in HDF5 1.8.13 in order to handle
- win32 thread cleanup. The preprocessor #ifdefs around the DllMain
- function allowed it to be compiled when the static library is built,
- which is incorrect behavior that can cause linkage problems in
- clients.
-
- The fix was to change the preprocessor #ifdefs to exclude compiling
- DllMain() in static builds. Our DllMain function is now only
- compiled when the shared, thread-safe library is built on Windows.
-
- (DER - 2014/06/13, HDFFV-8837)
-
- - Enforce Constraint on page_size Parameter in H5Pset_core_write_tracking()
-
- The reference manual states that the page_size parameter cannot be
- zero.
-
- This change checks the page_size parameter to see it is zero and
- returns an error code if it is.
-
- (DER - 2014/08/11, HDFFV-8891)
-
- - H5Ldelete_by_idx() fails on non-existent group name.
- (MSC - 2014/07/31, HDFFV-8888)
-
- - H5Ldelete_by_idx() Seg Fault on Non-existent Group Name
-
- If a non-existent group name was used by H5Ldelete_by_idx(), a
- segmentation fault would result.
-
- Bug was fixed.
-
- (MSC - 2014/07/31, HDFFV-8888)
-
- - Bug in Test When Building Parallel HDF5 on PVFS2
-
- There was a bug in a test when building Parallel HDF5 on PVFS2.
-
- The build now uses MPI_File_get_size() instead of stat().
-
- (MSC - 2014/07/14, HDFFV-8856)
-
- - MPI-IO Driver Tried to Allocate Space for Zero-length Dataset
-
- MPI-IO driver tried to allocate space for zero-length dataset
- and asserts.
-
- Fixed driver and added a regression test.
-
- (MSC - 2014/07/03, HDFFV-8761)
-
-
- Parallel Library
- ----------------
- - None
-
- Performance
- -------------
- - None
-
- Tools
- -----
- - None
-
- Fortran API
- -------
- - SIZEOF Replaced by C_SIZEOF and STORAGE_SIZE.
-
- The intrinsic function SIZEOF is non-standard and should be replaced with a
- standard intrinsic function.
-
- If the F2008 intrinsic C_SIZEOF and STORAGE_SIZE are available, then they will
- be used instead of the non-standard SIZEOF intrinsic, even when the SIZEOF
- function is available.
-
- (MSB - 2014/6/16, HDFFV-8653)
-
- - Non-functional API: h5pget_fill_value_f
-
- The Fortran wrapper h5pget_fill_value_f was calling the wrong C API.
-
- The correct C API, H5Pget_fill_value, is now called by the Fortran
- wrapper.
-
- (MSB - 2014/9/25, HDFFV-8879)
-
- - Interoperability with C HDF5: H5Literate and h5literate_f
-
- h5literate_f assumes the return value for the callback function to
- be of type int (or int_f in C). However, in the C wrapper the return
- value of H5Literate is type herr_t, and this could cause
- interoperability issues.
-
- The callback function should be declared INTEGER(C_INT) for
- portability. The tests were updated accordingly.
-
- (MSB - 2014/9/26, HDFFV-8909)
-
- - Interoperability with C HDF5: Constant INTEGER Parameters with the
- H5FD Interface
-
- Wrong type cast of constant Fortran INTEGER parameters was used.
-
- The following parameter constant types were changed from INTEGER to
- INTEGER(HID_T) to match the C types: H5FD_CORE, H5FD_FAMILY, H5FD_LOG,
- H5FD_MPIO, H5FD_MULTI, H5FD_SEC2, and H5FD_STDIO.
-
- Other internal 'int' types where changed to 'hid_t'; these are
- transparent to the user.
-
- (MSB - 2014/7/18, HDFFV-8748)
-
- C++ API
- ------
- - Memory Leaks
-
- There were several potential memory leaks in the library due to
- dynamically allocated strings not being freed when failure occurs.
-
- Applied user's patches to remove these potential memory leaks.
-
- (BMR - 2014/09/30, HDFFV-8928)
-
- - Disallow H5F_ACC_CREAT
-
- H5F_ACC_CREAT was included in the C++ API but the C library does not
- allow it at this time.
-
- Removed this flag from the functions in H5File class.
-
- (BMR - 2014/09/29, HDFFV-8852)
-
- - Missing Flags in Documentation: H5F_ACC_RDONLY and H5F_ACC_RDWR
-
- The H5F_ACC_RDONLY and H5F_ACC_RDWR flags were missing from the
- documentation of the H5File constructors.
-
- These two flags are now included in the documentation for opening
- files.
-
- (BMR - 2014/09/29, HDFFV-8852)
-
- High-level APIs:
- ------
- - Seg Faults in H5TBread_field_name and H5TBread_field_name_f
-
- When H5TBread_field_name or H5TBread_field_name_f were used to read a
- field and if the name of the field was wrong, a segmentation fault
- would result.
-
- Both C and Fortran APIs were fixed so they no longer seg fault if
- the name of the field is wrong, and both APIs return a negative
- value if the name of the field is wrong.
-
- (MSB - 2014/09/29, HDFFV-8912)
-
- - Possible Buffer Overflow in High-level (HL) APIs
-
- Multiple HL APIs (H5DSis_scale is one example) had issues:
- (1) The datatype from the file was re-used as the memory datatype,
- and
- (2) No effort was made to ensure that strings were actually
- null-terminated.
-
- All of the HL routines now check for NULL pointers, for null-terminated
- strings, and to see if string buffers are short enough not to overflow
- the buffer. The minimum length of the buffers is now used in strncmp
- to avoid overflow.
-
- (MSB - 2014/9/29, HDFFV-8670)
-
- - Behavior Change of H5LTdtype_to_text
-
- If a user buffer was passed in to H5LTdtype_to_text along with the
- length, then the function would not truncate at the end of the
- buffer, but would exceed the end of the user buffer.
-
- H5LTdtype_to_text was changed to truncate the string if the user
- buffer is too small.
-
- (MSB - 2014/9/29, HDFFV-8855)
-
- Fortran High-level APIs:
- ------
- - See entry for HDFFV-8912 above.
-
- Testing
- -------
- - A subtest in parallel h5diff (ph5diff) testing was bypassed for the
- local Linux 32 machine due to unknown issue in the previous version of
- Mpich. The failure no long exists in the current Mpich. Therefore the
- bypass is removed. (AKC - 2014/11/03 HDFFV-8954)
-
- - Fixed incorrect exit code values (was -1) in testframe which is commonly
- used by several test programs. (AKC - 2014/07/22 HDFFV-8881)
-
- - Fixed Incorrect Exit Code Values in Testframe
- The testframe which is commonly used by several test programs
- had some incorrect exit code values. Fixed the incorrect exit code
- values. (AKC - 2014/07/22, HDFFV-8881)
-
-Supported Platforms
-===================
-The following platforms are supported and have been tested for this release.
-They are built with the configure process unless specified otherwise.
-
- AIX 5.3 xlc 10.1.0.5
- (NASA G-ADA) xlC 10.1.0.5
- xlf90 12.1.0.6
-
- Linux 2.6.18-308.13.1.el5PAE GNU C (gcc), Fortran (gfortran), C++ (g++)
- #1 SMP i686 i686 i386 compilers for 32-bit applications;
- (jam) Version 4.1.2 20080704 (Red Hat 4.1.2-54)
- Version 4.8.2
- PGI C, Fortran, C++ Compilers for 32-bit
- applications;
- Version 13.7-0
- Intel(R) C, C++, Fortran Compiler for 32-bit
- applications;
- Version 14.0.2 (Build 20140120)
-
- Linux 2.6.18-371.6.1.el5 GNU C (gcc), Fortran (gfortran), C++ (g++)
- #1 SMP x86_64 GNU/Linux compilers for 64-bit applications;
- (koala) Version 4.1.2 20080704 (Red Hat 4.1.2-54)
- Version 4.8.2
- Intel(R) C, C++, Fortran Compilers for
- applications running on Intel(R) 64;
- Version 14.0.2 (Build 20140120)
-
- Linux 2.6.32-431.11.2.el6 GNU C (gcc), Fortran (gfortran), C++ (g++)
- #1 SMP x86_64 GNU/Linux compilers:
- (platypus) Version 4.4.7 20120313
- Version 4.8.2
- PGI C, Fortran, C++ for 64-bit target on
- x86-64;
- Version 13.7-0
- Intel(R) C (icc), C++ (icpc), Fortran (icc)
- compilers:
- Version 14.0.2 (Build 20140120)
-
- Linux 2.6.32-431.29.2.el6.ppc64 gcc (GCC) 4.4.7 20120313 (Red Hat 4.4.7-4)
- #1 SMP ppc64 GNU/Linux g++ (GCC) 4.4.7 20120313 (Red Hat 4.4.7-4)
- (ostrich) GNU Fortran (GCC) 4.4.7 20120313 (Red Hat 4.4.7-4)
- IBM XL C/C++ V13.1
- IBM XL Fortran V15.1
-
- SunOS 5.11 32- and 64-bit Sun C 5.12 SunOS_sparc
- (emu) Sun Fortran 95 8.6 SunOS_sparc
- Sun C++ 5.12 SunOS_sparc
-
- Windows 7 Visual Studio 2008 (cmake)
- Visual Studio 2010 w/ Intel Fortran 14 (cmake)
- Visual Studio 2012 w/ Intel Fortran 14 (cmake)
- Visual Studio 2013 w/ Intel Fortran 14 (cmake)
- Cygwin(CYGWIN_NT-6.1 1.7.32(0.274/5/3) gcc(4.8.3) compiler and gfortran)
- (cmake and autotools)
-
- Windows 7 x64 Visual Studio 2008 (cmake)
- Visual Studio 2010 w/ Intel Fortran 14 (cmake)
- Visual Studio 2012 w/ Intel Fortran 14 (cmake)
- Visual Studio 2013 w/ Intel Fortran 14 (cmake)
-
- Windows 8.1 Visual Studio 2012 w/ Intel Fortran 14 (cmake)
- Visual Studio 2013 w/ Intel Fortran 14 (cmake)
-
- Windows 8.1 x64 Visual Studio 2012 w/ Intel Fortran 14 (cmake)
- Visual Studio 2013 w/ Intel Fortran 14 (cmake)
-
- Mac OS X Lion 10.7.5 Apple clang/clang++ version 3.0 from Xcode 4.6.1
- 64-bit gfortran GNU Fortran (GCC) 4.8.2
- (duck) Intel icc/icpc/ifort version 13.0.3
-
- Mac OS X Mt. Lion 10.8.5 Apple clang/clang++ version 5.1 from Xcode 5.1
- 64-bit gfortran GNU Fortran (GCC) 4.8.2
- (swallow/kite) Intel icc/icpc/ifort version 14.0.2
-
- Mac OS X Mavericks 10.9.5 Apple clang/clang++ version 6.0 from Xcode 6.0.1
- 64-bit gfortran GNU Fortran (GCC) 4.8.2
- (wren) Intel icc/icpc/ifort version 14.0.2
-
-
-Tested Configuration Features Summary
-=====================================
-
- In the tables below
- y = tested
- n = not tested in this release
- C = Cluster
- W = Workstation
- x = not working in this release
- dna = does not apply
- ( ) = footnote appears below second table
- <blank> = testing incomplete on this feature or platform
-
-Platform C F90/ F90 C++ zlib SZIP
- parallel F2003 parallel
-Solaris2.11 32-bit n y/y n y y y
-Solaris2.11 64-bit n y/y n y y y
-Windows 7 y y/y n y y y
-Windows 7 x64 y y/y n y y y
-Windows 7 Cygwin n y/y n y y n
-Windows 8.1 n y/y n y y y
-Windows 8.1 x64 n y/y n y y y
-Mac OS X Lion 10.7.5 64-bit n y/y n y y y
-Mac OS X Mountain Lion 10.8.5 64-bit n y/y n y y y
-Mac OS X Mavericks 10.9.5 64-bit n y/y n y y ?
-AIX 5.3 32- and 64-bit n y/n n y y y
-CentOS 5.9 Linux 2.6.18-308 i686 GNU y y/y y y y y
-CentOS 5.9 Linux 2.6.18-308 i686 Intel n y/y n y y y
-CentOS 5.9 Linux 2.6.18-308 i686 PGI n y/y n y y y
-CentOS 5.9 Linux 2.6.18 x86_64 GNU n y/y n y y y
-CentOS 5.9 Linux 2.6.18 x86_64 Intel n y/y n y y y
-CentOS 6.4 Linux 2.6.32 x86_64 GNU y y/y y y y y
-CentOS 6.4 Linux 2.6.32 x86_64 Intel n y/y n y y y
-CentOS 6.4 Linux 2.6.32 x86_64 PGI n y/y n y y y
-Linux 2.6.32-431.11.2.el6.ppc64 n y/n n y y y
-
-Platform Shared Shared Shared Thread-
- C libs F90 libs C++ libs safe
-Solaris2.11 32-bit y y y y
-Solaris2.11 64-bit y y y y
-Windows 7 y y y y
-Windows 7 x64 y y y y
-Windows 7 Cygwin n n n y
-Windows 8.1 y y y y
-Windows 8.1 x64 y y y y
-Mac OS X Lion 10.7.5 64-bit y n y y
-Mac OS X Mountain Lion 10.8.5 64-bit y n y y
-Mac OS X Mavericks 10.9.5 64-bit y n y y
-AIX 5.3 32- and 64-bit y n n y
-CentOS 5.9 Linux 2.6.18-308 i686 GNU y y y y
-CentOS 5.9 Linux 2.6.18-308 i686 Intel y y y n
-CentOS 5.9 Linux 2.6.18-308 i686 PGI y y y n
-CentOS 5.9 Linux 2.6.18 x86_64 GNU y y y y
-CentOS 5.9 Linux 2.6.18 x86_64 Intel y y y n
-CentOS 6.4 Linux 2.6.32 x86_64 GNU y y y n
-CentOS 6.4 Linux 2.6.32 x86_64 Intel y y y n
-CentOS 6.4 Linux 2.6.32 x86_64 PGI y y y n
-Linux 2.6.32-431.11.2.el6.ppc64 y y y n
-
-Compiler versions for each platform are listed in the preceding
-"Supported Platforms" table.
-
-
-More Tested Platforms
-=====================
-The following platforms are not supported but have been tested for this release.
-
- Linux 2.6.18-308.13.1.el5PAE MPICH mpich 3.1.2 compiled with
- #1 SMP i686 i686 i386 gcc 4.9.1 and gfortran 4.9.1
- (jam) g95 (GCC 4.0.3 (g95 0.94!)
-
- Linux 2.6.18-431.11.2.el6 MPICH mpich 3.1.2 compiled with
- #1 SMP x86_64 GNU/Linux gcc 4.9.1 and gfortran 4.9.1
- (platypus) g95 (GCC 4.0.3 (g95 0.94!)
-
- FreeBSD 8.2-STABLE i386 gcc 4.5.4 [FreeBSD] 20110526
- (loyalty) gcc 4.6.1 20110527
- g++ 4.6.1 20110527
- gfortran 4.6.1 20110527
-
- FreeBSD 8.2-STABLE amd64 gcc 4.5.4 [FreeBSD] 20110526
- (freedom) gcc 4.6.1 20110527
- g++ 4.6.1 20110527
- gfortran 4.6.1 20110527
-
- Debian7.5.0 3.2.0-4-amd64 #1 SMP Debian 3.2.51-1 x86_64 GNU/Linux
- gcc (Debian 4.7.2-5) 4.7.2
- GNU Fortran (Debian 4.7.2-5) 4.7.2
- (cmake and autotools)
-
- Fedora20 3.15.3-200.fc20.x86_64 #1 SMP x86_64 x86_64 x86_64 GNU/Linux
- gcc (GCC) 4.8.3 20140624 (Red Hat 4.8.3-1)
- GNU Fortran (GCC) 4.8.3 20140624 (Red Hat 4.8.3-1)
- (cmake and autotools)
-
- SUSE 13.1 3.11.10-17-desktop #1 SMP PREEMPT x86_64 x86_64 x86_64 GNU/Linux
- gcc (SUSE Linux) 4.8.1
- GNU Fortran (SUSE Linux) 4.8.1
- (cmake and autotools)
-
- Ubuntu 14.04 3.13.0-35-generic #62-Ubuntu SMP x86_64 GNU/Linux
- gcc (Ubuntu/Linaro 4.9.1-0ubuntu1) 4.9.1
- GNU Fortran (Ubuntu/Linaro 4.9.1-0ubuntu1) 4.9.1
- (cmake and autotools)
-
- Cray Linux Environment (CLE) PrgEnv-pgi/4.2.34
- hopper.nersc.gov pgcc 13.6-0 64-bit target on x86-64 Linux -tp istanbul
- pgf90 13.6-0 64-bit target on x86-64 Linux -tp istanbul
- pgCC 13.6-0 64-bit target on x86-64 Linux -tp istanbul
-
-
-Known Problems
-==============
-* On cygwin platforms the feature to load dynamic filter libraries only looks
- for libraries with the a so extension. Support for cygwin cygxxx.dll libraries
- is planned for the next release.
- (ADB - 2014/11/04 - HDFFV-8736)
-
-* On windows platforms in debug configurations, the VFD flush1 tests will fail
- with the split and multi VFD drivers. These tests will display a modal debug
- dialog which must be answered or wait for the test timeout to expire.
- The flush1 and flush2 tests will be skipped under debug for this release.
- (ADB - 2014/06/23 - HDFFV-8851)
-
-* CLANG compiler with the options -fcatch-undefined-behavior and -ftrapv
- catches some undefined behavior in the alignment algorithm of the macro DETECT_I
- in H5detect.c (Issue 8147). Since the algorithm is trying to detect the alignment
- of integers, ideally the flag -fcatch-undefined-behavior shouldn't to be used for
- H5detect.c. In the future, we can separate flags for H5detect.c from the rest of
- the library. (SLU - 2013/10/16)
-
-* Make provided by Solaris fails in "make check". Solaris users should use
- gmake to build and install the HDF5 software. (AKC - 2013/10/08 - HDFFV-8534)
-
-* The h5dump and h5diff utilities occasionally produce different output
- between Linux and Windows systems. This is caused by lower-level library
- routines that fail to write fill values to the user's buffer when reading
- unallocated chunks from datasets that have a fill value set to
- H5D_FILL_VALUE_DEFAULT. Due to platform differences the return of
- spurious data values has only been encountered on Windows 32-bit systems.
- (Issue HDFFV-8247; JP - 2013/03/27)
-
-* The C++ and FORTRAN bindings are not currently working on FreeBSD with the
- native release 8.2 compilers (4.2.1), but are working with gcc 4.6 from the
- ports (and probably gcc releases after that).
- (QAK - 2012/10/19)
-
-* The STDIO VFD does not work on some architectures, possibly due to 32/64
- bit or large file issues. The basic STDIO VFD test is known to fail on
- 64-bit SunOS 5.10 on SPARC when built with -m64 and 32-bit OS X/Darwin
- 10.7.0. The STDIO VFD test has been disabled while we investigate and
- a fix should appear in a future release.
- (DER - 2011/10/14 - HDFFV-8235)
-
-* h5diff can report inconsistent results when comparing datasets of enum type
- that contain invalid values. This is due to how enum types are handled in
- the library and will be addressed in a future release.
- (DER - 2011/10/14 - HDFFV-7527)
-
-* The links test can fail under the stdio VFD due to some issues with external
- links. This will be investigated and fixed in a future release.
- (DER - 2011/10/14 - HDFFV-7768)
-
-* After the shared library support was fixed for some bugs, it was discovered
- that "make prefix=XXX install" no longer works for shared libraries. It
- still works correctly for static libraries. Therefore, if you want to
- install the HDF5 shared libraries in a location such as /usr/local/hdf5,
- you need to specify the location via the --prefix option during configure
- time. E.g, ./configure --prefix=/usr/local/hdf5 ...
- (AKC - 2011/05/07 - HDFFV-7583)
-
-* The parallel test, t_shapesame, in testpar/, may run for a long time and may
- be terminated by the alarm signal. If that happens, one can increase the
- alarm seconds (default is 1200 seconds = 20 minutes) by setting the
- environment variable, $HDF5_ALARM_SECONDS, to a larger value such as 3600
- (60 minutes). Note that the t_shapesame test may fail in some systems
- (see the "While working on the 1.8.6 release..." problem below). If
- it does, it will waste more time if $HDF5_ALARM_SECONDS is set
- to a larger value.
- (AKC - 2011/05/07)
-
-* Shared Fortran libraries are not quite working on AIX. While they are
- generated when --enable-shared is specified, the fortran and hl/fortran
- tests fail. We are looking into the issue. HL and C++ shared libraries
- should now be working as intended, however.
- (MAM - 2011/04/20)
-
-* The --with-mpe configure option does not work with Mpich2.
- (AKC - 2011/03/10)
-
-* While working on the 1.8.6 release of HDF5, a bug was discovered that can
- occur when reading from a dataset in parallel shortly after it has been
- written to collectively. The issue was exposed by a new test in the parallel
- HDF5 test suite, but had existed before that. We believe the problem lies with
- certain MPI implementations and/or file systems.
-
- We have provided a pure MPI test program, as well as a standalone HDF5
- program, that can be used to determine if this is an issue on your system.
- They should be run across multiple nodes with a varying number of processes.
- These programs can be found at:
- http://www.hdfgroup.org/ftp/HDF5/examples/known_problems/
- (NAF - 2011/01/19)
-
-* All the VFL drivers aren't backward compatible. In H5FDpublic.h, the
- structure H5FD_class_t changed in 1.8. There is new parameter added to
- get_eoa and set_eoa callback functions. A new callback function
- get_type_map was added in. The public function H5FDrealloc was taken
- out in 1.8. The problem only happens when users define their own driver
- for 1.6 and try to plug in 1.8 library. Because there's only one user
- complaining about it, we (Elena, Quincey, and I) decided to leave it as
- it is (see bug report #1279). Quincey will make a plan for 1.10.
- (SLU - 2010/02/02)
-
-* The --enable-static-exec configure flag will only statically link libraries
- if the static version of that library is present. If only the shared version
- of a library exists (i.e., most system libraries on Solaris, AIX, and Mac,
- for example, only have shared versions), the flag should still result in a
- successful compilation, but note that the installed executables will not be
- fully static. Thus, the only guarantee on these systems is that the
- executable is statically linked with just the HDF5 library.
- (MAM - 2009/11/04)
-
-* Parallel tests failed with 16 processes with data inconsistency at testphdf5
- / dataset_readAll. Parallel tests also failed with 32 and 64 processes with
- collective abort of all ranks at t_posix_compliant / allwrite_allread_blocks
- with MPI IO.
- (CMC - 2009/04/28)
-
-* A dataset created or rewritten with a v1.6.3 library or after cannot be read
- with the v1.6.2 library or before when the Fletcher32 EDC filter is enabled.
- There was a bug in the calculation of the Fletcher32 checksum in the
- library before v1.6.3; the checksum value was not consistent between big-
- endian and little-endian systems. This bug was fixed in Release 1.6.3.
- However, after fixing the bug, the checksum value was no longer the same as
- before on little-endian system. Library releases after 1.6.4 can still read
- datasets created or rewritten with an HDF5 library of v1.6.2 or before.
- (SLU - 2005/06/30)
-
-
-%%%%1.8.13%%%%
-
-
-HDF5 version 1.8.13 released on 2014-05-05
-================================================================================
-
-INTRODUCTION
-============
-
-This document describes the differences between HDF5-1.8.12 and
-HDF5-1.8.13, and contains information on the platforms tested and
-known problems in HDF5-1.8.13.
-For more details, see the files HISTORY-1_0-1_8_0_rc3.txt
-and HISTORY-1_8.txt in the release_docs/ directory of the HDF5 source.
-
-Links to the HDF5 1.8.13 source code, documentation, and additional materials
-can be found on the HDF5 web page at:
-
- http://www.hdfgroup.org/products/hdf5/
-
-The HDF5 1.8.13 release can be obtained from:
-
- http://www.hdfgroup.org/HDF5/release/obtain5.html
-
-User documentation for 1.8.13 can be accessed directly at this location:
-
- http://www.hdfgroup.org/HDF5/doc/
-
-New features in the HDF5-1.8.x release series, including brief general
-descriptions of some new and modified APIs, are described in the "What's New
-in 1.8.0?" document:
-
- http://www.hdfgroup.org/HDF5/doc/ADGuide/WhatsNew180.html
-
-All new and modified APIs are listed in detail in the "HDF5 Software Changes
-from Release to Release" document, in the section "Release 1.8.13 (current
-release) versus Release 1.8.12":
-
- http://www.hdfgroup.org/HDF5/doc/ADGuide/Changes.html
-
-If you have any questions or comments, please send them to the HDF Help Desk:
-
- help@hdfgroup.org
-
-
-CONTENTS
-========
-
-- New Features
-- Support for New Platforms, Languages, and Compilers
-- Bug Fixes since HDF5-1.8.12
-- Supported Platforms
-- Supported Configuration Features Summary
-- More Tested Platforms
-- Known Problems
-
-
-New Features
-============
-
- Configuration
- -------------
- - Autotools: Automake updated to 1.14.1 (ADB - 2014/04/08)
-
- - CMake: Moved minimum CMake version to 2.8.11 which enables better library
- include processing. (ADB - 2014/03/26)
-
- - When configuring a thread-safe HDF5 Library it is no longer necessary
- to specify --enable-threadsafe with --with-pthreads if the Pthreads
- library is in a standard location. (DER - 2014/04/11 HDFFV-8693)
-
- Library
- -------
- - Added an H5free_memory API call. This should be used to free memory
- that has been allocated by HDF5 API calls. H5Tget_member_name and
- H5Pget_class_name are two examples. The main motivation for this call
- is Windows, where it is common for application code and the HDF5 Library
- to be using different C run-time libraries (CRT). Using the new call
- ensures that the same CRT handles both the allocation and free. This
- new function can also be useful in any case where the library uses a
- different memory manager than the application, such as when a debug
- memory manager is in use or when the HDF5 Library is wrapped for use
- in a managed language like Python or Java. Fixes HDFFV-7710, 8519,
- and 8851. (DER - 2014/04/11)
-
- - The Core VFD (aka Memory VFD) can now be configured to track dirty
- regions in the file and only write out the changed regions on
- flush/close. Additionally, a "page aggregation" size can be set that
- will aggregate small writes into larger writes. For example, setting
- a 1 MiB page aggregation size will logically partition the the
- in-memory file into 1 MiB pages that will be written out in their
- entirety if even a single byte is dirtied. The feature is controlled
- via the new H5Pset/get_core_write_tracking() API call. A new
- "core_paged" target has been added to the check-vfd target in
- test/Makefile.am that exercises the feature over all HDF5 VFD-aware
- tests. (DER - 2014/04/12)
-
- Parallel Library
- ----------------
- - Removed MPI-POSIX VFD, as it wasn't helping anyone and was just
- generating support questions. Application developers performing
- parallel I/O should always use the MPI-IO VFD.
- (QAK - 2014/03/28 HDFFV-8659)
-
- - Improved parallel I/O support to allow collective I/O on point
- selections. (QAK - 2014/03/15)
-
- Tools
- -----
- - None
-
- High-Level APIs
- ---------------
- - None
-
- Fortran API
- -----------
- - Wrappers h5pset_file_image_f and h5pget_file_image_f were added to the
- library. (MSB - 2014/1/2014)
-
- C++ API
- -------
- - The following new features are added:
- + Wrappers to class H5Object to get an object's name (HDFFV-8548).
- ssize_t getObjName(char *obj_name, size_t buf_size = 0)
- ssize_t getObjName(H5std_string& obj_name, size_t len = 0)
- H5std_string getObjName()
- + Wrappers to class H5CommonFG to get a child object's type from a
- group or file (HDFFV-8367).
- H5O_type_t childObjType(const H5std_string& objname)
- H5O_type_t childObjType(const char* objname)
- H5O_type_t childObjType(hsize_t index,
- H5_index_t index_type=H5_INDEX_NAME,
- H5_iter_order_t order=H5_ITER_INC, const char* objname=".")
- + Wrappers to class DSetMemXferPropList for setting/getting a transform
- property list (HDFFV-7907).
- DSetMemXferPropList(const char* expression);
- void setDataTransform(const char* expression)
- void setDataTransform(const H5std_string& expression)
- ssize_t getDataTransform(char* exp, size_t buf_size=0)
- H5std_string getDataTransform()
- + Wrapper to CompType for setting size to compound datatype (HDFFV-8642).
- void setSize(size_t size)
- + Overloaded functions to provide prototypes that declare constant
- arguments const (HDFFV-3384). These include:
- DataSet::fillMemBuf
- DataSet::getVlenBufSize
- DataSpace::extentCopy
- DataType::commit
- FileAccPropList::setSplit
- H5File::getVFDHandle
- + Additional overload to class H5Location to get a comment as a char*
- ssize_t getComment(const char* name, size_t buf_size, char* comment)
- + Additional overloads to class Attribute to get an attribute's name for
- convenience:
- ssize_t getName(char* attr_name, size_t buf_size=0)
- ssize_t getName(H5std_string& attr_name, size_t buf_size=0)
- (BMR, 2014/04/15)
- + A static wrapper to Exception for printing the error stack without an
- instance of Exception
- static void printErrorStack(FILE* stream = stderr,
- hid_t err_stack = H5E_DEFAULT);
- (BMR, 2014/04/25)
-
-
-Support for New Platforms, Languages, and Compilers
-===================================================
- Mac OS X 10.6 Snow Leopard is not supported by Apple any more. In view of
- the added support of Mac OS X 10.9, Mac OS X 10.6 is retired from HDF5
- supported platforms. (AKC - 2014/03/14 HDFFV-8704)
-
- Mac OS X 10.9 Mavericks is supported. (AKC - 2014/03/04 HDFFV-8694)
-
-
-Bug Fixes since HDF5-1.8.12
-===========================
-
- Configuration
- -------------
- - CMake: When CMake commands are executed individually on the command line
- and the external filters are being built, the CMAKE_BUILD_TYPE define
- must be set to the same value as the configuration
- (-DCMAKE_BUILD_TYPE:STRING=Release if using -C Release). This is needed
- by the the szip and zlib filter build commands. (ADB - HDFFV-8695)
-
- - CMake: Removed use of the XLATE_UTILITY program.
- (ADB - 2014/03/28 HDFFV-8640)
-
- - CMake: Added missing quotes in setting the CMAKE_EXE_LINKER_FLAGS for the
- MPI option. (ADB - 2014/02/27 HDFFV-8674)
-
- - CMake: Configuration of the HDF5 C++ or Fortran libraries with the
- thread-safety feature.
-
- C++ and/or Fortran + thread-safe is enforced as a non-supported
- configuration. This matches the autotools. (DER - 2014/04/11)
-
- - CMake: Configuration of static HDF5 C library with the thread-safety
- feature.
-
- Static + thread-safe + Win32 threads is not a supported configuration
- due to the inability to automatically clean up thread-local storage.
- This is expected to be fixed in a future release. In the meantime, a
- work-around that uses internal functionality may allow the combination
- to be used without resource leaks. Contact the help desk for more
- information. (DER - 2014/04/11)
-
- - Autotools: Several changes were done to configure and installcheck.
-
- An export of LD_LIBRARY_PATH=<szip library location> was
- removed from configure; make installcheck was revised to run
- scripts installed in share/hdf5_examples to use the installed h5cc, etc.
- to compile and run example source files also installed there.
-
- Make installcheck will now fail when a shared szip or other external lib
- file cannot be found in the same manner that executables compiled and
- linked with h5cc will fail to run when those lib files cannot be found
- after install. Make installcheck should pass after setting
- LD_LIBRARY_PATH to the szip location. (LRK - 2014/04/16)
-
- Library
- -------
- - A Gnu Make directive (.NOTPARALLEL) is added to fortran/test/Makefile.
-
- AIX native make does not support this directive and would fail if
- parallel make (e.g. make -j4) is used to build the library. AIX users
- either do not use parallel make or install Gnu Make to build the library.
- (AKC 2014/04/08 HDFFV-8738)
-
- - H5R.c: H5Rget_name gave an assertion failure if the "name" parameter
- was NULL.
-
- Fixed H5Rget_name to return the size of the buffer needed to read a
- name of the referenced object in this case. The size doesn't include
- the NULL terminator. H5Rget_name returns negative on failure.
- (MSB - 2014/01/22 HDFFV-8620)
-
- - H5Z.c: H5Zfilter_avail didn't check if a filter was available as a
- dynamically loaded filter. The error manifested itself in the h5repack
- tool when removing user-defined dynamically loaded filter.
-
- Added a code to find the filter among the dynamically loaded filters
- after the function fails to find it among the registered filters.
- (ADB - 2014/03/03 HDFFV-8629)
-
- - Memory leak: a memory leak was observed in conjunction to the
- H5TS_errstk_key_g thread-local variable allocated in the H5E_get_stack
- function in H5E.c.
-
- The shared HDF5 thread-safe library now no longer leaks thread-local
- storage resources on Windows with Win32 threads. Currently, there is
- no solution for this problem when HDF5 is statically built. We
- disabled the build of the static HDF5 thread-safe library with
- Win32 threads. (DER - 2014/04/11 HDFFV-8518)
-
- - H5Dio.c: Improved handling of NULL pointers to H5Dread/H5Dwrite
- calls. Credit to Jason Newton (nevion@gmail.com) for the original patch.
-
- H5Dwrite/read failed when a NULL pointer was passed for a data buffer
- and 0 elements were selected. Fixed. (QAK - 2014/04/16 HDFFV-8705)
-
- - Deprecated API (1_6 API): Improved handling of closing the library and
- re-accessing it with a deprecated routine.
-
- When a program used a deprecated API (for example, H5Gcreate1),
- closed the library, and reopened it again to access a group, dataset,
- datatype, dataspace, attribute, or property list, HDF5 failed to
- provide an identifier for the object. Fixed.
- (NAF, QAK - 2014/04/16 HDFFV-8232)
-
- Parallel Library
- ----------------
- - Fixed a missing H5F_Provisional module in HDF5mpio.f90
- (MSB - 2014/2/7 HDFFV-8651)
-
- Performance
- -------------
- - None
-
- Tools
- -----
- - The h5diff tool would report that a datafile compared with an exact
- copy of the same datafile had differences. This was due to the issue
- below of reading un-written chunks. This problem is also fixed.
- (AKC - 2014/05/01 HDFFV-8637)
-
- - The h5dump and h5diff utilities occasionally produced different output
- between Linux and Windows systems. This has been fixed.
-
- This happened to datasets that used chunked storage, with default fill
- values, and some of the chunks had not been written.
- When the dataset was read, the library failed to write the default fill
- values to parts of the use buffer that were associated with the unwritten
- chunks. (JP - 2014/05/01 HDFFV-8247)
-
- - The compress option is retired from bin/release.
- (AKC - 2014/04/25 HDFFV-8755)
-
- - bin/release has a new option "zip" that produces a release zip file for
- the Windows platform. (AKC - 2014/04/24 HDFFV-8433)
-
- - h5diff: Several failures relating to handling of strings attributes
- are fixed.
-
- The tool crashed or gave an error message when one of the strings had
- fixed size type and another variable-length size type. h5diff now flags such
- strings as "not comparable". We plan to enhance the tool to handle
- strings of the different types in the future releases.
- (AKC - 2014/04/18 HDFFV-8625, 8639, 8745)
-
- - h5repack: h5repack would not remove user-defined filters.
- Fixed by modifying h5repack to check if the filter is registered or
- can be dynamically loaded. (ADB - 2014/03/03 HDFFV-8629)
-
- F90 API
- -------
- - H5D_CHUNK_CACHE_NSLOTS_DFLT_F and H5D_CHUNK_CACHE_NBYTES_DFLT_F were
- changed from the default KIND for INTEGER to INTEGER of KIND size_t.
- (MSB - 2014/3/31 HDFFV-8689)
-
- C++ API
- ------
- - Added throw() to all exception destructors. Credit to Jason Newton
- (nevion@gmail.com) for the patch. (BMR - 2014/4/15 HDFFV-8623)
- - Changed the default value for H5Location::getComment from 256 to 0
- to conform to C function and because it makes more sense.
- (BMR - 2014/4/15)
-
- High-Level APIs:
- ------
- - None
-
- Fortran High-Level APIs:
- ------
- - None
-
- Testing
- -------
- - testhdf5 now exits with EXIT_SUCCESS(0) if no errors, else
- EXIT_FAILURE(1). (AKC - 2014/01/27 HDFFV-8572)
-
- - The big test now pays attention to the HDF5_DRIVER environment variable.
- Previously, it would run all tests with the family, stdio, and sec2
- virtual file drivers (VFDs) for each VFD in the check-vfd make target,
- regardless of the variable setting. It now checks the variable and
- either runs the appropriate VFD-specific tests or skips as needed.
- This saves much testing time. Fixes HDFFV-8554. (DER - 2014/04/11)
-
-Supported Platforms
-===================
-The following platforms are supported and have been tested for this release.
-They are built with the configure process unless specified otherwise.
-
- AIX 5.3 xlc 10.1.0.5
- (NASA G-ADA) xlC 10.1.0.5
- xlf90 12.1.0.6
- gmake v3.82
-
- Linux 2.6.18-308.13.1.el5PAE GNU C (gcc), Fortran (gfortran), C++ (g++)
- #1 SMP i686 i686 i386 compilers for 32-bit applications;
- (jam) Version 4.1.2 20080704 (Red Hat 4.1.2-54)
- Version 4.8.2
- PGI C, Fortran, C++ Compilers for 32-bit
- applications;
- Version 13.7-0
- Intel(R) C, C++, Fortran Compiler for 32-bit
- applications;
- Version 14.0.2 (Build 20140120)
-
- Linux 2.6.18-371.6.1.el5 GNU C (gcc), Fortran (gfortran), C++ (g++)
- #1 SMP x86_64 GNU/Linux compilers for 64-bit applications;
- (koala) Version 4.1.2 20080704 (Red Hat 4.1.2-54)
- Version 4.8.2
- PGI C, Fortran, C++ for 64-bit target on
- x86-64;
- Version 13.7-0
- Intel(R) C, C++, Fortran Compilers for
- applications running on Intel(R) 64;
- Version 14.0.2 (Build 20140120)
-
- Linux 2.6.32-431.11.2.el6 GNU C (gcc), Fortran (gfortran), C++ (g++)
- #1 SMP x86_64 GNU/Linux compilers:
- (platypus) Version 4.4.7 20120313
- Version 4.8.2
- PGI C, Fortran, C++ for 64-bit target on
- x86-64;
- Version 13.7-0
- Intel(R) C (icc), C++ (icpc), Fortran (icc)
- compilers:
- Version 14.0.2 (Build 20140120)
-
- Linux 2.6.32-431.11.2.el6.ppc64 gcc (GCC) 4.4.7 20120313 (Red Hat 4.4.7-3)
- #1 SMP ppc64 GNU/Linux g++ (GCC) 4.4.7 20120313 (Red Hat 4.4.7-3)
- (ostrich) GNU Fortran (GCC) 4.4.7 20120313 (Red Hat 4.4.7-3)
- IBM XL C/C++ V11.1
- IBM XL Fortran V13.1
-
- SunOS 5.11 32- and 64-bit Sun C 5.12 SunOS_sparc
- (emu) Sun Fortran 95 8.6 SunOS_sparc
- Sun C++ 5.12 SunOS_sparc
-
- Windows 7 Visual Studio 2008 w/ Intel Fortran 14 (cmake)
- Visual Studio 2010 w/ Intel Fortran 14 (cmake)
- Visual Studio 2012 w/ Intel Fortran 14 (cmake)
- Cygwin(CYGWIN_NT-6.1 1.7.28(0.271/5/3) gcc(4.8.2) compiler and gfortran)
- (cmake and autotools)
-
- Windows 7 x64 Visual Studio 2008 w/ Intel Fortran 14 (cmake)
- Visual Studio 2010 w/ Intel Fortran 14 (cmake)
- Visual Studio 2012 w/ Intel Fortran 14 (cmake)
-
- Windows 8.1 Visual Studio 2012 w/ Intel Fortran 14 (cmake)
-
- Windows 8.1 x64 Visual Studio 2012 w/ Intel Fortran 14 (cmake)
-
- Mac OS X Lion 10.7.3 Apple clang/clang++ version 3.0 from Xcode 4.6.1
- 64-bit gfortran GNU Fortran (GCC) 4.6.2
- (duck) Intel icc/icpc/ifort version 13.0.3
-
- Mac OS X Mt. Lion 10.8.5 Apple clang/clang++ version 5.0 from Xcode 5.0.2
- 64-bit gfortran GNU Fortran (GCC) 4.8.2
- (swallow/kite) Intel icc/icpc/ifort version 14.0.2
-
- Mac OS X Mavericks 10.9.2 Apple clang/clang++ version 5.1 from Xcode 5.1
- 64-bit gfortran GNU Fortran (GCC) 4.8.2
- (wren/quail) Intel icc/icpc/ifort version 14.0.2
-
-
-Tested Configuration Features Summary
-=====================================
-
- In the tables below
- y = tested
- n = not tested in this release
- C = Cluster
- W = Workstation
- x = not working in this release
- dna = does not apply
- ( ) = footnote appears below second table
- <blank> = testing incomplete on this feature or platform
-
-Platform C F90/ F90 C++ zlib SZIP
- parallel F2003 parallel
-Solaris2.11 32-bit n y/y n y y y
-Solaris2.11 64-bit n y/y n y y y
-Windows 7 y y/y n y y y
-Windows 7 x64 y y/y n y y y
-Windows 7 Cygwin n y/y n y y y
-Windows 8.1 n y/y n y y y
-Windows 8.1 x64 n y/y n y y y
-Mac OS X Lion 10.7.3 64-bit n y/y n y y y
-Mac OS X Mountain Lion 10.8.1 64-bit n y/y n y y y
-Mac OS X Mavericks 10.9.1 64-bit n y/y n y y y
-AIX 5.3 32- and 64-bit n y/n n y y y
-CentOS 5.9 Linux 2.6.18-308 i686 GNU y y/y y y y y
-CentOS 5.9 Linux 2.6.18-308 i686 Intel n y/y n y y y
-CentOS 5.9 Linux 2.6.18-308 i686 PGI n y/y n y y y
-CentOS 5.9 Linux 2.6.18 x86_64 GNU n y/y n y y y
-CentOS 5.9 Linux 2.6.18 x86_64 Intel n y/y n y y y
-CentOS 6.4 Linux 2.6.32 x86_64 GNU y y/y y y y y
-CentOS 6.4 Linux 2.6.32 x86_64 Intel n y/y n y y y
-CentOS 6.4 Linux 2.6.32 x86_64 PGI n y/y n y y y
-Linux 2.6.32-431.11.2.el6.ppc64 n y/n n y y y
-OpenVMS IA64 V8.4 n y/n n y y n
-
-Platform Shared Shared Shared Thread-
- C libs F90 libs C++ libs safe
-Solaris2.11 32-bit y y y y
-Solaris2.11 64-bit y y y y
-Windows 7 y y y y
-Windows 7 x64 y y y y
-Windows 7 Cygwin n n n y
-Windows 8.1 y y y y
-Windows 8.1 x64 y y y y
-Mac OS X Lion 10.7.3 64-bit y n y y
-Mac OS X Mountain Lion 10.8.1 64-bit y n y y
-Mac OS X Mavericks 10.9.1 64-bit y n y y
-AIX 5.3 32- and 64-bit y n n y
-CentOS 5.9 Linux 2.6.18-308 i686 GNU y y y y
-CentOS 5.9 Linux 2.6.18-308 i686 Intel y y y n
-CentOS 5.9 Linux 2.6.18-308 i686 PGI y y y n
-CentOS 5.9 Linux 2.6.18 x86_64 GNU y y y y
-CentOS 5.9 Linux 2.6.18 x86_64 Intel y y y n
-CentOS 6.4 Linux 2.6.32 x86_64 GNU y y y n
-CentOS 6.4 Linux 2.6.32 x86_64 Intel y y y n
-CentOS 6.4 Linux 2.6.32 x86_64 PGI y y y n
-Linux 2.6.32-431.11.2.el6.ppc64 y y y n
-OpenVMS IA64 V8.4 n n n n
-
-Compiler versions for each platform are listed in the preceding
-"Supported Platforms" table.
-
-
-More Tested Platforms
-=====================
-The following platforms are not supported but have been tested for this release.
-
- Linux 2.6.18-308.13.1.el5PAE MPICH mpich 3.1 compiled with
- #1 SMP i686 i686 i386 gcc 4.8.2 and gfortran 4.8.2
- (jam) g95 (GCC 4.0.3 (g95 0.94!)
-
- Linux 2.6.18-431.11.2.el6 MPICH mpich 3.1 compiled with
- #1 SMP x86_64 GNU/Linux gcc 4.8.2 and gfortran 4.8.2
- (platypus) g95 (GCC 4.0.3 (g95 0.94!)
-
- FreeBSD 8.2-STABLE i386 gcc 4.5.4 [FreeBSD] 20110526
- (loyalty) gcc 4.6.1 20110527
- g++ 4.6.1 20110527
- gfortran 4.6.1 20110527
-
- FreeBSD 8.2-STABLE amd64 gcc 4.5.4 [FreeBSD] 20110526
- (freedom) gcc 4.6.1 20110527
- g++ 4.6.1 20110527
- gfortran 4.6.1 20110527
-
- Debian7.1.0 3.2.0-4-amd64 #1 SMP Debian 3.2.51-1 x86_64 GNU/Linux
- gcc (Debian 4.7.2-5) 4.7.2
- GNU Fortran (Debian 4.7.2-5) 4.7.2
- (cmake and autotools)
-
- Fedora20 3.11.10-301.fc20.x86_64 #1 SMP x86_64 x86_64 x86_64 GNU/Linux
- gcc (GCC) 4.8.2 20131212 (Red Hat 4.8.2-7)
- GNU Fortran (GCC) 4.8.2 20130603 (Red Hat 4.8.2-7)
- (cmake and autotools)
-
- SUSE 13.1 3.11.6-4-desktop #1 SMP PREEMPT x86_64 x86_64 x86_64 GNU/Linux
- gcc (SUSE Linux) 4.8.1
- GNU Fortran (SUSE Linux) 4.8.1
- (cmake and autotools)
-
- Ubuntu 13.10 3.11.0-13-generic #20-Ubuntu SMP x86_64 GNU/Linux
- gcc (Ubuntu/Linaro 4.8.1-10ubuntu8) 4.8.1
- GNU Fortran (Ubuntu/Linaro 4.8.1-10ubuntu8) 4.8.1
- (cmake and autotools)
-
- Cray Linux Environment (CLE) PrgEnv-pgi/4.0.46
- hopper.nersc.gov pgcc 12.5-0 64-bit target on x86-64 Linux -tp shanghai
- pgf90 12.5-0 64-bit target on x86-64 Linux -tp shanghai
- pgCC 12.5-0 64-bit target on x86-64 Linux -tp shanghai
-
-
-Known Problems
-==============
-* When reading or writing a dataset (H5Dread/H5Dwrite) with a large selection
- size (e.g., 2GB ~= 500 million of 4 bytes integers or floating point
- numbers), some I/O systems may not be able to process it correctly.
- We advise users to find out system limits before using large selections. If
- I/O size limits exist, application should use HDF5 partial I/O capabilities
- (e.g., H5Sselect_hyperslab(...)) to divide large requests into smaller sizes.
- In this case we also advise users not to use chunk storage sizes larger that
- 2GB since the HDF5 library performs I/O on the entire chunk. We will work
- on the HDF5 library to divide large data requests to smaller I/O requests.
- (AKC 2014/05/02 HDFFV-8479)
-
-* Due to an Intel compiler bug introduced in version 14.0.1, the HDF5 FORTRAN
- wrappers do not work with configure option --enable-fortran2003.
- However, the option --enable-fortran works with Intel 14.0.1. The compiler
- bug was fixed in Intel version 14.0.2 and resolved the issue.
- (MSB - 2014/4/15)
-
-* Due to a PGI compiler bug introduced in versions before 13.3 and versions
- after 14.2, the FORTRAN test 'Testing get file image' will fail.
- (MSB - 2014/4/15)
-
-* On CYGWIN, when building the library dynamically, testing will fail on
- dynamically loaded filters. The test process will build dynamic filter
- libraries with the *.dll.a extension, and the HDF5 Library will be looking
- for *.so libraries. Entered as issue HDFFV-8736. (ADB - 2014/04/14)
-
-* A Gnu Make directive (.NOTPARALLEL) is added to fortran/test/Makefile.
- AIX native make does not support this directive and would fail if
- parallel make (e.g. make -j4) is used to build the library. AIX users
- either do not use parallel make or install Gnu Make to build the library.
- (AKC 2014/04/08 HDFFV-8738)
-
-* CLANG compiler with the options -fcatch-undefined-behavior and -ftrapv
- catches some undefined behavior in the alignment algorithm of the macro
- DETECT_I in H5detect.c. Since the algorithm is trying to detect the alignment
- of integers, ideally the flag -fcatch-undefined-behavior should not to be
- used for H5detect.c. In the future, we can separate flags for H5detect.c
- from the rest of the library. (SLU - 2013/10/16 HDFFV-8147)
-
-* Make provided by Solaris fails in "make check". Solaris users should use
- gmake to build and install the HDF5 software. (AKC - 2013/10/08 - HDFFV-8534)
-
-* On OpenVMS, two soft conversion functions (H5T__conv_i_f and H5T__conv_f_i)
- have bugs. They convert data between floating-point numbers and integers.
- But the library's default is hard conversion. The user should avoid
- explicitly enabling soft conversion between floating-point numbers and
- integers. (Issue VMS-8; SLU - 2013/09/19)
-
-* On OpenVMS, ZLIB 1.2.8 library doesn't work properly. ZLIB 1.2.5 works
- fine. So please use ZLIB 1.2.5 to build HDF5 library. (Issue VMS-5;
- SLU 2013/09/19)
-
-* When building using the Cray compilers on Cray machines, HDF5
- configure mistakenly thinks the compiler is an intel compiler and
- sets the -std=c99 flag which breaks configure on Cray. To build HDF5
- properly on a Cray machine, please consult with the instructions in
- INSTALL_parallel for building on Hopper.
- (MSC - 2013/04/26 - HDFFV-8429)
-
-* The 5.9 C++ compiler on Sun failed to compile a C++ test ttypes.cpp. It
- complains with this message:
- "/home/hdf5/src/H5Vprivate.h", line 130: Error: __func__ is not defined.
-
- The reason is that __func__ is a predefined identifier in C99 standard. The
- HDF5 C library uses it in H5private.h. The test ttypes.cpp includes
- H5private.h (H5Tpkg.h<-H5Fprivate.h<-H5Vprivate.h<-H5private.h). Sun's 5.9
- C++ compiler doesn't support __func__, thus fails to compile the C++ test.
- But Sun's 5.11 C++ compiler does. To check whether your Sun C++ compiler
- knows this identifier, try to compile the following simple C++ program:
- #include<stdio.h>
-
- int main(void)
- {
- printf("%s\n", __func__);
- return 0;
- }
- (SLU - 2012/11/5)
-
-* The C++ and FORTRAN bindings are not currently working on FreeBSD with the
- native release 8.2 compilers (4.2.1), but are working with gcc 4.6 from the
- ports (and probably gcc releases after that).
- (QAK - 2012/10/19)
-
-* The following h5dump test case fails in BG/P machines (and potentially other
- machines that use a command script to launch executables):
-
- h5dump --no-compact-subset -d "AHFINDERDIRECT::ah_centroid_t[0] it=0 tl=0"
- tno-subset.h5
-
- This is due to the embedded spaces in the dataset name being interpreted
- by the command script launcher as meta-characters, thus passing three
- arguments to h5dump's -d flag. The command passes if run by hand, just
- not via the test script.
- (AKC - 2012/05/03)
-
-* On hopper, the build failed when RUNSERIAL and RUNPARALLEL are set
- to aprun -np X, because the H5lib_settings.c file was not generated
- properly. Not setting those environment variables works, because
- configure was able to automatically detect that it's a Cray system
- and used the proper launch commands when necessary.
- (MSC - 2012/04/18)
-
-* The data conversion test dt_arith.c fails in "long double" to integer
- conversion on Ubuntu 11.10 (3.0.0.13 kernel) with GCC 4.6.1 if the library
- is built with optimization -O3 or -O2. The older GCC (4.5) or newer kernel
- (3.2.2 on Fedora) doesn't have the problem. Users should lower the
- optimization level (-O1 or -O0) by defining CFLAGS in the command line of
- "configure" like:
-
- CFLAGS=-O1 ./configure
-
- This will overwrite the library's default optimization level.
- (SLU - 2012/02/07 - HDFFV-7829)
- This issue is no longer present on Ubuntu 12.10 (3.5.0 kernel) with
- gcc 4.7.2.
-
-* The STDIO VFD does not work on some architectures, possibly due to 32/64
- bit or large file issues. The basic STDIO VFD test is known to fail on
- 64-bit SunOS 5.10 on SPARC when built with -m64 and 32-bit OS X/Darwin
- 10.7.0. The STDIO VFD test has been disabled while we investigate and
- a fix should appear in a future release.
- (DER - 2011/10/14 - HDFFV-8235)
-
-* h5diff can report inconsistent results when comparing datasets of enum type
- that contain invalid values. This is due to how enum types are handled in
- the library and will be addressed in a future release.
- (DER - 2011/10/14 - HDFFV-7527)
-
-* The links test can fail under the stdio VFD due to some issues with external
- links. This will be investigated and fixed in a future release.
- (DER - 2011/10/14 - HDFFV-7768)
-
-* After the shared library support was fixed for some bugs, it was discovered
- that "make prefix=XXX install" no longer works for shared libraries. It
- still works correctly for static libraries. Therefore, if you want to
- install the HDF5 shared libraries in a location such as /usr/local/hdf5,
- you need to specify the location via the --prefix option during configure
- time. E.g, ./configure --prefix=/usr/local/hdf5 ...
- (AKC - 2011/05/07 - HDFFV-7583)
-
-* The parallel test, t_shapesame, in testpar/, may run for a long time and may
- be terminated by the alarm signal. If that happens, one can increase the
- alarm seconds (default is 1200 seconds = 20 minutes) by setting the
- environment variable, $HDF5_ALARM_SECONDS, to a larger value such as 3600
- (60 minutes). Note that the t_shapesame test may fail in some systems
- (see the "While working on the 1.8.6 release..." problem below). If
- it does, it will waste more time if $HDF5_ALARM_SECONDS is set
- to a larger value.
- (AKC - 2011/05/07)
-
-* The C++ and FORTRAN bindings are not currently working on FreeBSD.
- (QAK - 2011/04/26)
-
-* Shared Fortran libraries are not quite working on AIX. While they are
- generated when --enable-shared is specified, the fortran and hl/fortran
- tests fail. We are looking into the issue. HL and C++ shared libraries
- should now be working as intended, however.
- (MAM - 2011/04/20)
-
-* The --with-mpe configure option does not work with Mpich2.
- (AKC - 2011/03/10)
-
-* While working on the 1.8.6 release of HDF5, a bug was discovered that can
- occur when reading from a dataset in parallel shortly after it has been
- written to collectively. The issue was exposed by a new test in the parallel
- HDF5 test suite, but had existed before that. We believe the problem lies with
- certain MPI implementations and/or file systems.
-
- We have provided a pure MPI test program, as well as a standalone HDF5
- program, that can be used to determine if this is an issue on your system.
- They should be run across multiple nodes with a varying number of processes.
- These programs can be found at:
- http://www.hdfgroup.org/ftp/HDF5/examples/known_problems/
- (NAF - 2011/01/19)
-
-* All the VFL drivers aren't backward compatible. In H5FDpublic.h, the
- structure H5FD_class_t changed in 1.8. There is new parameter added to
- get_eoa and set_eoa callback functions. A new callback function
- get_type_map was added in. The public function H5FDrealloc was taken
- out in 1.8. The problem only happens when users define their own driver
- for 1.6 and try to plug in 1.8 library. Because there's only one user
- complaining about it, we (Elena, Quincey, and I) decided to leave it as
- it is (see bug report #1279). Quincey will make a plan for 1.10.
- (SLU - 2010/02/02)
-
-* The --enable-static-exec configure flag will only statically link libraries
- if the static version of that library is present. If only the shared version
- of a library exists (i.e., most system libraries on Solaris, AIX, and Mac,
- for example, only have shared versions), the flag should still result in a
- successful compilation, but note that the installed executables will not be
- fully static. Thus, the only guarantee on these systems is that the
- executable is statically linked with just the HDF5 library.
- (MAM - 2009/11/04)
-
-* Parallel tests failed with 16 processes with data inconsistency at testphdf5
- / dataset_readAll. Parallel tests also failed with 32 and 64 processes with
- collective abort of all ranks at t_posix_compliant / allwrite_allread_blocks
- with MPI IO.
- (CMC - 2009/04/28)
-
-* On an Intel 64 Linux cluster (RH 4, Linux 2.6.9) with Intel 10.0 compilers,
- use -mp -O1 compilation flags to build the libraries. A higher level of
- optimization causes failures in several HDF5 library tests.
-
-* A dataset created or rewritten with a v1.6.3 library or after cannot be read
- with the v1.6.2 library or before when the Fletcher32 EDC filter is enabled.
- There was a bug in the calculation of the Fletcher32 checksum in the
- library before v1.6.3; the checksum value was not consistent between big-
- endian and little-endian systems. This bug was fixed in Release 1.6.3.
- However, after fixing the bug, the checksum value was no longer the same as
- before on little-endian system. Library releases after 1.6.4 can still read
- datasets created or rewritten with an HDF5 library of v1.6.2 or before.
- (SLU - 2005/06/30)
-
-
-%%%%1.8.12%%%%
-
-
-HDF5 version 1.8.12 released on 2013-11-04
-================================================================================
-
-INTRODUCTION
-============
-
-This document describes the differences between HDF5-1.8.11 and
-HDF5-1.8.12, and contains information on the platforms tested and
-known problems in HDF5-1.8.12.
-For more details, see the files HISTORY-1_0-1_8_0_rc3.txt
-and HISTORY-1_8.txt in the release_docs/ directory of the HDF5 source.
-
-Links to the HDF5 1.8.12 source code, documentation, and additional materials
-can be found on the HDF5 web page at:
-
- http://www.hdfgroup.org/products/hdf5/
-
-The HDF5 1.8.12 release can be obtained from:
-
- http://www.hdfgroup.org/HDF5/release/obtain5.html
-
-User documentation for 1.8.12 can be accessed directly at this location:
-
- http://www.hdfgroup.org/HDF5/doc/
-
-New features in the HDF5-1.8.x release series, including brief general
-descriptions of some new and modified APIs, are described in the "What's New
-in 1.8.0?" document:
-
- http://www.hdfgroup.org/HDF5/doc/ADGuide/WhatsNew180.html
-
-All new and modified APIs are listed in detail in the "HDF5 Software Changes
-from Release to Release" document, in the section "Release 1.8.12 (current
-release) versus Release 1.8.11":
-
- http://www.hdfgroup.org/HDF5/doc/ADGuide/Changes.html
-
-If you have any questions or comments, please send them to the HDF Help Desk:
-
- help@hdfgroup.org
-
-
-CONTENTS
-========
-
-- New Features
-- Support for New Platforms, Languages, and Compilers
-- Bug Fixes since HDF5-1.8.11
-- Supported Platforms
-- Supported Configuration Features Summary
-- More Tested Platforms
-- Known Problems
-
-
-New Features
-============
-
- Configuration
- -------------
- - Added a configuration option to change the default plugin path.
- The configure option is --with-default-plugindir=location.
- The cmake option is -DH5_DEFAULT_PLUGINDIR:PATH=location.
- HDFFV-8513. (ADB 2013/09/04)
- - Renamed FFLAGS to FCFLAGS in configure. (ADB 2013/08/13)
- - CMake can now package a compressed examples file, the default for
- Windows binaries from HDF Group. (ADB - 2013/07/22)
-
- Library
- -------
- - None
-
- Parallel Library
- ----------------
- - None
-
- Tools
- -----
- - h5repack: Added the ability to use plugin filters to read and write
- files. The option uses the filter number. HDFFV-8345
- (ADB - 2013/09/04).
- - h5dump: Added the option -N --any_path, which searches the file for
- paths that match the search path. HDFFV-7989 (ADB - 2013/08/12).
- - h5dump: Added the optional arg 0 to -A, which excludes attributes
- from display. HDFFV-8134 (ADB - 2013/08/01).
-
- High-Level APIs
- ---------------
- - None
-
- Fortran API
- -----------
- - None
-
- C++ API
- -------
- - Added tutorial examples to C++/examples. They can be installed by
- "make install-examples" and, in the installed directory, they can be
- executed by running the script file run-c++-ex.sh. (BMR - 2013/09/28)
- - A new class, H5::H5Location, is added to represent the location concept
- in the C library. It is a base class to H5::H5File and H5::H5Ojbect,
- whose member functions are moved into H5::H5Location. H5::H5File can
- now inherent those functions. As a result, an H5::H5File object can have
- an attribute. (BMR - 2013/09/27)
- - Added wrappers for H5Rget_obj_type2 to retrieve the type of the object
- that an object reference points to. (BMR - 2013/09/27)
- H5O_type_t H5Location::getRefObjType(void *ref, H5R_type_t ref_type)
- - Added wrappers for H5Aexist to check whether an attribute exists given
- a name. (BMR - 2013/09/27)
- bool H5::H5Location::attrExists(const char* name)
- bool H5::H5Location::attrExists(const H5std_string& name)
- - Added a number of overloaded functions for convenience. (BMR - 2013/09/27)
-
-
-Support for New Platforms, Languages, and Compilers
-===================================================
- - None
-
-Bug Fixes since HDF5-1.8.11
-===========================
-
- Configuration
- -------------
- - Modified H5detect.c to scan floating point types for padding bits before
- analyzing the type further. This should fix problems with gcc 4.8.
- (NAF - 2013/09/19 - HDFFV-8523/HDFFV-8500)
- - HDF5 rpaths are no longer encoded in the library files when configured
- with --disable-sharedlib-rpath. (LRK-2013-09-23 - HDFFV-8276)
-
- Library
- -------
- - Added const qualifier to source buffer parameters in H5Dgather and
- H5D_scatter_func_t (H5Dscatter callback). (NAF - 2013/7/09)
-
- - CMake now creates *.so.{lt_version} files with the same version as
- configure. (ADB - 2013/06/05 HDFFV-8437)
-
- Parallel Library
- ----------------
- - None
-
- Performance
- -------------
- - None
-
- Tools
- -----
- - h5dump: Added the option -N --any_path, which searches the file for
- paths that match the search path. HDFFV-7989 (ADB - 2013/08/12).
- - h5dump: Added the optional arg 0 to -A, which excludes attributes
- from display. HDFFV-8134 (ADB - 2013/08/01).
- - h5dump correctly exports subsetted data to a file, using the --output
- option. (ADB - 2013/06/07 HDFFV-8447)
- - h5cc and other compile scripts now default to linking shared libraries
- when HDF5 is configured with the --disable-static option.
- (LRK - 2013-09-23 - HDFFV-8141)
-
- F90 API
- -------
- - None
-
- C++ API
- ------
- - None
-
- High-Level APIs:
- ------
- - None
-
- Fortran High-Level APIs:
- ------
- - None
-
- Testing
- -------
- - test/big sometimes failed with the message of "file selection+offset not
- within extent". This has been fixed. (AKC - 2013/09/28 HDFFV-8271).
- - tools/h5diff/testh5diff.sh is run in every "make check", even after it
- has passed in the previous run. It should not run again if there are no
- code changes. Fixed. (AKC - 2013/07/19 HDFFV-8392)
-
-Supported Platforms
-===================
-The following platforms are supported and have been tested for this release.
-They are built with the configure process unless specified otherwise.
-
- AIX 5.3 xlc 10.1.0.5
- (NASA G-ADA) xlC 10.1.0.5
- xlf90 12.1.0.6
-
- Linux 2.6.18-308.13.1.el5PAE GNU C (gcc), Fortran (gfortran), C++ (g++)
- #1 SMP i686 i686 i386 compilers for 32-bit applications;
- (jam) Version 4.1.2 20080704 (Red Hat 4.1.2-54)
- Version 4.8.1
- PGI C, Fortran, C++ Compilers for 32-bit
- applications;
- Version 13.7-0
- Intel(R) C, C++, Fortran Compiler for 32-bit
- applications;
- Version 13.1.3 (Build 20130607)
-
- Linux 2.6.18-308.16.1.el5 GNU C (gcc), Fortran (gfortran), C++ (g++)
- #1 SMP x86_64 GNU/Linux compilers for 64-bit applications;
- (koala) Version 4.1.2 20080704 (Red Hat 4.1.2-54)
- Version 4.8.1
- PGI C, Fortran, C++ for 64-bit target on
- x86-64;
- Version 13.7-0
- Intel(R) C, C++, Fortran Compilers for
- applications running on Intel(R) 64;
- Version 13.1.3 (Build 20130607)
-
- Linux 2.6.32-358.18.1.el6 GNU C (gcc), Fortran (gfortran), C++ (g++)
- #1 SMP x86_64 GNU/Linux compilers:
- (platypus) Version 4.4.7 20120313
- Version 4.8.1
- PGI C, Fortran, C++ for 64-bit target on
- x86-64;
- Version 13.7-0
- Intel(R) C (icc), C++ (icpc), Fortran (icc)
- compilers:
- Version 13.1.3 (Build 20130607)
-
- Linux 2.6.32-358.18.1.el6.ppc64 gcc (GCC) 4.4.7 20120313 (Red Hat 4.4.7-3)
- #1 SMP ppc64 GNU/Linux g++ (GCC) 4.4.7 20120313 (Red Hat 4.4.7-3)
- (ostrich) GNU Fortran (GCC) 4.4.7 20120313 (Red Hat 4.4.7-3)
- IBM XL C/C++ V11.1
- IBM XL Fortran V13.1
-
- SunOS 5.11 32- and 64-bit Sun C 5.12 SunOS_sparc
- (emu) Sun Fortran 95 8.6 SunOS_sparc
- Sun C++ 5.12 SunOS_sparc
-
- Windows 7 Visual Studio 2008 w/ Intel Fortran 11 (cmake)
- Visual Studio 2010 w/ Intel Fortran 12 (cmake)
- Visual Studio 2012 w/ Intel Fortran 13 (cmake)
- Cygwin(CYGWIN_NT-6.1 1.7.15(0.260/5/3) gcc(4.5.3) compiler and gfortran)
- (cmake and autotools)
-
- Windows 7 x64 Visual Studio 2008 w/ Intel Fortran 11 (cmake)
- Visual Studio 2010 w/ Intel Fortran 12 (cmake)
- Visual Studio 2012 w/ Intel Fortran 13 (cmake)
-
- Windows 8.1 Visual Studio 2012 w/ Intel Fortran 13 (cmake)
-
- Windows 8.1 x64 Visual Studio 2012 w/ Intel Fortran 13 (cmake)
-
- Mac OS X Snow Leopard 10.6.8 gcc i686-apple-darwin11-llvm-gcc-4.2 (GCC) 4.2.1 from Xcode 3.2.6
- Darwin Kernel Version 10.8.0 g++ i686-apple-darwin11-llvm-g++-4.2 (GCC) 4.2.1 from Xcode 3.2.6
- 64-bit gfortran GNU Fortran (GCC) 4.6.2
- (fred) Intel C (icc), Fortran (ifort), C++ (icpc)
- 12.1 Build 20120928
-
- Mac OS X Lion 10.7.3 Apple clang/clang++ version 3.0 from Xcode 4.6.1
- 64-bit gfortran GNU Fortran (GCC) 4.6.2
- (duck) Intel icc/icpc/ifort version 13.0.3
-
- Mac OS X Mountain Lion 10.8.1 Apple clang/clang++ version 4.2 from Xcode 4.6.1
- 64-bit gfortran GNU Fortran (GCC) 4.6.2
- (wren) Intel icc/icpc/ifort version 13.0.3
-
- OpenVMS IA64 V8.4 HP C V7.3-018
- HP Fortran V8.2-104939-50H96
- HP C++ V7.4-004
-
-Tested Configuration Features Summary
-=====================================
-
- In the tables below
- y = tested
- n = not tested in this release
- C = Cluster
- W = Workstation
- x = not working in this release
- dna = does not apply
- ( ) = footnote appears below second table
- <blank> = testing incomplete on this feature or platform
-
-Platform C F90/ F90 C++ zlib SZIP
- parallel F2003 parallel
-Solaris2.11 32-bit n y/y n y y y
-Solaris2.11 64-bit n y/y n y y y
-Windows 7 y y/y n y y y
-Windows 7 x64 y y/y n y y y
-Windows 7 Cygwin n y/n n y y y
-Windows 8.1 n y/y n y y y
-Windows 8.1 x64 n y/y n y y y
-Mac OS X Snow Leopard 10.6.8 64-bit n y/y n y y y
-Mac OS X Lion 10.7.3 64-bit n y/y n y y y
-Mac OS X Mountain Lion 10.8.1 64-bit n y/y n y y y
-AIX 5.3 32- and 64-bit n y/n n y y y
-CentOS 5.9 Linux 2.6.18-308 i686 GNU y y/y y y y y
-CentOS 5.9 Linux 2.6.18-308 i686 Intel n y/y n y y y
-CentOS 5.9 Linux 2.6.18-308 i686 PGI n y/y n y y y
-CentOS 5.9 Linux 2.6.18 x86_64 GNU y y/y y y y y
-CentOS 5.9 Linux 2.6.18 x86_64 Intel n y/y n y y y
-CentOS 5.9 Linux 2.6.18 x86_64 PGI n y/y n y y y
-CentOS 6.4 Linux 2.6.32 x86_64 GNU n y/y n y y y
-CentOS 6.4 Linux 2.6.32 x86_64 Intel n y/y n y y y
-Linux 2.6.32-358.2.1.el6.ppc64 n y/n n y y y
-OpenVMS IA64 V8.4 n y/n n y y n
-
-Platform Shared Shared Shared Thread-
- C libs F90 libs C++ libs safe
-Solaris2.11 32-bit y y y y
-Solaris2.11 64-bit y y y y
-Windows 7 y y y y
-Windows 7 x64 y y y y
-Windows 7 Cygwin n n n y
-Windows 8.1 y y y y
-Windows 8.1 x64 y y y y
-Mac OS X Snow Leopard 10.6.8 64-bit y n y n
-Mac OS X Lion 10.7.3 64-bit y n y y
-Mac OS X Mountain Lion 10.8.1 64-bit y n y y
-AIX 5.3 32- and 64-bit y n n y
-CentOS 5.9 Linux 2.6.18-308 i686 GNU y y y y
-CentOS 5.9 Linux 2.6.18-308 i686 Intel y y y n
-CentOS 5.9 Linux 2.6.18-308 i686 PGI y y y n
-CentOS 5.9 Linux 2.6.18 x86_64 GNU y y y y
-CentOS 5.9 Linux 2.6.18 x86_64 Intel y y y n
-CentOS 5.9 Linux 2.6.18 x86_64 PGI y y y n
-CentOS 6.4 Linux 2.6.32 x86_64 GNU y y y n
-CentOS 6.4 Linux 2.6.32 x86_64 Intel y y y n
-Linux 2.6.32-358.2.1.el6.ppc64 y y y n
-OpenVMS IA64 V8.4 n n n n
-
-Compiler versions for each platform are listed in the preceding
-"Supported Platforms" table.
-
-
-More Tested Platforms
-=====================
-The following platforms are not supported but have been tested for this release.
-
- Linux 2.6.18-308.13.1.el5PAE MPICH mpich2-1.4.1p1 compiled with
- #1 SMP i686 i686 i386 gcc 4.1.2 and gfortran 4.1.2
- (jam) g95 (GCC 4.0.3 (g95 0.94!)
-
- Linux 2.6.18-308.16.1.el5 MPICH mpich2-1.4.1p1 compiled with
- #1 SMP x86_64 GNU/Linux gcc 4.1.2 and gfortran 4.1.2
- (koala) g95 (GCC 4.0.3 (g95 0.94!)
-
- FreeBSD 8.2-STABLE i386 gcc 4.5.4 [FreeBSD] 20110526
- (loyalty) gcc 4.6.1 20110527
- g++ 4.6.1 20110527
- gfortran 4.6.1 20110527
-
- FreeBSD 8.2-STABLE amd64 gcc 4.5.4 [FreeBSD] 20110526
- (freedom) gcc 4.6.1 20110527
- g++ 4.6.1 20110527
- gfortran 4.6.1 20110527
-
- Debian7.1.0 3.2.0-4-amd64 #1 SMP Debian 3.2.46-1 x86_64 GNU/Linux
- gcc (Debian 4.7.2-5) 4.7.2
- GNU Fortran (Debian 4.7.2-5) 4.7.2
- (cmake and autotools)
-
- Fedora19 3.11.1-200.fc19.x86_64 #1 SMP x86_64 x86_64 x86_64 GNU/Linux
- gcc (GCC) 4.8.1 20130603 (Red Hat 4.8.1-1)
- GNU Fortran (GCC) 4.8.1 20130603 (Red Hat 4.8.1-1)
- (cmake and autotools)
-
- SUSE 12.3 3.7.10-1.16-desktop #1 SMP PREEMPT x86_64 x86_64 x86_64 GNU/Linux
- gcc (SUSE Linux) 4.7.2
- GNU Fortran (SUSE Linux) 4.7.2
- (cmake and autotools)
-
- Ubuntu 13.04 3.8.0-30-generic #44-Ubuntu SMP x86_64 GNU/Linux
- gcc (Ubuntu/Linaro 4.7.3-1ubuntu1) 4.7.3
- GNU Fortran (Ubuntu/Linaro 4.7.3-1ubuntu1) 4.7.3
- (cmake and autotools)
-
- Cray Linux Environment (CLE) PrgEnv-pgi/4.0.46
- hopper.nersc.gov pgcc 12.5-0 64-bit target on x86-64 Linux -tp shanghai
- pgf90 12.5-0 64-bit target on x86-64 Linux -tp shanghai
- pgCC 12.5-0 64-bit target on x86-64 Linux -tp shanghai
-
-
-Known Problems
-==============
-* Several HDF5 command-line tools and tests leave behind generated files
- that are not cleaned up with "make clean" or "make distclean" when software
- is built in place. The issue will be addressed in the 1.8.13 release. We
- recommend to use build directory to compile and test HDF5 as described
- in the INSTALL file, section 4.2.
-
-* Source directory names with spaces in them will cause failures in configure
- or make on Mac (HDFFV-8152), Linux, and probably all other platforms. If a
- configure command with a space is run from a build directory, it will exit
- with an error message: "checking whether build environment is sane...
- configure: error: unsafe srcdir value: '/scr/lrknox/hdf5 v1.8.12'". If
- configure is run inside or below the directory with the space in the name,
- libtool will get the directory path from the system, put the part of the
- path before the space in the libdir variable in .../src/libhdf5.la, and
- then fail to find the nonexistent directory. This is a known libtool issue
- and the suggested workaround is to rename the directory without spaces.
- (LRK - 2013/10/22)
-
-* CLANG compiler with the options -fcatch-undefined-behavior and -ftrapv
- catches some undefined behavior in the alignment algorithm of the macro
- DETECT_I in H5detect.c (HDFFV-8147). This issue will be addressed in the
- next release. (SLU - 2013/10/16)
-
-* Running make check for the tools can fail in the tools tests if make was not
- run prior. The tests for the tools use other tools in the tests, therefore
- all the tools should be built before testing the tools. (ADB - 2013/10/09)
-
-* Make provided by Solaris fails in "make check". Solaris users should use
- gmake to build and install HDF5 software. (AKC - 2013/10/08 - HDFFV-8534)
-
-* On OpenVMS, two soft conversion functions (H5T__conv_i_f and H5T__conv_f_i)
- have bugs. They convert data between floating-point numbers and integers.
- But the library's default is hard conversion. The user should avoid
- explicitly enabling soft conversion between floating-point numbers and
- integers. (Issue VMS-8; SLU - 2013/09/19)
-
-* On OpenVMS, ZLIB 1.2.8 library doesn't work properly. ZLIB 1.2.5 works
- fine. So please use ZLIB 1.2.5 to build HDF5 library. (Issue VMS-5;
- SLU 2013/09/19)
-
-* When building using the Cray compilers on Cray machines, HDF5
- configure mistakenly thinks the compiler is an intel compiler and
- sets the -std=c99 flag which breaks configure on Cray. To build HDF5
- properly on a Cray machine, please consult with the instructions in
- INSTALL_parallel for building on Hopper.
- (MSC - 2013/04/26 - HDFFV-8429)
-
-* The h5dump and h5diff utilities occasionally produce different output
- between Linux and Windows systems. This is caused by lower-level library
- routines that fail to write fill values to the user's buffer when reading
- unallocated chunks from datasets that have a fill value set to
- H5D_FILL_VALUE_DEFAULT. Due to platform differences the return of
- spurious data values has only been encountered on Windows 32-bit systems.
- (Issue HDFFV-8247; JP - 2013/03/27)
-
-* The 5.9 C++ compiler on Sun failed to compile a C++ test ttypes.cpp. It
- complains with this message:
- "/home/hdf5/src/H5Vprivate.h", line 130: Error: __func__ is not defined.
-
- The reason is that __func__ is a predefined identifier in C99 standard. The
- HDF5 C library uses it in H5private.h. The test ttypes.cpp includes
- H5private.h (H5Tpkg.h<-H5Fprivate.h<-H5Vprivate.h<-H5private.h). Sun's 5.9
- C++ compiler doesn't support __func__, thus fails to compile the C++ test.
- But Sun's 5.11 C++ compiler does. To check whether your Sun C++ compiler
- knows this identifier, try to compile the following simple C++ program:
- #include<stdio.h>
-
- int main(void)
- {
- printf("%s\n", __func__);
- return 0;
- }
- (SLU - 2012/11/5)
-
-* The C++ and FORTRAN bindings are not currently working on FreeBSD with the
- native release 8.2 compilers (4.2.1), but are working with gcc 4.6 from the
- ports (and probably gcc releases after that).
- (QAK - 2012/10/19)
-
-* The following h5dump test case fails in BG/P machines (and potentially other
- machines that use a command script to launch executables):
-
- h5dump --no-compact-subset -d "AHFINDERDIRECT::ah_centroid_t[0] it=0 tl=0"
- tno-subset.h5
-
- This is due to the embedded spaces in the dataset name being interpreted
- by the command script launcher as meta-characters, thus passing three
- arguments to h5dump's -d flag. The command passes if run by hand, just
- not via the test script.
- (AKC - 2012/05/03)
-
-* On hopper, the build failed when RUNSERIAL and RUNPARALLEL are set
- to aprun -np X, because the H5lib_settings.c file was not generated
- properly. Not setting those environment variables works, because
- configure was able to automatically detect that it is a Cray system
- and used the proper launch commands when necessary.
- (MSC - 2012/04/18)
-
-* The data conversion test dt_arith.c fails in "long double" to integer
- conversion on Ubuntu 11.10 (3.0.0.13 kernel) with GCC 4.6.1 if the library
- is built with optimization -O3 or -O2. The older GCC (4.5) or newer kernel
- (3.2.2 on Fedora) do not have the problem. Users should lower the
- optimization level (-O1 or -O0) by defining CFLAGS in the command line of
- "configure" like:
-
- CFLAGS=-O1 ./configure
-
- This will overwrite the library's default optimization level.
- (SLU - 2012/02/07 - HDFFV-7829)
- This issue is no longer present on Ubuntu 12.10 (3.5.0 kernel) with
- gcc 4.7.2.
-
-* The STDIO VFD does not work on some architectures, possibly due to 32/64
- bit or large file issues. The basic STDIO VFD test is known to fail on
- 64-bit SunOS 5.10 on SPARC when built with -m64 and 32-bit OS X/Darwin
- 10.7.0. The STDIO VFD test has been disabled while we investigate and
- a fix should appear in a future release.
- (DER - 2011/10/14 - HDFFV-8235)
-
-* h5diff can report inconsistent results when comparing datasets of enum type
- that contain invalid values. This is due to how enum types are handled in
- the library and will be addressed in a future release.
- (DER - 2011/10/14 - HDFFV-7527)
-
-* The links test can fail under the stdio VFD due to some issues with external
- links. This will be investigated and fixed in a future release.
- (DER - 2011/10/14 - HDFFV-7768)
-
-* After the shared library support was fixed for some bugs, it was discovered
- that "make prefix=XXX install" no longer works for shared libraries. It
- still works correctly for static libraries. Therefore, if you want to
- install the HDF5 shared libraries in a location such as /usr/local/hdf5,
- you need to specify the location via the --prefix option during configure
- time. E.g, ./configure --prefix=/usr/local/hdf5 ...
- (AKC - 2011/05/07 - HDFFV-7583)
-
-* The parallel test, t_shapesame, in testpar/, may run for a long time and may
- be terminated by the alarm signal. If that happens, one can increase the
- alarm seconds (default is 1200 seconds = 20 minutes) by setting the
- environment variable, $HDF5_ALARM_SECONDS, to a larger value such as 3600
- (60 minutes). Note that the t_shapesame test may fail in some systems
- (see the "While working on the 1.8.6 release..." problem below). If
- it does, it will waste more time if $HDF5_ALARM_SECONDS is set
- to a larger value.
- (AKC - 2011/05/07)
-
-* The C++ and FORTRAN bindings are not currently working on FreeBSD.
- (QAK - 2011/04/26)
-
-* Shared Fortran libraries are not quite working on AIX. While they are
- generated when --enable-shared is specified, the fortran and hl/fortran
- tests fail. We are looking into the issue. HL and C++ shared libraries
- should now be working as intended, however.
- (MAM - 2011/04/20)
-
-* The --with-mpe configure option does not work with Mpich2.
- (AKC - 2011/03/10)
-
-* While working on the 1.8.6 release of HDF5, a bug was discovered that can
- occur when reading from a dataset in parallel shortly after it has been
- written to collectively. The issue was exposed by a new test in the parallel
- HDF5 test suite, but had existed before that. We believe the problem lies with
- certain MPI implementations and/or file systems.
-
- We have provided a pure MPI test program, as well as a standalone HDF5
- program, that can be used to determine if this is an issue on your system.
- They should be run across multiple nodes with a varying number of processes.
- These programs can be found at:
- http://www.hdfgroup.org/ftp/HDF5/examples/known_problems/
- (NAF - 2011/01/19)
-
-* All the VFL drivers aren't backward compatible. In H5FDpublic.h, the
- structure H5FD_class_t changed in 1.8. There is new parameter added to
- get_eoa and set_eoa callback functions. A new callback function
- get_type_map was added in. The public function H5FDrealloc was taken
- out in 1.8. The problem only happens when users define their own driver
- for 1.6 and try to plug in 1.8 library. Because there's only one user
- complaining about it, we (Elena, Quincey, and I) decided to leave it as
- it is (see bug report #1279). Quincey will make a plan for 1.10.
- (SLU - 2010/02/02)
-
-* The --enable-static-exec configure flag will only statically link libraries
- if the static version of that library is present. If only the shared version
- of a library exists (i.e., most system libraries on Solaris, AIX, and Mac,
- for example, only have shared versions), the flag should still result in a
- successful compilation, but note that the installed executables will not be
- fully static. Thus, the only guarantee on these systems is that the
- executable is statically linked with just the HDF5 library.
- (MAM - 2009/11/04)
-
-* Parallel tests failed with 16 processes with data inconsistency at testphdf5
- / dataset_readAll. Parallel tests also failed with 32 and 64 processes with
- collective abort of all ranks at t_posix_compliant / allwrite_allread_blocks
- with MPI IO.
- (CMC - 2009/04/28)
-
-* On an Intel 64 Linux cluster (RH 4, Linux 2.6.9) with Intel 10.0 compilers,
- use -mp -O1 compilation flags to build the libraries. A higher level of
- optimization causes failures in several HDF5 library tests.
-
-* A dataset created or rewritten with a v1.6.3 library or after cannot be read
- with the v1.6.2 library or before when the Fletcher32 EDC filter is enabled.
- There was a bug in the calculation of the Fletcher32 checksum in the
- library before v1.6.3; the checksum value was not consistent between big-
- endian and little-endian systems. This bug was fixed in Release 1.6.3.
- However, after fixing the bug, the checksum value was no longer the same as
- before on little-endian system. Library releases after 1.6.4 can still read
- datasets created or rewritten with an HDF5 library of v1.6.2 or before.
- (SLU - 2005/06/30)
-
-
-%%%%1.8.11%%%%
-
-
-HDF5 version 1.8.11 released on 2013-05-08
-================================================================================
-
-INTRODUCTION
-============
-
-This document describes the differences between HDF5-1.8.10 and
-HDF5-1.8.11-*, and contains information on the platforms tested and
-known problems in HDF5-1.8.11-*.
-For more details, see the files HISTORY-1_0-1_8_0_rc3.txt
-and HISTORY-1_8.txt in the release_docs/ directory of the HDF5 source.
-
-Links to the HDF5 1.8.11 source code, documentation, and additional materials
-can be found on the HDF5 web page at:
-
- http://www.hdfgroup.org/products/hdf5/
-
-The HDF5 1.8.11 release can be obtained from:
-
- http://www.hdfgroup.org/HDF5/release/obtain5.html
-
-User documentation for 1.8.11 can be accessed directly at this location:
-
- http://www.hdfgroup.org/HDF5/doc/
-
-New features in the HDF5-1.8.x release series, including brief general
-descriptions of some new and modified APIs, are described in the "What's New
-in 1.8.0?" document:
-
- http://www.hdfgroup.org/HDF5/doc/ADGuide/WhatsNew180.html
-
-All new and modified APIs are listed in detail in the "HDF5 Software Changes
-from Release to Release" document, in the section "Release 1.8.11 (current
-release) versus Release 1.8.10":
-
- http://www.hdfgroup.org/HDF5/doc/ADGuide/Changes.html
-
-If you have any questions or comments, please send them to the HDF Help Desk:
-
- help@hdfgroup.org
-
-
-CONTENTS
-========
-
-- New Features
-- Support for New Platforms, Languages, and Compilers
-- Bug Fixes since HDF5-1.8.10
-- Supported Platforms
-- Supported Configuration Features Summary
-- More Tested Platforms
-- Known Problems
-
-
-New Features
-============
-
- Configuration
- -------------
- - Libtool version number is changed to 8.0.0 because there are API
- changes. See below for details. (AKC - 2013/05/07 HDFFV-8435)
- - Mac OS X 10.7 (Lion) and 10.8 (Mountain Lion) uses clang/clang++ as the
- default C and C++ compilers. (AKC - 2013/04/19 HDFFV-8245)
- - CMake minimum is now 2.8.10. (ADB 2013/1/14)
- - A new tool, cmakehdf5, which is a build command script similar to
- buildhdf5 is added and is available in the bin directory.
- (AKC - 2013/01/16 HDFFV-8336)
-
- Library
- -------
- - The library can load filter libraries dynamically during runtime. Users
- can set the search path through environment variable HDF5_PLUGIN_PATH
- and call H5Pset_filter to enable a dynamic filter. (SLU - 2013/04/08)
- - Added new API functions H5Dscatter and H5Dgather to scatter data to and
- and gather data from a selection within a memory buffer.
- (NAF - 2013/02/05)
- - The library now supports the data conversion from enumeration to numeric
- (integer and floating-point number) datatypes. See Issue HDFFV-8221.
- (SLU - 2012/10/23)
-
- Parallel Library
- ----------------
- - None
-
- Tools
- -----
- - h5dump: added new option -O or -ddl to output the ddl text to a file. This
- is a complement to the -o or --output option, which redirects the data to
- a file. HDFFV-8229 (ADB - 2013/2/25)
-
- High-Level APIs
- ---------------
- - A new API function, H5DOwrite_chunk. This function writes a data chunk
- directly into a file, bypassing hyperslab selection, data conversion,
- and the filter pipeline. The user must be careful with the function and
- clearly understand the I/O process of the library. (SLU - 2013/2/11)
-
- Fortran API
- -----------
- - New API functions added (MSB - 2013/3/23):
-
- h5odecr_refcount_f, h5oexists_by_name_f, h5oget_comment_f,
- h5oget_comment_by_name_f, h5oincr_refcount_f, h5oopen_by_idx_f,
- h5oset_comment_f, h5oset_comment_by_name_f, h5oset_comment_by_name_f
-
- F2003: h5oget_info_f, h5oget_info_by_idx_f, h5ovisit_by_name_f
-
-
- C++ API
- -------
- - None
-
-
-Support for New Platforms, Languages, and Compilers
-===================================================
- - SunOS 5.11 (emu) 32-bit and 64-bit with Sun C/C++ 5.12 compiler and
- Sun Fortran 95 8.6 compiler.
- - Visual Studio 2012 w/ Intel Fortran 13 on Windows 7
- - g95 released new version recently and is tested in this release.
-
-Bug Fixes since HDF5-1.8.10
-==========================
-
- Configuration
- -------------
- - Fixed Thread-safe configure failure for the AIX platform.
- (AKC - 2013/04/19 HDFFV-8390)
- - Configure will check the result of header searches before searching for
- the library.
- Fixes HDFFV-8257 (ADB 2013/03/04)
- - HDF does not support building SHARED Fortran libraries on OSX. Added
- CMake code to check for this condition.
- Fixes HDFFV-8227 (ADB 2013/03/04)
- - CMake builds on Windows will no longer use legacy naming for libraries.
- The "dll" tag will no longer be added to the name of *.lib and *.dll.
- The option HDF_LEGACY_NAMING is now OFF by default.
- Fixes HDFFV-8292 (ADB 2013/01/30)
-
- Library
- -------
- - The library now behaves correctly when performing large I/O operations
- on Mac OS-X. Previously, single I/O operations > 2 GB would fail
- since the Darwin read/write calls cannot handle the number of bytes
- that their parameter types imply.
- Fixes HDFFV-7975 and HDFFV-8240 (DER 2013/01/07)
- - Fixed a bug in the core VFD that causes failures when opening files
- > 2 GB.
- Fixes HDFFV-8124 and HDFFV-8158 (DER 2013/01/07)
- - Fixed a bug where uninitialized memory was read during variable-length
- type conversion. This caused segfaults in netCDF. Fixes HDFFV-8159.
- (DER 2013/03/30)
- - Removed the H5Pset/get_dxpl_multi functions from the library. The
- intended functionality for them was never fully implemented, and they
- have always been fundamentally broken. NOTE: This does not affect
- setting the multi VFD or any expected VFD functionality. Multi VFD
- usage remains unchanged.
- Fixes HDFFV-8296. (DER 2013/03/30)
-
- Parallel Library
- ----------------
- - None
-
- Performance
- -------------
- - None
-
- Tools
- -----
- - h5redeploy is changed to do this by default:
- Installation directories:
- prefix architecture-independent files.
- exec_prefix architecture-dependent files, default is <prefix>.
- libdir libraries, default is <exec_prefix>/lib.
- includedir header files, default is <prefix/include>.
- This allows users to just change the first line of prefix=<...> and the
- effect will change libdir and includedir too. (AKC 2013/04/05 HDFFV-8358)
- - h5repack: Fixed failure to convert the layout of a small chunked
- dataset (size < 1K) to contiguous layout. HDFFV-8214 (JKM 2013/03/26)
- - h5dump: Fixed displaying compression ratio for unknown or user-defined
- filters. HDFFV-8344 (XCAO 2013/03/19)
- - h5dump: Changed UNKNOWN_FILTER to USER_DEFINED_FILTER for user defined
- filter. HDFFV-8346 (XCAO 2013/03/19)
- - h5diff: Fixed to return the correct exit code 1 when the program
- detects a unique extra attribute. Prior to this fix, h5diff returned
- exit code 0 indicating the two files are identical.
- HDFFV-7643 (JKM 2013/02/15)
- - h5dump: Fixed writing nulls to a binary file when exporting a dataset
- with compound string datatype. HDFFV-8169 (ADB 2013/1/31)
- - The following h5stat test case failed in BG/P machines (and potentially
- other machines that display extra output if an MPI task returns with a
- non-zero code.)
- Testing h5stat notexist.h5
- The test script was fixed to ignore the extra output. HDFFV-8233
- (AKC - 2012/11/30)
- - h5diff: Improved speed when comparing HDF5 files with lots of
- attributes. Much slower performance was identified with release versions
- from 1.8.7 to 1.8.10 compared to 1.8.6. (JKM 2012/10/19)
-
- F90 API
- -------
- - The integer type of the 'offset' argument in h5pset_external_f and
- h5pget_external_f was changed to INTEGER(KIND=OFF_T) to support 8-byte
- integers, matching the C type definition of off_t. (MSB - 2013/3/23)
- - h5fc updated to recognize .f95, .f03 and .f08 file extensions.
-
- C++ API
- ------
- - The C++ wrappers DSetMemXferPropList::setMulti/getMulti were removed
- because the C functions H5Pset/get_dxpl_multi functions are removed
- from the library. Fixes HDFFV-8296 by DER. (BMR 2013/03/30)
- - An exception thrown by an internal function was not propagating to the
- test program during stack unwinding, so it couldn't be caught by the
- test, and the program terminated "without an active exception." It
- seemed that the problem happened when c_str() was used to generate
- an equivalent const char* from a std::string and the resulting string
- was passed to the internal function. As a work-around, we added a
- try/catch around the the call to the internal function and when the
- exception is caught there, it is re-thrown. Fixes HDFFV-8067.
- (BMR 2013/03/30)
-
- High-Level APIs:
- ------
- - Fixed a problem with H5DSget_scale_name including the NULL terminator
- in the size calculation returned by the function. The API was changed
- to NOT include the NULL terminator in the size of name returned
- (MSB- 2013/2/10)
-
- Fortran High-Level APIs:
- ------
- - None
-
- Testing
- -------
- - In some Mac systems, testlibinfo.sh failed with this error:
- Check file ../src/.libs/libhdf5.7.dylib
- strings: object: ../src/.libs/libhdf5.7.dylib malformed object \
- (unknown load command 15)
- The strings command of Mac systems inspects library files, and older
- versions of strings may not know newer library formats, resulting
- in errors. Fixed by sending the library file as stdin to the strings
- command to avoid this problem. (AKC - 2013/03/08 HDFFV-8305)
- - Fixed a typo in the ERROR macro in test/testhdf5.h. It segmentation
- faulted when used before. (AKC - 2013/02/12 HDFFV-8267)
-
-Supported Platforms
-===================
-The following platforms are supported and have been tested for this release.
-They are built with the configure process unless specified otherwise.
-
- AIX 5.3 xlc 10.1.0.5
- (NASA G-ADA) xlC 10.1.0.5
- xlf90 12.1.0.6
-
- Linux 2.6.18-308.13.1.el5PAE GNU C (gcc), Fortran (gfortran), C++ (g++)
- #1 SMP i686 i686 i386 compilers for 32-bit applications;
- (jam) Version 4.1.2 20080704 (Red Hat 4.1.2-54)
- Version 4.6.3
- PGI C, Fortran, C++ Compilers for 32-bit
- applications;
- Version 11.9-0
- Version 12.5-0
- Intel(R) C, C++, Fortran Compiler for 32-bit
- applications;
- Version 12.1 (Build 20110811)
- Version 12.1 (Build 20120212)
-
- Linux 2.6.18-308.16.1.el5 GNU C (gcc), Fortran (gfortran), C++ (g++)
- #1 SMP x86_64 GNU/Linux compilers for 64-bit applications;
- (koala) Version 4.1.2 20080704 (Red Hat 4.1.2-52)
- Version 4.6.3
- PGI C, Fortran, C++ for 64-bit target on
- x86-64;
- Version 11.9-0
- Version 12.5-0
- Intel(R) C, C++, Fortran Compilers for
- applications running on Intel(R) 64;
- Version 12.1 (Build 20110811)
- Version 12.1 (Build 20120212)
-
- Linux 2.6.32-358.2.1.el6 GNU C (gcc), Fortran (gfortran), C++ (g++)
- #1 SMP x86_64 GNU/Linux compilers:
- (platypus) Version 4.4.7 20120313
- Intel(R) C (icc), C++ (icpc), Fortran (icc)
- compilers:
- Version 12.1 20120212
-
- Linux 2.6.32-358.2.1.el6.ppc64 gcc (GCC) 4.4.7 20120313 (Red Hat 4.4.7-3)
- #1 SMP ppc64 GNU/Linux g++ (GCC) 4.4.7 20120313 (Red Hat 4.4.7-3)
- (ostrich) GNU Fortran (GCC) 4.4.7 20120313 (Red Hat 4.4.7-3)
- IBM XL C/C++ V11.1
- IBM XL Fortran V13.1
-
- SunOS 5.11 32- and 64-bit Sun C 5.12 SunOS_sparc
- (emu) Sun Fortran 95 8.6 SunOS_sparc
- Sun C++ 5.12 SunOS_sparc
-
- Windows 7 Visual Studio 2008 w/ Intel Fortran 11 (cmake)
- Visual Studio 2010 w/ Intel Fortran 12 (cmake)
- Visual Studio 2012 w/ Intel Fortran 13 (cmake)
- Cygwin(CYGWIN_NT-6.1 1.7.15(0.260/5/3) gcc(4.5.3) compiler and gfortran)
- (cmake and autotools)
-
- Windows 7 x64 Visual Studio 2008 w/ Intel Fortran 11 (cmake)
- Visual Studio 2010 w/ Intel Fortran 12 (cmake)
- Visual Studio 2012 w/ Intel Fortran 13 (cmake)
- Cygwin(CYGWIN_NT-6.1 1.7.15(0.260/5/3) gcc(4.5.3) compiler and gfortran)
- (cmake and autotools)
-
- Mac OS X Snow Leopard 10.6.8 gcc i686-apple-darwin11-llvm-gcc-4.2 (GCC) 4.2.1 from Xcode 3.2.6
- Darwin Kernel Version 10.8.0 g++ i686-apple-darwin11-llvm-g++-4.2 (GCC) 4.2.1 from Xcode 3.2.6
- 64-bit gfortran GNU Fortran (GCC) 4.6.2
- (fred) Intel C (icc), Fortran (ifort), C++ (icpc)
- 12.1 Build 20120928
-
- Mac OS X Lion 10.7.3 Apple clang/clang++ version 3.0 from Xcode 4.6.1
- 64-bit gfortran GNU Fortran (GCC) 4.6.2
- (duck) Intel icc/icpc/ifort version 13.0
-
- Mac OS X Mountain Lion 10.8.1 Apple clang/clang++ version 4.2 from Xcode 4.6.1
- 64-bit gfortran GNU Fortran (GCC) 4.6.2
- (wren) Intel icc/icpc/ifort version 13.0.1.119
-
-
-Tested Configuration Features Summary
-=====================================
-
- In the tables below
- y = tested
- n = not tested in this release
- C = Cluster
- W = Workstation
- x = not working in this release
- dna = does not apply
- ( ) = footnote appears below second table
- <blank> = testing incomplete on this feature or platform
-
-Platform C F90/ F90 C++ zlib SZIP
- parallel F2003 parallel
-Solaris2.11 32-bit n y/y n y y y
-Solaris2.11 64-bit n y/n n y y y
-Windows 7 y y/y n y y y
-Windows 7 x64 y y/y n y y y
-Windows 7 Cygwin n y/n n y y y
-Windows 7 x64 Cygwin n y/n n y y y
-Mac OS X Snow Leopard 10.6.8 64-bit n y/y n y y y
-Mac OS X Lion 10.7.3 64-bit n y/y n y y y
-Mac OS X Mountain Lion 10.8.1 64-bit n y/y n y y y
-AIX 5.3 32- and 64-bit n y/n n y y y
-CentOS 5.9 Linux 2.6.18-308 i686 GNU y y/y y y y y
-CentOS 5.9 Linux 2.6.18-308 i686 Intel n y/y n y y y
-CentOS 5.9 Linux 2.6.18-308 i686 PGI n y/y n y y y
-CentOS 5.9 Linux 2.6.18 x86_64 GNU y y/y y y y y
-CentOS 5.9 Linux 2.6.18 x86_64 Intel n y/y n y y y
-CentOS 5.9 Linux 2.6.18 x86_64 PGI n y/y n y y y
-CentOS 6.4 Linux 2.6.32 x86_64 GNU n y/n n y y y
-CentOS 6.4 Linux 2.6.32 x86_64 Intel n y/y n y y y
-Linux 2.6.32-358.2.1.el6.ppc64 n y/n n y y y
-
-
-Platform Shared Shared Shared Thread-
- C libs F90 libs C++ libs safe
-Solaris2.11 32-bit y y y y
-Solaris2.11 64-bit y y y y
-Windows 7 y y y y
-Windows 7 x64 y y y y
-Windows 7 Cygwin n n n y
-Windows 7 x64 Cygwin n n n y
-Mac OS X Snow Leopard 10.6.8 64-bit y n y n
-Mac OS X Lion 10.7.3 64-bit y n y y
-Mac OS X Mountain Lion 10.8.1 64-bit y n y y
-AIX 5.3 32- and 64-bit y n n y
-CentOS 5.9 Linux 2.6.18-308 i686 GNU y y y y
-CentOS 5.9 Linux 2.6.18-308 i686 Intel y y y n
-CentOS 5.9 Linux 2.6.18-308 i686 PGI y y y n
-CentOS 5.9 Linux 2.6.18 x86_64 GNU y y y y
-CentOS 5.9 Linux 2.6.18 x86_64 Intel y y y n
-CentOS 5.9 Linux 2.6.18 x86_64 PGI y y y n
-CentOS 6.4 Linux 2.6.32 x86_64 GNU y y y n
-CentOS 6.4 Linux 2.6.32 x86_64 Intel y y y n
-Linux 2.6.32-358.2.1.el6.ppc64 y y y n
-
-Compiler versions for each platform are listed in the preceding
-"Supported Platforms" table.
-
-
-More Tested Platforms
-=====================
-The following platforms are not supported but have been tested for this release.
-
- Linux 2.6.18-308.13.1.el5PAE MPICH mpich2-1.4.1p1 compiled with
- #1 SMP i686 i686 i386 gcc 4.1.2 and gfortran 4.1.2
- (jam) g95 (GCC 4.0.3 (g95 0.94!)
-
- Linux 2.6.18-308.16.1.el5 MPICH mpich2-1.4.1p1 compiled with
- #1 SMP x86_64 GNU/Linux gcc 4.1.2 and gfortran 4.1.2
- (koala) g95 (GCC 4.0.3 (g95 0.94!)
-
- FreeBSD 8.2-STABLE i386 gcc 4.2.1 [FreeBSD] 20070719
- (loyalty) gcc 4.6.1 20110422
- g++ 4.6.1 20110422
- gfortran 4.6.1 20110422
-
- FreeBSD 8.2-STABLE amd64 gcc 4.2.1 [FreeBSD] 20070719
- (freedom) gcc 4.6.1 20110422
- g++ 4.6.1 20110422
- gfortran 4.6.1 20110422
-
- Debian6.0.7 2.6.32-5-amd64 #1 SMP x86_64 GNU/Linux
- gcc (Debian 4.4.5-8) 4.4.5
- GNU Fortran (Debian 4.4.5-8) 4.4.5
- (cmake and autotools)
-
- Fedora18 3.7.9-205.fc18.x86_64 #1 SMP x86_64 x86_64 x86_64 GNU/Linux
- gcc (GCC) 4.7.2 20121109 (Red Hat 4.7.2-8)
- GNU Fortran (GCC) 4.7.2 20120507 (Red Hat 4.7.2-8)
- (cmake and autotools)
-
- SUSE 12.3 3.7.10-1.1-desktop #1 SMP PREEMPT x86_64 x86_64 x86_64 GNU/Linux
- gcc (SUSE Linux) 4.7.2
- GNU Fortran (SUSE Linux) 4.7.2
- (cmake and autotools)
-
- Ubuntu 12.10 3.5.0-25-generic #39-Ubuntu SMP x86_64 GNU/Linux
- gcc (Ubuntu/Linaro 4.7.2-2ubuntu1) 4.7.2
- GNU Fortran (Ubuntu/Linaro 4.7.2-2ubuntu1) 4.7.2
- (cmake and autotools)
-
- Cray Linux Environment (CLE) PrgEnv-pgi/4.0.46
- hopper.nersc.gov pgcc 12.5-0 64-bit target on x86-64 Linux -tp shanghai
- pgf90 12.5-0 64-bit target on x86-64 Linux -tp shanghai
- pgCC 12.5-0 64-bit target on x86-64 Linux -tp shanghai
-
-
-Known Problems
-==============
-
-* When building using the Cray compilers on Cray machines, HDF5
- configure mistakenly thinks the compiler is an intel compiler and
- sets the -std=c99 flag which breaks configure on Cray. To build HDF5
- properly on a Cray machine, please consult with the instructions in
- INSTALL_parallel for building on Hopper.
- (MSC - 2013/04/26 - HDFFV-8429)
-
-* The h5dump and h5diff utilities occasionally produce different output
- between Linux and Windows systems. This is caused by lower-level library
- routines that fail to write fill values to the user's buffer when reading
- unallocated chunks from datasets that have a fill value set to
- H5D_FILL_VALUE_DEFAULT. Due to platform differences the return of
- spurious data values has only been encountered on Windows 32-bit systems.
- (Issue HDFFV-8247; JP - 2013/03/27)
-
-* The 5.9 C++ compiler on Sun failed to compile a C++ test ttypes.cpp. It
- complains with this message:
- "/home/hdf5/src/H5Vprivate.h", line 130: Error: __func__ is not defined.
-
- The reason is that __func__ is a predefined identifier in C99 standard. The
- HDF5 C library uses it in H5private.h. The test ttypes.cpp includes
- H5private.h (H5Tpkg.h<-H5Fprivate.h<-H5Vprivate.h<-H5private.h). Sun's 5.9
- C++ compiler doesn't support __func__, thus fails to compile the C++ test.
- But Sun's 5.11 C++ compiler does. To check whether your Sun C++ compiler
- knows this identifier, try to compile the following simple C++ program:
- #include<stdio.h>
-
- int main(void)
- {
- printf("%s\n", __func__);
- return 0;
- }
- (SLU - 2012/11/5)
-
-* The C++ and FORTRAN bindings are not currently working on FreeBSD with the
- native release 8.2 compilers (4.2.1), but are working with gcc 4.6 from the
- ports (and probably gcc releases after that).
- (QAK - 2012/10/19)
-
-* The following h5dump test case fails in BG/P machines (and potentially other
- machines that use a command script to launch executables):
-
- h5dump --no-compact-subset -d "AHFINDERDIRECT::ah_centroid_t[0] it=0 tl=0"
- tno-subset.h5
-
- This is due to the embedded spaces in the dataset name being interpreted
- by the command script launcher as meta-characters, thus passing three
- arguments to h5dump's -d flag. The command passes if run by hand, just
- not via the test script.
- (AKC - 2012/05/03)
-
-* On hopper, the build failed when RUNSERIAL and RUNPARALLEL are set
- to aprun -np X, because the H5lib_settings.c file was not generated
- properly. Not setting those environment variables works, because
- configure was able to automatically detect that it's a Cray system
- and used the proper launch commands when necessary.
- (MSC - 2012/04/18)
-
-* The data conversion test dt_arith.c fails in "long double" to integer
- conversion on Ubuntu 11.10 (3.0.0.13 kernel) with GCC 4.6.1 if the library
- is built with optimization -O3 or -O2. The older GCC (4.5) or newer kernel
- (3.2.2 on Fedora) doesn't have the problem. Users should lower the
- optimization level (-O1 or -O0) by defining CFLAGS in the command line of
- "configure" like:
-
- CFLAGS=-O1 ./configure
-
- This will overwrite the library's default optimization level.
- (SLU - 2012/02/07 - HDFFV-7829)
- This issue is no longer present on Ubuntu 12.10 (3.5.0 kernel) with
- gcc 4.7.2.
-
-* The STDIO VFD does not work on some architectures, possibly due to 32/64
- bit or large file issues. The basic STDIO VFD test is known to fail on
- 64-bit SunOS 5.10 on SPARC when built with -m64 and 32-bit OS X/Darwin
- 10.7.0. The STDIO VFD test has been disabled while we investigate and
- a fix should appear in a future release.
- (DER - 2011/10/14 - HDFFV-8235)
-
-* h5diff can report inconsistent results when comparing datasets of enum type
- that contain invalid values. This is due to how enum types are handled in
- the library and will be addressed in a future release.
- (DER - 2011/10/14 - HDFFV-7527)
-
-* The links test can fail under the stdio VFD due to some issues with external
- links. This will be investigated and fixed in a future release.
- (DER - 2011/10/14 - HDFFV-7768)
-
-* After the shared library support was fixed for some bugs, it was discovered
- that "make prefix=XXX install" no longer works for shared libraries. It
- still works correctly for static libraries. Therefore, if you want to
- install the HDF5 shared libraries in a location such as /usr/local/hdf5,
- you need to specify the location via the --prefix option during configure
- time. E.g, ./configure --prefix=/usr/local/hdf5 ...
- (AKC - 2011/05/07 - HDFFV-7583)
-
-* The parallel test, t_shapesame, in testpar/, may run for a long time and may
- be terminated by the alarm signal. If that happens, one can increase the
- alarm seconds (default is 1200 seconds = 20 minutes) by setting the
- environment variable, $HDF5_ALARM_SECONDS, to a larger value such as 3600
- (60 minutes). Note that the t_shapesame test may fail in some systems
- (see the "While working on the 1.8.6 release..." problem below). If
- it does, it will waste more time if $HDF5_ALARM_SECONDS is set
- to a larger value.
- (AKC - 2011/05/07)
-
-* The C++ and FORTRAN bindings are not currently working on FreeBSD.
- (QAK - 2011/04/26)
-
-* Shared Fortran libraries are not quite working on AIX. While they are
- generated when --enable-shared is specified, the fortran and hl/fortran
- tests fail. We are looking into the issue. HL and C++ shared libraries
- should now be working as intended, however.
- (MAM - 2011/04/20)
-
-* The --with-mpe configure option does not work with Mpich2.
- (AKC - 2011/03/10)
-
-* While working on the 1.8.6 release of HDF5, a bug was discovered that can
- occur when reading from a dataset in parallel shortly after it has been
- written to collectively. The issue was exposed by a new test in the parallel
- HDF5 test suite, but had existed before that. We believe the problem lies with
- certain MPI implementations and/or file systems.
-
- We have provided a pure MPI test program, as well as a standalone HDF5
- program, that can be used to determine if this is an issue on your system.
- They should be run across multiple nodes with a varying number of processes.
- These programs can be found at:
- http://www.hdfgroup.org/ftp/HDF5/examples/known_problems/
- (NAF - 2011/01/19)
-
-* The library's test dt_arith.c showed a compiler's rounding problem on
- Cygwin when converting from unsigned long long to long double. The
- library's own conversion works fine. We defined a macro for Cygwin to
- skip this test until we can solve the problem.
- (SLU - 2010/05/05 - HDFFV-1264)
-
-* All the VFL drivers aren't backward compatible. In H5FDpublic.h, the
- structure H5FD_class_t changed in 1.8. There is new parameter added to
- get_eoa and set_eoa callback functions. A new callback function
- get_type_map was added in. The public function H5FDrealloc was taken
- out in 1.8. The problem only happens when users define their own driver
- for 1.6 and try to plug in 1.8 library. Because there's only one user
- complaining about it, we (Elena, Quincey, and I) decided to leave it as
- it is (see bug report #1279). Quincey will make a plan for 1.10.
- (SLU - 2010/02/02)
-
-* The --enable-static-exec configure flag will only statically link libraries
- if the static version of that library is present. If only the shared version
- of a library exists (i.e., most system libraries on Solaris, AIX, and Mac,
- for example, only have shared versions), the flag should still result in a
- successful compilation, but note that the installed executables will not be
- fully static. Thus, the only guarantee on these systems is that the
- executable is statically linked with just the HDF5 library.
- (MAM - 2009/11/04)
-
-* Parallel tests failed with 16 processes with data inconsistency at testphdf5
- / dataset_readAll. Parallel tests also failed with 32 and 64 processes with
- collective abort of all ranks at t_posix_compliant / allwrite_allread_blocks
- with MPI IO.
- (CMC - 2009/04/28)
-
-* On an Intel 64 Linux cluster (RH 4, Linux 2.6.9) with Intel 10.0 compilers,
- use -mp -O1 compilation flags to build the libraries. A higher level of
- optimization causes failures in several HDF5 library tests.
-
-* A dataset created or rewritten with a v1.6.3 library or after cannot be read
- with the v1.6.2 library or before when the Fletcher32 EDC filter is enabled.
- There was a bug in the calculation of the Fletcher32 checksum in the
- library before v1.6.3; the checksum value was not consistent between big-
- endian and little-endian systems. This bug was fixed in Release 1.6.3.
- However, after fixing the bug, the checksum value was no longer the same as
- before on little-endian system. Library releases after 1.6.4 can still read
- datasets created or rewritten with an HDF5 library of v1.6.2 or before.
- (SLU - 2005/06/30)
-
-
-%%%%1.8.10-patch1%%%%
-
-
-HDF5 version 1.8.10-patch1 released on 2013-01-22
-================================================================================
-
-INTRODUCTION
-============
-
-This document describes the differences between HDF5-1.8.9 and
-HDF5 1.8.10, and contains information on the platforms tested and
-known problems in HDF5-1.8.10.
-For more details, see the files HISTORY-1_0-1_8_0_rc3.txt
-and HISTORY-1_8.txt in the release_docs/ directory of the HDF5 source.
-
-Links to the HDF5 1.8.10 source code, documentation, and additional materials
-can be found on the HDF5 web page at:
-
- http://www.hdfgroup.org/products/hdf5/
-
-The HDF5 1.8.10 release can be obtained from:
-
- http://www.hdfgroup.org/HDF5/release/obtain5.html
-
-User documentation for 1.8.10 can be accessed directly at this location:
-
- http://www.hdfgroup.org/HDF5/doc/
-
-New features in the HDF5-1.8.x release series, including brief general
-descriptions of some new and modified APIs, are described in the "What's New
-in 1.8.0?" document:
-
- http://www.hdfgroup.org/HDF5/doc/ADGuide/WhatsNew180.html
-
-All new and modified APIs are listed in detail in the "HDF5 Software Changes
-from Release to Release" document, in the section "Release 1.8.10 (current
-release) versus Release 1.8.9":
-
- http://www.hdfgroup.org/HDF5/doc/ADGuide/Changes.html
-
-If you have any questions or comments, please send them to the HDF Help Desk:
-
- help@hdfgroup.org
-
-
-CONTENTS
-========
-
-- New Features
-- Support for New Platforms, Languages, and Compilers
-- Bug Fixes since HDF5-1.8.10
-- Bug Fixes since HDF5-1.8.9
-- Supported Platforms
-- Supported Configuration Features Summary
-- More Tested Platforms
-- Known Problems
-
-
-New Features
-============
-
- Configuration
- -------------
- - A new tool, cmakehdf5, which is a build command script similar to
- buildhdf5 is added and is available in the bin directory.
- (AKC - 2013/01/21)
-
- Library
- -------
- - Updated to latest autotools and changed all hard *.sh scripts to
- configure managed *.sh.in files. Removed overloading of autotools
- TESTS variable by examples and tests. Renamed configure.in to
- configure.ac. (ADB - 2012/08/23 - HDFFV-8129)
- - The data sieve buffer size was set for all the datasets in the file. It
- could waste memory if any dataset size is smaller than the sieve buffer
- size. Now the library picks the smaller one between the dataset size
- and the sieve buffer size from the file access property. See Issue 7934.
- (SLU - 2012/4/11)
-
- Parallel Library
- ----------------
- - Added the H5Pget_mpio_no_collective_cause() function that retrieves
- reasons why the collective I/O was broken during read/write IO access.
- (JKM - 2012/08/30 HDFFV-8143)
-
- - Added H5Pget_mpio_actual_io_mode_f (MSB - 2012/09/27)
-
- Tools
- -----
- - h5import: Changed to allow the use of h5dump output as input files to
- h5import. h5dump must include the "-p" option to print the properties;
- configuration file is captured output of h5dump. The restrictions are
- that only one dataset with a simple datatype (integer, floating-point,
- or string) can be processed. Integers and floating-point imports from
- h5dump must use the "binary" option for the data file. The string version
- uses the h5dump "-y --width=1" options to disable the indexing printouts,
- print single columns, and obviously NOT use the "binary" option.
- (ADB - 2012/07/19 HDFFV-721)
-
- High-Level APIs
- ---------------
- - None
-
- Fortran API
- -----------
- - Fixed a typo in return value of the nh5dread_f_c function (was 1
- instead of 0 on success); fixed the return value to make it consistent
- with other Fortran functions; cleaned debug statements from the code.
- (EIP - 2012/06/23)
-
- C++ API
- -------
- - None
-
-
-Support for New Platforms, Languages, and Compilers
-===================================================
- - None
-
-Bug Fixes since HDF5-1.8.10
-===========================
- Library
- -------
- - The library now behaves correctly when performing large I/O operations on
- Mac OS-X. Previously, single I/O operations > 2 GB would fail since the
- Darwin read/write calls cannot handle the number of bytes that their
- parameter types imply.
- Fixes HDFFV-7975 and HDFFV-8240 (DER - 07 JAN 2013)
- - Fixed a bug in the core VFD that cause failures when opening files > 2 GB.
- Fixes HDFFV-8124 and HDFFV-8158 (DER - 07 JAN 2013)
-
- Tools
- -----
- - The following h5stat test case failed in BG/P machines (and potentially
- other machines that display extra output if an MPI task returns with a
- non-zero code.)
- Testing h5stat notexist.h5
- The test script was fixed to ignore the extra output.
- HDFFV-8233 (AKC - 2012/12/17)
- - h5diff: Fixed slowness when comparing HDF5 files with many attributes.
- Much slower performance was identified with later release version
- (from 1.8.7 to 1.8.10) compared to 1.8.6. The issue was introduced
- from fixing an attribute related bug for 1.8.7 release in the past.
- HDFFV-8145 (JKM 2012/12/13)
-
- Testing
- -------
- - None
-
-Bug Fixes since HDF5-1.8.9
-==========================
-
- Configuration
- -------------
- - Fixed configure --enable-production to not use -O optimization for Lion
- and Mountain Lion systems when gcc (i686-apple-darwin11-llvm-gcc-4.2
- (GCC) 4.2.1) is used. Somehow the -O optimization will cause some of
- the hard conversion code in test/dt_arith.c to fail. HDFFV-8017.
- (AKC - 2012/10/10)
- - Fixed AIX Fortran compiler flags to use appropriate settings for
- debugging, profiling, and optimization situations. HDFFV-8069.
- (AKC 2012/09/27)
-
- Library
- -------
- - Fixed a memory leak exposed when inserting/removing a property
- from a property list several times. HDFFV-8022. (MSC 2012/05/18)
- - The file_image test will fail in the "initial file image and callbacks in
- the core VFD" sub-test if the source directory is read-only as the test
- fails to create its test files in the build directory. This has been
- fixed. HDFFV-8009 (AKC - 2012/07/06)
-
-
- Parallel Library
- ----------------
- - The MPI-POSIX VFD was updated to include the POSIX and Windows
- correctness features added that had already been added to the other VFDs.
- HDFFV-8058/7845. (DER 2012/09/17)
-
- Performance
- -------------
- - Removed program perform/benchpar from the enable-build-all list. The
- program will be retired or moved to another location. HDFFV-8156
- (AKC 2012/10/01)
- - Retired program perform/mpi-perf. Its purpose has been incorporated
- into h5perf. (AKC 2012/09/21)
-
- Tools
- -----
- - h5repack: "h5repack -f NONE file1.h5 out.h5" command failed if
- source file contains chunked dataset and a chunk dim is bigger than
- the dataset dim. Another issue is that the command changed max dims
- if chunk dim is smaller than the dataset dim. These issue occurred
- when dataset size is smaller than 64k (compact size limit) Fixed both.
- HDFFV-8012 (JKM 2012/09/24)
- - h5diff: Fixed the counter in verbose mode (-v, -r) so that it will no
- longer add together the differences between datasets and the differences
- between attributes of those datasets. This change makes the output of
- verbose mode consistent for datasets, groups, and committed datatypes.
- HDFFV-5919 (JKM 2012/09/10)
- - h5diff: Fixed the incorrect result when comparing attribute data
- values and the data type has the same class but different sizes.
- HDFFV-7942 (JKM 2012/08/15)
- - h5dump: Replaced single element fwrite with block writes.
- HDFFV-1208 (ADB 2012/08/13)
- - h5diff: Fixed test failure for "make check" due to failure of
- copying test files when performed in HDF5 source tree. Also applied
- to other tools. HDFFV-8107 (JKM 2012/08/01)
- - ph5diff: Fixed intermittent hang issue on a certain operation in
- parallel mode. It was detected by daily test for comparing
- non-comparable objects, but it could have occurred in other
- operations depending on machine condition. HDFFV-8003 (JKM 2012/08/01)
- - h5diff: Fixed the function COPY_TESTFILES_TO_TESTDIR() of testh5diff.sh
- to better report when there is an error in the file copying.
- HDFFV-8105 (AKC 2012/07/22)
- - h5dump: Fixed the sort by name display to maintain correct parent/child
- relationships between ascending/descending order.
- HDFFV-8095 (ADB 2012/07/12)
- - h5dump: Fixed the display by creation order when using option -n
- (print contents).
- HDFFV-5942 (ADB 2012/07/09)
- - h5dump: Changed to allow H5T_CSET_UTF8 to be displayed in h5dump output.
- Used technique similar to what was done in h5ls (matches library
- options).
- HDFFV-7999 (ADB 2012/05/23)
- - h5diff: Fixed the tool so that it will not check and display the status
- of dangling links without setting the --follow-symlinks option. This
- also improved performance when comparing lots of external links without
- the --follow-symlinks option.
- HDFFV-7998 (JKM 2012/04/26)
-
- F90 API
- -------
-
- - Fixed a typo in return value of the nh5dread_f_c function (was 1
- instead of 0 on success); fixed the return value to make it consistent
- with other Fortran functions; cleaned debug statements from the code.
- (EIP - 2012/06/23)
-
- - Fixed a problem writing/reading control characters to a dataset; writing
- a string containing alerts, backspace, carriage_return, form_feed,
- horizontal_tab, vertical_tab, or new_line is now tested and working.
- (MSB - 2012/09/01)
-
- - Corrected the integer type of H5S_UNLIMITED_F to HSIZE_T (MSB - 2012/09/01)
-
- - Corrected the number of continuation lines in the src files
- to be less than 32 lines for F95 compliance. (MSB - 2012/10/01)
-
- C++ API
- ------
- - None
-
- High-Level APIs:
- ------
-
- - Fixed problem with H5TBdelete_record destroying all data following the
- deletion of a row. (MSB- 2012/7/26)
-
- - Fixed H5LTget_attribute_string not closing an object identifier when an
- error occurs. (MSB- 2012/7/21)
-
- - Corrected the return type of H5TBAget_fill from herr_t to htri_t to
- reflect that a return value of 1 indicates that a fill value is
- present, 0 indicates a fill value is not present, and <0 indicates an
- error.
-
- Fortran High-Level APIs:
- ------
- - None
-
-Supported Platforms
-===================
- AIX 5.3 xlc 10.1.0.5
- (NASA G-ADA) xlC 10.1.0.5
- xlf90 12.1.0.6
-
- Linux 2.6.18-308.13.1.el5PAE GNU C (gcc), Fortran (gfortran), C++ (g++)
- #1 SMP i686 i686 i386 compilers for 32-bit applications;
- (jam) Version 4.1.2 20080704 (Red Hat 4.1.2-52)
- Version 4.6.3
- PGI C, Fortran, C++ Compilers for 32-bit
- applications;
- Version 11.9-0
- Intel(R) C, C++, Fortran Compiler for 32-bit
- applications;
- Version 12.1
- MPICH mpich2-1.4.1p1 compiled with
- gcc 4.1.2 and gfortran 4.1.2
-
- Linux 2.6.18-308.16.1.el5 GNU C (gcc), Fortran (gfortran), C++ (g++)
- #1 SMP x86_64 GNU/Linux compilers for 32-bit applications;
- (koala) Version 4.1.2 20080704 (Red Hat 4.1.2-52)
- Version 4.6.3
- PGI C, Fortran, C++ for 64-bit target on
- x86-64;
- Version 11.9-0
- Version 12.5-0
- Intel(R) C, C++, Fortran Compilers for
- applications running on Intel(R) 64;
- Version 12.1 (Build 20110811)
- Version 12.1 (Build 20120212)
- MPICH mpich2-1.4.1p1 compiled with
- gcc 4.1.2 and gfortran 4.1.2
-
- Linux 2.6.32-220.7.1.el6.ppc64 gcc (GCC) 4.4.6 20110731 (Red Hat 4.4.6-3)
- #1 SMP ppc64 GNU/Linux g++ (GCC) 4.4.6 20110731
- (ostrich) GNU Fortran (GCC) 4.4.6 20110731 (Red Hat 4.4.6-3)
-
- Linux 2.6.32-220.23.1.1chaos Intel C, C++, Fortran Compilers
- ch5.x86_64 GNU/Linux Version 12.1.5.339
- (LLNL Aztec)
-
- IBM Blue Gene/P XL C for Blue Gene/P, bgxlc V9.0
- (LLNL uDawn) XL C++ for Blue Gene/P, bgxlC V9.0
- XL Fortran for Blue Gene/P, bgxlf90 V11.1
-
- SunOS 5.10 32- and 64-bit Sun C 5.9 Sun OS_sparc Patch 124867-16
- (linew) Sun Fortran 95 8.3 Sun OS_sparc Patch 127000-13
- Sun C++ 5.9 Sun OS_sparc Patch 124863-26
- Sun C 5.11 SunOS_sparc
- Sun Fortran 95 8.5 SunOS_sparc
- Sun C++ 5.11 SunOS_sparc
-
- Windows XP Visual Studio 2008 w/ Intel Fortran 10.1 (project files)
-
- Windows XP x64 Visual Studio 2008 w/ Intel Fortran 10.1 (project files)
-
- Windows 7 Visual Studio 2008 w/ Intel Fortran 11.1 (cmake)
- Visual Studio 2010 w/ Intel Fortran 12 (cmake)
- Cygwin(CYGWIN_NT-6.1 1.7.15(0.260/5/3) gcc(4.5.3) compiler and gfortran)
- (cmake and autotools)
-
- Windows 7 x64 Visual Studio 2008 w/ Intel Fortran 11.1 (cmake)
- Visual Studio 2010 w/ Intel Fortran 12 (cmake)
- Cygwin(CYGWIN_NT-6.1 1.7.15(0.260/5/3) gcc(4.5.3) compiler and gfortran)
- (cmake and autotools)
-
- Mac OS X Snow Leopard 10.6.8 gcc i686-apple-darwin11-llvm-gcc-4.2 (GCC) 4.2.1 from Xcode 3.2.6
- Darwin Kernel Version 10.8.0 g++ i686-apple-darwin11-llvm-g++-4.2 (GCC) 4.2.1 from Xcode 3.2.6
- (fred) gfortran GNU Fortran (GCC) 4.6.2
- Intel C (icc), Fortran (ifort), C++ (icpc)
- 12.1.0.038 Build 20110811
-
- Mac OS X Snow Leopard 10.6.8 gcc i686-apple-darwin11-llvm-gcc-4.2 (GCC) 4.2.1 from Xcode 3.2.6
- Darwin Kernel Version 10.8.0 g++ i686-apple-darwin11-llvm-g++-4.2 (GCC) 4.2.1 from Xcode 3.2.6
- Intel 32-bit gfortran GNU Fortran (GCC) 4.6.1
- (tejeda) Intel C (icc), Fortran (ifort), C++ (icpc)
- 12.1.0.038 Build 20110811
-
- Mac OS X Lion 10.7.3 gcc i686-apple-darwin11-llvm-gcc-4.2 (GCC) 4.2.1 from Xcode 4.2.1
- 32- and 64-bit g++ i686-apple-darwin11-llvm-g++-4.2 (GCC) 4.2.1 from Xcode 4.2.1
- (duck) gfortran GNU Fortran (GCC) 4.6.2
-
- Mac OS X Mountain Lion 10.8.1 cc Apple clang version 4.0 from Xcode 4.5.1
- (owl) c++ Apple clang version 4.0 from Xcode 4.5.1
- gcc i686-apple-darwin11-llvm-gcc-4.2 (GCC) 4.2.1 from Xcode 4.5.1
- g++ i686-apple-darwin11-llvm-g++-4.2 (GCC) 4.2.1 from Xcode 4.5.1
- gfortran GNU Fortran (GCC) 4.6.2
-
-
-Tested Configuration Features Summary
-=====================================
-
- In the tables below
- y = tested
- n = not tested in this release
- C = Cluster
- W = Workstation
- x = not working in this release
- dna = does not apply
- ( ) = footnote appears below second table
- <blank> = testing incomplete on this feature or platform
-
-Platform C F90/ F90 C++ zlib SZIP
- parallel F2003 parallel
-Solaris2.10 32-bit n y/y n y y y
-Solaris2.10 64-bit n y/n n y y y
-Windows 7 y y/n n y y y
-Windows 7 x64 y y/n n y y y
-Mac OS X Snow Leopard 10.6.8 32-bit n y/y n y y n
-Mac OS X Snow Leopard 10.6.8 64-bit n y/y n y y y
-Mac OS X Lion 10.7.3 32-bit n y/y n y y n
-Mac OS X Lion 10.7.3 64-bit n y/y n y y y
-Mac OS X Mountain Lion 10.8.1 64-bit n y/n n y y n
-AIX 5.3 32- and 64-bit y y/n y y y y
-CentOS 5.5 Linux 2.6.18-308 i686 GNU y y/y y y y y
-CentOS 5.5 Linux 2.6.18-308 i686 Intel n y/y n y y y
-CentOS 5.5 Linux 2.6.18-308 i686 PGI n y/y n y y y
-CentOS 5.5 Linux 2.6.18 x86_64 GNU y y/y y y y y
-CentOS 5.5 Linux 2.6.18 x86_64 Intel n y/y n y y y
-CentOS 5.5 Linux 2.6.18 x86_64 PGI n y/y n y y y
-Linux 2.6.32-220.7.1.el6.ppc64 n y/n n y y y
-
-
-Platform Shared Shared Shared Thread-
- C libs F90 libs C++ libs safe
-Solaris2.10 32-bit y y y y
-Solaris2.10 64-bit n n n n
-Windows 7 y y y y
-Windows 7 x64 y y y y
-Mac OS X Snow Leopard 10.6.8 32-bit y n y n
-Mac OS X Snow Leopard 10.6.8 64-bit y n y n
-Mac OS X Lion 10.7.3 32-bit y n y y
-Mac OS X Lion 10.7.3 64-bit y n y y
-Mac OS X Mountain Lion 10.8.1 64-bit y n y y
-AIX 5.3 32- and 64-bit n n n y
-CentOS 5.5 Linux 2.6.18-308 i686 GNU y y y y
-CentOS 5.5 Linux 2.6.18-308 i686 Intel y y y n
-CentOS 5.5 Linux 2.6.18-308 i686 PGI y y y n
-CentOS 5.5 Linux 2.6.18 x86_64 GNU y y y y
-CentOS 5.5 Linux 2.6.18 x86_64 Intel y y y n
-CentOS 5.5 Linux 2.6.18 x86_64 PGI y y y n
-Linux 2.6.32-220.7.1.el6.ppc64 y y y n
-
-Compiler versions for each platform are listed in the preceding
-"Supported Platforms" table.
-
-
-More Tested Platforms
-=====================
-The following platforms are not supported but have been tested for this release.
-
- FreeBSD 8.2-STABLE i386 gcc 4.2.1 [FreeBSD] 20070719
- (loyalty) gcc 4.6.1 20110422
- g++ 4.6.1 20110422
- gfortran 4.6.1 20110422
-
- FreeBSD 8.2-STABLE amd64 gcc 4.2.1 [FreeBSD] 20070719
- (freedom) gcc 4.6.1 20110422
- g++ 4.6.1 20110422
- gfortran 4.6.1 20110422
-
- Debian6.0.3 2.6.32-5-686 #1 SMP i686 GNU/Linux
- gcc (Debian 4.4.5-8) 4.4.5
- GNU Fortran (Debian 4.4.5-8) 4.4.5
- (cmake and autotools)
-
- Debian6.0.3 2.6.32-5-amd64 #1 SMP x86_64 GNU/Linux
- gcc (Debian 4.4.5-8) 4.4.5
- GNU Fortran (Debian 4.4.5-8) 4.4.5
- (cmake and autotools)
-
- Fedora17 3.5.2-1.fc17.i6866 #1 SMP i686 i686 i386 GNU/Linux
- gcc (GCC) 4.7.0 20120507 (Red Hat 4.7.0-5)
- GNU Fortran (GCC) 4.7.0 20120507 (Red Hat 4.7.0-5)
- (cmake and autotools)
-
- Fedora17 3.5.2-1.fc17.x86_64 #1 SMP x86_64 x86_64 x86_64 GNU/Linux
- gcc (GCC) 4.7.0 20120507 (Red Hat 4.7.0-5)
- GNU Fortran (GCC) 4.7.0 20120507 (Red Hat 4.7.0-5)
- (cmake and autotools)
-
- SUSE 12.2 3.4.6-2.10-desktop #1 SMP PREEMPT i686 i686 i386 GNU/Linux
- gcc (SUSE Linux) 4.7.1
- GNU Fortran (SUSE Linux) 4.7.1
- (cmake and autotools)
-
- SUSE 12.2 3.4.6-2.10-desktop #1 SMP PREEMPT x86_64 x86_64 x86_64 GNU/Linux
- gcc (SUSE Linux) 4.7.1
- GNU Fortran (SUSE Linux) 4.7.1
- (cmake and autotools)
-
- Ubuntu 12.04 3.2.0-29-generic #46-Ubuntu SMP i686 GNU/Linux
- gcc (Ubuntu/Linaro 4.6.3-1ubuntu5) 4.6.3
- GNU Fortran (Ubuntu/Linaro 4.6.3-1ubuntu5) 4.6.3
- (cmake and autotools)
-
- Ubuntu 12.04 3.2.0-29-generic #46-Ubuntu SMP x86_64 GNU/Linux
- gcc (Ubuntu/Linaro 4.6.3-1ubuntu5) 4.6.3
- GNU Fortran (Ubuntu/Linaro 4.6.3-1ubuntu5) 4.6.3
- (cmake and autotools)
- (Use optimization level -O1)
-
- Cray Linux Environment (CLE) PrgEnv-pgi/4.0.46
- hopper.nersc.gov pgcc 12.5-0 64-bit target on x86-64 Linux -tp shanghai
- pgf90 12.5-0 64-bit target on x86-64 Linux -tp shanghai
- pgCC 12.5-0 64-bit target on x86-64 Linux -tp shanghai
-
-
-Known Problems
-==============
-* The C++ and FORTRAN bindings are not currently working on FreeBSD with the
- native release 8.2 compilers (4.2.1), but are working with gcc 4.6 from the
- ports (and probably gcc releases after that).
- (QAK - 2012/10/19)
-
-* The following h5dump test case fails in BG/P machines (and potentially other
- machines that use a command script to launch executables):
-
- h5dump --no-compact-subset -d "AHFINDERDIRECT::ah_centroid_t[0] it=0 tl=0"
- tno-subset.h5
-
- This is due to the embedded spaces in the dataset name being interpreted
- by the command script launcher as meta-characters, thus passing three
- arguments to h5dump's -d flag. The command passes if run by hand, just
- not via the test script.
- (AKC - 2012/05/03)
-
-* On hopper, the build failed when RUNSERIAL and RUNPARALLEL are set
- to aprun -np X, because the H5lib_settings.c file was not generated
- properly. Not setting those environment variables works, because
- configure was able to automatically detect that it's a Cray system
- and used the proper launch commands when necessary.
- (MSC - 2012/04/18)
-
-* The data conversion test dt_arith.c fails in "long double" to integer
- conversion on Ubuntu 11.10 (3.0.0.13 kernel) with GCC 4.6.1 if the library
- is built with optimization -O3 or -O2. The older GCC (4.5) or newer kernel
- (3.2.2 on Fedora) doesn't have the problem. Users should lower the
- optimization level (-O1 or -O0) by defining CFLAGS in the command line of
- "configure" like:
-
- CFLAGS=-O1 ./configure
-
- This will overwrite the library's default optimization level.
- (SLU - 2012/02/07 - HDFFV-7829)
-
-* The STDIO VFD does not work on some architectures, possibly due to 32/64
- bit or large file issues. The basic STDIO VFD test is known to fail on
- 64-bit SunOS 5.10 on SPARC when built with -m64 and 32-bit OS X/Darwin
- 10.7.0. The STDIO VFD test has been disabled while we investigate and
- a fix should appear in a future release.
- (DER - 2011/10/14 - HDFFV-8235)
-
-* h5diff can report inconsistent results when comparing datasets of enum type
- that contain invalid values. This is due to how enum types are handled in
- the library and will be addressed in a future release.
- (DER - 2011/10/14 - HDFFV-7527)
-
-* The links test can fail under the stdio VFD due to some issues with external
- links. This will be investigated and fixed in a future release.
- (DER - 2011/10/14 - HDFFV-7768)
-
-* After the shared library support was fixed for some bugs, it was discovered
- that "make prefix=XXX install" no longer works for shared libraries. It
- still works correctly for static libraries. Therefore, if you want to
- install the HDF5 shared libraries in a location such as /usr/local/hdf5,
- you need to specify the location via the --prefix option during configure
- time. E.g, ./configure --prefix=/usr/local/hdf5 ...
- (AKC - 2011/05/07 - HDFFV-7583)
-
-* The parallel test, t_shapesame, in testpar/, may run for a long time and may
- be terminated by the alarm signal. If that happens, one can increase the
- alarm seconds (default is 1200 seconds = 20 minutes) by setting the
- environment variable, $HDF5_ALARM_SECONDS, to a larger value such as 3600
- (60 minutes). Note that the t_shapesame test may fail in some systems
- (see the "While working on the 1.8.6 release..." problem below). If
- it does, it will waste more time if $HDF5_ALARM_SECONDS is set
- to a larger value.
- (AKC - 2011/05/07)
-
-* The C++ and FORTRAN bindings are not currently working on FreeBSD.
- (QAK - 2011/04/26)
-
-* Shared Fortran libraries are not quite working on AIX. While they are
- generated when --enable-shared is specified, the fortran and hl/fortran
- tests fail. We are looking into the issue. HL and C++ shared libraries
- should now be working as intended, however.
- (MAM - 2011/04/20)
-
-* The --with-mpe configure option does not work with Mpich2.
- (AKC - 2011/03/10)
-
-* While working on the 1.8.6 release of HDF5, a bug was discovered that can
- occur when reading from a dataset in parallel shortly after it has been
- written to collectively. The issue was exposed by a new test in the parallel
- HDF5 test suite, but had existed before that. We believe the problem lies with
- certain MPI implementations and/or file systems.
-
- We have provided a pure MPI test program, as well as a standalone HDF5
- program, that can be used to determine if this is an issue on your system.
- They should be run across multiple nodes with a varying number of processes.
- These programs can be found at:
- http://www.hdfgroup.org/ftp/HDF5/examples/known_problems/
- (NAF - 2011/01/19)
-
-* The library's test dt_arith.c showed a compiler's rounding problem on
- Cygwin when converting from unsigned long long to long double. The
- library's own conversion works fine. We defined a macro for Cygwin to
- skip this test until we can solve the problem.
- (SLU - 2010/05/05 - HDFFV-1264)
-
-* All the VFL drivers aren't backward compatible. In H5FDpublic.h, the
- structure H5FD_class_t changed in 1.8. There is new parameter added to
- get_eoa and set_eoa callback functions. A new callback function
- get_type_map was added in. The public function H5FDrealloc was taken
- out in 1.8. The problem only happens when users define their own driver
- for 1.6 and try to plug in 1.8 library. Because there's only one user
- complaining about it, we (Elena, Quincey, and I) decided to leave it as
- it is (see bug report #1279). Quincey will make a plan for 1.10.
- (SLU - 2010/02/02)
-
-* The --enable-static-exec configure flag will only statically link libraries
- if the static version of that library is present. If only the shared version
- of a library exists (i.e., most system libraries on Solaris, AIX, and Mac,
- for example, only have shared versions), the flag should still result in a
- successful compilation, but note that the installed executables will not be
- fully static. Thus, the only guarantee on these systems is that the
- executable is statically linked with just the HDF5 library.
- (MAM - 2009/11/04)
-
-* Parallel tests failed with 16 processes with data inconsistency at testphdf5
- / dataset_readAll. Parallel tests also failed with 32 and 64 processes with
- collective abort of all ranks at t_posix_compliant / allwrite_allread_blocks
- with MPI IO.
- (CMC - 2009/04/28)
-
-* On an Intel 64 Linux cluster (RH 4, Linux 2.6.9) with Intel 10.0 compilers,
- use -mp -O1 compilation flags to build the libraries. A higher level of
- optimization causes failures in several HDF5 library tests.
-
-* A dataset created or rewritten with a v1.6.3 library or after cannot be read
- with the v1.6.2 library or before when the Fletcher32 EDC filter is enabled.
- There was a bug in the calculation of the Fletcher32 checksum in the
- library before v1.6.3; the checksum value was not consistent between big-
- endian and little-endian systems. This bug was fixed in Release 1.6.3.
- However, after fixing the bug, the checksum value was no longer the same as
- before on little-endian system. Library releases after 1.6.4 can still read
- datasets created or rewritten with an HDF5 library of v1.6.2 or before.
- (SLU - 2005/06/30)
-
-
-%%%%1.8.10%%%%
-
-
-HDF5 version 1.8.10 released on 2012-10-26
-================================================================================
-
-INTRODUCTION
-============
-
-This document describes the differences between HDF5-1.8.9 and
-HDF5 1.8.10, and contains information on the platforms tested and
-known problems in HDF5-1.8.10.
-For more details, see the files HISTORY-1_0-1_8_0_rc3.txt
-and HISTORY-1_8.txt in the release_docs/ directory of the HDF5 source.
-
-Links to the HDF5 1.8.10 source code, documentation, and additional materials
-can be found on the HDF5 web page at:
-
- http://www.hdfgroup.org/products/hdf5/
-
-The HDF5 1.8.10 release can be obtained from:
-
- http://www.hdfgroup.org/HDF5/release/obtain5.html
-
-User documentation for 1.8.10 can be accessed directly at this location:
-
- http://www.hdfgroup.org/HDF5/doc/
-
-New features in the HDF5-1.8.x release series, including brief general
-descriptions of some new and modified APIs, are described in the "What's New
-in 1.8.0?" document:
-
- http://www.hdfgroup.org/HDF5/doc/ADGuide/WhatsNew180.html
-
-All new and modified APIs are listed in detail in the "HDF5 Software Changes
-from Release to Release" document, in the section "Release 1.8.10 (current
-release) versus Release 1.8.9":
-
- http://www.hdfgroup.org/HDF5/doc/ADGuide/Changes.html
-
-If you have any questions or comments, please send them to the HDF Help Desk:
-
- help@hdfgroup.org
-
-
-CONTENTS
-========
-
-- New Features
-- Support for New Platforms, Languages, and Compilers
-- Bug Fixes since HDF5-1.8.9
-- Supported Platforms
-- Supported Configuration Features Summary
-- More Tested Platforms
-- Known Problems
-
-
-New Features
-============
-
- Configuration
- -------------
- - None
-
- Library
- -------
- - Updated to latest autotools and changed all hard *.sh scripts to
- configure managed *.sh.in files. Removed overloading of autotools
- TESTS variable by examples and tests. Renamed configure.in to
- configure.ac. (ADB - 2012/08/23 - HDFFV-8129)
- - The data sieve buffer size was set for all the datasets in the file. It
- could waste memory if any dataset size is smaller than the sieve buffer
- size. Now the library picks the smaller one between the dataset size
- and the sieve buffer size from the file access property. See Issue 7934.
- (SLU - 2012/4/11)
-
- Parallel Library
- ----------------
- - Added the H5Pget_mpio_no_collective_cause() function that retrieves
- reasons why the collective I/O was broken during read/write IO access.
- (JKM - 2012/08/30 HDFFV-8143)
-
- - Added H5Pget_mpio_actual_io_mode_f (MSB - 2012/09/27)
-
- Tools
- -----
- - h5import: Changed to allow the use of h5dump output as input files to
- h5import. h5dump must include the "-p" option to print the properties;
- configuration file is captured output of h5dump. The restrictions are
- that only one dataset with a simple datatype (integer, floating-point,
- or string) can be processed. Integers and floating-point imports from
- h5dump must use the "binary" option for the data file. The string version
- uses the h5dump "-y --width=1" options to disable the indexing printouts,
- print single columns, and obviously NOT use the "binary" option.
- (ADB - 2012/07/19 HDFFV-721)
-
- High-Level APIs
- ---------------
- - None
-
- Fortran API
- -----------
- - Fixed a typo in return value of the nh5dread_f_c function (was 1
- instead of 0 on success); fixed the return value to make it consistent
- with other Fortran functions; cleaned debug statements from the code.
- (EIP - 2012/06/23)
-
- C++ API
- -------
- - None
-
-
-Support for New Platforms, Languages, and Compilers
-===================================================
- - None
-
-Bug Fixes since HDF5-1.8.9
-==========================
-
- Configuration
- -------------
- - Fixed configure --enable-production to not use -O optimization for Lion
- and Mountain Lion systems when gcc (i686-apple-darwin11-llvm-gcc-4.2
- (GCC) 4.2.1) is used. Somehow the -O optimization will cause some of
- the hard conversion code in test/dt_arith.c to fail. HDFFV-8017.
- (AKC - 2012/10/10)
- - Fixed AIX Fortran compiler flags to use appropriate settings for
- debugging, profiling, and optimization situations. HDFFV-8069.
- (AKC 2012/09/27)
-
- Library
- -------
- - Fixed a memory leak exposed when inserting/removing a property
- from a property list several times. HDFFV-8022. (MSC 2012/05/18)
- - The file_image test will fail in the "initial file image and callbacks in
- the core VFD" sub-test if the source directory is read-only as the test
- fails to create its test files in the build directory. This has been
- fixed. HDFFV-8009 (AKC - 2012/07/06)
-
-
- Parallel Library
- ----------------
- - The MPI-POSIX VFD was updated to include the POSIX and Windows
- correctness features added that had already been added to the other VFDs.
- HDFFV-8058/7845. (DER 2012/09/17)
-
- Performance
- -------------
- - Removed program perform/benchpar from the enable-build-all list. The
- program will be retired or moved to another location. HDFFV-8156
- (AKC 2012/10/01)
- - Retired program perform/mpi-perf. Its purpose has been incorporated
- into h5perf. (AKC 2012/09/21)
-
- Tools
- -----
- - h5repack: "h5repack -f NONE file1.h5 out.h5" command failed if
- source file contains chunked dataset and a chunk dim is bigger than
- the dataset dim. Another issue is that the command changed max dims
- if chunk dim is smaller than the dataset dim. These issue occurred
- when dataset size is smaller than 64k (compact size limit) Fixed both.
- HDFFV-8012 (JKM 2012/09/24)
- - h5diff: Fixed the counter in verbose mode (-v, -r) so that it will no
- longer add together the differences between datasets and the differences
- between attributes of those datasets. This change makes the output of
- verbose mode consistent for datasets, groups, and committed datatypes.
- HDFFV-5919 (JKM 2012/09/10)
- - h5diff: Fixed the incorrect result when comparing attribute data
- values and the data type has the same class but different sizes.
- HDFFV-7942 (JKM 2012/08/15)
- - h5dump: Replaced single element fwrite with block writes.
- HDFFV-1208 (ADB 2012/08/13)
- - h5diff: Fixed test failure for "make check" due to failure of
- copying test files when performed in HDF5 source tree. Also applied
- to other tools. HDFFV-8107 (JKM 2012/08/01)
- - ph5diff: Fixed intermittent hang issue on a certain operation in
- parallel mode. It was detected by daily test for comparing
- non-comparable objects, but it could have occurred in other
- operations depending on machine condition. HDFFV-8003 (JKM 2012/08/01)
- - h5diff: Fixed the function COPY_TESTFILES_TO_TESTDIR() of testh5diff.sh
- to better report when there is an error in the file copying.
- HDFFV-8105 (AKC 2012/07/22)
- - h5dump: Fixed the sort by name display to maintain correct parent/child
- relationships between ascending/descending order.
- HDFFV-8095 (ADB 2012/07/12)
- - h5dump: Fixed the display by creation order when using option -n
- (print contents).
- HDFFV-5942 (ADB 2012/07/09)
- - h5dump: Changed to allow H5T_CSET_UTF8 to be displayed in h5dump output.
- Used technique similar to what was done in h5ls (matches library
- options).
- HDFFV-7999 (ADB 2012/05/23)
- - h5diff: Fixed the tool so that it will not check and display the status
- of dangling links without setting the --follow-symlinks option. This
- also improved performance when comparing lots of external links without
- the --follow-symlinks option.
- HDFFV-7998 (JKM 2012/04/26)
-
- F90 API
- -------
-
- - Fixed a typo in return value of the nh5dread_f_c function (was 1
- instead of 0 on success); fixed the return value to make it consistent
- with other Fortran functions; cleaned debug statements from the code.
- (EIP - 2012/06/23)
-
- - Fixed a problem writing/reading control characters to a dataset; writing
- a string containing alerts, backspace, carriage_return, form_feed,
- horizontal_tab, vertical_tab, or new_line is now tested and working.
- (MSB - 2012/09/01)
-
- - Corrected the integer type of H5S_UNLIMITED_F to HSIZE_T (MSB - 2012/09/01)
-
- - Corrected the number of continuation lines in the src files
- to be less than 32 lines for F95 compliance. (MSB - 2012/10/01)
-
- C++ API
- ------
- - None
-
- High-Level APIs:
- ------
-
- - Fixed problem with H5TBdelete_record destroying all data following the
- deletion of a row. (MSB- 2012/7/26)
-
- - Fixed H5LTget_attribute_string not closing an object identifier when an
- error occurs. (MSB- 2012/7/21)
-
- - Corrected the return type of H5TBAget_fill from herr_t to htri_t to
- reflect that a return value of 1 indicates that a fill value is
- present, 0 indicates a fill value is not present, and <0 indicates an
- error.
-
- Fortran High-Level APIs:
- ------
- - None
-
-Supported Platforms
-===================
- AIX 5.3 xlc 10.1.0.5
- (NASA G-ADA) xlC 10.1.0.5
- xlf90 12.1.0.6
-
- Linux 2.6.18-308.13.1.el5PAE GNU C (gcc), Fortran (gfortran), C++ (g++)
- #1 SMP i686 i686 i386 compilers for 32-bit applications;
- (jam) Version 4.1.2 20080704 (Red Hat 4.1.2-52)
- Version 4.6.3
- PGI C, Fortran, C++ Compilers for 32-bit
- applications;
- Version 11.9-0
- Intel(R) C, C++, Fortran Compiler for 32-bit
- applications;
- Version 12.1
- MPICH mpich2-1.4.1p1 compiled with
- gcc 4.1.2 and gfortran 4.1.2
-
- Linux 2.6.18-308.16.1.el5 GNU C (gcc), Fortran (gfortran), C++ (g++)
- #1 SMP x86_64 GNU/Linux compilers for 32-bit applications;
- (koala) Version 4.1.2 20080704 (Red Hat 4.1.2-52)
- Version 4.6.3
- PGI C, Fortran, C++ for 64-bit target on
- x86-64;
- Version 11.9-0
- Version 12.5-0
- Intel(R) C, C++, Fortran Compilers for
- applications running on Intel(R) 64;
- Version 12.1 (Build 20110811)
- Version 12.1 (Build 20120212)
- MPICH mpich2-1.4.1p1 compiled with
- gcc 4.1.2 and gfortran 4.1.2
-
- Linux 2.6.32-220.7.1.el6.ppc64 gcc (GCC) 4.4.6 20110731 (Red Hat 4.4.6-3)
- #1 SMP ppc64 GNU/Linux g++ (GCC) 4.4.6 20110731
- (ostrich) GNU Fortran (GCC) 4.4.6 20110731 (Red Hat 4.4.6-3)
-
- Linux 2.6.32-220.23.1.1chaos Intel C, C++, Fortran Compilers
- ch5.x86_64 GNU/Linux Version 12.1.5.339
- (LLNL Aztec)
-
- IBM Blue Gene/P XL C for Blue Gene/P, bgxlc V9.0
- (LLNL uDawn) XL C++ for Blue Gene/P, bgxlC V9.0
- XL Fortran for Blue Gene/P, bgxlf90 V11.1
-
- SunOS 5.10 32- and 64-bit Sun C 5.9 Sun OS_sparc Patch 124867-16
- (linew) Sun Fortran 95 8.3 Sun OS_sparc Patch 127000-13
- Sun C++ 5.9 Sun OS_sparc Patch 124863-26
- Sun C 5.11 SunOS_sparc
- Sun Fortran 95 8.5 SunOS_sparc
- Sun C++ 5.11 SunOS_sparc
-
- Windows XP Visual Studio 2008 w/ Intel Fortran 10.1 (project files)
-
- Windows XP x64 Visual Studio 2008 w/ Intel Fortran 10.1 (project files)
-
- Windows 7 Visual Studio 2008 w/ Intel Fortran 11.1 (cmake)
- Visual Studio 2010 w/ Intel Fortran 12 (cmake)
- Cygwin(CYGWIN_NT-6.1 1.7.15(0.260/5/3) gcc(4.5.3) compiler and gfortran)
- (cmake and autotools)
-
- Windows 7 x64 Visual Studio 2008 w/ Intel Fortran 11.1 (cmake)
- Visual Studio 2010 w/ Intel Fortran 12 (cmake)
- Cygwin(CYGWIN_NT-6.1 1.7.15(0.260/5/3) gcc(4.5.3) compiler and gfortran)
- (cmake and autotools)
-
- Mac OS X Snow Leopard 10.6.8 gcc i686-apple-darwin11-llvm-gcc-4.2 (GCC) 4.2.1 from Xcode 3.2.6
- Darwin Kernel Version 10.8.0 g++ i686-apple-darwin11-llvm-g++-4.2 (GCC) 4.2.1 from Xcode 3.2.6
- (fred) gfortran GNU Fortran (GCC) 4.6.2
- Intel C (icc), Fortran (ifort), C++ (icpc)
- 12.1.0.038 Build 20110811
-
- Mac OS X Snow Leopard 10.6.8 gcc i686-apple-darwin11-llvm-gcc-4.2 (GCC) 4.2.1 from Xcode 3.2.6
- Darwin Kernel Version 10.8.0 g++ i686-apple-darwin11-llvm-g++-4.2 (GCC) 4.2.1 from Xcode 3.2.6
- Intel 32-bit gfortran GNU Fortran (GCC) 4.6.1
- (tejeda) Intel C (icc), Fortran (ifort), C++ (icpc)
- 12.1.0.038 Build 20110811
-
- Mac OS X Lion 10.7.3 gcc i686-apple-darwin11-llvm-gcc-4.2 (GCC) 4.2.1 from Xcode 4.2.1
- 32- and 64-bit g++ i686-apple-darwin11-llvm-g++-4.2 (GCC) 4.2.1 from Xcode 4.2.1
- (duck) gfortran GNU Fortran (GCC) 4.6.2
-
- Mac OS X Mountain Lion 10.8.1 cc Apple clang version 4.0 from Xcode 4.5.1
- (owl) c++ Apple clang version 4.0 from Xcode 4.5.1
- gcc i686-apple-darwin11-llvm-gcc-4.2 (GCC) 4.2.1 from Xcode 4.5.1
- g++ i686-apple-darwin11-llvm-g++-4.2 (GCC) 4.2.1 from Xcode 4.5.1
- gfortran GNU Fortran (GCC) 4.6.2
-
-
-Tested Configuration Features Summary
-=====================================
-
- In the tables below
- y = tested
- n = not tested in this release
- C = Cluster
- W = Workstation
- x = not working in this release
- dna = does not apply
- ( ) = footnote appears below second table
- <blank> = testing incomplete on this feature or platform
-
-Platform C F90/ F90 C++ zlib SZIP
- parallel F2003 parallel
-Solaris2.10 32-bit n y/y n y y y
-Solaris2.10 64-bit n y/n n y y y
-Windows 7 y y/n n y y y
-Windows 7 x64 y y/n n y y y
-Mac OS X Snow Leopard 10.6.8 32-bit n y/y n y y n
-Mac OS X Snow Leopard 10.6.8 64-bit n y/y n y y y
-Mac OS X Lion 10.7.3 32-bit n y/y n y y n
-Mac OS X Lion 10.7.3 64-bit n y/y n y y y
-Mac OS X Mountain Lion 10.8.1 64-bit n y/n n y y n
-AIX 5.3 32- and 64-bit y y/n y y y y
-CentOS 5.5 Linux 2.6.18-308 i686 GNU y y/y y y y y
-CentOS 5.5 Linux 2.6.18-308 i686 Intel n y/y n y y y
-CentOS 5.5 Linux 2.6.18-308 i686 PGI n y/y n y y y
-CentOS 5.5 Linux 2.6.18 x86_64 GNU y y/y y y y y
-CentOS 5.5 Linux 2.6.18 x86_64 Intel n y/y n y y y
-CentOS 5.5 Linux 2.6.18 x86_64 PGI n y/y n y y y
-Linux 2.6.32-220.7.1.el6.ppc64 n y/n n y y y
-
-
-Platform Shared Shared Shared Thread-
- C libs F90 libs C++ libs safe
-Solaris2.10 32-bit y y y y
-Solaris2.10 64-bit n n n n
-Windows 7 y y y y
-Windows 7 x64 y y y y
-Mac OS X Snow Leopard 10.6.8 32-bit y n y n
-Mac OS X Snow Leopard 10.6.8 64-bit y n y n
-Mac OS X Lion 10.7.3 32-bit y n y y
-Mac OS X Lion 10.7.3 64-bit y n y y
-Mac OS X Mountain Lion 10.8.1 64-bit y n y y
-AIX 5.3 32- and 64-bit n n n y
-CentOS 5.5 Linux 2.6.18-308 i686 GNU y y y y
-CentOS 5.5 Linux 2.6.18-308 i686 Intel y y y n
-CentOS 5.5 Linux 2.6.18-308 i686 PGI y y y n
-CentOS 5.5 Linux 2.6.18 x86_64 GNU y y y y
-CentOS 5.5 Linux 2.6.18 x86_64 Intel y y y n
-CentOS 5.5 Linux 2.6.18 x86_64 PGI y y y n
-Linux 2.6.32-220.7.1.el6.ppc64 y y y n
-
-Compiler versions for each platform are listed in the preceding
-"Supported Platforms" table.
-
-
-More Tested Platforms
-=====================
-The following platforms are not supported but have been tested for this release.
-
- FreeBSD 8.2-STABLE i386 gcc 4.2.1 [FreeBSD] 20070719
- (loyalty) gcc 4.6.1 20110422
- g++ 4.6.1 20110422
- gfortran 4.6.1 20110422
-
- FreeBSD 8.2-STABLE amd64 gcc 4.2.1 [FreeBSD] 20070719
- (freedom) gcc 4.6.1 20110422
- g++ 4.6.1 20110422
- gfortran 4.6.1 20110422
-
- Debian6.0.3 2.6.32-5-686 #1 SMP i686 GNU/Linux
- gcc (Debian 4.4.5-8) 4.4.5
- GNU Fortran (Debian 4.4.5-8) 4.4.5
- (cmake and autotools)
-
- Debian6.0.3 2.6.32-5-amd64 #1 SMP x86_64 GNU/Linux
- gcc (Debian 4.4.5-8) 4.4.5
- GNU Fortran (Debian 4.4.5-8) 4.4.5
- (cmake and autotools)
-
- Fedora17 3.5.2-1.fc17.i6866 #1 SMP i686 i686 i386 GNU/Linux
- gcc (GCC) 4.7.0 20120507 (Red Hat 4.7.0-5)
- GNU Fortran (GCC) 4.7.0 20120507 (Red Hat 4.7.0-5)
- (cmake and autotools)
-
- Fedora17 3.5.2-1.fc17.x86_64 #1 SMP x86_64 x86_64 x86_64 GNU/Linux
- gcc (GCC) 4.7.0 20120507 (Red Hat 4.7.0-5)
- GNU Fortran (GCC) 4.7.0 20120507 (Red Hat 4.7.0-5)
- (cmake and autotools)
-
- SUSE 12.2 3.4.6-2.10-desktop #1 SMP PREEMPT i686 i686 i386 GNU/Linux
- gcc (SUSE Linux) 4.7.1
- GNU Fortran (SUSE Linux) 4.7.1
- (cmake and autotools)
-
- SUSE 12.2 3.4.6-2.10-desktop #1 SMP PREEMPT x86_64 x86_64 x86_64 GNU/Linux
- gcc (SUSE Linux) 4.7.1
- GNU Fortran (SUSE Linux) 4.7.1
- (cmake and autotools)
-
- Ubuntu 12.04 3.2.0-29-generic #46-Ubuntu SMP i686 GNU/Linux
- gcc (Ubuntu/Linaro 4.6.3-1ubuntu5) 4.6.3
- GNU Fortran (Ubuntu/Linaro 4.6.3-1ubuntu5) 4.6.3
- (cmake and autotools)
-
- Ubuntu 12.04 3.2.0-29-generic #46-Ubuntu SMP x86_64 GNU/Linux
- gcc (Ubuntu/Linaro 4.6.3-1ubuntu5) 4.6.3
- GNU Fortran (Ubuntu/Linaro 4.6.3-1ubuntu5) 4.6.3
- (cmake and autotools)
- (Use optimization level -O1)
-
- Cray Linux Environment (CLE) PrgEnv-pgi/4.0.46
- hopper.nersc.gov pgcc 12.5-0 64-bit target on x86-64 Linux -tp shanghai
- pgf90 12.5-0 64-bit target on x86-64 Linux -tp shanghai
- pgCC 12.5-0 64-bit target on x86-64 Linux -tp shanghai
-
-
-Known Problems
-==============
-* The following h5stat test case fails in BG/P machines (and potentially other
- machines that display extra output if an MPI task returns with a non-zero
- code.)
- Testing h5stat notexist.h5
-
- The test actually runs and passes as expected. It is the extra output from
- the MPI process that causes the test script to fail. This will be fixed
- in the next release. (AKC - 2012/10/25 - HDFFV-8233)
-
-* The C++ and FORTRAN bindings are not currently working on FreeBSD with the
- native release 8.2 compilers (4.2.1), but are working with gcc 4.6 from the
- ports (and probably gcc releases after that).
- (QAK - 2012/10/19)
-
-* The following h5dump test case fails in BG/P machines (and potentially other
- machines that use a command script to launch executables):
-
- h5dump --no-compact-subset -d "AHFINDERDIRECT::ah_centroid_t[0] it=0 tl=0"
- tno-subset.h5
-
- This is due to the embedded spaces in the dataset name being interpreted
- by the command script launcher as meta-characters, thus passing three
- arguments to h5dump's -d flag. The command passes if run by hand, just
- not via the test script.
- (AKC - 2012/05/03)
-
-* On hopper, the build failed when RUNSERIAL and RUNPARALLEL are set
- to aprun -np X, because the H5lib_settings.c file was not generated
- properly. Not setting those environment variables works, because
- configure was able to automatically detect that it's a Cray system
- and used the proper launch commands when necessary.
- (MSC - 2012/04/18)
-
-* The data conversion test dt_arith.c fails in "long double" to integer
- conversion on Ubuntu 11.10 (3.0.0.13 kernel) with GCC 4.6.1 if the library
- is built with optimization -O3 or -O2. The older GCC (4.5) or newer kernel
- (3.2.2 on Fedora) doesn't have the problem. Users should lower the
- optimization level (-O1 or -O0) by defining CFLAGS in the command line of
- "configure" like:
-
- CFLAGS=-O1 ./configure
-
- This will overwrite the library's default optimization level.
- (SLU - 2012/02/07 - HDFFV-7829)
-
-* The STDIO VFD does not work on some architectures, possibly due to 32/64
- bit or large file issues. The basic STDIO VFD test is known to fail on
- 64-bit SunOS 5.10 on SPARC when built with -m64 and 32-bit OS X/Darwin
- 10.7.0. The STDIO VFD test has been disabled while we investigate and
- a fix should appear in a future release.
- (DER - 2011/10/14 - HDFFV-8235)
-
-* h5diff can report inconsistent results when comparing datasets of enum type
- that contain invalid values. This is due to how enum types are handled in
- the library and will be addressed in a future release.
- (DER - 2011/10/14 - HDFFV-7527)
-
-* The links test can fail under the stdio VFD due to some issues with external
- links. This will be investigated and fixed in a future release.
- (DER - 2011/10/14 - HDFFV-7768)
-
-* After the shared library support was fixed for some bugs, it was discovered
- that "make prefix=XXX install" no longer works for shared libraries. It
- still works correctly for static libraries. Therefore, if you want to
- install the HDF5 shared libraries in a location such as /usr/local/hdf5,
- you need to specify the location via the --prefix option during configure
- time. E.g, ./configure --prefix=/usr/local/hdf5 ...
- (AKC - 2011/05/07 - HDFFV-7583)
-
-* The parallel test, t_shapesame, in testpar/, may run for a long time and may
- be terminated by the alarm signal. If that happens, one can increase the
- alarm seconds (default is 1200 seconds = 20 minutes) by setting the
- environment variable, $HDF5_ALARM_SECONDS, to a larger value such as 3600
- (60 minutes). Note that the t_shapesame test may fail in some systems
- (see the "While working on the 1.8.6 release..." problem below). If
- it does, it will waste more time if $HDF5_ALARM_SECONDS is set
- to a larger value.
- (AKC - 2011/05/07)
-
-* The C++ and FORTRAN bindings are not currently working on FreeBSD.
- (QAK - 2011/04/26)
-
-* Shared Fortran libraries are not quite working on AIX. While they are
- generated when --enable-shared is specified, the fortran and hl/fortran
- tests fail. We are looking into the issue. HL and C++ shared libraries
- should now be working as intended, however.
- (MAM - 2011/04/20)
-
-* The --with-mpe configure option does not work with Mpich2.
- (AKC - 2011/03/10)
-
-* While working on the 1.8.6 release of HDF5, a bug was discovered that can
- occur when reading from a dataset in parallel shortly after it has been
- written to collectively. The issue was exposed by a new test in the parallel
- HDF5 test suite, but had existed before that. We believe the problem lies with
- certain MPI implementations and/or file systems.
-
- We have provided a pure MPI test program, as well as a standalone HDF5
- program, that can be used to determine if this is an issue on your system.
- They should be run across multiple nodes with a varying number of processes.
- These programs can be found at:
- http://www.hdfgroup.org/ftp/HDF5/examples/known_problems/
- (NAF - 2011/01/19)
-
-* The library's test dt_arith.c showed a compiler's rounding problem on
- Cygwin when converting from unsigned long long to long double. The
- library's own conversion works fine. We defined a macro for Cygwin to
- skip this test until we can solve the problem.
- (SLU - 2010/05/05 - HDFFV-1264)
-
-* All the VFL drivers aren't backward compatible. In H5FDpublic.h, the
- structure H5FD_class_t changed in 1.8. There is new parameter added to
- get_eoa and set_eoa callback functions. A new callback function
- get_type_map was added in. The public function H5FDrealloc was taken
- out in 1.8. The problem only happens when users define their own driver
- for 1.6 and try to plug in 1.8 library. Because there's only one user
- complaining about it, we (Elena, Quincey, and I) decided to leave it as
- it is (see bug report #1279). Quincey will make a plan for 1.10.
- (SLU - 2010/02/02)
-
-* The --enable-static-exec configure flag will only statically link libraries
- if the static version of that library is present. If only the shared version
- of a library exists (i.e., most system libraries on Solaris, AIX, and Mac,
- for example, only have shared versions), the flag should still result in a
- successful compilation, but note that the installed executables will not be
- fully static. Thus, the only guarantee on these systems is that the
- executable is statically linked with just the HDF5 library.
- (MAM - 2009/11/04)
-
-* Parallel tests failed with 16 processes with data inconsistency at testphdf5
- / dataset_readAll. Parallel tests also failed with 32 and 64 processes with
- collective abort of all ranks at t_posix_compliant / allwrite_allread_blocks
- with MPI IO.
- (CMC - 2009/04/28)
-
-* On an Intel 64 Linux cluster (RH 4, Linux 2.6.9) with Intel 10.0 compilers,
- use -mp -O1 compilation flags to build the libraries. A higher level of
- optimization causes failures in several HDF5 library tests.
-
-* A dataset created or rewritten with a v1.6.3 library or after cannot be read
- with the v1.6.2 library or before when the Fletcher32 EDC filter is enabled.
- There was a bug in the calculation of the Fletcher32 checksum in the
- library before v1.6.3; the checksum value was not consistent between big-
- endian and little-endian systems. This bug was fixed in Release 1.6.3.
- However, after fixing the bug, the checksum value was no longer the same as
- before on little-endian system. Library releases after 1.6.4 can still read
- datasets created or rewritten with an HDF5 library of v1.6.2 or before.
- (SLU - 2005/06/30)
-
-
-%%%%1.8.9%%%%
-
-
-HDF5 version 1.8.9 released on 2012-05-09
-================================================================================
-
-INTRODUCTION
-============
-
-This document describes the differences between HDF5-1.8.8 and
-HDF5 1.8.9. It also contains information on the platforms tested and
-known problems in HDF5-1.8.9.
-
-For more details, see the files HISTORY-1_0-1_8_0_rc3.txt
-and HISTORY-1_8.txt in the release_docs/ directory of the HDF5 source.
-
-Links to the HDF5 1.8.9 source code, documentation, and additional materials
-can be found on the HDF5 web page at:
-
- http://www.hdfgroup.org/products/hdf5/
-
-The HDF5 1.8.9 release can be obtained from:
-
- http://www.hdfgroup.org/HDF5/release/obtain5.html
-
-User documentation for 1.8.9 can be accessed directly at this location:
-
- http://www.hdfgroup.org/HDF5/doc/
-
-New features in the HDF5-1.8.x release series, including brief general
-descriptions of some new and modified APIs, are described in the "What's New
-in 1.8.0?" document:
-
- http://www.hdfgroup.org/HDF5/doc/ADGuide/WhatsNew180.html
-
-All new and modified APIs are listed in detail in the "HDF5 Software Changes
-from Release to Release" document, in the section "Release 1.8.9 (current
-release) versus Release 1.8.8":
-
- http://www.hdfgroup.org/HDF5/doc/ADGuide/Changes.html
-
-If you have any questions or comments, please send them to the HDF Help Desk:
-
- help@hdfgroup.org
-
-
-CONTENTS
-========
-
-- New Features
-- Support for New Platforms, Languages, and Compilers
-- Bug Fixes since HDF5-1.8.8
-- Platforms Tested
-- Supported Configuration Features Summary
-- Known Problems
-
-
-New Features
-============
-
- Configuration
- -------------
- - None
-
- Library
- -------
- - Added new feature to merge committed datatypes when copying objects,
- using new H5O_COPY_MERGE_COMMITTED_DTYPE_FLAG, modified by new API
- routines: H5Padd_merge_committed_dtype_path(),
- H5Pfree_merge_committed_dtype_paths(), H5Pset_mcdt_search_cb() and
- H5Pget_mcdt_search_cb(). (QAK - 2012/03/30)
- - Added new feature which allows working with files in memory in the
- same ways files are worked with on disk. New API routines include
- H5Pset_file_image, H5Pget_file_image, H5Pset_file_image_callbacks,
- H5Pget_file_image_callbacks, H5Fget_file_image, and
- H5LTopen_file_image. (QAK - 2012/04/17)
-
- Parallel Library
- ----------------
- - Corrected memory allocation error in MPI datatype construction code.
- (QAK - 2012/04/23)
- - Add two new routines to set/get the atomicity parameter in the
- MPI library to perform atomic operations. Some file systems (for
- example PVFS2) do not support atomic updates, so those routines
- would not be supported. (MSC - 2012/03/27 - HDFFV-7961)
-
- Tools
- -----
- - h5repack: Added ability to set the metadata block size of the output
- file, with the '-M'/'--metadata_block_size' command line parameter.
- (QAK - 2012/03/30)
- - h5stat: Added ability to display a summary of the file space usage for a
- file, with the '-S'/'--summary' command line parameter. (QAK - 2012/03/28)
- - h5dump: Added capability for "-a" option to show attributes containing "/"
- by using an escape character. For example, for a dataset "/dset"
- containing attribute "speed(m/h)", use "h5dump -a "/dset/speed(\/h)"
- to show the content of the attribute. (PC - 2012/03/12 - HDFFV-7523)
- - h5dump: Added ability to apply command options across multiple files using a
- wildcard in the filename. Unix example; "h5dump -H -d Dataset1 tarr*.h5".
- Cross platform example; "h5dump -H -d Dataset1 tarray1.h5 tarray2.h5 tarray3.h5".
- (ADB - 2012/03/12 - HDFFV-7876).
- - h5dump: Added new option --no-compact-subset. This option will not
- interpret the '[' character as starting the compact form of
- subsetting. This is useful when the "h5dump error: unable to
- open dataset "datset_name"" message is output because a dataset
- name contains a '[' character. (ADB - 2012/03/05 - HDFFV-7689).
- - h5repack: Improved performance for big chunked datasets (size > 128MB)
- when used with the layout (-l) or compression (-f) options.
- Before this change, repacking datasets with chunks with a large first
- dimension would take extremely long. For example, repacking a dataset
- with chunk dimensions of 1024x5x1 might take many hours to process
- while changing a dataset with chunk dimensions set to 1x5x1024
- might take under an hour. After this change, processing the dataset
- with chunk dimensions of 1024x5x1 takes about 15 minutes, and processing
- a dataset with chunk dimensions of 1x5x1024 takes about 14 minutes.
- (JKM - 2012/03/01 - HDFFV-7862)
-
- High-Level APIs
- ---------------
- - New API: H5LTpath_valid (Fortran: h5ltpath_valid_f) checks
- if a path is correct, determines if a link resolves to a valid
- object, and checks that the link does not dangle. (MSB - 2012/03/15)
-
- Fortran API
- -----------
-
- - Added for the C API the Fortran wrapper:
- h5ocopy_f (MSB - 2012/03/22)
-
- C++ API
- -------
- - None
-
-
-Support for New Platforms, Languages, and Compilers
-===================================================
- - None
-
-Bug Fixes since HDF5-1.8.8
-==========================
-
- Configuration
- -------------
- - Fixed Makefile issue in which "-Wl," was not properly specified
- prior to -rpath when building parallel Fortran libraries with
- an Intel compiler. (MAM - 2012/03/26)
- - Makefiles generated by other packages using h5cc as the compiler
- no longer error when 'make' is invoked more than once in order
- to 'rebuild' after changes to source. (MAM - 2012/03/26)
- - Added code to display the version information of XL Fortran and C++
- in the summary of configure. (AKC - 2012/02/28 - HDFFV-7793)
- - Updated all CMakeLists.txt files to indicate the minimum CMake version is
- the current standard of 2.8.6 (ADB - 2011/12/05 - HDFFV-7854)
-
- Library
- -------
- - Windows and STDIO correctness changes have been propagated from the SEC2
- and old Windows drivers to the STDIO VFD. (DER - 2012/03/30 - HDFFV-7917)
- - Fixed an error that would occur when copying an object with attribute
- creation order tracked and indexed. (NAF - 2012/03/28 - HDFFV-7762)
- - Fixed a bug in H5Ocopy(): When copying an opened object, call the
- object's flush class action to ensure that cached data is flushed so
- that H5Ocopy will get the correct data. (VC - 2012/03/27 - HDFFV-7853)
- - The istore test will now skip the sparse 50x50x50 test when the VFD does
- not support sparse files on that platform. The most important platforms
- on which this will be skipped are Windows (NTFS sparse files are not
- supported) and Mac OS-X (HFS sparse files are not supported). This
- fixes CTest timeout issues on Windows. (DER - 2012/03/27 - HDFFV-7769)
- - Windows and POSIX correctness changes have been propagated from the SEC2
- VFD to the Core VFD. This mainly affects file operations on the
- driver's backing store and fixes a problem on Windows where large files
- could not be read. (DER - 2012/03/27 - HDFFV-7916 - HDFFV-7603)
- - When an application tries to write or read many small data chunks and
- runs out of memory, the library had a segmentation fault. The fix is to
- return the error stack with proper information.
- (SLU - 2012/03/23 - HDFFV-7785)
- - H5Pset_data_transform had a segmentation fault in some cases like x*-100.
- It works correctly now and handles other cases like 100-x or 2/x.
- (SLU - 2012/03/15 - HDFFV-7922)
- - Fixed rare corruption bugs that could occur when using the new object
- header format. (NAF - 2012/03/15 - HDFFV-7879)
- - Fixed an error that occurred when creating a contiguous dataset with a
- zero-sized dataspace and space allocation time set to 'early'.
- (QAK - 2012/03/12)
- - Changed Windows thread creation to use _beginthread() instead of
- CreateThread(). Threads created by the latter can be killed in
- low-memory situations. (DER - 2012/02/10 - HDFFV-7780)
- - Creating a dataset in a read-only file caused a segmentation fault when
- the file is closed. It's fixed. The attempt to create a dataset will
- fail with an error indicating the file is read-only.
- (SLU - 2012/01/25 - HDFFV-7756)
- - Fixed a segmentation fault that could occur when shrinking a dataset
- with chunks larger than 1 MB. (NAF - 2011/11/30 - HDFFV-7833)
- - Fixed a bug that could cause H5Oget_info to return the wrong address
- after copying a committed (named) datatype. (NAF - 2011/11/14)
- - The library allowed the conversion of strings between ASCII and UTF8
- We have corrected it to report an error under this situation.
- (SLU - 2011/11/8 - HDFFV-7582)
- - Fixed a segmentation fault when the library tried to shrink the size
- of a compound datatype through H5Tset_size immediately after the
- datatype was created. (SLU - 2011/11/4 - HDFFV-7618)
-
- Parallel Library
- ----------------
- - None
-
- Tools
- -----
- - h5unjam: Fixed a segmentation fault that occurred when h5unjam was used
- with the -V (show version) option. (JKM - 2012/04/19 - HDFFV-8001)
- - h5repack: Fixed a failure that occurred when repacking the chunk size
- of a specified chunked dataset with unlimited max dims.
- (JKM - 2012/04/11 - HDFFV-7993)
- - h5diff: Fixed a failure when comparing groups. Before the fix, if an
- object in a group was compared with an object in another group where
- both had the same name but the object type was different, then h5diff
- would fail. After the fix, h5diff detects such cases as non-comparable
- and displays appropriate error messages.
- (JKM - 2012/03/28 - HDFFV-7644)
- - h5diff: If unique objects exist only in one file and if h5diff is set to
- exclude the unique objects with the --exclude-path option, then h5diff
- might miss excluding some objects. This was fixed to correctly exclude
- objects. (JKM - 2012/03/20 - HDFFV-7837)
- - h5diff: When two symbolic dangling links are compared with the
- --follow-symlinks option, the result should be the same. This worked when
- comparing two files, but didn't work when comparing two objects.
- h5diff now works when comparing two objects.
- (JKM - 2012/03/09 - HDFFV-7835)
- - h5dump: Added the tools library error stack to properly catch error
- information generated within the library. (ADB - 2012/03/12 - HDFFV-7958)
- - h5dump: Changed the process where an open link used to fail. Now dangling
- links no longer throw error messages. (ADB - 2012/03/12 - HDFFV-7839)
- - h5dump: Refactored code to remove duplicated functions. Split XML
- functions from DDL functions. Corrected indentation and formatting
- errors. Also fixed subsetting counting overflow (HDFFV-5874). Verified
- all tools call tools_init() in main. The USER_BLOCK data now correctly
- displays within the SUPER_BLOCK info. NOTE: WHITESPACE IN THE OUTPUT
- HAS CHANGED. (ADB - 2012/02/17 - HDFFV-7560)
- - h5diff: Fixed to prevent from displaying error stack message when
- comparing two dangling symbolic links with the follow-symlinks option.
- (JKM - 2012/01/13 - HDFFV-7836)
- - h5repack: Fixed a memory leak that occurred with the handling of
- variable length strings in attributes.
- (JKM - 2012/01/10 - HDFFV-7840)
- - h5ls: Fixed a segmentation fault that occurred when accessing region
- reference data in an attribute. (JKM - 2012/01/06 - HDFFV-7838)
-
- F90 API
- -------
- - None
-
- C++ API
- ------
- - None
-
- High-Level APIs:
- ------
- - None
-
- Fortran High-Level APIs:
- ------
- - h5ltget_attribute_string_f: The h5ltget_attribute_string_f used to return
- the C NULL character in the returned character buffer. The returned
- character buffer now does not return the C NULL character; the buffer
- is blank-padded if needed. (MSB - 2012/03/23)
-
-
-Platforms Tested
-================
-The following platforms and compilers have been tested for this release.
-
- AIX 5.3 xlc 10.1.0.5
- (NASA G-ADA) xlC 10.1.0.5
- xlf90 12.1.0.6
-
- FreeBSD 8.2-STABLE i386 gcc 4.2.1 [FreeBSD] 20070719
- (loyalty) g++ 4.2.1 [FreeBSD] 20070719
- gcc 4.6.1 20110422
- g++ 4.6.1 20110422
- gfortran 4.6.1 20110422
-
- FreeBSD 8.2-STABLE amd64 gcc 4.2.1 [FreeBSD] 20070719
- (freedom) g++ 4.2.1 [FreeBSD] 20070719
- gcc 4.6.1 20110422
- g++ 4.6.1 20110422
- gfortran 4.6.1 20110422
-
- Linux 2.6.18-194.3.1.el5PAE GNU C (gcc), Fortran (gfortran), C++ (g++)
- #1 SMP i686 i686 i386 compilers for 32-bit applications;
- (jam) Version 4.1.2 20080704 (Red Hat 4.1.2-52)
- Version 4.5.2
- PGI C, Fortran, C++ Compilers for 32-bit
- applications;
- Version 11.8-0
- Version 11.9-0
- Intel(R) C, C++, Fortran Compiler for 32-bit
- applications;
- Version 12.0
- Version 12.1
- MPICH mpich2-1.3.1 compiled with
- gcc 4.1.2 and gfortran 4.1.2
-
- Linux 2.6.18-308.1.1.el5 GNU C (gcc), Fortran (gfortran), C++ (g++)
- #1 SMP x86_64 GNU/Linux compilers for 32-bit applications;
- (koala) Version 4.1.2 20080704 (Red Hat 4.1.2-52)
- Version 4.5.2
- PGI C, Fortran, C++ for 64-bit target on
- x86-64;
- Version 11.9-0 (64-bit)
- Version 11.8-0 (32-bit)
- Intel(R) C, C++, Fortran Compilers for
- applications running on Intel(R) 64;
- Version 12.0
- Version 12.1
- MPICH mpich2-1.3.1 compiled with
- gcc 4.1.2 and gfortran 4.1.2
-
- Linux 2.6.32-220.7.1.el6.ppc64 gcc (GCC) 4.4.6 20110731 (Red Hat 4.4.6-3)
- #1 SMP ppc64 GNU/Linux g++ (GCC) 4.4.6 20110731
- (ostrich) GNU Fortran (GCC) 4.4.6 20110731 (Red Hat 4.4.6-3)
-
- Linux 2.6.18-108chaos Intel C, C++, Fortran Compilers Version 11.1
- #1 SMP x86_64 GNU/Linux
- (LLNL Aztec)
-
- IBM Blue Gene/P XL C for Blue Gene/P, bgxlc V9.0
- (LLNL uDawn) XL C++ for Blue Gene/P, bgxlC V9.0
- XL Fortran for Blue Gene/P, bgxlf0 V11.1
-
- SunOS 5.10 32- and 64-bit Sun C 5.9 Sun OS_sparc Patch 124867-16
- (linew) Sun Fortran 95 8.3 Sun OS_sparc Patch 127000-13
- Sun C++ 5.9 Sun OS_sparc Patch 124863-26
- Sun C 5.11 SunOS_sparc
- Sun Fortran 95 8.5 SunOS_sparc
- Sun C++ 5.11 SunOS_sparc
-
- SGI Altix UV Intel(R) C, Fortran Compilers
- SGI ProPack 7 Linux Version 11.1 20100806
- 2.6.32.24-0.2.1.2230.2.PTF- SGI MPT 2.02
- default #1 SMP
- (NCSA ember)
-
- Dell NVIDIA Cluster Intel(R) C, Fortran Compilers
- Red Hat Enterprise Linux 6 Version 12.0.4 20110427
- 2.6.32-131.4.1.el6.x86_64 mvapich2 1.7rc1-intel-12.0.4
- (NCSA forge)
-
- Windows XP Visual Studio 2008 w/ Intel Fortran 10.1 (project files)
- Visual Studio 2008 w/ Intel Fortran 11.1 (cmake)
- Visual Studio 2010 w/ Intel Fortran 12 (cmake)
-
- Windows XP x64 Visual Studio 2008 w/ Intel Fortran 10.1 (project files)
- Visual Studio 2008 w/ Intel Fortran 11.1 (cmake)
- Visual Studio 2010 w/ Intel Fortran 12 (cmake)
-
- Windows 7 Visual Studio 2008 w/ Intel Fortran 11.1 (cmake)
- Visual Studio 2010 w/ Intel Fortran 12 (cmake)
- Cygwin(1.7.9 native gcc(4.5.3) compiler and gfortran)
-
- Windows 7 x64 Visual Studio 2008 w/ Intel Fortran 11.1 (cmake)
- Visual Studio 2010 w/ Intel Fortran 12 (cmake)
- Cygwin(1.7.9 native gcc(4.5.3) compiler and gfortran)
-
- Mac OS X Snow Leopard 10.6.8 i686-apple-darwin10-gcc-4.2.1 (GCC) 4.2.1 (gcc)
- Darwin Kernel Version 10.8.0 i686-apple-darwin10-g++-4.2.1 (GCC) 4.2.1 (g++)
- Intel 64-bit (Apple Inc. build 5666) (dot 3)
- (fred) GNU Fortran (GCC) 4.6.1 (gfortran)
- Intel C (icc), Fortran (ifort), C++ (icpc)
- 12.1.0.038 Build 20110811
-
- Mac OS X Snow Leopard 10.6.8 i686-apple-darwin10-gcc-4.2.1 (GCC) 4.2.1 (gcc)
- Darwin Kernel Version 10.8.0 i686-apple-darwin10-g++-4.2.1 (GCC) 4.2.1 (g++)
- Intel 32-bit (Apple Inc. build 5666) (dot 3)
- (tejeda) GNU Fortran (GCC) 4.6.1 (gfortran)
- Intel C (icc), Fortran (ifort), C++ (icpc)
- 12.1.0.038 Build 20110811
-
- Mac OS X Lion 10.7.3 GCC 4.2.1 gcc
- 32- and 64-bit GNU Fortran (GCC) 4.6.1 gfortran
- (duck) GCC 4.2.1. g++
-
- Debian6.0.3 2.6.32-5-686 #1 SMP i686 GNU/Linux
- gcc (Debian 4.4.5-8) 4.4.5
- GNU Fortran (Debian 4.4.5-8) 4.4.5
-
- Debian6.0.3 2.6.32-5-amd64 #1 SMP x86_64 GNU/Linux
- gcc (Debian 4.4.5-8) 4.4.5
- GNU Fortran (Debian 4.4.5-8) 4.4.5
-
- Fedora16 3.2.9-2.fc16.i6866 #1 SMP i686 i686 i386 GNU/Linux
- gcc (GCC) 4.6.2 20111027 (Red Hat 4.6.2-1)
- GNU Fortran (GCC) 4.6.2 20111027 (Red Hat 4.6.2-1)
-
- Fedora16 3.2.9-2.fc16.x86_64 #1 SMP x86_64 x86_64 x86_64 GNU/Linux
- gcc (GCC) 4.6.2 20111027 (Red Hat 4.6.2-1)
- GNU Fortran (GCC) 4.6.2 20111027 (Red Hat 4.6.2-1)
-
- SUSE 12.1 3.1.9-1.4-desktop #1 SMP PREEMPT i686 i686 i386 GNU/Linux
- gcc (SUSE Linux) 4.6.2
- GNU Fortran (SUSE Linux) 4.6.2
-
- SUSE 12.1 3.1.9-1.4-desktop #1 SMP PREEMPT x86_64 x86_64 x86_64 GNU/Linux
- gcc (SUSE Linux) 4.6.2
- GNU Fortran (SUSE Linux) 4.6.2
-
- Ubuntu 11.10 3.0.0-16-generic #29-Ubuntu SMP i686 GNU/Linux
- gcc (Ubuntu/Linaro 4.6.1-9ubuntu3) 4.6.1
- GNU Fortran (Ubuntu/Linaro 4.6.4-9ubuntu3) 4.6.1
-
- Ubuntu 11.10 3.0.0-16-generic #29-Ubuntu SMP x86_64 GNU/Linux
- gcc (Ubuntu/Linaro 4.6.1-9ubuntu3) 4.6.1
- GNU Fortran (Ubuntu/Linaro 4.6.1-9ubuntu3) 4.6.1
-
- Cray Linux Environment (CLE) PrgEnv-pgi 2.2.74
- hopper.nersc.gov pgcc 11.9-0 64-bit target on x86-64 Linux -tp k8e
- pgf90 11.9-0 64-bit target on x86-64 Linux -tp k8e
- pgCC 11.9-0 64-bit target on x86-64 Linux -tp k8e
-
-
-Tested Configuration Features Summary
-=====================================
-
- In the tables below
- y = tested
- n = not tested in this release
- C = Cluster
- W = Workstation
- x = not working in this release
- dna = does not apply
- ( ) = footnote appears below second table
- <blank> = testing incomplete on this feature or platform
-
-Platform C F90 F90 C++ zlib SZIP
- parallel parallel
-Solaris2.10 32-bit n y n y y y
-Solaris2.10 64-bit n y n y y y
-Windows XP n y(4) n y y y
-Windows XP x64 n y(4) n y y y
-Windows Vista n y(4) n y y y
-Windows Vista x64 n y(4) n y y y
-Mac OS X Snow Leopard 10.6.8 32-bit n y n y y n
-Mac OS X Snow Leopard 10.6.8 64-bit n y n y y y
-Mac OS X Lion 10.7.3 32-bit n y n y y n
-Mac OS X Lion 10.7.3 64-bit n y n y y y
-AIX 5.3 32- and 64-bit y y y y y y
-FreeBSD 8.2-STABLE 32&64 bit n x n x y y
-CentOS 5.5 Linux 2.6.18-194 i686 GNU (1)W y y(2) y y y y
-CentOS 5.5 Linux 2.6.18-194 i686 Intel W n y n y y y
-CentOS 5.5 Linux 2.6.18-194 i686 PGI W n y n y y y
-CentOS 5.5 Linux 2.6.18 x86_64 GNU (1) W y y(3) y y y y
-CentOS 5.5 Linux 2.6.18 x86_64 Intel W n y n y y y
-CentOS 5.5 Linux 2.6.18 x86_64 PGI W n y n y y y
-Linux 2.6.32-220.7.1.el6.ppc64 n y n y y y
-SGI ProPack 7 Linux 2.6.32.24 y y y y y y
-Red Hat Enterprise Linux 6 y y y y y y
-CLE hopper.nersc.gov y y(3) y y y n
-
-
-Platform Shared Shared Shared Thread-
- C libs F90 libs C++ libs safe
-Solaris2.10 32-bit y y y y
-Solaris2.10 64-bit n n n n
-Windows XP y y(4) y n
-Windows XP x64 y y(4) y n
-Windows Vista y y(4) y y
-Windows Vista x64 y y(4) y y
-Mac OS X Snow Leopard 10.6.8 32-bit y n y n
-Mac OS X Snow Leopard 10.6.8 64-bit y n y n
-Mac OS X Lion 10.7.3 32-bit y n y y
-Mac OS X Lion 10.7.3 64-bit y n y y
-AIX 5.3 32- and 64-bit n n n y
-FreeBSD 8.2-STABLE 32&64 bit y x x y
-CentOS 5.5 Linux 2.6.18-194 i686 GNU (1)W y y(2) y y
-CentOS 5.5 Linux 2.6.18-194 i686 Intel W y y y n
-CentOS 5.5 Linux 2.6.18-194 i686 PGI W y y y n
-CentOS 5.5 Linux 2.6.18 x86_64 GNU (1) W y y y y
-CentOS 5.5 Linux 2.6.18 x86_64 Intel W y y y n
-CentOS 5.5 Linux 2.6.18 x86_64 PGI W y y y n
-Linux 2.6.32-220.7.1.el6.ppc64 y y y n
-SGI ProPack 7 Linux 2.6.32.24 y y y n
-Red Hat Enterprise Linux 6 y y y n
-CLE hopper.nersc.gov n n n n
-
- (1) Fortran compiled with gfortran.
- (2) With PGI and Absoft compilers.
- (3) With PGI compiler for Fortran.
- (4) Using Visual Studio 2008 w/ Intel Fortran 10.1 (Cygwin shared libraries are not supported)
- (5) C and C++ shared libraries will not be built when Fortran is enabled.
- Compiler versions for each platform are listed in the preceding
- "Platforms Tested" table.
-
-
-Known Problems
-==============
-* The h5repacktst test fails on AIX 32-bit because the test uses more
- memory than the default amount. The failure message typically looks like:
-
- "time: 0551-010 The process was stopped abnormally. Try again."
-
- This is an issue with the test only and does not represent a problem with
- the library. To allow the test to pass, request more memory when testing
- via appropriate command such as:
-
- $ env LDR_CNRTL=MAXDATA=0x20000000@DSA make check
-
- (AKC - 2012/05/09 - HDFFV-8016)
-
-* The file_image test will fail in the "initial file image and callbacks in
- the core VFD" sub-test if the source directory is read-only as the test
- fails to create its test files in the build directory. This will be
- resolved in a future release.
- (AKC - 2012/05/05 - HDFFV-8009)
-
-* The dt_arith test reports several errors involving "long double" on
- Mac OS X 10.7 Lion when any level of optimization is enabled. The test does
- not fail in debug mode. This will be addressed in a future release.
- (SLU - 2012/05/08)
-
-* The following h5dump test case fails in BG/P machines (and potentially other
- machines that use a command script to launch executables):
-
- h5dump --no-compact-subset -d "AHFINDERDIRECT::ah_centroid_t[0] it=0 tl=0"
- tno-subset.h5
-
- This is due to the embedded spaces in the dataset name being interpreted
- by the command script launcher as meta-characters, thus passing three
- arguments to h5dump's -d flag. The command passes if run by hand, just
- not via the test script.
- (AKC - 2012/05/03)
-
-* The ph5diff (parallel h5diff) tool can intermittently hang in parallel mode
- when comparing two HDF5 files that contain objects with the same names but
- with different object types.
- (JKM - 2012/04/27)
-
-* On hopper, the build failed when RUNSERIAL and RUNPARALLEL are set
- to aprun -np X, because the H5lib_settings.c file was not generated
- properly. Not setting those environment variables works, because
- configure was able to automatically detect that it's a Cray system
- and used the proper launch commands when necessary.
- (MSC - 2012/04/18)
-
-* The data conversion test dt_arith.c fails in "long double" to integer
- conversion on Ubuntu 11.10 (3.0.0.13 kernel) with GCC 4.6.1 if the library
- is built with optimization -O3 or -O2. The older GCC (4.5) or newer kernel
- (3.2.2 on Fedora) doesn't have the problem. Users should lower the
- optimization level (-O1 or -O0) by defining CFLAGS in the command line of
- "configure" like:
-
- CFLAGS=-O1 ./configure
-
- This will overwrite the library's default optimization level.
- (SLU - 2012/02/07 - HDFFV-7829)
-
-* The STDIO VFD does not work on some architectures, possibly due to 32/64
- bit or large file issues. The basic STDIO VFD test is known to fail on
- 64-bit SunOS 5.10 on SPARC when built with -m64 and 32-bit OS X/Darwin
- 10.7.0. The STDIO VFD test has been disabled while we investigate and
- a fix should appear in a future release.
- (DER - 2011/10/14)
-
-* h5diff can report inconsistent results when comparing datasets of enum type
- that contain invalid values. This is due to how enum types are handled in
- the library and will be addressed in a future release.
- (DER - 2011/10/14 - HDFFV-7527)
-
-* The links test can fail under the stdio VFD due to some issues with external
- links. This will be investigated and fixed in a future release.
- (DER - 2011/10/14 - HDFFV-7768)
-
-* After the shared library support was fixed for some bugs, it was discovered
- that "make prefix=XXX install" no longer works for shared libraries. It
- still works correctly for static libraries. Therefore, if you want to
- install the HDF5 shared libraries in a location such as /usr/local/hdf5,
- you need to specify the location via the --prefix option during configure
- time. E.g, ./configure --prefix=/usr/local/hdf5 ...
- (AKC - 2011/05/07 - HDFFV-7583)
-
-* The parallel test, t_shapesame, in testpar/, may run for a long time and may
- be terminated by the alarm signal. If that happens, one can increase the
- alarm seconds (default is 1200 seconds = 20 minutes) by setting the
- environment variable, $HDF5_ALARM_SECONDS, to a larger value such as 3600
- (60 minutes). Note that the t_shapesame test may fail in some systems
- (see the "While working on the 1.8.6 release..." problem below). If
- it does, it will waste more time if $HDF5_ALARM_SECONDS is set
- to a larger value.
- (AKC - 2011/05/07)
-
-* The C++ and FORTRAN bindings are not currently working on FreeBSD.
- (QAK - 2011/04/26)
-
-* Shared Fortran libraries are not quite working on AIX. While they are
- generated when --enable-shared is specified, the fortran and hl/fortran
- tests fail. We are looking into the issue. HL and C++ shared libraries
- should now be working as intended, however.
- (MAM - 2011/04/20)
-
-* The --with-mpe configure option does not work with Mpich2.
- (AKC - 2011/03/10)
-
-* While working on the 1.8.6 release of HDF5, a bug was discovered that can
- occur when reading from a dataset in parallel shortly after it has been
- written to collectively. The issue was exposed by a new test in the parallel
- HDF5 test suite, but had existed before that. We believe the problem lies with
- certain MPI implementations and/or file systems.
-
- We have provided a pure MPI test program, as well as a standalone HDF5
- program, that can be used to determine if this is an issue on your system.
- They should be run across multiple nodes with a varying number of processes.
- These programs can be found at:
- http://www.hdfgroup.org/ftp/HDF5/examples/known_problems/
- (NAF - 2011/01/19)
-
-* The library's test dt_arith.c showed a compiler's rounding problem on
- Cygwin when converting from unsigned long long to long double. The
- library's own conversion works fine. We defined a macro for Cygwin to
- skip this test until we can solve the problem.
- (SLU - 2010/05/05 - HDFFV-1264)
-
-* All the VFL drivers aren't backward compatible. In H5FDpublic.h, the
- structure H5FD_class_t changed in 1.8. There is new parameter added to
- get_eoa and set_eoa callback functions. A new callback function
- get_type_map was added in. The public function H5FDrealloc was taken
- out in 1.8. The problem only happens when users define their own driver
- for 1.6 and try to plug in 1.8 library. Because there's only one user
- complaining about it, we (Elena, Quincey, and I) decided to leave it as
- it is (see bug report #1279). Quincey will make a plan for 1.10.
- (SLU - 2010/02/02)
-
-* MinGW has a missing libstdc++.dll.a library file and will not successfully link
- C++ applications/tests. Do not use the enable-cxx configure option. Read all of
- the INSTALL_MINGW.txt file for all restrictions.
- (ADB - 2009/11/11)
-
-* The --enable-static-exec configure flag will only statically link libraries
- if the static version of that library is present. If only the shared version
- of a library exists (i.e., most system libraries on Solaris, AIX, and Mac,
- for example, only have shared versions), the flag should still result in a
- successful compilation, but note that the installed executables will not be
- fully static. Thus, the only guarantee on these systems is that the
- executable is statically linked with just the HDF5 library.
- (MAM - 2009/11/04)
-
-* The PathScale MPI implementation, accessing a Panasas file system, would
- cause H5Fcreate() with H5F_ACC_EXCL to fail even when the file does not
- exist. This is due to the MPI_File_open() call failing if the mode has
- the MPI_MODE_EXCL bit set.
- (AKC - 2009/08/11 - HDFFV-988)
-
-* Parallel tests failed with 16 processes with data inconsistency at testphdf5
- / dataset_readAll. Parallel tests also failed with 32 and 64 processes with
- collective abort of all ranks at t_posix_compliant / allwrite_allread_blocks
- with MPI IO.
- (CMC - 2009/04/28)
-
-* For Red Storm, a Cray XT3 system, the tools/h5ls/testh5ls.sh and
- tools/h5copy/testh5copy.sh will fail some of its sub-tests. These sub-tests
- are expected to fail and should exit with a non-zero code but the yod
- command does not propagate the exit code of the executables. Yod always
- returns 0 if it can launch the executable. The test suite shell expects
- a non-zero for this particular test, therefore it concludes the test has
- failed when it receives 0 from yod. Skip all the "failing" test for now
- by changing them as following.
-
- ======== Original tools/h5ls/testh5ls.sh =========
- TOOLTEST tgroup-1.ls 1 -w80 -r -g tgroup.h5
- ======== Change to ===============================
- echo SKIP TOOLTEST tgroup-1.ls 1 -w80 -r -g tgroup.h5
- ==================================================
-
- ======== Original tools/h5copy/testh5copy.sh =========
- TOOLTEST_FAIL -i $TESTFILE -o $FILEOUT -v -s grp_dsets -d grp_rename
- TOOLTEST_FAIL -i $TESTFILE -o $FILEOUT -v -s grp_dsets -d /grp_rename/grp_dsets
- TOOLTEST_FAIL -i $TESTFILE -o $FILEOUT -vp -s /grp_dsets -d /E/F/grp_dsets
- TOOLTEST_FAIL -i $TESTFILE -o $FILEOUT -vp -s /grp_nested -d /G/H/grp_nested
- H5LSTEST $FILEOUT
- ======== Change to ===============================
- echo SKIP TOOLTEST_FAIL -i $TESTFILE -o $FILEOUT -v -s grp_dsets -d grp_rename
- echo SKIP TOOLTEST_FAIL -i $TESTFILE -o $FILEOUT -v -s grp_dsets -d /grp_rename/grp_dsets
- echo SKIP TOOLTEST_FAIL -i $TESTFILE -o $FILEOUT -vp -s /grp_dsets -d /E/F/grp_dsets
- echo SKIP TOOLTEST_FAIL -i $TESTFILE -o $FILEOUT -vp -s /grp_nested -d /G/H/grp_nested
- echo SKIP H5LSTEST $FILEOUT
- ==================================================
- (AKC - 2008/11/10)
-
-* For Red Storm, a Cray XT3 system, the yod command sometimes gives the
- message, "yod allocation delayed for node recovery". This interferes with
- test suites that do not expect to see this message. See the section of "Red
- Storm" in file INSTALL_parallel for a way to deal with this problem.
- (AKC - 2008/05/28)
-
-* On an Intel 64 Linux cluster (RH 4, Linux 2.6.9) with Intel 10.0 compilers,
- use -mp -O1 compilation flags to build the libraries. A higher level of
- optimization causes failures in several HDF5 library tests.
-
-* On mpich 1.2.5 and 1.2.6, if more than two processes contribute no IO and
- the application asks to do collective IO, we have found that when using 4
- processors, a simple collective write will sometimes be hung. This can be
- verified with t_mpi test under testpar.
-
-* A dataset created or rewritten with a v1.6.3 library or after cannot be read
- with the v1.6.2 library or before when the Fletcher32 EDC filter is enabled.
- There was a bug in the calculation of the Fletcher32 checksum in the
- library before v1.6.3; the checksum value was not consistent between big-
- endian and little-endian systems. This bug was fixed in Release 1.6.3.
- However, after fixing the bug, the checksum value was no longer the same as
- before on little-endian system. Library releases after 1.6.4 can still read
- datasets created or rewritten with an HDF5 library of v1.6.2 or before.
- (SLU - 2005/06/30)
-
-* On IBM AIX systems, parallel HDF5 mode will fail some tests with error
- messages like "INFO: 0031-XXX ...". This is from the command `poe'.
- Set the environment variable MP_INFOLEVEL to 0 to minimize the messages
- and run the tests again.
-
- The tests may fail with messages like "The socket name is already in use",
- but HDF5 does not use sockets. This failure is due to problems with the
- poe command trying to set up the debug socket. To resolve this problem,
- check to see whether there are many old /tmp/s.pedb.* files staying around.
- These are sockets used by the poe command and left behind due to failed
- commands. First, ask your system administrator to clean them out.
- Lastly, request IBM to provide a means to run poe without the debug socket.
- (AKC - 2004/12/08)
-
-
-%%%%1.8.8%%%%
-
-
-HDF5 version 1.8.8 released on 2011-11-15
-================================================================================
-
-INTRODUCTION
-============
-
-This document describes the differences between HDF5-1.8.7 and
-HDF5 1.8.8, and contains information on the platforms tested and
-known problems in HDF5-1.8.8.
-For more details, see the files HISTORY-1_0-1_8_0_rc3.txt
-and HISTORY-1_8.txt in the release_docs/ directory of the HDF5 source.
-
-Links to the HDF5 1.8.8 source code, documentation, and additional materials
-can be found on the HDF5 web page at:
-
- http://www.hdfgroup.org/products/hdf5/
-
-The HDF5 1.8.8 release can be obtained from:
-
- http://www.hdfgroup.org/HDF5/release/obtain5.html
-
-User documentation for 1.8.8 can be accessed directly at this location:
-
- http://www.hdfgroup.org/HDF5/doc/
-
-New features in the HDF5-1.8.x release series, including brief general
-descriptions of some new and modified APIs, are described in the "What's New
-in 1.8.0?" document:
-
- http://www.hdfgroup.org/HDF5/doc/ADGuide/WhatsNew180.html
-
-All new and modified APIs are listed in detail in the "HDF5 Software Changes
-from Release to Release" document, in the section "Release 1.8.8 (current
-release) versus Release 1.8.7":
-
- http://www.hdfgroup.org/HDF5/doc/ADGuide/Changes.html
-
-If you have any questions or comments, please send them to the HDF Help Desk:
-
- help@hdfgroup.org
-
-
-CONTENTS
-========
-
-- New Features
-- Support for New Platforms, Languages, and Compilers
-- Bug Fixes since HDF5-1.8.7
-- Platforms Tested
-- Supported Configuration Features Summary
-- Known Problems
-
-
-New Features
-============
-
- Configuration
- -------------
- - Added the --enable-fortran2003 flag to enable Fortran2003 support
- in the HDF5 Fortran library. The flag should be used along with the
- --enable-fortran flag and takes affect only when the Fortran compiler
- is Fortran2003 compliant. (EIP - 2011/11/14)
- - Added checks for clock_gettime and mach/mach_time.h to both configure and
- CMake. This will support the move from gettimeofday to clock_gettime's
- monotonic timer in the profiling code in a future release.
- (DER - 2011/10/12)
-
- Library
- -------
- - The Windows VFD code has been removed with the exception of the functions
- which set it (H5Pset_fapl_windows, for example). Setting the Windows
- VFD now really sets the SEC2 VFD. The WINDOWS_MAX_BUF and
- WINDOWS_USE_STDIO configuration options and #defines have also been
- removed. NOTE: Since the Windows VFD was a clone of the SEC2 VFD, this
- change should be transparent to users.
- (DER - 2011/10/12 - HDFFV-7740, HDFFV-7744)
- - H5Tcreate now supports the string type (fixed-length and variable-
- length). (SLU - 2011/05/20)
-
- Parallel Library
- ----------------
- - Added new H5Pget_mpio_actual_chunk_opt_mode and
- H5Pget_mpio_actual_io_mode API routines for querying whether/how
- a collective I/O operation completed. (QAK - 2011/10/12)
-
- Tools
- -----
- - None
-
- High-Level APIs
- ---------------
- - Added the following Fortran wrappers for the Dimension Scale APIs:
- h5dsset_scale_f
- h5dsattach_scale_f
- h5dsdetach_scale_f
- h5dsis_attached_f
- h5dsis_scale_f
- h5dsset_label_f
- h5dsget_label_f
- h5dsget_scale_name_f
- h5dsget_num_scales_f
- (EIP for SB - 2011/10/13 - HDFFV-3797)
-
- Fortran API
- -----------
- - The HDF5 Fortran library was enhanced to support the Fortran 2003 standard.
- The following features are available when the HDF5 library is configured
- using the --enable-fortran and --enable-fortran2003 configure flags AND
- if the Fortran compiler is Fortran 2003 compliant:
-
- - Subroutines overloaded with the C_PTR derived type:
- h5pget_f
- h5pget_fill_value_f
- h5pinsert_f
- h5pregister_f
- h5pset_f
- h5pset_fill_value_f
- h5rcreate_f
- h5rderefrence_f
- h5rget_name_f
- h5rget_obj_type_f
- - Subroutines overloaded with the C_PTR derived type
- and simplified signatures:
- h5aread_f
- h5awrite_f
- h5dread_f
- h5dwrite_f
- - New subroutines
- h5dvlen_reclaim_f
- h5literate_by_name_f
- h5literate_f
- h5ovisit_f
- h5tconvert_f
- h5pset_nbit_f
- h5pset_scaleoffset_f
- - Subroutines with additional optional parameters:
- h5pcreate_class_f
- (EIP - 2011/10/14)
-
- C++ API
- -------
- - None
-
-
-Support for New Platforms, Languages, and Compilers
-===================================================
- - None
-
-Bug Fixes since HDF5-1.8.7
-==========================
-
- Configuration
- -------------
- - Changed the size of H5_SIZEOF_OFF_T to 4 bytes (was 8) in the VMS
- h5pubconf.h based on the output of a test program. (DER - 2011/10/12)
- - The Windows and VMS versions of H5pubconf.h were brought into sync with
- the linux/posix version. (DER - 2011/10/12)
- - Fixed a bug in the bin/trace Perl script where API functions
- that take a variable number of arguments were not processed for
- trace statement fixup. (DER - 2011/08/25)
- - The --enable-h5dump-packed-bits configure option has been removed.
- The h5dump code that this option conditionally enabled is now always
- compiled into h5dump. Please refer to the h5dump reference manual for
- usage of the packed bits feature. (MAM - 2011/06/23 - HDFFV-7592)
- - Configure now uses the same flags and symbols in its tests that are
- used to build the library. (DER - 2011/05/24)
-
- Library
- -------
- - Corrected the error when copying attributes between files which are using
- different versions of the file format. (QAK - 2011/10/20 - HDFFV-7718)
- - Corrected the error when loading local heaps from the file, which could
- cause the size of the local heap's data block to increase dramatically.
- (QAK - 2011/10/14 - HDFFV-7767)
- - An application does not need to do H5O_move_msgs_forward() when writing
- attributes. Tests were checked into the performance suite.
- (VC - 2011/10/13 - HDFFV-7640)
- - Fixed a bug that occurred when using H5Ocopy on a committed datatype
- containing an attribute using that committed datatype.
- (NAF - 2011/10/13 - HDFFV-5854)
- - Added generic VFD I/O types to the SEC2 and log VFDs to ensure correct
- I/O sizes (and remove compiler warnings) between Windows and true POSIX
- systems. (DER - 2011/10/12)
- - Corrected some Windows behavior in the SEC2 and log VFDs. This mainly
- involved datatype correctness fixes, Windows API call error checks,
- and adding the volume serial number to the VFD cmp functions.
- (DER - 2011/10/12)
- - Converted post-checks for the appropriate POSIX I/O sizes to pre-checks
- in order to avoid platform-specific or undefined behavior.
- (DER - 2011/10/12)
- - #ifdef _WIN32 instances have been changed to #ifdef H5_HAVE_WIN32_API.
- H5_HAVE_VISUAL_STUDIO checks have been added where necessary. This is in
- CMake only as configure never sets _WIN32. (ADB - 2011/09/12)
- - CLANG compiler with the options -fcatch-undefined-behavior and -ftrapv
- discovered 3 problems in tests and tools' library:
- 1. In dsets.c, left shifting an unsigned int for 32 bits or more
- caused undefined behavior.
- 2. In dt_arith.c, the INIT_INTEGER macro definition has an overflow
- when the value is a negative minimal and is being subtracted from one.
- 3. In tools/lib/h5tools_str.c, right shifting an int value for 32 bits
- or more caused undefined behavior.
- All the problems have been corrected. (SLU - 2011/09/02 - HDFFV-7674)
- - H5Epush2() now has the correct trace functionality (this is related to the
- bin/trace Perl script bug noted in the configure section).
- (DER - 2011/08/25)
- - Corrected mismatched function name typo of h5pget_dxpl_mpio_c and
- h5pfill_value_defined_c. (AKC - 2011/08/22 - HDFFV-7641)
- - Corrected an internal error in the library where objects that use committed
- (named) datatypes and were accessed from two different file IDs could confuse
- the two and cause erroneous failures. (QAK - 2011/07/18 - HDFFV-7638)
- - In v1.6 of the library, there was an EOA for the whole MULTI file saved in the
- super block. We took it out in v1.8 of the library because it's meaningless
- for the MULTI file. v1.8 of the library saves the EOA for the metadata file
- instead, but this caused a backward compatibility problem.
- A v1.8 library couldn't open the file created with the v1.6 library. We
- fixed the problem by checking the EOA value to detect the file
- created with v1.6 library. (SLU - 2011/06/22)
- - When a dataset had filters and reading data failed, the error message
- didn't say which filter wasn't registered. It's fixed now. (SLU - 2011/06/03)
-
- Parallel Library
- ----------------
- - The Special Collective IO (IO when some processes do not contribute to the
- IO) and the Complex Derived Datatype MPI functionalities are no longer
- conditionally enabled in the library by configure. They are always
- enabled in order to take advantage of performance boosts from these
- behaviors. Older MPI implementations that do not allow for these
- functionalities can no longer by used by HDF5.
- (MAM - 2011/07/08 - HDFFV-7639).
-
- Tools
- -----
- - h5diff: fixed segfault over non-comparable attribute with different
- dimension or rank, along with '-c' option to display details.
- (JKM - 2011/10/24 - HDFFV-7770)
- - Fixed h5diff to display all the comparable objects and attributes
- regardless of detecting non-comparables. (JKM - 2011/09/16 - HDFFV-7693)
- - Fixed h5repack to update the values of references(object and region) of
- attributes in h5repack for 1) references, 2) arrays of references,
- 3) variable-length references, and 4) compound references.
- (PC - 2011/09/14 - HDFFV-5932)
- - h5diff: fixed a segfault over a dataset with container types
- array and variable-length (vlen) along with multiple nested compound types.
- Example: compound->array->compound, compound->vlen->compound.
- (JKM - 2011/09/01 - HDFFV-7712)
- - h5repack: added macro to handle a failure in H5Dread/write when memory
- allocation failed inside the library. (PC - 2011/08/19)
- - Fixed h5jam to not to allow the specifying of an HDF5 formatted file as
- an input file for the -u (user block file) option. The original HDF5 file
- would not be accessible if this behavior was allowed.
- (JKM - 2011/08/19 - HDFFV-5941)
- - Revised the command help pages of h5jam and h5unjam. The descriptions
- were not up to date and some were missing.
- (JKM - 2011/08/15 - HDFFV-7515)
- - Fixed h5dump to correct the schema location:
- <hdf5:HDF5-File
- xmlns:hdf5="http://hdfgroup.org/HDF5/XML/schema/HDF5-File"
- xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
- xsi:schemaLocation="http://hdfgroup.org/HDF5/XML/schema/HDF5-File
- http://www.hdfgroup.org/HDF5/XML/schema/HDF5-File.xsd">
- (ADB - 2011/08/10)
- - h5repack: h5repack failed to copy a dataset if the layout is changed
- from chunked with unlimited dimensions to contiguous.
- (PC - 2011/07/15 - HDFFV-7649)
- - Fixed h5diff: the "--delta" option considers two NaN of the same type
- are different. This is wrong based on the h5diff description in the
- Reference Manual. (PC - 2011/07/15 - HDFFV-7656)
- - Fixed h5diff to display an instructive error message and exit with
- an instructive error message when mutually exclusive options
- (-d, -p and --use-system-epsilon) are used together.
- (JKM - 2011/07/07 - HDFFV-7600)
- - Fixed h5dump so that it displays the first line of each element in correct
- position for multiple dimension array types. Before this fix,
- the first line of each element in an array was
- displayed after the last line of previous element without
- moving to the next line (+indentation).
- (JKM - 2011/06/15 - HDFFV-5878)
- - Fixed h5dump so that it will display the correct value for
- H5T_STD_I8LE datasets on the Blue-gene system (ppc64, linux, Big-Endian,
- clustering). (AKC & JKM - 2011/05/12 - HDFFV-7594)
- - Fixed h5diff to compare a file to itself correctly. Previously h5diff
- reported either the files were different or not compatible in certain
- cases even when comparing a file to itself. This fix also improves
- performance when comparing the same target objects through verifying
- the object and file addresses before comparing the details
- in the objects. Examples of details are datasets and attributes.
- (XCAO & JKM - 2011/05/06 - HDFFV-5928)
-
- F90 API
- -------
- - Modified the h5open_f and h5close_f subroutines to not to call H5open
- and H5close correspondingly. While the H5open call just adds overhead,
- the H5close call called by a Fortran application shuts down the HDF5
- library. This makes the library inaccessible to the application.
- (EIP & SB - 2011/10/13 - HDFFV-915)
- - Fixed h5tget_tag_f where the length of the C string was used to
- repack the C string into the Fortran string. This lead to memory
- corruption in the calling program. (SB - 2011/07/26)
- - Added defined constants:
- H5T_ORDER_MIXED_F (HDFFV-2767)
- H5Z_SO_FLOAT_DSCALE_F
- H5Z_SO_FLOAT_ESCALE_F
- H5Z_SO_INT_F
- H5Z_SO_INT_MINBITS_DEFAULT_F
- H5O_TYPE_UNKNOWN_F
- H5O_TYPE_GROUP_F
- H5O_TYPE_DATASET_F
- H5O_TYPE_NAMED_DATATYPE_F
- H5O_TYPE_NTYPES_F
-
- C++ API
- ------
- - None
-
- High-Level APIs:
- ------
- - Fixed the H5LTdtype_to_text function. It had some memory problems when
- dealing with some complicated data types. (SLU - 2011/10/19 - HDFFV-7701)
- - Fixed H5DSset_label seg faulting when retrieving the length of a
- dimension label that was not set. (SB - 2011/08/07 - HDFFV-7673)
- - Fixed a dimension scale bug where if you create a dimscale, attach two
- datasets to it, and then unattach them, you get an error if they are
- unattached in order, but no error if you unattach them in reverse order.
- (SB - 2011/06/07 - HDFFV-7605)
-
- Fortran High-Level APIs:
- ------
- - None
-
-
-Platforms Tested
-================
-The following platforms and compilers have been tested for this release.
-
- AIX 5.3 xlc 10.1.0.5
- (NASA G-ADA) xlC 10.1.0.5
- xlf90 12.1.0.6
-
- FreeBSD 8.2-STABLE i386 gcc 4.2.1 [FreeBSD] 20070719
- (loyalty) g++ 4.2.1 [FreeBSD] 20070719
- gcc 4.6.1 20110422
- g++ 4.6.1 20110422
- gfortran 4.6.1 20110422
-
- FreeBSD 8.2-STABLE amd64 gcc 4.2.1 [FreeBSD] 20070719
- (freedom) g++ 4.2.1 [FreeBSD] 20070719
- gcc 4.6.1 20110422
- g++ 4.6.1 20110422
- gfortran 4.6.1 20110422
-
- IBM Blue Gene/P bgxlc 9.0.0.9
- (LLNL uDawn) bgxlf90 11.1.0.7
- bgxlC 9.0.0.9
-
- Linux 2.6.16.60-0.54.5-smp Intel(R) C, C++, Fortran Compilers
- x86_64 Version 11.1 20090630
- (INL Icestorm)
-
- Linux 2.6.18-194.el5 x86_64 Intel(R) C, C++, Fortran Compilers
- (INL Fission) Version 12.0.2 20110112
-
- Linux 2.6.18-108chaos x86_64 Intel(R) C, C++, Fortran Compilers
- (LLNL Aztec) Version 11.1 20090630
-
- Linux 2.6.18-194.3.1.el5PAE gcc (GCC) 4.1.2 and 4.4.2
- #1 SMP i686 i686 i386 GNU Fortran (GCC) 4.1.2 20080704
- (jam) (Red Hat 4.1.2-48) and 4.4.2
- PGI C, Fortran, C++ 10.4-0 32-bit
- PGI C, Fortran, C++ 10.6-0 32-bit
- Intel(R) C Compiler for 32-bit
- applications, Version 11.1
- Intel(R) C++ Compiler for 32-bit
- applications, Version 11.1
- Intel(R) Fortran Compiler for 32-bit
- applications, Version 11.1
- MPICH mpich2-1.3.1 compiled with
- gcc 4.1.2 and gfortran 4.1.2
-
- Linux 2.6.18-238.12.1.el5 gcc 4.1.2 and 4.4.2
- #1 SMP x86_64 GNU/Linux GNU Fortran (GCC) 4.1.2 20080704
- (koala) (Red Hat 4.1.2-46) and 4.4.2
- tested for both 32- and 64-bit binaries
- Intel(R) C, C++, Fortran Compilers for
- applications running on Intel(R) 64,
- Version 11.1.
- PGI C, Fortran, C++ Version 9.0-4
- for 64-bit target on x86-64
- MPICH mpich2-1.3.1 compiled with
- gcc 4.1.2 and gfortran 4.1.2
-
- SGI Altix UV Intel(R) C, Fortran Compilers
- SGI ProPack 7 Linux Version 11.1 20100806
- 2.6.32.24-0.2.1.2230.2.PTF- SGI MPT 2.02
- default #1 SMP
- (NCSA ember)
-
- Dell NVIDIA Cluster Intel(R) C, Fortran Compilers
- Red Hat Enterprise Linux 6 Version 12.0.4 20110427
- 2.6.32-131.4.1.el6.x86_64 mvapich2 1.7rc1-intel-12.0.4
- (NCSA forge)
-
- SunOS 5.10 32- and 64-bit Sun C 5.11 SunOS_sparc 2010/08/13
- Sun Fortran 95 8.5 SunOS_sparc 2010/08/13
- Sun C++ 5.11 SunOS_sparc 2010/08/13
-
- Windows XP Visual Studio 2008 w/ Intel Fortran 10.1 (project files)
- Visual Studio 2008 w/ Intel Fortran 11.1 (cmake)
- Visual Studio 2010 (cmake)
- Cygwin(1.7.9 native gcc(4.5.3) compiler and gfortran)
-
- Windows XP x64 Visual Studio 2008 w/ Intel Fortran 10.1 (project files)
- Visual Studio 2008 w/ Intel Fortran 11.1 (cmake)
- Visual Studio 2010 (cmake)
- Cygwin(1.7.9 native gcc(4.5.3) compiler and gfortran)
-
- Windows Vista Visual Studio 2008 w/ Intel Fortran 11.1 (cmake)
-
- Windows Vista x64 Visual Studio 2008 w/ Intel Fortran 11.1 (cmake)
-
- Windows 7 Visual Studio 2008 w/ Intel Fortran 11.1 (cmake)
-
- Windows 7 x64 Visual Studio 2008 w/ Intel Fortran 11.1 (cmake)
-
- Mac OS X 10.8.0 (Intel 64-bit) i686-apple-darwin10-gcc-4.2.1 (GCC) 4.2.1 (Apple Inc. build 5666) (dot 3)
- Darwin Kernel Version 10.8.0 GNU Fortran (GCC) 4.6.1
- Intel C, C++ and Fortran compilers 12.1.0
-
- Mac OS X 10.8.0 (Intel 32-bit) i686-apple-darwin10-gcc-4.2.1 (GCC) 4.2.1 (Apple Inc. build 5666) (dot 3)
- Darwin Kernel Version 10.8.0 GNU Fortran (GCC) version 4.6.1
- Intel C, C++ and Fortran compilers 12.1.0
-
- Fedora 12 2.6.32.16-150.fc12.ppc64 #1 SMP ppc64 GNU/Linux
- gcc (GCC) 4.4.4 20100630 (Red Hat 4.4.4-10)
- GNU Fortran (GCC) 4.4.4 20100630 (Red Hat 4.4.4-10)
-
- Debian6.0.3 2.6.32-5-686 #1 SMP i686 GNU/Linux
- gcc (Debian 4.4.5-8) 4.4.5
- GNU Fortran (Debian 4.4.5-8) 4.4.5
-
- Debian6.0.3 2.6.32-5-amd64 #1 SMP x86_64 GNU/Linux
- gcc (Debian 4.4.5-8) 4.4.5
- GNU Fortran (Debian 4.4.5-8) 4.4.5
-
- Fedora15 2.6.40.6-0.fc15.i686.PAE #1 SMP i686 i686 i386 GNU/Linux
- gcc (GCC) 4.6.1 20110908 (Red Hat 4.6.1-9)
- GNU Fortran (GCC) 4.6.1 20110908 (Red Hat 4.6.1-9)
-
- Fedora15 2.6.40.6-0.fc15.x86_64 #1 SMP x86_64 x86_64 x86_64 GNU/Linux
- gcc (GCC) 4.6.1 20110908 (Red Hat 4.6.1-9)
- GNU Fortran (GCC) 4.6.1 20110908 (Red Hat 4.6.1-9)
-
- SUSE 11.4 2.6.37.6-0.7-desktop #1 SMP PREEMPT i686 i686 i386 GNU/Linux
- gcc (SUSE Linux) 4.5.1 20101208
- GNU Fortran (SUSE Linux) 4.5.1 20101208
-
- SUSE 11.4 2.6.37.6-0.7-desktop #1 SMP PREEMPT x86_64 x86_64 x86_64 GNU/Linux
- gcc (SUSE Linux) 4.5.1 20101208
- GNU Fortran (SUSE Linux) 4.5.1 20101208
-
- Ubuntu 11.10 3.0.0-12-generic #20-Ubuntu SMP i686 GNU/Linux
- gcc (Ubuntu/Linaro 4.6.1-9ubuntu3) 4.6.1
- GNU Fortran (Ubuntu/Linaro 4.6.4-9ubuntu3) 4.6.1
-
- Ubuntu 11.10 3.0.0-12-generic #20-Ubuntu SMP x86_64 GNU/Linux
- gcc (Ubuntu/Linaro 4.6.1-9ubuntu3) 4.6.1
- GNU Fortran (Ubuntu/Linaro 4.6.1-9ubuntu3) 4.6.1
-
- OpenVMS Alpha 8.3 HP C V7.3-009
- HP Fortran V8.2-104679-48H9K
- HP C++ V7.3-009
-
- Cray Linux Environment (CLE) PrgEnv-pgi 2.2.74
- hopper.nersc.gov pgcc 11.7-0 64-bit target on x86-64 Linux -tp k8e
- franklin.nersc.gov pgf90 11.7-0 64-bit target on x86-64 Linux -tp k8e
- pgCC 11.7-0 64-bit target on x86-64 Linux -tp k8e
-
-Tested Configuration Features Summary
-=====================================
-
- In the tables below
- y = tested
- n = not tested in this release
- C = Cluster
- W = Workstation
- x = not working in this release
- dna = does not apply
- ( ) = footnote appears below second table
- <blank> = testing incomplete on this feature or platform
-
-Platform C F90 F90 C++ zlib SZIP
- parallel parallel
-Solaris2.10 32-bit n y n y y y
-Solaris2.10 64-bit n y n y y y
-Windows XP n y(4) n y y y
-Windows XP x64 n y(4) n y y y
-Windows Vista n y(4) n y y y
-Windows Vista x64 n y(4) n y y y
-OpenVMS Alpha n y n y y n
-Mac OS X 10.8 Intel 32-bit n y n y y y
-Mac OS X 10.8 Intel 64-bit n y n y y y
-AIX 5.3 32- and 64-bit n y n y y y
-FreeBSD 8.2-STABLE 32&64 bit n x n x y y
-CentOS 5.5 Linux 2.6.18-194 i686 GNU (1)W y y(2) y y y y
-CentOS 5.5 Linux 2.6.18-194 i686 Intel W n y n y y n
-CentOS 5.5 Linux 2.6.18-194 i686 PGI W n y n y y n
-CentOS 5.5 Linux 2.6.16 x86_64 GNU (1) W y y(3) y y y y
-CentOS 5.5 Linux 2.6.16 x86_64 Intel W n y n y y n
-CentOS 5.5 Linux 2.6.16 x86_64 PGI W n y n y y y
-Fedora 12 Linux 2.6.32.16-150.fc12.ppc64 n y n y y y
-SGI ProPack 7 Linux 2.6.32.24 y y y y y y
-Red Hat Enterprise Linux 6 y y y y y y
-CLE hopper.nersc.gov y y(3) y y y n
-CLE franklin.nersc.gov y y(3) y y y n
-
-
-Platform Shared Shared Shared Thread-
- C libs F90 libs C++ libs safe
-Solaris2.10 32-bit y y y y
-Solaris2.10 64-bit y y y y
-Windows XP y y(4) y n
-Windows XP x64 y y(4) y n
-Windows Vista y y(4) y y
-Windows Vista x64 y y(4) y y
-OpenVMS Alpha n n n n
-Mac OS X 10.8 Intel 32-bit y(5) n y n
-Mac OS X 10.8 Intel 64-bit y(5) n y n
-AIX 5.3 32- and 64-bit n n n y
-FreeBSD 8.2-STABLE 32&64 bit y x x y
-CentOS 5.5 Linux 2.6.18-128 i686 GNU (1)W y y(2) y y
-CentOS 5.5 Linux 2.6.18-128 i686 Intel W y y y n
-CentOS 5.5 Linux 2.6.18-128 i686 PGI W y y y n
-CentOS 5.5 Linux 2.6.16 x86_64 GNU (1) W y y y y
-CentOS 5.5 Linux 2.6.16 x86_64 Intel W y y y n
-CentOS 5.5 Linux 2.6.16 x86_64 PGI W y y y n
-Fedora 12 Linux 2.6.32.16-150.fc12.ppc64 y y y y
-SGI ProPack 7 Linux 2.6.32.24 y y y n
-Red Hat Enterprise Linux 6 y y y n
-CLE hopper.nersc.gov n n n n
-CLE franklin.nersc.gov n n n n
-
- (1) Fortran compiled with gfortran.
- (2) With PGI and Absoft compilers.
- (3) With PGI compiler for Fortran.
- (4) Using Visual Studio 2008 w/ Intel Fortran 10.1 (Cygwin shared libraries are not supported)
- (5) C and C++ shared libraries will not be built when Fortran is enabled.
- Compiler versions for each platform are listed in the preceding
- "Platforms Tested" table.
-
-
-Known Problems
-==============
-
-* The STDIO VFD does not work on some architectures, possibly due to 32/64
- bit or large file issues. The basic STDIO VFD test is known to fail on
- 64-bit SunOS 5.10 on SPARC when built with -m64 and 32-bit OS X/Darwin
- 10.7.0. The STDIO VFD test has been disabled while we investigate and
- a fix should appear in a future release, possibly 1.8.9.
- (DER - 2011/10/14)
-
-* h5diff can report inconsistent results when comparing datasets of enum type
- that contain invalid values. This is due to how enum types are handled in
- the library and will be addressed in the next release.
- (DER - 2011/10/14 - HDFFV-7527)
-
-* The links test can fail under the stdio VFD due to some issues with external
- links. This will be investigated and fixed in a future release.
- (DER - 2011/10/14 - HDFFV-7768)
-
-* After the shared library support was fixed for some bugs, it was discovered
- that "make prefix=XXX install" no longer works for shared libraries. It
- still works correctly for static libraries. Therefore, if you want to
- install the HDF5 shared libraries in a location such as /usr/local/hdf5,
- you need to specify the location via the --prefix option during configure
- time. E.g, ./configure --prefix=/usr/local/hdf5 ...
- (AKC - 2011/05/07 - HDFFV-7583)
-
-* The parallel test, t_shapesame, in testpar/, may run for a long time and may
- be terminated by the alarm signal. If that happens, one can increase the
- alarm seconds (default is 1200 seconds = 20 minutes) by setting the
- environment variable, $HDF5_ALARM_SECONDS, to a larger value such as 3600
- (60 minutes). Note that the t_shapesame test may fail in some systems
- (see the "While working on the 1.8.6 release..." problem below). If
- it does, it will waste more time if $HDF5_ALARM_SECONDS is set
- to a larger value. (AKC - 2011/05/07)
-
-* The C++ and FORTRAN bindings are not currently working on FreeBSD.
- (QAK - 2011/04/26)
-
-* Shared Fortran libraries are not quite working on AIX. While they are
- generated when --enable-shared is specified, the fortran and hl/fortran
- tests fail. We are looking into the issue. HL and C++ shared libraries
- should now be working as intended, however. (MAM - 2011/04/20)
-
-* The --with-mpe configure option does not work with Mpich2. (AKC - 2011/03/10)
-
-* While working on the 1.8.6 release of HDF5, a bug was discovered that can
- occur when reading from a dataset in parallel shortly after it has been
- written to collectively. The issue was exposed by a new test in the parallel
- HDF5 test suite, but had existed before that. We believe the problem lies with
- certain MPI implementations and/or file systems.
-
- We have provided a pure MPI test program, as well as a standalone HDF5
- program, that can be used to determine if this is an issue on your system.
- They should be run across multiple nodes with a varying number of processes.
- These programs can be found at:
- http://www.hdfgroup.org/ftp/HDF5/examples/known_problems/
- (NAF - 2011/01/19)
-
-* The library's test dt_arith.c showed a compiler's rounding problem on
- Cygwin when converting from unsigned long long to long double. The
- library's own conversion works fine. We defined a macro for Cygwin to
- skip this test until we can solve the problem.
- (SLU - 2010/05/05 - HDFFV-1264)
-
-* All the VFL drivers aren't backward compatible. In H5FDpublic.h, the
- structure H5FD_class_t changed in 1.8. There is new parameter added to
- get_eoa and set_eoa callback functions. A new callback function
- get_type_map was added in. The public function H5FDrealloc was taken
- out in 1.8. The problem only happens when users define their own driver
- for 1.6 and try to plug in 1.8 library. Because there's only one user
- complaining about it, we (Elena, Quincey, and I) decided to leave it as
- it is (see bug report #1279). Quincey will make a plan for 1.10.
- (SLU - 2010/02/02)
-
-* MinGW has a missing libstdc++.dll.a library file and will not successfully link
- C++ applications/tests. Do not use the enable-cxx configure option. Read all of
- the INSTALL_MINGW.txt file for all restrictions. (ADB - 2009/11/11)
-
-* The --enable-static-exec configure flag will only statically link libraries
- if the static version of that library is present. If only the shared version
- of a library exists (i.e., most system libraries on Solaris, AIX, and Mac,
- for example, only have shared versions), the flag should still result in a
- successful compilation, but note that the installed executables will not be
- fully static. Thus, the only guarantee on these systems is that the
- executable is statically linked with just the HDF5 library.
- (MAM - 2009/11/04)
-
-* The PathScale MPI implementation, accessing a Panasas file system, would
- cause H5Fcreate() with H5F_ACC_EXCL to fail even when the file does not
- exist. This is due to the MPI_File_open() call failing if the mode has
- the MPI_MODE_EXCL bit set. (AKC - 2009/08/11 - HDFFV-988)
-
-* Parallel tests failed with 16 processes with data inconsistency at testphdf5
- / dataset_readAll. Parallel tests also failed with 32 and 64 processes with
- collective abort of all ranks at t_posix_compliant / allwrite_allread_blocks
- with MPI IO. (CMC - 2009/04/28)
-
-* For Red Storm, a Cray XT3 system, the tools/h5ls/testh5ls.sh and
- tools/h5copy/testh5copy.sh will fail some of its sub-tests. These sub-tests
- are expected to fail and should exit with a non-zero code but the yod
- command does not propagate the exit code of the executables. Yod always
- returns 0 if it can launch the executable. The test suite shell expects
- a non-zero for this particular test, therefore it concludes the test has
- failed when it receives 0 from yod. Skip all the "failing" test for now
- by changing them as following.
-
- ======== Original tools/h5ls/testh5ls.sh =========
- TOOLTEST tgroup-1.ls 1 -w80 -r -g tgroup.h5
- ======== Change to ===============================
- echo SKIP TOOLTEST tgroup-1.ls 1 -w80 -r -g tgroup.h5
- ==================================================
-
- ======== Original tools/h5copy/testh5copy.sh =========
- TOOLTEST_FAIL -i $TESTFILE -o $FILEOUT -v -s grp_dsets -d grp_rename
- TOOLTEST_FAIL -i $TESTFILE -o $FILEOUT -v -s grp_dsets -d /grp_rename/grp_dsets
- TOOLTEST_FAIL -i $TESTFILE -o $FILEOUT -vp -s /grp_dsets -d /E/F/grp_dsets
- TOOLTEST_FAIL -i $TESTFILE -o $FILEOUT -vp -s /grp_nested -d /G/H/grp_nested
- H5LSTEST $FILEOUT
- ======== Change to ===============================
- echo SKIP TOOLTEST_FAIL -i $TESTFILE -o $FILEOUT -v -s grp_dsets -d grp_rename
- echo SKIP TOOLTEST_FAIL -i $TESTFILE -o $FILEOUT -v -s grp_dsets -d /grp_rename/grp_dsets
- echo SKIP TOOLTEST_FAIL -i $TESTFILE -o $FILEOUT -vp -s /grp_dsets -d /E/F/grp_dsets
- echo SKIP TOOLTEST_FAIL -i $TESTFILE -o $FILEOUT -vp -s /grp_nested -d /G/H/grp_nested
- echo SKIP H5LSTEST $FILEOUT
- ==================================================
- (AKC - 2008/11/10)
-
-* For Red Storm, a Cray XT3 system, the yod command sometimes gives the
- message, "yod allocation delayed for node recovery". This interferes with
- test suites that do not expect to see this message. See the section of "Red
- Storm" in file INSTALL_parallel for a way to deal with this problem.
- (AKC - 2008/05/28)
-
-* On an Intel 64 Linux cluster (RH 4, Linux 2.6.9) with Intel 10.0 compilers,
- use -mp -O1 compilation flags to build the libraries. A higher level of
- optimization causes failures in several HDF5 library tests.
-
-* On mpich 1.2.5 and 1.2.6, if more than two processes contribute no IO and
- the application asks to do collective IO, we have found that when using 4
- processors, a simple collective write will sometimes be hung. This can be
- verified with t_mpi test under testpar.
-
-* A dataset created or rewritten with a v1.6.3 library or after cannot be read
- with the v1.6.2 library or before when the Fletcher32 EDC filter is enabled.
- There was a bug in the calculation of the Fletcher32 checksum in the
- library before v1.6.3; the checksum value was not consistent between big-
- endian and little-endian systems. This bug was fixed in Release 1.6.3.
- However, after fixing the bug, the checksum value was no longer the same as
- before on little-endian system. Library releases after 1.6.4 can still read
- datasets created or rewritten with an HDF5 library of v1.6.2 or before.
- (SLU - 2005/06/30)
-
-* On IBM AIX systems, parallel HDF5 mode will fail some tests with error
- messages like "INFO: 0031-XXX ...". This is from the command `poe'.
- Set the environment variable MP_INFOLEVEL to 0 to minimize the messages
- and run the tests again.
-
- The tests may fail with messages like "The socket name is already in use",
- but HDF5 does not use sockets. This failure is due to problems with the
- poe command trying to set up the debug socket. To resolve this problem,
- check to see whether there are many old /tmp/s.pedb.* files staying around.
- These are sockets used by the poe command and left behind due to failed
- commands. First, ask your system administrator to clean them out.
- Lastly, request IBM to provide a means to run poe without the debug socket.
- (AKC - 2004/12/08)
-
-
-%%%%1.8.7%%%%
-
-
-HDF5 version 1.8.7 released on Tue May 10 09:24:44 CDT 2011
-================================================================================
-
-INTRODUCTION
-============
-
-This document describes the differences between HDF5-1.8.6 and
-HDF5 1.8.7, and contains information on the platforms tested and
-known problems in HDF5-1.8.7.
-For more details, see the files HISTORY-1_0-1_8_0_rc3.txt
-and HISTORY-1_8.txt in the release_docs/ directory of the HDF5 source.
-
-Links to the HDF5 1.8.7 source code, documentation, and additional materials
-can be found on the HDF5 web page at:
-
- http://www.hdfgroup.org/products/hdf5/
-
-The HDF5 1.8.7 release can be obtained from:
-
- http://www.hdfgroup.org/HDF5/release/obtain5.html
-
-User documentation for 1.8.7 can be accessed directly at this location:
-
- http://www.hdfgroup.org/HDF5/doc/
-
-New features in the HDF5-1.8.x release series, including brief general
-descriptions of some new and modified APIs, are described in the "What's New
-in 1.8.0?" document:
-
- http://www.hdfgroup.org/HDF5/doc/ADGuide/WhatsNew180.html
-
-All new and modified APIs are listed in detail in the "HDF5 Software Changes
-from Release to Release" document, in the section "Release 1.8.7 (current
-release) versus Release 1.8.6":
-
- http://www.hdfgroup.org/HDF5/doc/ADGuide/Changes.html
-
-If you have any questions or comments, please send them to the HDF Help Desk:
-
- help@hdfgroup.org
-
-
-CONTENTS
-========
-
-- New Features
-- Support for New Platforms, Languages, and Compilers
-- Bug Fixes since HDF5-1.8.6
-- Platforms Tested
-- Supported Configuration Features Summary
-- Known Problems
-
-
-New Features
-============
-
- Configuration
- -------------
- - Configure now generates Makefiles that build in "silent make mode"
- by default in which compile and link lines are significantly
- simplified for clarity. To override this and view actual compile and
- link lines during building, the --disable-silent-rules flag can be used
- at configure time, or the 'make' command can be followed by V=1, to
- indicate a "verbose" make. (MAM - 2011/4/14).
- - Added mpicc and mpif90 as the default C and Fortran compilers for Linux
- systems when --enable-parallel is specified but no $CC or $FC is defined.
- (AKC - 2011/2/7)
- - Added a new configure option, "--enable-unsupported", which can
- be used to stop configure from preventing the use of unsupported
- configure option combinations, such as c++ in parallel or Fortran
- with threadsafe. Use at your own risk, as it may result in a
- library that won't compile or run as expected!
- (MAM - 2010/11/17 - Bug 2061)
-
- Library
- -------
- - The library allows the dimension size of a dataspace to be zero. In
- the past, the library would allow this only if the maximal dimension
- size was unlimited. Now there is no such restriction, but no data
- can be written to this kind of dataset. (SLU - 2011/4/20)
- - We added two new macros, H5_VERSION_GE and H5_VERSION_LE, to let users
- compare certain version numbers with the library being used. (SLU -
- 2011/4/20)
- - Added ability to cache files opened through external links. Added new
- public functions H5Pset_elink_file_cache_size(),
- H5Pget_elink_file_cache_size(), and H5Fclear_elink_file_cache().
- (NAF - 2011/02/17)
- - Finished implementing all options for 'log' VFD. (QAK - 2011/1/25)
- - Removed all old code for Metrowerks compilers, bracketed by
- __MWERKS__). Metrowerks compiler is long gone. (AKC - 2010/11/17)
-
- Parallel Library
- ----------------
- - None
-
- Tools
- -----
- - h5diff: Added new "verbose with levels" option, '-vN, --verbose=N'.
- The old '-v, --verbose' option is deprecated but remains available;
- it is exactly equivalent to '-v0, --verbose=0'.
- The new levels 1 ('-v1' or '--verbose=1') and 2 ('-v2' or
- '--verbose=2') can be specified to view more information regarding
- attributes differences. Bug #2121 (JKM 2011/3/23)
- - h5dump: Added new option --enable-error-stack. This option will
- display error stack information in the output stream. This is
- useful when the "h5dump: Unable to print data" message is output.
- (ADB - 2011/03/03)
-
- High-Level APIs
- ---------------
- - Fortran LT make datasets routines (H5LTmake_dataset_f,
- h5ltmake_dataset_int_f, h5ltmake_dataset_float_f, h5ltmake_dataset_double_f)
- and LT read datasets routines (h5ltread_dataset_f,h5ltread_dataset_int_f,
- h5ltread_dataset_float_f, 5ltread_dataset_double_f) can now handle
- 4-dimensional to 7-dimensional rank datasets. HDFFV-1217 (MSB-2011/4/24/2011)
-
- F90 API
- -------
- - None
-
- C++ API
- -------
- - None
-
-
-Support for New Platforms, Languages, and Compilers
-===================================================
- - Intel V11.1 uses now -O3 optimization in production mode (EIP - 2010/10/08)
-
-
-
-Bug Fixes since HDF5-1.8.6
-==========================
-
- Configuration
- -------------
- - Shared C++ and HL libraries on AIX should now be working correctly.
- Note that Fortran shared libraries are still not working on AIX.
- (See the Known Problems section, below). (MAM - 2011/4/20)
- - Removed config/ibm-aix6.x. All IBM-AIX settings are in one file,
- ibm-aix. (AKC - 2011/4/14)
- - Shared C libraries are no longer disabled on Mac when Fortran
- is enabled. Shared Fortran libraries are still not supported on Mac,
- so configure will disable them by default, but this is overridable
- with the new --enable-unsupported configure option. The configure
- summary has been updated to reflect the fact that the shared-ness of
- the C++/Fortran wrapper libraries may not align with the C library.
- (MAM - 2011/04/11 - HDFFV-4353).
-
- Library
- -------
- - Changed assertion failure when decoding a compound datatype with no
- fields into a normal error failure. Also prohibit using this sort
- of datatype for creating an attribute (as is already the case for
- datasets and committed (named) datatypes). (QAK - 2011/04/15, Jira
- issue #HDFFV-2766)
- - Tell the VFL flush call that the file will be closing, allowing
- the VFDs to avoid sync'ing the file (particularly valuable in parallel).
- (QAK - 2011/03/09)
- - The datatype handler created with H5Tencode/decode used to have the
- reference count 0 (zero); it now has the reference count 1 (one).
- (SLU - 2011/2/18)
- - Fixed the definition of H5_HAVE_GETTIMEOFDAY on Windows so that
- HDgettimeofday() is defined and works properly. Bug HDFFV-5931
- (DER - 2011/04/14)
- - Added basic VFD tests for the Windows, STDIO and log VFD tests.
- (DER - 2011/04/11)
-
- Parallel Library
- ----------------
- - None
-
- Tools
- -----
- - Updated h5dump test case script to prevent entire test failure when
- source directory is read-only. Bug #HDFFV-4342 (JKM 2011/4/12)
- - Fixed h5dump displaying incorrect values for H5T_STD_I8BE type data in
- attribute on Big-Endian machine. H5T_STD_I8BE is unsigned 8bit type,
- so h5dump is supposed to display -2 instead of 254. It worked correctly
- on Little-Endian system , but not on Big-Endian system. Bug #HDFFV-4358
- (JKM 04/08/2011)
- - Updated some HDF5 tools to standardize the option name as
- '--enable-error-stack' for printing HDF5 error stack messages. h5ls and
- h5dump have been updated. For h5ls, this replaces "-e/--errors" option,
- which is deprecated. For h5dump, this is a new option. Bug #2182
- (JKM 2011/3/30)
- - Fixed the h5diff --use-system-epsilon option. The formula used in the
- calculation was changed from ( |a - b| / b ) to ( |a - b| ).
- This was done to improve performance. Bug #2184 (JKM 2011/3/24)
- - Fixed output for H5T_REFERENCE in h5dump. According to the BNF document
- the output of a H5T_REFERENCE should be followed by the type;
- <reference> ::= H5T_REFERENCE { <ref_type> }
- <ref_type> ::= H5T_STD_REF_OBJECT | H5T_STD_REF_DSETREG
- Previously this was only displayed if the -R option was used.
- Bug #1725 (ADB 2011/3/28)
- - Fixed two h5diff issues. 1) h5diff compared attributes correctly only
- when two objects had the same number of attributes and the attribute
- names were identical. 2) h5diff did not display useful information about
- attribute differences. Bug #2121 (JKM 2011/3/17)
- - Fixed a memory leak in h5diff that occurred when accessing symbolic links
- with the --follow-symlink option. Bug #2214 (JKM 2011/3/18)
- - Fixed a memory leak in h5diff that occurred when accessing variable length
- string data. Bug #2216 (JKM 2011/3/18)
- - Fixed and improved the help page for h5ls -a, --address option.
- Bug #1904 (JKM 2011/3/11)
- - Fixed h5copy to enable copying an object into the same HDF5 file.
- Previously h5copy displayed an error message when the target file
- was the same as the source file. (XCAO 2011/3/8)
- - Fixed an h5dump problem that caused the tool to skip some data elements
- in large datasets with a large array datatype on Windows. This issue
- arose only on Windows due to the different return behavior of the
- _vsnprintf() function. Bug #2161 (JKM 2011/3/3)
- - Fixed h5dump which was skipping some array indices in large datasets
- with a relatively large array datatype. The interval of skipped indices
- varied according to the size of the array. Bug #2092 (JKM 2011/2/15)
- - Fixed h5diff which was segfaulting when comparing compound datasets
- with a combination of fixed-length string datatypes and variable-length
- string datatypes in certain orders. Bug #2089 (JKM 2010/12/28)
- - Improved h5diff performance. 1) Now use HDmemcmp() before comparing two
- elements. 2) Replace expensive H5Tequals() calls. 3) Retrieve datatype
- information at dataset level, not at each element level for compound
- datasets. HDFFV-7516 (JKM 2011/4/18)
- - Fixed h5ls to display nested compound types with curly brackets
- when -S (--simple) option is used with -l (--label), so it shows
- which members (in curly brackets) belong to which nested compound type,
- making the output clearer. Bug #1979 (JKM 2010/11/09)
- - Fixed h5diff to handle variable-length strings in a compound dataset
- and variable-length string arrays in a compound dataset correctly.
- Garbage values were previously displayed when h5diff compared multiple
- variable-length strings in a compound type dataset.
- Bug #1989 (JKM 2010/10/28)
- - Fixed h5copy to fail gracefully when copying an object to a non-
- existing group without the -p option. Bug #2040 (JKM 2010/10/18)
-
- F90 API
- ------
- - None
-
- C++ API
- ------
- - None
-
- High-Level APIs:
- ------
- - None
-
- Fortran High-Level APIs:
- ------
- - h5tbmake_table_f: Fixed error in passing an array of characters with different
- length field names.
- - h5tget_field_info_f: Fixed error with packing the C strings into a Fortran
- array of strings. Added optional argument called 'maxlen_out' which returns
- the maximum string character length in a field name element.
- Bug HDFFV-1255 (MSB- 4/17/2011)
-
-
-
-
-Platforms Tested
-================
-The following platforms and compilers have been tested for this release.
-
- AIX 6.1 xlc 11.1.0.3
- (NCSA BP) xlC 11.1.0.3
- xlf90 13.1.0.3
- mpcc_r 11.1.0.3
- mpxlf90_r 13.1.0.3
-
- FreeBSD 8.2-STABLE i386 gcc 4.2.1 [FreeBSD] 20070719
- (loyalty) g++ 4.2.1 [FreeBSD] 20070719
- gcc 4.6.1 20110422
- g++ 4.6.1 20110422
- gfortran 4.6.1 20110422
-
- FreeBSD 8.2-STABLE amd64 gcc 4.2.1 [FreeBSD] 20070719
- (freedom) g++ 4.2.1 [FreeBSD] 20070719
- gcc 4.6.1 20110422
- g++ 4.6.1 20110422
- gfortran 4.6.1 20110422
-
- Linux 2.6.18-194.3.1.el5PAE gcc (GCC) 4.1.2 and 4.4.2
- #1 SMP i686 i686 i386 G95 (GCC 4.0.3 (g95 0.93!) Apr 21 2010)
- (jam) GNU Fortran (GCC) 4.1.2 20080704
- (Red Hat 4.1.2-48) and 4.4.2
- PGI C, Fortran, C++ 10.4-0 32-bit
- PGI C, Fortran, C++ 10.6-0 32-bit
- Intel(R) C Compiler for 32-bit
- applications, Version 11.1
- Intel(R) C++ Compiler for 32-bit
- applications, Version 11.1
- Intel(R) Fortran Compiler for 32-bit
- applications, Version 11.1
- Absoft 32-bit Fortran 95 10.0.7
- MPICH mpich2-1.3.1 compiled with
- gcc 4.1.2 and gfortran 4.1.2
-
- Linux 2.6.18-194.17.1.el5 gcc 4.1.2 and 4.4.2
- #1 SMP x86_64 GNU/Linux G95 (GCC 4.0.3 (g95 0.93!) Apr 21 2010)
- (amani) tested for both 32- and 64-bit binaries
- GNU Fortran (GCC) 4.1.2 20080704
- (Red Hat 4.1.2-46) and 4.4.2
- Intel(R) C, C++, Fortran Compilers for
- applications running on Intel(R) 64,
- Version 11.1.
- PGI C, Fortran, C++ Version 9.0-4
- for 64-bit target on x86-64
- MPICH mpich2-1.3.1 compiled with
- gcc 4.1.2 and gfortran 4.1.2
-
- SGI ProPack 7 Linux Intel(R) C++ Version 11.1 20100806
- 2.6.32.24-0.2.1.2230.2.PTF- Intel(R) Fortran Version 11.1 20100806
- default #1 SMP SGI MPT 2.01
- SGI Altix UV
- (NCSA ember)
-
- SunOS 5.10 32- and 64-bit Sun C 5.9 Sun OS_sparc Patch 124867-16
- (linew) Sun Fortran 95 8.3 Sun OS_sparc Patch 127000-13
- Sun C++ 5.9 Sun OS_sparc Patch 124863-26
- Sun C 5.10 SunOS_sparc Patch 141861-07
- Sun Fortran 95 8.4 SunOS_sparc Patch 128231-06
- Sun C++ 5.10 SunOS_sparc 128228-11
-
- Intel Xeon Linux 2.6.18- gcc 4.2.4
- 92.1.10.el5_lustre.1.6.6smp- Intel(R) C++ Version 10.1.017
- perfctr #8 SMP Intel(R) Fortran Compiler Version 10.1.017
- (NCSA abe) Open MPI 1.3.2
- MVAPICH2-1.5.1_pgi-10.8
-
- Windows XP Visual Studio 2008 w/ Intel Fortran 10.1 (project files)
- Visual Studio 2008 w/ Intel Fortran 11.1 (cmake)
- Visual Studio 2010 (cmake)
- Cygwin(1.7.7 native gcc(4.3.4) compiler and gfortran)
-
- Windows XP x64 Visual Studio 2008 w/ Intel Fortran 10.1 (project files)
- Visual Studio 2008 w/ Intel Fortran 11.1 (cmake)
- Visual Studio 2010 (cmake)
- Cygwin(1.7.7 native gcc(4.3.4) compiler and gfortran)
-
- Windows Vista Visual Studio 2008 w/ Intel Fortran 11.1 (cmake)
-
- Windows Vista x64 Visual Studio 2008 w/ Intel Fortran 11.1 (cmake)
-
- Windows 7 Visual Studio 2008 w/ Intel Fortran 11.1 (cmake)
-
- Windows 7 x64 Visual Studio 2008 w/ Intel Fortran 11.1 (cmake)
-
- Mac OS X 10.7.0 (Intel 64-bit) i686-apple-darwin10-gcc-4.2.1 (GCC) 4.2.1
- Darwin Kernel Version 10.7.0 GNU Fortran (GCC) 4.6.0 20101106 (experimental)
- Intel C, C++ and Fortran compilers 12.0.1.122 20101110
-
- Mac OS X 10.7.0 (Intel 32-bit) i686-apple-darwin10-gcc-4.2.1 (GCC) 4.2.1 (Apple Inc. build 5666) (dot 3)
- Darwin Kernel Version 10.7.0 GNU Fortran (GCC) version 4.4.0 20090123 (experimental)
- [trunk revision 143587]
-
- Fedora 12 2.6.32.16-150.fc12.ppc64 #1 SMP ppc64 GNU/Linux
- gcc (GCC) 4.4.4 20100630 (Red Hat 4.4.4-10)
- GNU Fortran (GCC) 4.4.4 20100630 (Red Hat 4.4.4-10)
-
- Debian6.01 2.6.32-5-686 #1 SMP i686 GNU/Linux
- gcc (Debian 4.4.5-8) 4.4.5
- GNU Fortran (Debian 4.4.5-8) 4.4.5
-
- Debian6.01 2.6.32-5-amd64 #1 SMP x86_64 GNU/Linux
- gcc (Debian 4.4.5-8) 4.4.5
- GNU Fortran (Debian 4.4.5-8) 4.4.5
-
- Fedora14 2.6.35.12-88.fc14.i686.PAE #1 SMP i686 i686 i386 GNU/Linux
- gcc (GCC) 4.5.1 20100924 (Red Hat 4.5.1-4)
- GNU Fortran (GCC) 4.5.1 20100924 (Red Hat 4.5.1-4)
-
- Fedora14 2.6.35.12-88.fc14.x86_64 #1 SMP x86_64 x86_64 x86_64 GNU/Linux
- gcc (GCC) 4.5.1 20100924 (Red Hat 4.5.1-4)
- GNU Fortran (GCC) 4.5.1 20100924 (Red Hat 4.5.1-4)
-
- SUSE 11.4 2.6.37.1-1.2-desktop #1 SMP PREEMPT i686 i686 i386 GNU/Linux
- gcc (SUSE Linux) 4.5.1 20101208
- GNU Fortran (SUSE Linux) 4.5.1 20101208
-
- SUSE 11.4 2.6.37.1-1.2-desktop #1 SMP PREEMPT x86_64 x86_64 x86_64 GNU/Linux
- gcc (SUSE Linux) 4.5.1 20101208
- GNU Fortran (SUSE Linux) 4.5.1 20101208
-
- Ubuntu 10.10 2.6.35-28-generic #50-Ubuntu SMP i686 GNU/Linux
- gcc (Ubuntu/Linaro 4.4.4-14ubuntu5) 4.4.5
- GNU Fortran (Ubuntu/Linaro 4.4.4-14ubuntu5) 4.4.5
-
- Ubuntu 10.10 2.6.35-28-generic #50-Ubuntu SMP x86_64 GNU/Linux
- gcc (Ubuntu/Linaro 4.4.4-14ubuntu5) 4.4.5
- GNU Fortran (Ubuntu/Linaro 4.4.4-14ubuntu5) 4.4.5
-
- OpenVMS Alpha 8.3 HP C V7.3-009
- HP Fortran V8.2-104679-48H9K
- HP C++ V7.3-009
-
-Tested Configuration Features Summary
-========================================
-
- In the tables below
- y = tested
- n = not tested in this release
- C = Cluster
- W = Workstation
- x = not working in this release
- dna = does not apply
- ( ) = footnote appears below second table
- <blank> = testing incomplete on this feature or platform
-
-Platform C F90 F90 C++ zlib SZIP
- parallel parallel
-Solaris2.10 32-bit n y n y y y
-Solaris2.10 64-bit n y n y y y
-Windows XP n y(4) n y y y
-Windows XP x64 n y(4) n y y y
-Windows Vista n y(4) n y y y
-Windows Vista x64 n y(4) n y y y
-OpenVMS Alpha n y n y y n
-Mac OS X 10.7 Intel 32-bit n y n y y y
-Mac OS X 10.7 Intel 64-bit n y n y y y
-AIX 6.1 32- and 64-bit y y y y y y
-FreeBSD 8.2-STABLE 32&64 bit n x n x y y
-CentOS 5.5 Linux 2.6.18-194 i686 GNU (1)W y y(2) y y y y
-CentOS 5.5 Linux 2.6.18-194 i686 Intel W n y n y y n
-CentOS 5.5 Linux 2.6.18-194 i686 PGI W n y n y y n
-CentOS 5.5 Linux 2.6.16 x86_64 GNU (1) W y y(3) y y y y
-CentOS 5.5 Linux 2.6.16 x86_64 Intel W n y n y y n
-CentOS 5.5 Linux 2.6.16 x86_64 PGI W n y n y y y
-RedHat EL4 2.6.18 Xeon Lustre C y y y y y n
-Fedora 12 Linux 2.6.32.16-150.fc12.ppc64 n y n y y y
-SGI Linux 2.6.32.19 y y y y y y
-
-
-Platform Shared Shared Shared Thread-
- C libs F90 libs C++ libs safe
-Solaris2.10 32-bit y y y y
-Solaris2.10 64-bit y y y y
-Windows XP y y(4) y n
-Windows XP x64 y y(4) y n
-Windows Vista y y(4) y y
-Windows Vista x64 y y(4) y y
-OpenVMS Alpha n n n n
-Mac OS X 10.7 Intel 32-bit y(5) n y n
-Mac OS X 10.7 Intel 64-bit y(5) n y n
-AIX 6.1 32- and 64-bit n n n y
-FreeBSD 8.2-STABLE 32&64 bit y x x y
-CentOS 5.5 Linux 2.6.18-128 i686 GNU (1)W y y(2) y y
-CentOS 5.5 Linux 2.6.18-128 i686 Intel W y y y n
-CentOS 5.5 Linux 2.6.18-128 i686 PGI W y y y n
-CentOS 5.5 Linux 2.6.16 x86_64 GNU (1) W y y y y
-CentOS 5.5 Linux 2.6.16 x86_64 Intel W y y y n
-CentOS 5.5 Linux 2.6.16 x86_64 PGI W y y y n
-RedHat EL4 2.6.18 Xeon Lustre C y y y n
-Fedora 12 Linux 2.6.32.16-150.fc12.ppc64 y y y y
-SGI Linux 2.6.32.19 y y y y
-
- (1) Fortran compiled with gfortran.
- (2) With PGI and Absoft compilers.
- (3) With PGI compiler for Fortran.
- (4) Using Visual Studio 2008 w/ Intel Fortran 10.1 (Cygwin shared libraries are not supported)
- (5) C and C++ shared libraries will not be built when Fortran is enabled.
- Compiler versions for each platform are listed in the preceding
- "Platforms Tested" table.
-
-
-Known Problems
-==============
-* After the shared library support was fixed for some bugs, it was discovered
- that "make prefix=XXX install" no longer works for shared libraries. It
- still works correctly for static libraries. Therefore, if you want to
- install the HDF5 shared libraries in a location such as /usr/local/hdf5,
- you need to specify the location via the --prefix option during configure
- time. E.g, ./configure --prefix=/usr/local/hdf5 ...
- (AKC - 2011/05/07 HDFFV-7583)
-
-* The parallel test, t_shapesame, in testpar/, may run for a long time and may
- be terminated by the alarm signal. If that happens, one can increase the
- alarm seconds (default is 1200 seconds = 20 minutes) by setting the
- environment variable, $HDF5_ALARM_SECONDS, to a larger value such as 3600
- (60 minutes). Note that the t_shapesame test may fail in some systems
- (see the "While working on the 1.8.6 release..." problem below). If
- it does, it will waste more time if $HDF5_ALARM_SECONDS is set
- to a larger value. (AKC - 2011/05/07)
-
-* The C++ and FORTRAN bindings are not currently working on FreeBSD.
- (QAK - 2011/04/26)
-
-* Shared Fortran libraries are not quite working on AIX. While they are
- generated when --enable-shared is specified, the fortran and hl/fortran
- tests fail. We are looking into the issue. HL and C++ shared libraries
- should now be working as intended, however. (MAM - 2011/04/20)
-
-* The --with-mpe configure option does not work with Mpich2. AKC - 2011/03/10
-
-* If parallel gmake (e.g., gmake -j 4) is used, the "gmake clean" command
- sometimes fails in the perform directory due to the attempt to remove the
- executable of h5perf or h5perf_serial by two "parallel" commands. This error
- has no consequence on the functionality of the HDF5 library or install. It
- is fixed in the next release. AKC - 2011/01/25
-
-* While working on the 1.8.6 release of HDF5, a bug was discovered that can
- occur when reading from a dataset in parallel shortly after it has been
- written to collectively. The issue was exposed by a new test in the parallel
- HDF5 test suite, but had existed before that. We believe the problem lies with
- certain MPI implementations and/or file systems.
-
- We have provided a pure MPI test program, as well as a standalone HDF5
- program, that can be used to determine if this is an issue on your system.
- They should be run across multiple nodes with a varying number of processes.
- These programs can be found at:
- http://www.hdfgroup.org/ftp/HDF5/examples/known_problems/
-
-* The library's test dt_arith.c showed a compiler's rounding problem on
- Cygwin when converting from unsigned long long to long double. The
- library's own conversion works fine. We defined a macro for Cygwin to
- skip this test until we can solve the problem. Please see bug #1813.
- SLU - 2010/5/5
-
-* All the VFL drivers aren't backward compatible. In H5FDpublic.h, the
- structure H5FD_class_t changed in 1.8. There is new parameter added to
- get_eoa and set_eoa callback functions. A new callback function
- get_type_map was added in. The public function H5FDrealloc was taken
- out in 1.8. The problem only happens when users define their own driver
- for 1.6 and try to plug in 1.8 library. Because there's only one user
- complaining about it, we (Elena, Quincey, and I) decided to leave it as
- it is (see bug report #1279). Quincey will make a plan for 1.10.
- SLU - 2010/2/2
-
-* MinGW has a missing libstdc++.dll.a library file and will not successfully link
- C++ applications/tests. Do not use the enable-cxx configure option. Read all of
- the INSTALL_MINGW.txt file for all restrictions. ADB - 2009/11/11
-
-* The PathScale MPI implementation, accessing a Panasas file system, would
- cause H5Fcreate() with H5F_ACC_EXCL to fail even when the file does not
- exist. This is due to the MPI_File_open() call failing if the mode has
- the MPI_MODE_EXCL bit set. (See bug 1468 for details.) AKC - 2009/8/11
-
-* Parallel tests failed with 16 processes with data inconsistency at testphdf5
- / dataset_readAll. Parallel tests also failed with 32 and 64 processes with
- collective abort of all ranks at t_posix_compliant / allwrite_allread_blocks
- with MPI IO. CMC - 2009/04/28
-
-* For Red Storm, a Cray XT3 system, the tools/h5ls/testh5ls.sh and
- tools/h5copy/testh5copy.sh will fail some of its sub-tests. These sub-tests
- are expected to fail and should exit with a non-zero code but the yod
- command does not propagate the exit code of the executables. Yod always
- returns 0 if it can launch the executable. The test suite shell expects
- a non-zero for this particular test, therefore it concludes the test has
- failed when it receives 0 from yod. Skip all the "failing" test for now
- by changing them as following.
-
- ======== Original tools/h5ls/testh5ls.sh =========
- TOOLTEST tgroup-1.ls 1 -w80 -r -g tgroup.h5
- ======== Change to ===============================
- echo SKIP TOOLTEST tgroup-1.ls 1 -w80 -r -g tgroup.h5
- ==================================================
-
- ======== Original tools/h5copy/testh5copy.sh =========
- TOOLTEST_FAIL -i $TESTFILE -o $FILEOUT -v -s grp_dsets -d grp_rename
- TOOLTEST_FAIL -i $TESTFILE -o $FILEOUT -v -s grp_dsets -d /grp_rename/grp_dsets
- TOOLTEST_FAIL -i $TESTFILE -o $FILEOUT -vp -s /grp_dsets -d /E/F/grp_dsets
- TOOLTEST_FAIL -i $TESTFILE -o $FILEOUT -vp -s /grp_nested -d /G/H/grp_nested
- H5LSTEST $FILEOUT
- ======== Change to ===============================
- echo SKIP TOOLTEST_FAIL -i $TESTFILE -o $FILEOUT -v -s grp_dsets -d grp_rename
- echo SKIP TOOLTEST_FAIL -i $TESTFILE -o $FILEOUT -v -s grp_dsets -d /grp_rename/grp_dsets
- echo SKIP TOOLTEST_FAIL -i $TESTFILE -o $FILEOUT -vp -s /grp_dsets -d /E/F/grp_dsets
- echo SKIP TOOLTEST_FAIL -i $TESTFILE -o $FILEOUT -vp -s /grp_nested -d /G/H/grp_nested
- echo SKIP H5LSTEST $FILEOUT
- ==================================================
- AKC - 2008/11/10
-
-* For Red Storm, a Cray XT3 system, the yod command sometimes gives the
- message, "yod allocation delayed for node recovery". This interferes with
- test suites that do not expect to see this message. See the section of "Red
- Storm" in file INSTALL_parallel for a way to deal with this problem.
- AKC - 2008/05/28
-
-* On an Intel 64 Linux cluster (RH 4, Linux 2.6.9) with Intel 10.0 compilers,
- use -mp -O1 compilation flags to build the libraries. A higher level of
- optimization causes failures in several HDF5 library tests.
-
-* On mpich 1.2.5 and 1.2.6, if more than two processes contribute no IO and
- the application asks to do collective IO, we have found that when using 4
- processors, a simple collective write will sometimes be hung. This can be
- verified with t_mpi test under testpar.
-
-* A dataset created or rewritten with a v1.6.3 library or after cannot be read
- with the v1.6.2 library or before when the Fletcher32 EDC filter is enabled.
- There was a bug in the calculation of the Fletcher32 checksum in the
- library before v1.6.3; the checksum value was not consistent between big-
- endian and little-endian systems. This bug was fixed in Release 1.6.3.
- However, after fixing the bug, the checksum value was no longer the same as
- before on little-endian system. Library releases after 1.6.4 can still read
- datasets created or rewritten with an HDF5 library of v1.6.2 or before.
- SLU - 2005/6/30
-
-* On IBM AIX systems, parallel HDF5 mode will fail some tests with error
- messages like "INFO: 0031-XXX ...". This is from the command `poe'.
- Set the environment variable MP_INFOLEVEL to 0 to minimize the messages
- and run the tests again.
-
- The tests may fail with messages like "The socket name is already in use",
- but HDF5 does not use sockets. This failure is due to problems with the
- poe command trying to set up the debug socket. To resolve this problem,
- check to see whether there are many old /tmp/s.pedb.* files staying around.
- These are sockets used by the poe command and left behind due to failed
- commands. First, ask your system administrator to clean them out.
- Lastly, request IBM to provide a means to run poe without the debug socket.
-
-* The --enable-static-exec configure flag will only statically link libraries
- if the static version of that library is present. If only the shared version
- of a library exists (i.e., most system libraries on Solaris, AIX, and Mac,
- for example, only have shared versions), the flag should still result in a
- successful compilation, but note that the installed executables will not be
- fully static. Thus, the only guarantee on these systems is that the
- executable is statically linked with just the HDF5 library.
-
-* There is also a configure error on Altix machines that incorrectly reports
- when a version of Szip without an encoder is being used.
-
-* On cobalt, an SGI Altix SMP ia64 system, Intel compiler version 10.1 (which
- is the default on that system) does not work properly and results in
- failures during make check (in a static build) and make installcheck (during
- a shared build). This appears to be a compiler optimization problem.
- Reducing optimization by setting CFLAGS to -O1 or below resolves the issue.
- Alternatively, using a newer version of the compiler (11.0) also works as
- intended. MAM - 2010/06/01
-
-* h5diff will not report enum value differences when one or both of the values
- is not a valid enumeration value. The source of this bug has been identified
- and it will be fixed in 1.8.8. DER - 2011/04/27
-
-
-%%%%1.8.6%%%%
-
-
-HDF5 version 1.8.6 released on Mon Feb 14 10:26:30 CST 2011
-================================================================================
-
-INTRODUCTION
-============
-
-This document describes the differences between HDF5-1.8.5 and
-HDF5 1.8.6, and contains information on the platforms tested and
-known problems in HDF5-1.8.6.
-For more details, see the files HISTORY-1_0-1_8_0_rc3.txt
-and HISTORY-1_8.txt in the release_docs/ directory of the HDF5 source.
-
-Links to the HDF5 1.8.6 source code, documentation, and additional materials
-can be found on the HDF5 web page at:
-
- http://www.hdfgroup.org/products/hdf5/
-
-The HDF5 1.8.6 release can be obtained from:
-
- http://www.hdfgroup.org/HDF5/release/obtain5.html
-
-User documentation for 1.8.6 can be accessed directly at this location:
-
- http://www.hdfgroup.org/HDF5/doc/
-
-New features in the HDF5-1.8.x release series, including brief general
-descriptions of some new and modified APIs, are described in the "What's New
-in 1.8.0?" document:
-
- http://www.hdfgroup.org/HDF5/doc/ADGuide/WhatsNew180.html
-
-All new and modified APIs are listed in detail in the "HDF5 Software Changes
-from Release to Release" document, in the section "Release 1.8.6 (current
-release) versus Release 1.8.5":
-
- http://www.hdfgroup.org/HDF5/doc/ADGuide/Changes.html
-
-If you have any questions or comments, please send them to the HDF Help Desk:
-
- help@hdfgroup.org
-
-
-CONTENTS
-========
-
-- New Features
-- Support for New Platforms, Languages, and Compilers
-- Bug Fixes since HDF5-1.8.5
-- Platforms Tested
-- Supported Configuration Features Summary
-- Known Problems
-
-
-New Features
-============
-
- Configuration
- -------------
- - CMake: Improved CPack packaging, added parallel commands, improved
- configuration options (better similarity to configure), added more
- tests, better support for use in external cmake projects.
- (ADB - 2010/10/07)
- - The default configuration setting for official releases is
- --enable-production. For unofficial releases, the default configuration
- setting has been --disable-production. (AKC - 2010/05/28)
- Library
- -------
- - Added support for thread safety on Windows using the Windows threads
- library. Use the HDF5_ENABLE_THREADSAFE option in CMake on a Windows
- platform to enable this functionality. This is supported on Windows
- Vista and newer Windows operating systems. (MAM - 2010/09/10)
- - H5Tset_order and H5Tget_order now support all datatypes. A new byte
- order, H5T_ORDER_MIXED, has been added specifically for a compound
- datatype and its derived type. (SLU - 2010/8/23)
- - Improved performance of metadata I/O by changing the default algorithm
- to perform I/O from all processes (instead of just process 0) when using
- parallel I/O drivers. (QAK - 2010/07/19)
- - Improved performance of I/O on datasets with the same shape, but
- different rank. (QAK - 2010/07/19)
- - Improved performance of the chunk cache by avoiding unnecessary b-tree
- lookups of chunks already in cache. (NAF - 2010/06/15)
-
- Parallel Library
- ----------------
- - None
-
- Tools
- -----
- - h5diff: Added a new flag: --exclude-path. The specified path to an
- object will be excluded when comparing two files or two groups. If a
- group is specified to be excluded, all member objects of that group
- will be excluded. (JKM - 2010/09/16).
- - h5ls: Added a new flag: --no-dangling-links. See --help output for
- details. (JKM - 2010/06/15)
- - h5ls: Added a new flag --follow-symlinks. See --help output for
- details. (JKM - 2010/05/25)
-
- High-Level APIs
- ---------------
- - None
-
- F90 API
- -------
- - None
-
- C++ API
- -------
- - None
-
-
-Support for New Platforms, Languages, and Compilers
-===================================================
- - Sun C and C++ 5.10 and Sun Fortran 95 8.4.
- - Mac OS X 10.6.4 with gcc 4.2.1 and gfortran 4.6
-
-
-Bug Fixes since HDF5-1.8.5
-==========================
-
- Configuration
- -------------
- - The default number of MPI processes for testing purposes has been
- changed from 3 to 6. (AKC - 2010/11/11)
- - Some tests in tools/h5repack may fail in AIX systems when -q32 mode is
- used. The error is caused by not requesting enough memory in default.
- Added "env LDR_CNTRL=MAXDATA=0x20000000@DSA" into the $RUNSERIAL and
- $RUNPARALLE in the AIX config file so that executables are tested with
- more memory. (AKC - 2010/11/11)
- - Removed recognition of the parallel compilers of LAM(hcc) and
- ChMPIon(cmpicc) since we have no access to these two MPI implementations
- and cannot verify their correctness. (AKC - 2010/07/14 - Bug 1921)
- - PHDF5 was changed to use "mpiexec" instead of mpirun as the default
- MPI applications startup command as defined in the MPI-2 definition,
- section 4.1. (AKC - 2010/06/11 - Bug 1921)
-
- Library
- -------
- - Fixed a bug that caused big endian machines to generate corrupt files
- when using the scale-offset filter with floating point data or fill
- values. Note that such datasets will no longer be readable by any
- by any machine after this patch. (NAF - 2010/02/02 - Bug 2131)
- - Retrieving a link's name by index in the case where the link is external
- and the file that the link refers to doesn't exist will now fail
- gracefully rather than cause a segmentation fault. (MAM - 2010/11/17)
- - Modified metadata accumulator to better track accumulated dirty metadata
- in an effort to reduce unnecessary I/O in certain situations and to
- fix some other corner cases which were prone to error. (MAM - 2010/10/15)
- - Added a new set of unit tests that are run during 'make check' to verify
- the behavior of the metadata accumulator. (MAM - 2010/10/15)
- - Modified library to always cache symbol table information. Libraries
- from version 1.6.3 and earlier have a bug which causes them to require
- this information for some operations. (NAF - 2010/09/21 - Bug 1864)
- - Fixed a bug where the library could generate an assertion/core dump when
- a file that had been created with H5Pset_libver_bounds(fapl,
- H5F_LIBVER_LATEST, H5F_LIBVER_LATEST) but didn't have a superblock
- extension was later reopened. (QAK - 2010/09/16 - Bug 1968)
- - Fixed a bug that could occur when getting information for a new-style
- group that was previously opened through a file handle that was later
- closed. (NAF - 2010/09/15)
- - Added define check in H5public.h if stdint.h is supported by the C++
- compiler. This define is only available on Windows with VS2010 and using
- CMake to build the library. (ADB - 2010/09/13 - Bug 1938)
- - When a mandatory filter failed to write data chunks, the dataset
- couldn't close (bug 1260). The fix releases all resources and closes
- the dataset but returns a failure. (SLU - 2010/09/08)
- - H5Eset_current_stack now also closes the error stack set as the
- default. This is to avoid a potential problem.
- (SLU - 2010/09/07 - Bug 1799)
- - Corrected situation where 1-D chunked dataset could get created by an
- application without calling H5Pset_chunk(). H5Pset_chunk is now
- required for creating all chunked datasets. (QAK - 2010/09/02)
- - Fixed many memory issues that valgrind exposed. (QAK - 2010/08/24)
- - Fixed the bug in the filter's public CAN_APPLY function. The return
- value should be htri_t not herr_t. (SLU - 2010/08/05 - Bug 1239)
- - Fixed the STDIO VFD to use fseeko64 instead of fseek64 for 64-bit I/O
- support. (AKC - 2010/7/30)
- - Fixed a bug in the direct I/O driver that could render files with certain
- kinds of unaligned data unreadable or corrupt them. (NAF - 2010/07/28)
- - valgrind reported an error of copying data to itself when a new attribute
- is written. Fixed by taking out the memcpy step in the attribute code.
- (SLU - 2010/07/28 - Bug 1956)
- - Corrected various issues in the MPI datatype creation code which could
- cause resource leaks or incorrect behavior (and may improve the
- performance as well). (QAK - 2010/07/19)
- - Fixed a bug that could cause file corruption when using non-default sizes
- of addresses and/or lengths. This bug could also cause uncorrupted files
- with this property to be unreadable. This bug was introduced in 1.8.5.
- (NAF - 2010/07/16 - Bug 1951)
-
- Parallel Library
- ----------------
- - None
-
- Tools
- -----
- - Fixed h5diff to compare member objects and groups recursively when
- two files or groups are compared. (JKM - 2010/9/16 - Bug 1975)
- - Fixed h5repack to be able to convert a dataset to COMPACT layout.
- (JKM - 2010/09/15 - Bug 1896)
- - Changed h5ls to not interpret special characters in object or attribute
- names for output. (JKM - 2010/06/28 - Bug 1784)
- - Revised the order of arguments for h5cc, h5fc, h5c++, h5pcc and h5pfc.
- CPPFLAGS, CFLAGS, LDFLAGS, and LIBS have been duplicated with an H5BLD_
- prefix to put the flags and paths from the hdf5 build in the correct
- places and allow the script user to add entries in CPPFLAGS, CFLAGS,
- LDFLAGS, and LIBS that will take precedence over those from the hdf5
- build. The user can make these entries persistent by editing
- CFLAGSBASE, CPPFLAGSBASE, LDFLAGSBASE, and LIBSBASE near the top of
- the script or temporary by setting HDF5_CFLAGS, HDF5_CPPFLAGS,
- HDF5_LDFLAGS, or HDF5_LIBS in the environment. The new order of
- arguments in these scripts is $CLINKER $H5BLD_CPPFLAGS $CPPFLAGS
- $H5BLD_CFLAGS $CFLAGS $LDFLAGS $clibpath $link_objs $LIBS $link_args
- $shared_link. (LRK - 2010/10/25 - Bug 1973)
-
- F90 API
- ------
- - None
-
- C++ API
- ------
- - None
-
- High-Level APIs:
- ------
- - None
-
- Fortran High-Level APIs:
- ------
- - None
-
-
-Platforms Tested
-================
-The following platforms and compilers have been tested for this release.
-
- AIX 6.1 xlc 11.1.0.3
- (NCSA BP) xlC 11.1.0.3
- xlf 13.1.0.3
- mpcc_r 11.1.0.3
- mpxlf_r 13.1.0.3
-
- FreeBSD 6.3-STABLE i386 gcc 3.4.6 [FreeBSD] 20060305
- (duty) g++ 3.4.6 [FreeBSD] 20060305
- gcc 4.4.5 20100803
- g++ 4.4.5 20100803
- gfortran 4.4.5 20100803
-
- FreeBSD 6.3-STABLE amd64 gcc 3.4.6 [FreeBSD] 20060305
- (liberty) g++ 3.4.6 [FreeBSD] 20060305
- gcc 4.4.5 20100803
- g++ 4.4.5 20100803
- gfortran 4.4.5 20100803
-
- Linux 2.6.18-194.3.1.el5PAE gcc (GCC) 4.1.2 and 4.4.2
- #1 SMP i686 i686 i386 G95 (GCC 4.0.3 (g95 0.93!) Apr 21 2010)
- (jam) GNU Fortran (GCC) 4.1.2 20080704
- (Red Hat 4.1.2-48) and 4.4.2
- PGI C, Fortran, C++ 10.4-0 32-bit
- PGI C, Fortran, C++ 10.6-0 32-bit
- Intel(R) C Compiler for 32-bit
- applications, Version 11.1
- Intel(R) C++ Compiler for 32-bit
- applications, Version 11.1
- Intel(R) Fortran Compiler for 32-bit
- applications, Version 11.1
- Absoft 32-bit Fortran 95 10.0.7
- MPICH mpich2-1.3.1 compiled with
- gcc 4.1.2 and gfortran 4.1.2
-
- Linux 2.6.18-194.17.1.el5 gcc 4.1.2 and 4.4.2
- #1 SMP x86_64 GNU/Linux G95 (GCC 4.0.3 (g95 0.93!) Apr 21 2010)
- (amani) tested for both 32- and 64-bit binaries
- GNU Fortran (GCC) 4.1.2 20080704
- (Red Hat 4.1.2-46) and 4.4.2
- Intel(R) C, C++, Fortran Compilers for
- applications running on Intel(R) 64,
- Version 11.1.
- PGI C, Fortran, C++ Version 9.0-4
- for 64-bit target on x86-64
- MPICH mpich2-1.3.1 compiled with
- gcc 4.1.2 and gfortran 4.1.2
-
- SGI ProPack 7 Linux Intel(R) C++ Version 11.1 20100806
- 2.6.32.19-0.3.1.1982.0.PTF- Intel(R) Fortran Version 11.1 20100806
- default #1 SMP SGI MPT 2.01
- SGI Altix UV
- (NCSA ember)
-
- SunOS 5.10 32- and 64-bit Sun C 5.9 Sun OS_sparc Patch 124867-16
- (linew) Sun Fortran 95 8.3 Sun OS_sparc Patch 127000-13
- Sun C++ 5.9 Sun OS_sparc Patch 124863-62
- Sun C 5.10 SunOS_sparc Patch 141861-07
- Sun Fortran 95 8.4 SunOS_sparc Patch 128231-06
- Sun C++ 5.10 SunOS_sparc 128228-11
-
- Intel Xeon Linux 2.6.18- gcc 4.2.4
- 92.1.10.el5_lustre.1.6.6smp- Intel(R) C++ Version 10.1.017
- perfctr #8 SMP Intel(R) Fortran Compiler Version 10.1.017
- (NCSA abe) Open MPI 1.3.2
- MVAPICH2-1.5.1_pgi-10.8
-
- Windows XP Visual Studio 2008 w/ Intel Fortran 10.1 (project files)
- Visual Studio 2008 w/ Intel Fortran 11.1 (cmake)
- Visual Studio 2010 (cmake)
- Cygwin(1.7.7 native gcc(4.3.4) compiler and gfortran)
-
- Windows XP x64 Visual Studio 2008 w/ Intel Fortran 10.1 (project files)
- Visual Studio 2008 w/ Intel Fortran 11.1 (cmake)
- Visual Studio 2010 (cmake)
- Cygwin(1.7.7 native gcc(4.3.4) compiler and gfortran)
-
- Windows Vista Visual Studio 2008 w/ Intel Fortran 10.1 (project files)
- Visual Studio 2008 w/ Intel Fortran 11.1 (cmake)
-
- Windows Vista x64 Visual Studio 2008 w/ Intel Fortran 10.1 (project files)
- Visual Studio 2008 w/ Intel Fortran 11.1 (cmake)
-
- Windows 7 Visual Studio 2008 w/ Intel Fortran 11.1 (cmake)
-
- Windows 7 x64 Visual Studio 2008 w/ Intel Fortran 11.1 (cmake)
-
- Mac OS X 10.6.3 (Intel 64-bit) i686-apple-darwin10-gcc-4.2.1 (GCC) 4.2.1
- Darwin Kernel Version 10.3.1 GNU Fortran (GCC) 4.5.0 20090910
- Intel C, C++ and Fortran compilers 11.1 20100806
-
- Mac OS X 10.6.4 (Intel 32-bit) i686-apple-darwin10-gcc-4.2.1 (GCC) 4.2.1
- Darwin Kernel Version 10.4.0 GNU Fortran (GCC) 4.6.0 20101106
- Intel C, C++ and Fortran compilers 12.0.0 20101110
-
- Mac OS X 10.6.4 (Intel 64-bit) i686-apple-darwin10-gcc-4.2.1 (GCC) 4.2.1 (Apple Inc. build 5659)
- Darwin Kernel Version 10.6.0 GNU Fortran (GCC) 4.5.0 20090910
- Intel C, C++ and Fortran compilers 11.1 20100806
-
- Fedora 12 2.6.32.16-150.fc12.ppc64 #1 SMP ppc64 GNU/Linux
- gcc (GCC) 4.4.4 20100630 (Red Hat 4.4.4-10)
- GNU Fortran (GCC) 4.4.4 20100630 (Red Hat 4.4.4-10)
-
- Debian5.06 2.6.26-2-686 #1 SMP i686 GNU/Linux
- gcc (Debian 4.3.2-1.1) 4.3.2
- GNU Fortran (Debian 4.3.2-1.1) 4.3.2
-
- Debian5.06 2.6.26-2-amd64 #1 SMP x86_64 GNU/Linux
- gcc (Debian 4.3.2-1.1) 4.3.2
- GNU Fortran (Debian 4.3.2-1.1) 4.3.2
-
- Fedora14 2.6.35.6-48.fc14.i686.PAE #1 SMP i686 i686 i386 GNU/Linux
- gcc (GCC) 4.5.1 20100924 (Red Hat 4.5.1-4)
- GNU Fortran (GCC) 4.5.1 20100924 (Red Hat 4.5.1-4)
-
- Fedora14 2.6.35.6-48.fc14.x86_64 #1 SMP x86_64 x86_64 x86_64 GNU/Linux
- gcc (GCC) 4.5.1 20100924 (Red Hat 4.5.1-4)
- GNU Fortran (GCC) 4.5.1 20100924 (Red Hat 4.5.1-4)
-
- SUSE 11.3 2.6.34.7-0.7-desktop #1 SMP PREEMPT i686 i686 i386 GNU/Linux
- gcc (SUSE Linux) 4.5.0 20100604 [gcc-4_5-branch revision 160292]
- GNU Fortran (SUSE Linux) 4.5.0 20100604 [gcc-4_5-branch revision 160292]
-
- SUSE 11.3 2.6.34.7-0.7-desktop #1 SMP PREEMPT x86_64 x86_64 x86_64 GNU/Linux
- gcc (SUSE Linux) 4.5.0 20100604 [gcc-4_5-branch revision 160292]
- GNU Fortran (SUSE Linux) 4.5.0 20100604 [gcc-4_5-branch revision 160292]
-
- Ubuntu 10.10 2.6.35-25-generic #44-Ubuntu SMP i686 GNU/Linux
- gcc (Ubuntu/Linaro 4.4.4-14ubuntu5) 4.4.5
- GNU Fortran (Ubuntu/Linaro 4.4.4-14ubuntu5) 4.4.5
-
- Ubuntu 10.10 2.6.35-25-generic #44-Ubuntu SMP x86_64 GNU/Linux
- gcc (Ubuntu/Linaro 4.4.4-14ubuntu5) 4.4.5
- GNU Fortran (Ubuntu/Linaro 4.4.4-14ubuntu5) 4.4.5
-
- OpenVMS Alpha 8.3 HP C V7.3-009
- HP Fortran V8.2-104679-48H9K
- HP C++ V7.3-009
-
-Tested Configuration Features Summary
-========================================
-
- In the tables below
- y = tested
- n = not tested in this release
- C = Cluster
- W = Workstation
- x = not working in this release
- dna = does not apply
- ( ) = footnote appears below second table
- <blank> = testing incomplete on this feature or platform
-
-Platform C F90 F90 C++ zlib SZIP
- parallel parallel
-Solaris2.10 32-bit n y n y y y
-Solaris2.10 64-bit n y n y y y
-Windows XP n y(4) n y y y
-Windows XP x64 n y(4) n y y y
-Windows Vista n y(4) n y y y
-Windows Vista x64 n y(4) n y y y
-OpenVMS Alpha n y n y y n
-Mac OS X 10.6 Intel n y n y y y
-AIX 6.1 32- and 64-bit y y y y y y
-FreeBSD 6.3-STABLE 32&64 bit n y n y y y
-CentOS 5.5 Linux 2.6.18-194 i686 GNU (1)W y y(2) y y y y
-CentOS 5.5 Linux 2.6.18-194 i686 Intel W n y n y y n
-CentOS 5.5 Linux 2.6.18-194 i686 PGI W n y n y y n
-CentOS 5.5 Linux 2.6.16 x86_64 GNU (1) W y y(3) y y y y
-CentOS 5.5 Linux 2.6.16 x86_64 Intel W n y n y y n
-CentOS 5.5 Linux 2.6.16 x86_64 PGI W n y n y y y
-RedHat EL4 2.6.18 Xeon Lustre C y y y y y n
-Fedora 12 Linux 2.6.32.16-150.fc12.ppc64 n y n y y y
-SGI Linux 2.6.32.19 y y y y y y
-
-
-Platform Shared Shared Shared Thread-
- C libs F90 libs C++ libs safe
-Solaris2.10 32-bit y y y y
-Solaris2.10 64-bit y y y y
-Windows XP y y(4) y n
-Windows XP x64 y y(4) y n
-Windows Vista y y(4) y y
-Windows Vista x64 y y(4) y y
-OpenVMS Alpha n n n n
-Mac OS X 10.6 y(5) n y n
-AIX 6.1 32- and 64-bit n n n y
-FreeBSD 6.3-STABLE 32&64 bit y n y y
-CentOS 5.5 Linux 2.6.18-128 i686 GNU (1)W y y(2) y y
-CentOS 5.5 Linux 2.6.18-128 i686 Intel W y y y n
-CentOS 5.5 Linux 2.6.18-128 i686 PGI W y y y n
-CentOS 5.5 Linux 2.6.16 x86_64 GNU (1) W y y y y
-CentOS 5.5 Linux 2.6.16 x86_64 Intel W y y y n
-CentOS 5.5 Linux 2.6.16 x86_64 PGI W y y y n
-RedHat EL4 2.6.18 Xeon Lustre C y y y n
-Fedora 12 Linux 2.6.32.16-150.fc12.ppc64 y y y y
-SGI Linux 2.6.32.19 y y y y
-
- (1) Fortran compiled with gfortran.
- (2) With PGI and Absoft compilers.
- (3) With PGI compiler for Fortran.
- (4) Using Visual Studio 2008 w/ Intel Fortran 10.1 (Cygwin shared libraries are not supported)
- (5) C and C++ shared libraries will not be built when Fortran is enabled.
- Compiler versions for each platform are listed in the preceding
- "Platforms Tested" table.
-
-
-Known Problems
-==============
-* examples/run-all-ex.sh does not work on Cygwin. (NAF - 2011/02/11)
-
-* Parallel test, t_shapesame in testpar, is rather unstable as it continues to
- have occasional errors in AIX and quite often in NCSA Abe. It is being built
- but it is not run automatically in the "make check" command. One would have to
- run it by hand to see if it works in a particular machine. AKC - 2011/01/28
-
-* Although OpenVMS Alpha is supported, there are several problems with the C
- test suite - getname.c, lheap.c, lheap.c, mtime.c, and stab.c. The test
- suite for h5diff also fails. These failures are from the tests, not the
- library. We have fixed these failures. But it's too late to put the fixes
- into this release. If you install the 1.8.6 library, it should still work
- despite of these test failures. If you want the working copy without any
- test failure, you can request it from us. SLU - 2011/01/26
-
-* If parallel gmake (e.g., gmake -j 4) is used, the "gmake clean" command
- sometimes fails in the perform directory due to the attempt to remove the
- executable of h5perf or h5perf_serial by two "parallel" commands. This error
- has no consequence on the functionality of the HDF5 library or install. It
- is fixed in the next release. AKC - 2011/01/25
-
-* While working on the 1.8.6 release of HDF5, a bug was discovered that can
- occur when reading from a dataset in parallel shortly after it has been
- written to collectively. The issue was exposed by a new test in the parallel
- HDF5 test suite, but had existed before that. We believe the problem lies with
- certain MPI implementations and/or filesystems.
-
- We have provided a pure MPI test program, as well as a standalone HDF5
- program, that can be used to determine if this is an issue on your system.
- They should be run across multiple nodes with a varying number of processes.
- These programs can be found at:
- http://www.hdfgroup.org/ftp/HDF5/examples/known_problems/
-
-* The h5diff tool can display garbage values when variable-length strings in
- a compound type dataset are compared. This also occurs with variable-length
- string arrays in a compound type dataset. See bug #1989. This will be fixed
- in the next release. JKM - 2010/11/05
-
-* The AIX --enable-shared setting does not quite work. It can produce a shared
- library, but there cannot be more than one shared library that is
- interlinked. This means that the high level APIs will not work which is not
- very useful. We hope to have a solution in the next release.
- (AKC - 2010/10/15)
-
-* H5Eset_auto can cause a seg fault for a library API call if the application
- compiles with -DH5_USE_16_API (see bug 1707). It will be fixed in the
- next release. SLU - 2010/10/5
-
-* The library's test dt_arith.c showed a compiler's rounding problem on
- Cygwin when converting an unsigned long long to a long double. The
- library's own conversion works fine. We defined a macro for Cygwin to
- skip this test until we can solve the problem. Please see bug #1813.
- SLU - 2010/5/5
-
-* All the VFL drivers aren't backwardly compatible. In H5FDpublic.h, the
- structure H5FD_class_t changed in 1.8. A new parameter was added to the
- get_eoa and set_eoa callback functions, and a new callback function
- get_type_map was added. The public function H5FDrealloc was taken out in
- 1.8. The problem only happens when users define their own driver for 1.6
- and try to plug in a 1.8 library. This will be fixed in 1.10. SLU - 2010/2/2
-
-* MinGW has a missing libstdc++.dll.a library file and will not successfully link
- C++ applications/tests. Do not use the enable-cxx configure option. Read all of
- the INSTALL_MINGW.txt file for all restrictions. ADB - 2009/11/11
-
-* The PathScale MPI implementation, accessing a Panasas file system, would
- cause H5Fcreate() with H5F_ACC_EXCL to fail even when the file does not
- exist. This is due to the MPI_File_open() call failing if the amode has
- the MPI_MODE_EXCL bit set. (See bug 1468 for details.) AKC - 2009/8/11
-
-* Parallel tests failed with 16 processes with data inconsistency at testphdf5
- / dataset_readAll. Parallel tests also failed with 32 and 64 processes with
- collective abort of all ranks at t_posix_compliant / allwrite_allread_blocks
- with MPI IO. CMC - 2009/04/28
-
-* For Red Storm, a Cray XT3 system, the tools/h5ls/testh5ls.sh and
- tools/h5copy/testh5copy.sh will fail some of their sub-tests. These
- sub-tests are expected to fail and should exit with a non-zero code but
- the yod command does not propagate the exit code of the executables. Yod
- always returns 0 if it can launch the executable. The test suite shell
- expects a non-zero for this particular test. Therefore, it concludes the
- test has failed when it receives 0 from yod. To skip all the "failing"
- tests for now, change them as shown below.
-
- ======== Original tools/h5ls/testh5ls.sh =========
- TOOLTEST tgroup-1.ls 1 -w80 -r -g tgroup.h5
- ======== Change to ===============================
- echo SKIP TOOLTEST tgroup-1.ls 1 -w80 -r -g tgroup.h5
- ==================================================
-
- ======== Original tools/h5copy/testh5copy.sh =========
- TOOLTEST_FAIL -i $TESTFILE -o $FILEOUT -v -s grp_dsets -d grp_rename
- TOOLTEST_FAIL -i $TESTFILE -o $FILEOUT -v -s grp_dsets -d /grp_rename/grp_dsets
- TOOLTEST_FAIL -i $TESTFILE -o $FILEOUT -vp -s /grp_dsets -d /E/F/grp_dsets
- TOOLTEST_FAIL -i $TESTFILE -o $FILEOUT -vp -s /grp_nested -d /G/H/grp_nested
- H5LSTEST $FILEOUT
- ======== Change to ===============================
- echo SKIP TOOLTEST_FAIL -i $TESTFILE -o $FILEOUT -v -s grp_dsets -d grp_rename
- echo SKIP TOOLTEST_FAIL -i $TESTFILE -o $FILEOUT -v -s grp_dsets -d /grp_rename/grp_dsets
- echo SKIP TOOLTEST_FAIL -i $TESTFILE -o $FILEOUT -vp -s /grp_dsets -d /E/F/grp_dsets
- echo SKIP TOOLTEST_FAIL -i $TESTFILE -o $FILEOUT -vp -s /grp_nested -d /G/H/grp_nested
- echo SKIP H5LSTEST $FILEOUT
- ==================================================
- AKC - 2008/11/10
-
-* For Red Storm, a Cray XT3 system, the yod command sometimes gives the
- message "yod allocation delayed for node recovery." This interferes
- with test suites that do not expect to see this message. See the "Red Storm"
- section in file INSTALL_parallel for a way to deal with this problem.
- AKC - 2008/05/28
-
-* On an Intel 64 Linux cluster (RH 4, Linux 2.6.9) with Intel 10.0 compilers,
- use the -mp -O1 compilation flags to build the libraries. A higher level
- of optimization causes failures in several HDF5 library tests.
-
-* On mpich 1.2.5 and 1.2.6 on a system using four processors, if more than
- two processes contribute no I/O and the application asks to do collective
- I/O, we have found that a simple collective write will sometimes hang. This
- can be verified with the t_mpi test under testpar.
-
-* A dataset created or rewritten with a v1.6.3 or later library cannot be
- read with the v1.6.2 or earlier library when the Fletcher32 EDC filter
- is enabled. There was a bug in the calculation of the Fletcher32 checksum
- in the library before v1.6.3; the checksum value was not consistent
- between big-endian and little-endian systems. This bug was fixed in
- Release 1.6.3. However, after fixing the bug, the checksum value was no
- longer the same as before on little-endian system. Library releases after
- 1.6.4 can still read datasets created or rewritten with an HDF5 library of
- v1.6.2 or earlier. SLU - 2005/6/30
-
-* On IBM AIX systems, parallel HDF5 mode will fail some tests with error
- messages like "INFO: 0031-XXX ...". This is from the command `poe'. To
- work around this, set the environment variable MP_INFOLEVEL to 0 to
- minimize the messages and run the tests again. The tests may fail with
- messages like "The socket name is already in use", but HDF5 does not use
- sockets. This failure is due to problems with the poe command trying to
- set up the debug socket. To resolve this problem, check to see whether
- there are any old /tmp/s.pedb.* files around. These are sockets used by
- the poe command and left behind if the command failed at some point. To
- resolve this, ask your system administrator to remove the
- old/tmp/s.pedb.* files, and then ask IBM to provide a means to run poe
- without the debug socket.
-
-* The --enable-static-exec configure flag will only statically link
- libraries if the static version of that library is present. If only the
- shared version of a library exists (i.e., most system libraries on
- Solaris, AIX, and Mac, for example, only have shared versions), the flag
- should still result in a successful compilation, but note that the
- installed executables will not be fully static. Thus, the only guarantee
- on these systems is that the executable is statically linked with just
- the HDF5 library.
-
-* On an SGI Altix SMP ia64 system, the Intel compiler version 10.1 (which
- is the default on that system) does not work properly and results in
- failures during the make check (in a static build) and the make
- installcheck (in a shared build). This appears to be a compiler
- optimization problem. Reducing the optimization by setting CFLAGS to
- -O1 or below resolves the issue. Using a newer version of the compiler
- (11.0) avoids the issue. MAM - 2010/06/01
-
-* On solaris systems, when running the examples with the scripts installed in
- .../share/hdf5_examples, two of the c tests, h5_extlink and h5_elink_unix2win
- may fail or generate HDF5 errors because the script commands in c/run-c-ex.sh
- fail to create test directories red, blue, and u2w. Moving the '!' in lines
- 67, 70, 73 of run-c-ex.sh will fix the problem. For example the script command
- "if ! test -d red; then" will work on solaris if changed to
- "if test ! -d red; then".
-
-
-%%%%1.8.5%%%%
-
-
-HDF5 version 1.8.5 released on Fri Jun 4 13:27:31 CDT 2010
-================================================================================
-
-INTRODUCTION
-============
-
-This document describes the differences between HDF5-1.8.4 and HDF5 1.8.5, and
-contains information on the platforms tested and known problems in HDF5-1.8.5.
-For more details, see the files HISTORY-1_0-1_8_0_rc3.txt and HISTORY-1_8.txt
-in the release_docs/ directory of the HDF5 source.
-
-Links to the HDF5 1.8.5 source code, documentation, and additional materials
-can be found on the HDF5 web page at:
-
- http://www.hdfgroup.org/products/hdf5/
-
-The HDF5 1.8.5 release can be obtained from:
-
- http://www.hdfgroup.org/HDF5/release/obtain5.html
-
-User documentation for 1.8.5 can be accessed directly at this location:
-
- http://www.hdfgroup.org/HDF5/doc/
-
-New features in the HDF5-1.8.x release series, including brief general
-descriptions of some new and modified APIs, are described in the "What's New
-in 1.8.0?" document:
-
- http://www.hdfgroup.org/HDF5/doc/ADGuide/WhatsNew180.html
-
-All new and modified APIs are listed in detail in the "HDF5 Software Changes
-from Release to Release" document, in the section "Release 1.8.5 (current
-release) versus Release 1.8.4":
-
- http://www.hdfgroup.org/HDF5/doc/ADGuide/Changes.html
-
-If you have any questions or comments, please send them to the HDF Help Desk:
-
- help@hdfgroup.org
-
-
-CONTENTS
-========
-
-- New Features
-- Support for New Platforms, Languages, and Compilers
-- Bug Fixes since HDF5-1.8.4
-- Platforms Tested
-- Supported Configuration Features Summary
-- Known Problems
-
-
-New Features
-============
-
- Configuration
- -------------
- - CMake Early Access: This release adds support for building HDF5 using
- the CMake system. Initial work has targeted Windows, but other platforms
- can be used. See the CMake.TXT file for more information. Version
- 2.8.1 of CMake is required.
- - Configure now adds appropriate defines for supporting large (64-bit)
- files on all systems, where supported, by default, instead of only Linux.
- This large file support is controllable with the --enable-largefile
- configure option. The Linux-specific --enable-linux-lfs option has been
- deprecated in favor of this new option. Please note that specifying
- --disable-large does NOT attempt to "turn off" largefile support if it
- is natively supported by the compiler, but rather just disables
- configure from actively trying to add any additional compiler flags.
- (MAM - 2010/05/05 - Bug # 1772/1434)
- - Fixed an signal handling mask error in H5detect that might result in
- SIGBUS or SIGSEGV failures in some platforms such as Linux on Sparc.
- (AKC - 2010/4/28 - Bug # 1764)
- - Fixed various "strict aliasing" problems, allowing higher levels
- of compiler optimization (in particular, allowing '-O3' to work
- with recent versions of GCC). (QAK - 2010/04/26)
- - Upgraded versions of autotools used to generate configuration suite.
- We now use Automake 1.11.1, Autoconf 2.65, and Libtool 2.2.6b.
- (MAM - 2010/04/15)
- - Added the xlc-* and mpcc_r-* BASENAME patterns to be recognized as IBM
- compilers so that the IBM compiler options can be added properly. This
- allows non-system-default compiler command names (e.g. xlc-m.n.k.l) be
- recognized. (AKC - 2009/11/26)
-
- Library
- -------
- - Performance is substantially improved when extending a dataset with early
- allocation. (NAF - 2010/03/24 - Bug # 1637)
- - Added support for filtering densely stored groups. Many of the API
- functions related to filters have been extended to support dense groups
- as well as datasets. Pipeline messages can now be stored in a group's
- object header. (NAF/QAK - 2009/11/3)
-
- Parallel Library
- ----------------
- - None
-
- Tools
- -----
- - h5dump: Added the new packed bits feature which prints packed bits stored
- in an integer dataset. (AKC/ADB - 2010/5/7)
- - h5diff: Fixed incorrect behavior (hang) in parallel mode when specifying
- invalid options (ex: -v and -q). (JKM - 2010/02/17)
- - h5diff: Added new flag --no-dangling-links (see --help for details).
- (JKM - 2010/02/10)
- - h5diff: Added new flag --follow-symlinks (see --help for details).
- (JKM - 2010/01/25)
- - h5diff: Added a fix to correct the display of garbage values when
- displaying big-endian data on a little-endian machine. (JKM - 2009/11/20)
-
- High-Level APIs
- ---------------
- - None
-
- F90 API
- -------
- - None
-
- C++ API
- -------
- - New member functions
- + Overloaded CommonFG::getObjnameByIdx to take char* for name.
- + Overloaded CommonFG::getObjTypeByIdx to return type name as a char*.
- (BMR - 2010/05/10)
- + Added DataSet::getInMemDataSize() to simplify getting the dataset's
- data size in memory. (BMR - 2009/07/26)
-
-
-Support for New Platforms, Languages, and Compilers
-===================================================
- - AIX 6.1 has been added. (AKC - 2010/1/4)
-
-
-Bug Fixes since HDF5-1.8.4
-==========================
-
- Configuration
- -------------
- - Fixed various "strict aliasing" problems, allowing higher levels
- of compiler optimization (in particular, allowing '-O3' to work
- with recent versions of GCC). (QAK - 2010/04/26)
-
- Library
- -------
- - Fixed a file corruption bug that could happen when shrinking a compressed
- dataset. (NAF - 2010/05/20)
- - Fixed some memory leaks in VL datatype conversion when strings are
- used as fill values. (MAM - 2010/05/12 - Bug # 1826)
- - Fixed an H5Rcreate failure when passing in a -1 for the dataspace
- identifier. (ADB - 2010/4/28)
- - Fixed a bug when copying objects with NULL references with the
- H5O_COPY_EXPAND_REFERENCE_FLAG flag set. (NAF - 2010/04/08 - Bug # 1815)
- - Added a mechanism to the H5I interface to save returned object identifier
- structures for immediate re-use if needed. This addresses a potential
- performance issue by delaying the case when the next identifier to be
- registered has grown so large that it wraps around and needs to be
- checked to see whether it is available for distribution.
- (MAM - 2010/03/15 - Bug # 1730)
- - Files can now be concurrently opened more than once using the core file
- driver, as long as the backing store is used. (NAF - 2010/03/09)
- - Added support for H5O_COPY_EXPAND_EXT_LINK_FLAG to H5Ocopy. External
- links will now be expanded if this flag is set.
- (NAF - 2010/03/05 - Bug # 1733)
- - Fixed a bug where the library, when traversing an external link, would
- reopen the source file if nothing else worked. (NAF - 2010/03/05)
- - Fixed a bug where fractal heap identifiers for attributes and shared
- object header messages could be incorrectly encoded in the file for
- files created on big-endian platforms.
- Please see http://www.hdfgroup.org/HDF5/release/known_problems if you
- suspect you have a file with this problem.
- (QAK - 2010/02/23 - Bug # 1755)
- - Fixed an intermittent bug in the b-tree code which could be triggered
- by expanding and shrinking chunked datasets in certain ways.
- (NAF - 2010/02/16)
- - H5Tdetect_class said a VL string is a string type. But when it's in
- a compound type, it said it's a VL type. THis has been fixed to be
- consistent; it now always returns a string type.
- (SLU - 2009/12/10 - Bug # 1584)
- - Allow "child" files from external links to be correctly located when
- relative to a "parent" file that is opened through a symbolic link.
- (QAK - 2009/12/01)
-
- Parallel Library
- ----------------
- - Parallel mode in AIX will fail some of the testcheck_version.sh tests
- where it treats "exit(134) the same as if process 0 had received an abort
- signal. Fixed. (AKC - 2009/11/3)
-
- Tools
- -----
- - Fixed h5ls to return exit code 1 (error) when a non-existent file is
- specified. (JKM - 2010/04/27 - Bug # 1793)
- - Fixed h5copy failure when copying a dangling link that is specified
- directly. (JKM - 2010/04/22 - Bug # 1817)
- - Fixed an h5repack failure that lost attributes from a dataset of
- reference type. (JKM - 2010/3/25 - Bug # 1726)
- - Fixed h5repack error that set NULL for object reference values for
- datasets, groups, or named datatypes. (JKM - 2010/03/19 - Bug # 1814)
-
- F90 API
- ------
- - None
-
- C++ API
- ------
- - The constructor PropList::PropList(id) was fixed to act properly
- according to the nature of 'id'. When 'id' is a property class
- identifier, a new property list will be created. When 'id' is a
- property list identifier, a copy of the property list will be made.
- (BMR - 2010/5/9)
- - The parameters 'size' and 'bufsize' in CommonFG::getLinkval and
- CommonFG::getComment, respectively, now have default values for the
- user's convenience. (BMR - 2009/10/23)
- - NULL pointer accessing was fixed. (BMR - 2009/10/05 - Bug # 1061)
- - Read/write methods of DataSet and Attribute classes were fixed
- to handle string correctly. (BMR - 2009/07/26)
-
- High-Level APIs:
- ------
- - Fixed a bug in H5DSattach_scale, H5DSis_attached, and H5DSdetach_scale
- caused by using the H5Tget_native_type function to determine the native
- type for reading the REFERENCE_LIST attribute. This bug was exposed
- on Mac PPC. (EIP - 2010/05/22 - Bug # 1851)
- - Fixed a bug in the H5DSdetach_scale function when 0 bytes were
- allocated after the last reference to a dimension scale was removed
- from the list of references in a VL element of the DIMENSION_LIST
- attribute. Modified the function to comply with the specification:
- the DIMENSION_LIST attribute is now deleted when no dimension scales
- are left attached. (EIP - 2010/05/14 - Bug # 1822)
-
- Fortran High-Level APIs:
- ------
- - None
-
-
-Platforms Tested
-================
-The following platforms and compilers have been tested for this release.
-
- AIX 5.3 xlc 7.0.0.9, 8.0.0.20, 9.0.0.4
- (LLNL Up) xlC 7.0.0.9, 8.0.0.20, 9.0.0.4
- xlf 9.1.0.9, 10.1.0.9, 11.1.0.7
- mpcc_r 7.0.0.9
- mpxlf_r 09.01.0000.0008
-
- AIX 6.1 xlc 10.1.0.6
- (NCSA BP) xlC 10.1.0.6
- xlf 12.1.0.7
-
- Cray XT3 (2.1.56) cc (pgcc) 10.0-0
- (SNL red storm) ftn (pgf90) 10.0-0
- CC (pgCC) 10.0-0
-
- FreeBSD 6.3-STABLE i386 gcc 3.4.6 [FreeBSD] 20060305
- (duty) g++ 3.4.6 [FreeBSD] 20060305
- gcc 4.3.4 20090419
- g++ 4.3.4 20090419
- gfortran 4.3.4 20090419
-
- FreeBSD 6.3-STABLE amd64 gcc 3.4.6 [FreeBSD] 20060305
- (liberty) g++ 3.4.6 [FreeBSD] 20060305
- gcc 4.4.1 20090421
- g++ 4.4.1 20090421
- gfortran 4.4.1 20090421
-
- Linux 2.6.18-128.1.6.el5xen gcc (GCC) 4.1.2 20080704 and 4.4.2
- #1 SMP i686 i686 i386 GNU Fortran (GCC) 4.1.2 20080704 and 4.4.2
- (jam) g++ (GCC) 4.1.2 20080704 and 4.4.2
- G95 (GCC 4.0.3 (g95 0.93!) Apr 21 2010)
- Absoft 32-bit Fortran 95 10.0.7
- PGI C, Fortran, C++ 10.4-0 32-bit
- Intel(R) C, C++, Fortran Compilers for 32-bit
- applications, Version 11.1 Build 20090827
- MPICH mpich2-1.0.8 compiled with
- gcc 4.1.2 and GNU Fortran (GCC) 4.1.2
-
- Linux 2.6.18-164.el5 #1 SMP gcc 4.1.2 20080704 and gcc 4.4.2
- x86_64 GNU/Linux GNU Fortran (GCC) 4.1.2 20080704 and 4.4.2
- (amani) g++ (GCC) 4.1.2 20080704 and 4.4.2
- G95 (GCC 4.0.3 (g95 0.93!) Apr 21 2010)
- Intel(R) C, C++, Fortran Compilers for
- applications running on Intel(R) 64,
- Version 11.1 Build 20090827.
- PGI C, Fortran, C++ Version 10.4-0
- for 32 & 64-bit target on x86-64
- MPICH mpich2-1.0.8 compiled with
- gcc 4.1.2 and GNU Fortran (GCC) 4.1.2
-
- Linux 2.6.16.54-0.2.5 #1 Intel(R) C++ Version 11.0.074
- SGI Altix SMP ia64 Intel(R) Fortran Itanium(R) Version 11.0.074
- (cobalt) SGI MPI 1.38
-
- SunOS 5.10 32- and 64-bit Sun C 5.9 SunOS_sparc Patch 124867-14
- (linew) Sun Fortran 95 8.3 SunOS_sparc
- Patch 127000-13
- Sun C++ 5.9 SunOS_sparc Patch 124863-23
-
- Intel Xeon Linux 2.6.18- Intel(R) C++ Version 10.0.026
- 92.1.10.el5_lustre.1.6.6smp- Intel(R) Fortran Compiler Version 10.0.026
- perfctr #7 SMP Open MPI 1.2.2
- (abe) MVAPICH2-0.9.8p28p2patched-intel-ofed-1.2
- compiled with icc v10.0.026 and ifort 10.0.026
-
- Linux 2.6.18-76chaos #1 SMP Intel(R) C, C++, Fortran Compilers for
- SMP x86_64 GNU/Linux applications running on Intel(R) 64,
- (SNL Glory) Versions 11.1.
-
- Windows XP Visual Studio 2008 w/ Intel Fortran 10.1
- Cygwin(1.7.5 native gcc(4.3.4) compiler and
- gfortran)
-
- Windows XP x64 Visual Studio 2008 w/ Intel Fortran 10.1
-
- Windows Vista Visual Studio 2008 w/ Intel Fortran 10.1
-
- Windows Vista x64 Visual Studio 2008 w/ Intel Fortran 10.1
-
- MAC OS 10.6.3 (Intel) i686-apple-darwin10-gcc-4.2.1 (GCC) 4.2.1
- (pahra) GNU Fortran (GCC) 4.5.0 20090910
- i686-apple-darwin10-g++-4.2.1 (GCC) 4.2.1
- Intel C, C++ and Fortran compilers 11.1
-
- MAC OS 10.5.8 (Intel) i686-apple-darwin9-gcc-4.0.1 (GCC) 4.0.1
- (tejeda)
-
- MAC OS 10.5 (PPC) powerpc-apple-darwin9-gcc-4.0.1 (GCC) 4.0.1
- (juniper-w)
-
- OpenVMS Alpha V8.3 HP C V7.3-009
- HP C++ V7.3-009
- HP Fortran V8.0-1-104669-48GBT
-
-Supported Configuration Features Summary
-========================================
-
- In the tables below
- y = tested and supported
- n = not supported or not tested in this release
- C = Cluster
- W = Workstation
- x = not working in this release
- dna = does not apply
- ( ) = footnote appears below second table
- <blank> = testing incomplete on this feature or platform
-
-Platform C F90 F90 C++ zlib SZIP
- parallel parallel
-Solaris2.10 32-bit n y n y y y
-Solaris2.10 64-bit n y n y y y
-Windows XP n y(4) n(4) y y y
-Windows XP x64 n y(4) n(4) y y y
-Windows Vista n y(4) n(4) y y y
-Windows Vista x64 n y(4) n(4) y y y
-Mac OS X 10.5 PPC n n n n y n
-Mac OS X 10.5 Intel n y n y y y
-Mac OS X 10.6 Intel n y n y y y
-AIX 5.3 32- and 64-bit n y n y y n
-AIX 6.1 32- and 64-bit n y n y y n
-FreeBSD 6.3-STABLE 32&64 bit n y n y y y
-RedHat EL4 2.6.9-42 i686 GNU (1) W y y y y y y
-RedHat EL5 2.6.18-128 i686 GNU (1)W y y(2) y y y y
-RedHat EL5 2.6.18-128 i686 Intel W n y n y y n
-RedHat EL5 2.6.18-128 i686 PGI W n y n y y n
-SuSe Linux 2.6.16 x86_64 GNU (1) W y y(3) y y y y
-SuSe Linux 2.6.16 x86_64 Intel W n y n y y n
-SuSe Linux 2.6.16 x86_64 PGI W n y n y y y
-SuSe Linux 2.6.16 SGI Altix ia64 C y y y y y y
-RedHat EL4 2.6.18 Xeon Lustre C y y y y y n
-Cray XT3 2.1.56 y y y y y n
-OpenVMS Alpha V8.3 n y n y y n
-
-Platform Shared Shared Shared Thread-
- C libs F90 libs C++ libs safe
-Solaris2.10 32-bit y y y y
-Solaris2.10 64-bit y y y y
-Windows XP y y(4) y n
-Windows XP x64 y y(4) y n
-Windows Vista y y(4) y n
-Windows Vista x64 y y(4) y n
-Mac OS X 10.5 PPC y n n n
-Mac OS X 10.5 (Intel) y(5) n y n
-Mac OS X 10.6 (Intel) y(5) n y n
-AIX 5.3 32- and 64-bit n n n n
-AIX 6.1 32- and 64-bit n n n n
-FreeBSD 6.3-STABLE 32&64 bit y n y y
-RedHat EL4 2.6.9-42 i686 GNU (1) W y y y y
-RedHat EL5 2.6.18-128 i686 GNU (1)W y y(2) y y
-RedHat EL5 2.6.18-128 i686 Intel W y y y n
-RedHat EL5 2.6.18-128 i686 PGI W y y y n
-SuSe Linux 2.6.16 x86_64 GNU (1) W y y y y
-SuSe Linux 2.6.16 x86_64 Intel W y y y n
-SuSe Linux 2.6.16 x86_64 PGI W y y y n
-SuSe Linux 2.6.16 SGI Altix ia64 C y n
-RedHat EL4 2.6.18 Xeon Lustre C y y y n
-Cray XT3 2.1.56 n n n n
-OpenVMS Alpha V8.3 n n n n
-
- (1) Fortran compiled with g95.
- (2) With PGI and Absoft compilers.
- (3) With PGI compiler for Fortran.
- (4) Using Visual Studio 2008. (Cygwin shared libraries are not
- supported.)
- (5) Shared C and C++ are disabled when Fortran is configured in.
- Compiler versions for each platform are listed in the preceding
- "Platforms Tested" table.
-
-
-Known Problems
-==============
-* The library's test dt_arith.c exposed a compiler's rounding problem on
- Cygwin when converting from unsigned long long to long double. The
- library's own conversion works correctly. A macro is defined for Cygwin
- to skip this test until we can solve the problem. (Please see bug #1813.)
- SLU - 2010/5/5
-
-* All the VFL drivers aren't backward compatible. In H5FDpublic.h, the
- structure H5FD_class_t changed in 1.8. There is a new parameter added to
- get_eoa and set_eoa callback functions. A new callback function
- get_type_map was added. The public function H5FDrealloc was taken
- out in 1.8. The problem only happens when users define their own driver
- for 1.6 and try to plug it into a 1.8 library. This affects a very small
- number of users. (See bug report #1279.) SLU - 2010/2/2
-
-* MinGW has a missing libstdc++.dll.a library file and will not successfully
- link C++ applications/tests. Do not use the enable-cxx configure option.
- Read all of the INSTALL_MINGW.txt file for all restrictions.
- ADB - 2009/11/11
-
-* Some tests in tools/h5repack may fail in AIX systems when -q32 mode is used.
- The error is due to insufficient memory requested. Request a large amount
- of runtime memory by setting the following environment variable for more
- memory.
- LDR_CNTRL=MAXDATA=0x20000000@DSA
- AKC - 2009/10/31
-
-* The PathScale MPI implementation, accessing a Panasas file system, would
- cause H5Fcreate() with H5F_ACC_EXCL to fail even when the file is not
- existing. This is due to the MPI_File_open() call failing if the amode has
- the MPI_MODE_EXCL bit set. (See bug 1468 for details.) AKC - 2009/8/11
-
-* Parallel tests failed with 16 processes with data inconsistency at testphdf5
- / dataset_readAll. Parallel tests also failed with 32 and 64 processes with
- collective abort of all ranks at t_posix_compliant / allwrite_allread_blocks
- with MPI IO. CMC - 2009/04/28
-
-* For gcc v4.3 and v4.4, with production mode, if -O3 is used, H5Tinit.c
- would fail to compile. Actually bad H5Tinit.c is produced. If -O (same
- as -O1) is used, H5Tinit.c compiled okay but test/dt_arith would fail.
- When -O0 (no optimizatio) is used, H5Tinit.c compilete okay and all
- tests passed. Therefore, -O0 is imposed for v4.3 and v4.4 of gcc.
- AKC - 2009/04/20
-
-* For Red Storm, a Cray XT3 system, the tools/h5ls/testh5ls.sh and
- tools/h5copy/testh5copy.sh will fail some of its sub-tests. These sub-tests
- are expected to fail and should exit with a non-zero code but the yod
- command does not propagate the exit code of the executables. Yod always
- returns 0 if it can launch the executable. The test suite shell expects
- a non-zero for this particular test, therefore it concludes the test has
- failed when it receives 0 from yod. Skip all the "failing" test for now
- by changing them as following.
-
- ======== Original tools/h5ls/testh5ls.sh =========
- TOOLTEST tgroup-1.ls 1 -w80 -r -g tgroup.h5
- ======== Change to ===============================
- echo SKIP TOOLTEST tgroup-1.ls 1 -w80 -r -g tgroup.h5
- ==================================================
-
- ======== Original tools/h5copy/testh5copy.sh =========
- TOOLTEST_FAIL -i $TESTFILE -o $FILEOUT -v -s grp_dsets -d grp_rename
- TOOLTEST_FAIL -i $TESTFILE -o $FILEOUT -v -s grp_dsets -d /grp_rename/grp_dsets
- TOOLTEST_FAIL -i $TESTFILE -o $FILEOUT -vp -s /grp_dsets -d /E/F/grp_dsets
- TOOLTEST_FAIL -i $TESTFILE -o $FILEOUT -vp -s /grp_nested -d /G/H/grp_nested
- H5LSTEST $FILEOUT
- ======== Change to ===============================
- echo SKIP TOOLTEST_FAIL -i $TESTFILE -o $FILEOUT -v -s grp_dsets -d grp_rename
- echo SKIP TOOLTEST_FAIL -i $TESTFILE -o $FILEOUT -v -s grp_dsets -d /grp_rename/grp_dsets
- echo SKIP TOOLTEST_FAIL -i $TESTFILE -o $FILEOUT -vp -s /grp_dsets -d /E/F/grp_dsets
- echo SKIP TOOLTEST_FAIL -i $TESTFILE -o $FILEOUT -vp -s /grp_nested -d /G/H/grp_nested
- echo SKIP H5LSTEST $FILEOUT
- ==================================================
- AKC - 2008/11/10
-
-* For Red Storm, a Cray XT3 system, the yod command sometimes gives the
- message, "yod allocation delayed for node recovery". This interferes with
- test suites that do not expect seeing this message. See the section of "Red
- Storm" in file INSTALL_parallel for a way to deal with this problem.
- AKC - 2008/05/28
-
-* On Intel 64 Linux cluster (RH 4, Linux 2.6.9) with Intel 10.0 compilers,
- use -mp -O1 compilation flags to build the libraries. A higher level of
- optimization causes failures in several HDF5 library tests.
-
-* On mpich 1.2.5 and 1.2.6, if more than two processes contribute no IO and
- the application asks to do collective IO, we have found that when using 4
- processors, a simple collective write will sometimes be hung. This can be
- verified with t_mpi test under testpar.
-
-* A dataset created or rewritten with a v1.6.3 library or after cannot be read
- with the v1.6.2 library or before when the Fletcher32 EDC filter is enabled.
- There was a bug in the calculation of the Fletcher32 checksum in the
- library before v1.6.3; the checksum value was not consistent between big-
- endian and little-endian systems. This bug was fixed in Release 1.6.3.
- However, after fixing the bug, the checksum value was no longer the same as
- before on little-endian system. Library releases after 1.6.4 can still read
- datasets created or rewritten with an HDF5 library of v1.6.2 or before.
- SLU - 2005/6/30
-
-* On IBM AIX systems, parallel HDF5 mode will fail some tests with error
- messages like "INFO: 0031-XXX ...". This is from the command `poe'.
- Set the environment variable MP_INFOLEVEL to 0 to minimize the messages
- and run the tests again.
-
- The tests may fail with messages like "The socket name is already in use,"
- but HDF5 does not use sockets. This failure is due to problems with the
- poe command trying to set up the debug socket. To resolve this problem,
- check to see whether there are many old /tmp/s.pedb.* files staying around.
- These are sockets used by the poe command and left behind due to failed
- commands. First, ask your system administrator to clean them out.
- Lastly, request IBM to provide a means to run poe without the debug socket.
-
-* The --enable-static-exec configure flag will only statically link libraries
- if the static version of that library is present. If only the shared version
- of a library exists (i.e., most system libraries on Solaris, AIX, and Mac,
- for example, only have shared versions), the flag should still result in a
- successful compilation, but note that the installed executables will not be
- fully static. Thus, the only guarantee on these systems is that the
- executable is statically linked with just the HDF5 library.
-
-* There is also a configure error on Altix machines that incorrectly reports
- when a version of Szip without an encoder is being used.
-
-* On FREE-BSD systems when shared libraries are disabled, make install fails
- in install-examples with the error '"Makefile", line 635: Need an operator'.
- When this error occurs removing or commenting out the line "export
- LD_LIBRARY_PATH=$(LL_PATH)" (line 635 in examples/Makefile) will allow make
- install to finish installing examples. The problem will be fixed in the
- next release. LRK - 2010/05/26
-
-* On cobalt, an SGI Altix SMP ia64 system, Intel compiler version 10.1 (which
- is the default on that system) does not work properly and results in
- failures during make check (in a static build) and make installcheck (during
- a shared build). This appears to be a compiler optimization problem.
- Reducing optimization by setting CFLAGS to -O1 or below resolves the issue.
- Alternatively, using a newer version of the compiler (11.0) also works as
- intended. MAM - 2010/06/01
-
-
-%%%%1.8.4%%%%
-
-
-HDF5 version 1.8.4 released on Tue Nov 10 15:33:14 CST 2009
-================================================================================
-
-INTRODUCTION
-============
-
-This document describes the differences between HDF5-1.8.3 and
-HDF5 1.8.4, and contains information on the platforms tested and
-known problems in HDF5-1.8.4
-For more details, see the files HISTORY-1_0-1_8_0_rc3.txt
-and HISTORY-1_8.txt in the release_docs/ directory of the HDF5 source.
-
-Links to the HDF5 1.8.4 source code, documentation, and additional materials
-can be found on the HDF5 web page at:
-
- http://www.hdfgroup.org/products/hdf5/
-
-The HDF5 1.8.4 release can be obtained from:
-
- http://www.hdfgroup.org/HDF5/release/obtain5.html
-
-User documentation for 1.8.4 can be accessed directly at this location:
-
- http://www.hdfgroup.org/HDF5/doc/
-
-New features in the HDF5-1.8.x release series, including brief general
-descriptions of some new and modified APIs, are described in the "What's New
-in 1.8.0?" document:
-
- http://www.hdfgroup.org/HDF5/doc/ADGuide/WhatsNew180.html
-
-All new and modified APIs are listed in detail in the "HDF5 Software Changes
-from Release to Release" document, in the section "Release 1.8.4 (current
-release) versus Release 1.8.3":
-
- http://www.hdfgroup.org/HDF5/doc/ADGuide/Changes.html
-
-If you have any questions or comments, please send them to the HDF Help Desk:
-
- help@hdfgroup.org
-
-
-CONTENTS
-========
-
-- New Features
-- Support for New Platforms, Languages, and Compilers
-- Bug Fixes since HDF5-1.8.3
-- Platforms Tested
-- Supported Configuration Features Summary
-- Known Problems
-
-
-New Features
-============
-
- Configuration
- -------------
- - Configuration suite now uses Automake 1.11 and Autoconf 2.64.
- MAM 2009/08/31.
- - Changed default Gnu fortran compiler from g95 to gfortran since
- gfortran is more likely installed with gcc now. -AKC 2009/07/19-
-
- Library
- -------
- - The embedded library information is displayed by H5check_version() if a
- version mismatch is detected. Also changed H5check_version() to
- suppress the warning message totally if $HDF5_DISABLE_VERSION_CHECK is 2
- or higher. (Old behavior treated 3 or higher the same as 1, that is
- print a warning and allows the program to continue. (AKC - 2009/9/28)
- - If a user does not care for the extra library information insert
- in the executables, he may turn it off by --disable-embedded-libinfo
- during configure. (AKC - 2009/9/15)
-
- Parallel Library
- ----------------
- - None
-
- Tools
- -----
- - h5diff: h5diff treats two INFINITY values different. Fixed by checking
- (value==expect) before call ABS(...) at h5diff_array.c. This will make
- that (INF==INF) is true (INF is treated as an number instead of NaN)
- (PC -- 2009/07/28)
- - h5diff: add option "--use-system-epsilon" to print difference if
- (|a-b| > EPSILON).
- Change default to use strict equality (PC -- 2009/09/12)
-
- High-Level APIs
- ---------------
- - None
-
- F90 API
- -------
- - Added H5Oopen_by_addr_f MSB - 9/14/09
-
- C++ API
- -------
- - None
-
-
-Support for New Platforms, Languages, and Compilers
-===================================================
- - PathScale compilers are recognized and can build the HDF5 library
- properly. AKC - 2009/7/28 -
-
-
-Bug Fixes since HDF5-1.8.3
-==========================
-
- Configuration
- -------------
- - Removed the following config files, as we no longer support them:
- config/dec-osf*, config/hpux11.00, config/irix5.x,
- config/powerpc-ibm-aix4.x config/rs6000-ibm-aix5.x config/unicos*
- MAM - 2009/10/08
- - Modified configure and make process to properly preserve user's CFLAGS
- (and company) environment variables. Build will now properly use
- automake's AM_CFLAGS for any compiler flags set by the configure
- process. Configure will no longer modify CFLAGS directly, nor will
- setting CFLAGS during make completely replace what configure has set up.
- MAM - 2009/10/08
- - Support for TFLOPS, config/intel-osf1, is removed since the TFLOPS
- machine has long retired. AKC - 2009/10/06.
- - Added $(EXEEXT) extension to H5detect when it's executed in the
- src/Makefile to generate H5Tinit.c so it works correctly on platforms
- that require the full extension when running executables.
- MAM - 2009/10/01 - BZ #1613
- - Configure will now set FC and CXX to "no" when fortran and c++
- are not being compiled, respectively, so configure will not run
- some of the compiler tests for these languages when they are not
- being used. MAM - 2009/10/01
- - The --enable-static-exec flag will now properly place the -static flag
- on the link line of all installed executables. This will force the
- executable to link with static libraries over shared libraries, provided
- the static libraries are available. MAM - 2009/08/31 - BZ #1583
- - The PathScale compiler (v3.2) was mistaken as gcc v4.2.0 but it fails to
- recognize some gcc options. Fixed. (see bug 1301). AKC - 2009/7/28 -
-
- Library
- -------
- - Fixed a bug where writing and deleting many global heap objects (i.e.
- variable length data) would render the file unreadable. Previously
- created files exhibiting this problem should now be readable.
- NAF - 2009/10/27 - 1483
- - Fixed error in library's internal caching mechanisms which could cause
- an assertion failure (and attendant core dump) when encountering an
- unusually formatted file. (QAK - 2009/10/13)
- - Fixed incorrect return value for H5Pget_preserve. AKC - 2009/10/08 - 1628
- - Fixed an assertion failure that occurred when H5Ocopy was called on a
- dataset using a vlen inside a compound. NAF - 2009/10/02 - 1597
- - Fixed incorrect return value for H5Pget_filter_by_id1/2 in H5Ppublic.h.
- NAF - 2009/09/25 - 1620
- - Fixed a bug where properties weren't being compared with the registered
- compare callback. NAF - 2009/09/25 - 1555
- - Corrected problem where library would re-write the superblock in a file
- opened for R/W access, even when no changes were made to the file.
- (QAK - 2009/08/20, Bz#1473)
- - Fixed a bug where H5Pget_filter_by_id would succeed when called for a
- filter that wasn't present. NAF - 2009/06/25 - 1250
- - Fixed an issue with committed compound datatypes containing a vlen. Also
- fixed memory leaks involving committed datatypes. NAF - 2009/06/10 - 1593
-
- Parallel Library
- ----------------
- - None
-
- Tools
- -----
- - h5dump/h5ls display buffer resize fixed in tools library.
- ADB - 2009/7/21 - 1520
- - perf_serial test added to Windows projects and check batch file.
- ADB - 2009/06/11 -1504
-
-
- F90 API
- ------
- - Fixed bug in h5lget_info_by_idx_f by adding missing arguments,
- consequently changing the API. New API is:
-
- SUBROUTINE h5lget_info_by_idx_f(loc_id, group_name, index_field, order, n, &
- link_type, f_corder_valid, corder, cset, address, val_size, hdferr, lapl_id)
-
- MSB - 2009/9/17 - 1652
-
- - Corrected the values for the H5L_flags FORTRAN constants:
- H5L_LINK_ERROR_F, H5L_LINK_HARD_F, H5L_LINK_SOFT_F, H5L_LINK_EXTERNAL_F
- MSB - 2009-09-17 - 1653
-
- - Added FORTRAN equivalent of C constant H5T_ORDER_NONE: H5T_ORDER_NONE_F
- MSB - 2009-9-24 - 1471
-
- C++ API
- ------
- - None
-
- High-Level APIs:
- ------
- - Fixed a bug where the H5TB API would forget the order of fields when added
- out of offset order. NAF - 2009/10/27 - 1582
- - H5DSis_attached failed to account for different platform types. Added a
- get native type call. ADB - 2009/9/29 - 1562
-
- Fortran High-Level APIs:
- ------
- - Lite: the h5ltread_dataset_string_f and h5ltget_attribute_string_f functions
- had memory problems with the g95 fortran compiler. (PVN � 5/13/2009) 1522
-
-
-
-Platforms Tested
-================
-The following platforms and compilers have been tested for this release.
-
- AIX 5.3 xlc 7.0.0.8
- (LLNL Up) xlf 09.01.0000.0008
- xlC 7.0.0.8
- mpcc_r 7.0.0.8
- mpxlf_r 09.01.0000.0008
-
- Cray XT3 (2.0.41) cc (pgcc) 7.1-4
- (SNL red storm) ftn (pgf90) 7.1-4
- CC (pgCC) 7.1-4
-
- FreeBSD 6.3-STABLE i386 gcc 3.4.6 [FreeBSD] 20060305
- (duty) g++ 3.4.6 [FreeBSD] 20060305
- gcc 4.3.5 20091004
- g++ 4.3.5 20091004
- gfortran 4.3.5 20091004
-
- FreeBSD 6.3-STABLE amd64 gcc 3.4.6 [FreeBSD] 20060305
- (liberty) g++ 3.4.6 [FreeBSD] 20060305
- gcc 4.4.2 20091006
- g++ 4.4.2 20091006
- gfortran 4.4.2 20091006
-
- Linux 2.6.18-164.el5 gcc (GCC) 4.1.2 20080704
- #1 SMP i686 i686 i386 G95 (GCC 4.0.3 (g95 0.92!) Jun 24 2009)
- (jam) GNU Fortran (GCC) 4.1.2 20080704
- (Red Hat 4.1.2-46)
- PGI C, Fortran, C++ 8.0-5 32-bit
- PGI C, Fortran, C++ 8.0-1 32-bit
- Intel(R) C Compiler for 32-bit
- applications, Versions 11.0, 11.1
- Intel(R) C++ Compiler for 32-bit
- applications, Version 11.0, 11.1
- Intel(R) Fortran Compiler for 32-bit
- applications, Version 11.0, 11.1
- Absoft 32-bit Fortran 95 10.0.7
- MPICH mpich2-1.0.8 compiled with
- gcc (GCC) 4.1.2 and G95
- (GCC 4.0.3 (g95 0.92!)
-
- Linux 2.6.18-164.el5 #1 SMP gcc 4.1.2 20080704
- x86_64 GNU/Linux G95 (GCC 4.0.3 (g95 0.92!) Jun 24 2009)
- (amani) tested for both 32- and 64-bit binaries
- Intel(R) C, C++, Fortran Compilers for
- applications running on Intel(R) 64,
- Versions 11.1.
- PGI C, Fortran, C++ Version 9.0-4
- for 64-bit target on x86-64
- gcc 4.1.2 and G95 (GCC 4.0.3 (g95 0.92!)
- MPICH mpich2-1.0.8 compiled with
- gcc 4.1.2 and G95 (GCC 4.0.3 (g95 0.92!)
- GNU Fortran (GCC) 4.1.2 20080704
- (Red Hat 4.1.2-46)
-
-
- Linux 2.6.16.60-0.42.5 #1 Intel(R) C++ Version 10.1.017
- SGI Altix SMP ia64 Intel(R) Fortran Itanium(R) Version 10.1.017
- (cobalt) SGI MPI 1.38
-
- SunOS 5.10 32- and 64-bit Sun C 5.9 SunOS_sparc Patch 124867-11 2009/04/30
- (linew) Sun Fortran 95 8.3 SunOS_sparc
- Patch 127000-11 2009/10/06
- Sun C++ 5.9 SunOS_sparc
- Patch 124863-16 2009/09/15
-
- Intel Xeon Linux 2.6.18- Intel(R) C++ Version 10.0.026
- 92.1.10.el5_lustre.1.6.6smp- Intel(R) Fortran Compiler Version 10.0.026
- perfctr #6 SMP Open MPI 1.2.2
- (abe) MVAPICH2-0.9.8p28p2patched-intel-ofed-1.2
- compiled with icc v10.0.026 and ifort 10.0.026
-
- IA-64 Linux 2.4.21-309.tg1 gcc (GCC) 3.2.2
- #1 SMP ia64 Intel(R) C++ Version 8.1.037
- (NCSA tg-login) Intel(R) Fortran Compiler Version 8.1.033
- mpich-gm-1.2.7p1..16-intel-8.1.037-r1
-
- Linux 2.6.9-55.0.9.EL_lustre Intel(R) C, C++, Fortran Compilers for
- .1.4.11.1smp #1 SMP applications running on Intel(R) 64,
- SMP x86_64 GNU/Linux Versions 10.1.
- (SNL Thunderbird)
-
- Linux 2.6.18-76chaos #1 SMP Intel(R) C, C++, Fortran Compilers for
- SMP x86_64 GNU/Linux applications running on Intel(R) 64,
- (SNL Glory) Versions 10.1.
-
- Windows XP Visual Studio 2005 w/ Intel Fortran 9.1
- Cygwin(native gcc compiler and g95)
-
- Windows XP x64 Visual Studio 2005 w/ Intel Fortran 9.1
-
- Windows Vista Visual Studio 2005 w/ Intel Fortran 9.1
-
- Windows Vista x64 Visual Studio 2005 w/ Intel Fortran 9.1
-
- MAC OS 10.5.6 (Intel) i686-apple-darwin9-gcc-4.0.1 (GCC) 4.0.1
- GNU Fortran (GCC) 4.3.0 20070810
- G95 (GCC 4.0.3 (g95 0.91!) Apr 24 2008)
- Intel C, C++ and Fortran compilers 10.1
-
-
-Supported Configuration Features Summary
-========================================
-
- In the tables below
- y = tested and supported
- n = not supported or not tested in this release
- C = Cluster
- W = Workstation
- x = not working in this release
- dna = does not apply
- ( ) = footnote appears below second table
- <blank> = testing incomplete on this feature or platform
-
-Platform C F90 F90 C++ zlib SZIP
- parallel parallel
-Solaris2.10 32-bit n y n y y y
-Solaris2.10 64-bit n y n y y y
-Windows XP n y(4) n(4) y y y
-Windows XP x64 n y(4) n(4) y y y
-Windows Vista n n n y y y
-Mac OS X 10.5 Intel n y n y y y
-AIX 5.3 32- and 64-bit n y n y y n
-FreeBSD 6.3-STABLE 32&64 bit n y n y y y
-RedHat EL5 2.6.18-164 i686 GNU (1)W y y(2) y y y y
-RedHat EL5 2.6.18-164 i686 Intel W n y n y y n
-RedHat EL5 2.6.18-164 i686 PGI W n y n y y n
-RedHat EL5 2.6.18-164 x86_64 GNU(1)W y y(3) y y y y
-RedHat EL5 2.6.18-164 x86_64 IntelW n y n y y n
-RedHat EL5 2.6.18-164 x86_64 PGI W n y n y y y
-SuSe Linux 2.6.16 SGI Altix ia64 C y y y y y y
-RedHat EL4 2.6.18 Xeon Lustre C y y y y y n
-SuSe Linux 2.4.21 ia64 Intel C y y y y y n
-Cray XT3 2.0.62 y y y y y n
-
-
-Platform Shared Shared Shared Thread-
- C libs F90 libs C++ libs safe
-Solaris2.10 32-bit y y y y
-Solaris2.10 64-bit y y y y
-Windows XP y y(4) y y
-Windows XP x64 y y(4) y y
-Windows Vista y n n y
-Mac OS X 10.5 y n y n
-AIX 5.3 32- and 64-bit n n n n
-FreeBSD 6.3-STABLE 32&64 bit y y y y
-RedHat EL5 2.6.18-164 i686 GNU (1)W y y(2) y y
-RedHat EL5 2.6.18-164 i686 Intel W y y y n
-RedHat EL5 2.6.18-164 i686 PGI W y y y n
-RedHat EL5 2.6.18-164 x86_64 GNU(1)W y y y y
-RedHat EL5 2.6.18-164 x86_64 IntelW y y y n
-RedHat EL5 2.6.18-164 x86_64 PGI W y y y n
-SuSe Linux 2.6.16 SGI Altix ia64 C y n
-RedHat EL4 2.6.18 Xeon Lustre C y y y n
-SuSe Linux 2.4.21 ia64 Intel C y y y n
-Cray XT3 2.0.62 n n n n
-
- (1) Fortran compiled with g95.
- (2) With PGI and Absoft compilers.
- (3) With PGI compiler for Fortran.
- (4) Using Visual Studio 2005 or Cygwin
- Compiler versions for each platform are listed in the preceding
- "Platforms Tested" table.
-
-
-Known Problems
-==============
-* Parallel mode in AIX will fail some of the testcheck_version.sh tests where
- it treats "exit(134) the same as if process 0 had received an abort signal.
- This is fixed and will be available in the next release. AKC - 2009/11/3
-
-* Some tests in tools/h5repack may fail in AIX systems when -q32 mode is used.
- The error is due to insufficient memory requested. Request a large amount
- of runtime memory by setting the following environment variable for more
- memory.
- LDR_CNTRL=MAXDATA=0x20000000@DSA
- AKC - 2009/10/31
-
-* The PathScale MPI implementation, accessing a Panasas file system, would
- cause H5Fcreate() with H5F_ACC_EXCL to fail even when the file is not
- existing. This is due to the MPI_File_open() call failing if the amode has
- the MPI_MODE_EXCL bit set. (See bug 1468 for details.) AKC - 2009/8/11
-
-* Parallel tests failed with 16 processes with data inconsistency at testphdf5
- / dataset_readAll. Parallel tests also failed with 32 and 64 processes with
- collective abort of all ranks at t_posix_compliant / allwrite_allread_blocks
- with MPI IO. CMC - 2009/04/28
-
-* There is a known issue in which HDF5 will change the timestamp on a file
- simply by opening it with read/write permissions, even if the file is not
- modified in any way. This is due to the way in which HDF5 manages the file
- superblock. A fix is currently underway and should be included in the 1.8.4
- release of HDF5. MAM - 2009/04/28
-
-* For gcc v4.3 and v4.4, with production mode, if -O3 is used, H5Tinit.c
- would fail to compile. Actually bad H5Tinit.c is produced. If -O (same
- as -O1) is used, H5Tinit.c compiled okay but test/dt_arith would fail.
- When -O0 (no optimizatio) is used, H5Tinit.c compilete okay and all
- tests passed. Therefore, -O0 is imposed for v4.3 and v4.4 of gcc.
- AKC - 2009/04/20
-
-* For Red Storm, a Cray XT3 system, the tools/h5ls/testh5ls.sh and
- tools/h5copy/testh5copy.sh will fail some of its sub-tests. These sub-tests
- are expected to fail and should exit with a non-zero code but the yod
- command does not propagate the exit code of the executables. Yod always
- returns 0 if it can launch the executable. The test suite shell expects
- a non-zero for this particular test, therefore it concludes the test has
- failed when it receives 0 from yod. Skip all the "failing" test for now
- by changing them as following.
-
- ======== Original tools/h5ls/testh5ls.sh =========
- TOOLTEST tgroup-1.ls 1 -w80 -r -g tgroup.h5
- ======== Change to ===============================
- echo SKIP TOOLTEST tgroup-1.ls 1 -w80 -r -g tgroup.h5
- ==================================================
-
- ======== Original tools/h5copy/testh5copy.sh =========
- TOOLTEST_FAIL -i $TESTFILE -o $FILEOUT -v -s grp_dsets -d grp_rename
- TOOLTEST_FAIL -i $TESTFILE -o $FILEOUT -v -s grp_dsets -d /grp_rename/grp_dsets
- TOOLTEST_FAIL -i $TESTFILE -o $FILEOUT -vp -s /grp_dsets -d /E/F/grp_dsets
- TOOLTEST_FAIL -i $TESTFILE -o $FILEOUT -vp -s /grp_nested -d /G/H/grp_nested
- H5LSTEST $FILEOUT
- ======== Change to ===============================
- echo SKIP TOOLTEST_FAIL -i $TESTFILE -o $FILEOUT -v -s grp_dsets -d grp_rename
- echo SKIP TOOLTEST_FAIL -i $TESTFILE -o $FILEOUT -v -s grp_dsets -d /grp_rename/grp_dsets
- echo SKIP TOOLTEST_FAIL -i $TESTFILE -o $FILEOUT -vp -s /grp_dsets -d /E/F/grp_dsets
- echo SKIP TOOLTEST_FAIL -i $TESTFILE -o $FILEOUT -vp -s /grp_nested -d /G/H/grp_nested
- echo SKIP H5LSTEST $FILEOUT
- ==================================================
- AKC - 2008/11/10
-
-* For Red Storm, a Cray XT3 system, the yod command sometimes gives the
- message, "yod allocation delayed for node recovery". This interferes with
- test suites that do not expect seeing this message. See the section of "Red
- Storm" in file INSTALL_parallel for a way to deal with this problem.
- AKC - 2008/05/28
-
-* On Intel 64 Linux cluster (RH 4, Linux 2.6.9) with Intel 10.0 compilers,
- use -mp -O1 compilation flags to build the libraries. A higher level of
- optimization causes failures in several HDF5 library tests.
-
-* On mpich 1.2.5 and 1.2.6, if more than two processes contribute no IO and
- the application asks to do collective IO, we have found that when using 4
- processors, a simple collective write will sometimes be hung. This can be
- verified with t_mpi test under testpar.
-
-* A dataset created or rewritten with a v1.6.3 library or after cannot be read
- with the v1.6.2 library or before when the Fletcher32 EDC filter is enabled.
- There was a bug in the calculation of the Fletcher32 checksum in the
- library before v1.6.3; the checksum value was not consistent between big-
- endian and little-endian systems. This bug was fixed in Release 1.6.3.
- However, after fixing the bug, the checksum value was no longer the same as
- before on little-endian system. Library releases after 1.6.4 can still read
- datasets created or rewritten with an HDF5 library of v1.6.2 or before.
- SLU - 2005/6/30
-
-* On IBM AIX systems, parallel HDF5 mode will fail some tests with error
- messages like "INFO: 0031-XXX ...". This is from the command `poe'.
- Set the environment variable MP_INFOLEVEL to 0 to minimize the messages
- and run the tests again.
-
- The tests may fail with messages like "The socket name is already in use",
- but HDF5 does not use sockets. This failure is due to problems with the
- poe command trying to set up the debug socket. To resolve this problem,
- check to see whether there are many old /tmp/s.pedb.* files staying around.
- These are sockets used by the poe command and left behind due to failed
- commands. First, ask your system administrator to clean them out.
- Lastly, request IBM to provide a means to run poe without the debug socket.
-
-* The --enable-static-exec configure flag will only statically link libraries
- if the static version of that library is present. If only the shared version
- of a library exists (i.e., most system libraries on Solaris, AIX, and Mac,
- for example, only have shared versions), the flag should still result in a
- successful compilation, but note that the installed executables will not be
- fully static. Thus, the only guarantee on these systems is that the
- executable is statically linked with just the HDF5 library.
-
-* There is also a configure error on Altix machines that incorrectly reports
- when a version of Szip without an encoder is being used.
-
-%%%%1.8.3%%%%
-
-
-HDF5 version 1.8.3 released on Mon May 4 09:21:00 CDT 2009
-================================================================================
-
-INTRODUCTION
-============
-
-This document describes the differences between HDF5-1.8.2 and
-HDF5 1.8.3, and contains information on the platforms tested and
-known problems in HDF5-1.8.3.
-For more details, see the files HISTORY-1_0-1_8_0_rc3.txt
-and HISTORY-1_8.txt in the release_docs/ directory of the HDF5 source.
-
-Links to the HDF5 1.8.3 source code, documentation, and additional materials
-can be found on the HDF5 web page at:
-
- http://www.hdfgroup.org/products/hdf5/
-
-The HDF5 1.8.3 release can be obtained from:
-
- http://www.hdfgroup.org/HDF5/release/obtain5.html
-
-User documentation for 1.8.3 can be accessed directly at this location:
-
- http://www.hdfgroup.org/HDF5/doc/
-
-New features in the HDF5-1.8.x release series, including brief general
-descriptions of some new and modified APIs, are described in the "What's New
-in 1.8.0?" document:
-
- http://www.hdfgroup.org/HDF5/doc/ADGuide/WhatsNew180.html
-
-All new and modified APIs are listed in detail in the "HDF5 Software Changes
-from Release to Release" document, in the section "Release 1.8.3 (current
-release) versus Release 1.8.2":
-
- http://www.hdfgroup.org/HDF5/doc/ADGuide/Changes.html
-
-If you have any questions or comments, please send them to the HDF Help Desk:
-
- help@hdfgroup.org
-
-
-CONTENTS
-========
-
-- New Features
-- Support for New Platforms, Languages, and Compilers
-- Bug Fixes since HDF5-1.8.2
-- Platforms Tested
-- Supported Configuration Features Summary
-- Known Problems
-
-
-New Features
-============
-
- Configuration
- -------------
- - Added libtool version numbers to generated c++, fortran, and
- hl libraries. MAM 2009/04/19.
- - Regenerated Makefile.ins using Automake 1.10.2. MAM 2009/04/19.
- - Added a Make target of check-all-install to test the correctness of
- installing via the prefix= or $DESTDIR options. AKC - 2009/04/14
-
- Library
- -------
- - Embed the content of libhdf5.settings into the hdf5 executables
- so that an "orphaned" executables can display (via the Unix
- strings command, for example) the library settings used to build
- the executables. This is a prototype implementation. Improvement will
- be added in next release. AKC - 2009/04/20
- - Separated "factory" free list class from block free lists. These free
- lists are dynamically created and manage blocks of a fixed size.
- H5set_free_list_limits() will use the same settings specified for block
- free lists for factory free lists. NAF - 2009/04/08
- - Added support for dense attributes to H5Ocopy. XCao/NAF - 2009/01/29
- - Added H5Pset_elink_cb and H5Pget_elink_cb functions to support a
- user-defined callback function for external link traversal.
- NAF - 2009/01/08
- - Added H5Pset_elink_acc_flags and H5Pget_elink_acc_flags functions to
- allow the user to specify the file access flags used to open the target
- file of an external link. NAF - 2009/01/08
- - Added H5Pset_chunk_cache() and H5Pget_chunk_cache() functions to allow
- individual rdcc configuration for each dataset. Added
- H5Dget_access_plist() function to retrieve a dataset access property
- list from a dataset. NAF - 2008/11/12
- - Added H5Iis_valid() function to check if an id is valid without
- producing an error message. NAF - 2008/11/5
- - Added code to maintain a min_clean_fraction in the metadata cache when
- in serial mode. MAM - 2009/01/9
-
- Parallel Library
- ----------------
- - Modified parallel tests to run with arbitrary number of processes. The
- modified tests are testphdf5 (parallel dataset access), t_chunk_alloc
- (chunk allocation), and t_posix_compliant (posix compliance). The rest of
- the parallel tests already use in the code the number of processes
- available in the communicator. (CMC - 2009/04/28)
-
- Tools
- -----
- - h5diff new flag, -c, --compare, list objects that are not comparable.
- PVN - 2009/4/2 - 1368
- - h5diff new flag, -N, --nan, avoids NaNs detection. PVN - 2009/4/2
- - h5dump correctly specifies XML dtd / schema urls ADB - 2009/4/3 - 1519
- - h5repack now handles group creation order. PVN - 2009/4/2 - 1402
- - h5repack: When user doesn't specify a chunk size, h5repack now
- defines a default chunk size as the same size of the size of the
- hyperslab used to read the chunks. The size of the hyperslabs are
- defined as the size of each dimension or a predefined constant,
- whatever is smaller. This assures that the chunk read fits in the
- chunk cache. PVN - 2008/11/21
-
- High-Level APIs
- ---------------
- - Table: In version 3.0 of Table, the writing of the "NROWS" attribute
- (used to store number of records) was deprecated. PVN - 2008/11/24
-
- F90 API
- -------
- - Added for the C APIs the Fortran wrappers:
- h5dget_access_plist_f
- h5iis_valid_f
- h5pset_chunk_cache_f
- h5pget_chunk_cache_f
- MSB - 2009/04/17
-
- C++ API
- -------
- - None
-
-
-Support for New Platforms, Languages, and Compilers
-===================================================
-
-
-Bug Fixes since HDF5-1.8.2
-==========================
-
- Configuration
- -------------
- - The --includedir=DIR configuration option now works as intended, and
- can be used to specify the location to install C header files. The
- default location remains unchanged, residing at ${prefix}/include.
- MAM - 2009/03/10 - BZ #1381
- - Configure no longer removes the '-g' flag from CFLAGS when in production
- mode if it has been explicitly set in the CFLAGS environment variable
- prior to configuration. MAM - 2009/03/09 - BZ #1401
-
- Library
- -------
- - Added versioning to H5Z_class_t struct to allow compatibility with 1.6
- API. NAF - 2009/04/20 - 1533
- - Fixed a problem with using data transforms with non-native types in the
- file. NAF - 2009/04/20 - 1548
- - Added direct.h include file to windows section of H5private.h
- to fix _getcwd() warning. ADB - 2009/04/14 - 1536
- - Fixed a bug that prevented external links from working after calling
- H5close(). NAF - 2009/04/10 - 1539
- - Modified library to write cached symbol table information to the
- superblock, to allow library versions 1.3.0 to 1.6.3 to read files created
- by this version. NAF - 2009/04/08 - 1423
- - Changed skip lists to use a deterministic algorithm. The library should
- now never call rand() or srand(). NAF - 2009/04/08 - 503
- - Fixed a bug where H5Lcopy and H5Lmove wouldn't create intermediate groups
- when that property was set. NAF - 2009/04/07 - 1526
- - Fixed a bug that caused files with a user block to grow by the size of the
- user block every time they were opened. NAF - 2009/03/26 - 1499
- - Fixed a rare problem that could occur with files using the old (pre 1.4)
- array datatype. NAF - 2009/03/23
- - Modified library to be able to open files with corrupt root group symbol
- table messages, and correct these errors if they are found. Such files
- can only be successfully opened with write access. NAF - 2009/03/23 - 1189
- - Removed the long_long #define and replaced all instances with
- "long long". This caused problems with third party products. All
- currently supported compilers support the type. ADB - 2009/03/05
- - Fixed various bugs that could prevent the fill value from being written
- in certain rare cases. NAF - 2009/02/26 - 1469
- - Fixed a bug that prevented more than one dataset chunk from being cached
- at a time. NAF - 2009/02/12 - 1015
- - Fixed an assertion failure caused by opening an attribute multiple times
- through multiple file handles. NAF - 2009/02/12 - 1420
- - Fixed a problem that could prevent the user from adding attributes (or any
- object header message) in some circumstances. NAF - 2009/02/12 - 1427
- - Fixed a bug that could cause problems when an attribute was added to a
- committed datatype using the committed datatype's datatype.
- NAF - 2009/02/12
- - Fixed a bug that could cause problems when copying an object with a shared
- message in its own object header. NAF - 2009/01/29
- - Changed H5Tset_order to properly reject H5T_ORDER_NONE for most datatypes.
- NAF - 2009/01/27 - 1443
- - Fixed a bug where H5Tpack wouldn't remove trailing space from an otherwise
- packed compound type. NAF - 2009/01/14
- - Fixed up some old v2 btree assertions that get run in debug mode that
- were previously failing on compilation, and removed some of the
- more heavily outdated and non-rewritable ones. MAM - 2008/12/15
- - Fixed a bug that could cause problems when "automatically" unmounting
- multiple files. NAF - 2008/11/17
- - H5Dset_extent: when shrinking dimensions, some chunks were not deleted.
- PVN - 2009/01/8
-
- Parallel Library
- ----------------
- - None
-
- Tools
- -----
- - Fixed many problems that could occur when using h5repack with named
- datatypes. NAF - 2009/4/20 - 1516/1466
- - h5dump, h5diff, h5repack were not reading (by hyperslabs) datasets
- that have a datatype datum size greater than H5TOOLS_BUFSIZE, a constant
- defined as 1024Kb, such as array types with large dimensions.
- PVN - 2009/4/1 - 1501
- - h5import: By selecting a compression type, a big endian byte order
- was being selected. PVN - 2009/3/11 - 1462
- - zip_perf.c had missing argument on one of the open() calls. Fixed.
- AKC - 2008/12/9
-
- F90 API
- ------
- - None
-
- C++ API
- ------
- - None
-
- High-Level APIs:
- ------
- - Dimension scales: The scale index return value in H5DSiterate_scales
- was not always incremented. PVN - 2009/4/8 - 1538
-
- Fortran High-Level APIs:
- ------
- - Lite: The h5ltget_dataset_info_f function (gets information about
- a dataset) was not correctly returning the dimension array
- PVN - 2009/3/23
-
-
-Platforms Tested
-================
-The following platforms and compilers have been tested for this release.
-
- AIX 5.3 xlc 7.0.0.8
- (LLNL Up) xlf 09.01.0000.0008
- xlC 7.0.0.8
- mpcc_r 7.0.0.8
- mpxlf_r 09.01.0000.0008
-
- Cray XT3 (2.0.41) cc (pgcc) 7.1-4
- (SNL red storm) ftn (pgf90) 7.1-4
- CC (pgCC) 7.1-4
-
- FreeBSD 6.3-STABLE i386 gcc 3.4.6 [FreeBSD] 20060305
- (duty) g++ 3.4.6 [FreeBSD] 20060305
- gcc 4.3.4 20090419
- g++ 4.3.4 20090419
- gfortran 4.3.4 20090419
-
- FreeBSD 6.3-STABLE amd64 gcc 3.4.6 [FreeBSD] 20060305
- (liberty) g++ 3.4.6 [FreeBSD] 20060305
- gcc 4.4.1 20090421
- g++ 4.4.1 20090421
- gfortran 4.4.1 20090421
-
- IRIX64 6.5 (64 & n32) MIPSpro cc 7.4.4m
- F90 MIPSpro 7.4.4m
- C++ MIPSpro cc 7.4.4m
-
- Linux 2.6.18-128.1.6.el5xen gcc (GCC) 4.1.2
- #1 SMP i686 i686 i386 G95 (GCC 4.0.3 (g95 0.92!) Feb 4 2009)
- (jam) PGI C, Fortran, C++ 7.2-1 32-bit
- PGI C, Fortran, C++ 8.0-1 32-bit
- Intel(R) C Compiler for 32-bit
- applications, Versions 10.1, 11.0
- Intel(R) C++ Compiler for 32-bit
- applications, Version 10.1, 11.0
- Intel(R) Fortran Compiler for 32-bit
- applications, Version 10.1, 11.0
- Absoft 32-bit Fortran 95 10.0.7
- MPICH mpich2-1.0.8 compiled with
- gcc 4.1.2 and G95 (GCC 4.0.3 (g95 0.92!)
-
- Linux 2.6.9-42.0.10.ELsmp #1 gcc (GCC) 3.4.6
- SMP i686 i686 i386 G95 (GCC 4.0.3 (g95 0.92!) Feb 4 2009)
- (kagiso) MPICH mpich2-1.0.8 compiled with
- gcc 3.4.6 and G95 (GCC 4.0.3 (g95 0.92!)
-
- Linux 2.6.16.60-0.37-smp #1 gcc 4.1.2
- SMP x86_64 GNU/Linux G95 (GCC 4.0.3 (g95 0.92!) Feb 4 2009)
- (smirom) Intel(R) C, C++, Fortran Compilers for
- applications running on Intel(R) 64,
- Versions 10.1, 11.0.
- PGI C, Fortran, C++ Version 7.2-1, 8.0-1
- for 64-bit target on x86-64
- gcc 4.1.2 and G95 (GCC 4.0.3 (g95 0.92!)
- MPICH mpich2-1.0.8 compiled with
- gcc 4.1.2 and G95 (GCC 4.0.3 (g95 0.92!)
- tested for both 32- and 64-bit binaries
-
- Linux 2.6.16.54-0.2.5 #1 Intel(R) C++ Version 10.1.017
- SGI Altix SMP ia64 Intel(R) Fortran Itanium(R) Version 10.1.017
- (cobalt) SGI MPI 1.38
-
- SunOS 5.10 32- and 64-bit Sun WorkShop 6 update 2 C 5.9 Patch 124867-09
- (linew) Sun WorkShop 6 update 2 Fortran 95 8.3
- Patch 127000-07
- Sun WorkShop 6 update 2 C++ 5.8
- Patch 124863-11
-
- Intel Xeon Linux 2.6.18- gcc 3.4.6 20060404
- 92.1.10.el5_lustre.1.6.6smp- Intel(R) C++ Version 10.0.026
- perfctr #2 SMP Intel(R) Fortran Compiler Version 10.0.026
- (abe) Open MPI 1.2.2
- MVAPICH2-0.9.8p28p2patched-intel-ofed-1.2
- compiled with icc v10.0.026 and ifort 10.0.026
-
- IA-64 Linux 2.4.21-309.tg1 gcc (GCC) 3.2.2
- #1 SMP ia64 Intel(R) C++ Version 8.1.037
- (NCSA tg-login) Intel(R) Fortran Compiler Version 8.1.033
- mpich-gm-1.2.7p1..16-intel-8.1.037-r1
-
- Linux 2.6.9-55.0.9.EL_lustre Intel(R) C, C++, Fortran Compilers for
- .1.4.11.1smp #1 SMP applications running on Intel(R) 64,
- SMP x86_64 GNU/Linux Versions 9.1.
- (SNL Spirit)
-
- Linux 2.6.9-55.0.9.EL_lustre Intel(R) C, C++, Fortran Compilers for
- .1.4.11.1smp #1 SMP applications running on Intel(R) 64,
- SMP x86_64 GNU/Linux Versions 10.1.
- (SNL Thunderbird)
-
- Linux 2.6.18-63chaos #1 SMP Intel(R) C, C++, Fortran Compilers for
- SMP x86_64 GNU/Linux applications running on Intel(R) 64,
- (SNL Glory) Versions 10.1.
-
- Linux 2.6.18-63chaos #1 SMP Intel(R) C, C++, Fortran Compilers for
- SMP x86_64 GNU/Linux applications running on Intel(R) 64,
- (LLNL Zeus) Versions 9.1.
- gcc/gfortran/g++ (GCC) 4.1.2.
-
- Windows XP Visual Studio .NET
- Visual Studio 2005 w/ Intel Fortran 9.1
- Cygwin(native gcc compiler and g95)
-
- Windows XP x64 Visual Studio 2005 w/ Intel Fortran 9.1
-
- Windows Vista Visual Studio 2005
-
- MAC OS 10.5.6 (Intel) i686-apple-darwin9-gcc-4.0.1 (GCC) 4.0.1
- GNU Fortran (GCC) 4.3.0 20070810
- G95 (GCC 4.0.3 (g95 0.91!) Apr 24 2008)
- Intel C, C++ and Fortran compilers 10.1
-
-
-Supported Configuration Features Summary
-========================================
-
- In the tables below
- y = tested and supported
- n = not supported or not tested in this release
- C = Cluster
- W = Workstation
- x = not working in this release
- dna = does not apply
- ( ) = footnote appears below second table
- <blank> = testing incomplete on this feature or platform
-
-Platform C F90 F90 C++ zlib SZIP
- parallel parallel
-Solaris2.10 32-bit n y n y y y
-Solaris2.10 64-bit n y n y y y
-IRIX64_6.5 32-bit n n n n y y
-IRIX64_6.5 64-bit n y y y y y
-Windows XP n y(4) n(4) y y y
-Windows XP x64 n y(4) n(4) y y y
-Windows Vista n n n y y y
-Mac OS X 10.5 Intel n y n y y y
-AIX 5.3 32- and 64-bit n y n y y n
-FreeBSD 6.3-STABLE 32&64 bit n y n y y y
-RedHat EL4 2.6.9-42 i686 GNU (1) W y y y y y y
-RedHat EL5 2.6.18-128 i686 GNU (1)W y y(2) y y y y
-RedHat EL5 2.6.18-128 i686 Intel W n y n y y n
-RedHat EL5 2.6.18-128 i686 PGI W n y n y y n
-SuSe Linux 2.6.16 x86_64 GNU (1) W y y(3) y y y y
-SuSe Linux 2.6.16 x86_64 Intel W n y n y y n
-SuSe Linux 2.6.16 x86_64 PGI W n y n y y y
-SuSe Linux 2.6.16 SGI Altix ia64 C y y y y y y
-RedHat EL4 2.6.18 Xeon Lustre C y y y y y n
-SuSe Linux 2.4.21 ia64 Intel C y y y y y n
-Cray XT3 2.0.41 y y y y y n
-
-
-Platform Shared Shared Shared Thread-
- C libs F90 libs C++ libs safe
-Solaris2.10 32-bit y y y y
-Solaris2.10 64-bit y y y y
-IRIX64_6.5 32-bit y dna y y
-IRIX64_6.5 64-bit y y n y
-Windows XP y y(4) y y
-Windows XP x64 y y(4) y y
-Windows Vista y n n y
-Mac OS X 10.5 y n y n
-AIX 5.3 32- and 64-bit n n n n
-FreeBSD 6.3-STABLE 32&64 bit y n y y
-RedHat EL4 2.6.9-42 i686 GNU (1) W y y y y
-RedHat EL5 2.6.18-128 i686 GNU (1)W y y(2) y y
-RedHat EL5 2.6.18-128 i686 Intel W y y y n
-RedHat EL5 2.6.18-128 i686 PGI W y y y n
-SuSe Linux 2.6.16 x86_64 GNU (1) W y y y y
-SuSe Linux 2.6.16 x86_64 Intel W y y y n
-SuSe Linux 2.6.16 x86_64 PGI W y y y n
-SuSe Linux 2.6.16 SGI Altix ia64 C y n
-RedHat EL4 2.6.18 Xeon Lustre C y y y n
-SuSe Linux 2.4.21 ia64 Intel C y y y n
-Cray XT3 2.0.41 n n n n
-
- (1) Fortran compiled with g95.
- (2) With PGI and Absoft compilers.
- (3) With PGI compiler for Fortran.
- (4) Using Visual Studio 2005 or Cygwin
- Compiler versions for each platform are listed in the preceding
- "Platforms Tested" table.
-
-
-Known Problems
-==============
-* Parallel tests failed with 16 processes with data inconsistency at testphdf5
- / dataset_readAll. Parallel tests also failed with 32 and 64 processes with
- collective abort of all ranks at t_posix_compliant / allwrite_allread_blocks
- with MPI IO. CMC - 2009/04/28
-
-* There is a known issue in which HDF5 will change the timestamp on a file
- simply by opening it with read/write permissions, even if the file is not
- modified in any way. This is due to the way in which HDF5 manages the file
- superblock. A fix is currently underway and should be included in the 1.8.4
- release of HDF5. MAM - 2009/04/28
-
-* For gcc v4.3 and v4.4, with production mode, if -O3 is used, H5Tinit.c
- would fail to compile. Actually bad H5Tinit.c is produced. If -O (same
- as -O1) is used, H5Tinit.c compiled okay but test/dt_arith would fail.
- When -O0 (no optimizatio) is used, H5Tinit.c compilete okay and all
- tests passed. Therefore, -O0 is imposed for v4.3 and v4.4 of gcc.
- AKC - 2009/04/20
-
-* For Red Storm, a Cray XT3 system, the tools/h5ls/testh5ls.sh and
- tools/h5copy/testh5copy.sh will fail some of its sub-tests. These sub-tests
- are expected to fail and should exit with a non-zero code but the yod
- command does not propagate the exit code of the executables. Yod always
- returns 0 if it can launch the executable. The test suite shell expects
- a non-zero for this particular test, therefore it concludes the test has
- failed when it receives 0 from yod. Skip all the "failing" test for now
- by changing them as following.
-
- ======== Original tools/h5ls/testh5ls.sh =========
- TOOLTEST tgroup-1.ls 1 -w80 -r -g tgroup.h5
- ======== Change to ===============================
- echo SKIP TOOLTEST tgroup-1.ls 1 -w80 -r -g tgroup.h5
- ==================================================
-
- ======== Original tools/h5copy/testh5copy.sh =========
- TOOLTEST_FAIL -i $TESTFILE -o $FILEOUT -v -s grp_dsets -d grp_rename
- TOOLTEST_FAIL -i $TESTFILE -o $FILEOUT -v -s grp_dsets -d /grp_rename/grp_dsets
- TOOLTEST_FAIL -i $TESTFILE -o $FILEOUT -vp -s /grp_dsets -d /E/F/grp_dsets
- TOOLTEST_FAIL -i $TESTFILE -o $FILEOUT -vp -s /grp_nested -d /G/H/grp_nested
- H5LSTEST $FILEOUT
- ======== Change to ===============================
- echo SKIP TOOLTEST_FAIL -i $TESTFILE -o $FILEOUT -v -s grp_dsets -d grp_rename
- echo SKIP TOOLTEST_FAIL -i $TESTFILE -o $FILEOUT -v -s grp_dsets -d /grp_rename/grp_dsets
- echo SKIP TOOLTEST_FAIL -i $TESTFILE -o $FILEOUT -vp -s /grp_dsets -d /E/F/grp_dsets
- echo SKIP TOOLTEST_FAIL -i $TESTFILE -o $FILEOUT -vp -s /grp_nested -d /G/H/grp_nested
- echo SKIP H5LSTEST $FILEOUT
- ==================================================
- AKC - 2008/11/10
-
-* For Red Storm, a Cray XT3 system, the yod command sometimes gives the
- message, "yod allocation delayed for node recovery". This interferes with
- test suites that do not expect seeing this message. See the section of "Red
- Storm" in file INSTALL_parallel for a way to deal with this problem.
- AKC - 2008/05/28
-
-* We have discovered two problems when running collective IO parallel HDF5
- tests with chunking storage on the ChaMPIon MPI compiler on tungsten, a
- Linux cluster at NCSA.
-
- Under some complex selection cases:
- 1) MPI_Get_element returns the wrong value.
- 2) MPI_Type_struct also generates the wrong derived datatype and corrupt
- data may be generated.
- These issues arise only when turning on collective IO with chunking storage
- with some complex selections. We have not found these problems on other
- MPI-IO compilers. If you encounter these problems, you may use independent
- IO instead.
-
- To avoid this behavior, change the following line in your code
- H5Pset_dxpl_mpio(xfer_plist, H5FD_MPIO_COLLECTIVE);
- to
- H5Pset_dxpl_mpio(xfer_plist, H5FD_MPIO_INDEPENDENT);
- KY - 2007/08/24
-
-* On Intel 64 Linux cluster (RH 4, Linux 2.6.9) with Intel 10.0 compilers,
- use -mp -O1 compilation flags to build the libraries. A higher level of
- optimization causes failures in several HDF5 library tests.
-
-* For LLNL, uP: both serial and parallel tests pass.
- Zeus: Serial tests pass but parallel tests fail with a known problem in MPI.
- ubgl: Serial tests pass but parallel tests fail.
-
-* On mpich 1.2.5 and 1.2.6, if more than two processes contribute no IO and
- the application asks to do collective IO, we have found that when using 4
- processors, a simple collective write will sometimes be hung. This can be
- verified with t_mpi test under testpar.
-
-* On IRIX6.5, when the C compiler version is greater than 7.4, complicated
- MPI derived datatype code will work. However, the user should increase
- the value of the MPI_TYPE_MAX environment variable to some appropriate value
- to use collective irregular selection code. For example, the current
- parallel HDF5 test needs to raise MPI_TYPE_MAX to 200,000 to pass the test.
-
-* A dataset created or rewritten with a v1.6.3 library or after cannot be read
- with the v1.6.2 library or before when the Fletcher32 EDC filter is enabled.
- There was a bug in the calculation of the Fletcher32 checksum in the
- library before v1.6.3; the checksum value was not consistent between big-
- endian and little-endian systems. This bug was fixed in Release 1.6.3.
- However, after fixing the bug, the checksum value was no longer the same as
- before on little-endian system. Library releases after 1.6.4 can still read
- datasets created or rewritten with an HDF5 library of v1.6.2 or before.
- SLU - 2005/6/30
-
-* On IBM AIX systems, parallel HDF5 mode will fail some tests with error
- messages like "INFO: 0031-XXX ...". This is from the command `poe'.
- Set the environment variable MP_INFOLEVEL to 0 to minimize the messages
- and run the tests again.
-
- The tests may fail with messages like "The socket name is already in use",
- but HDF5 does not use sockets. This failure is due to problems with the
- poe command trying to set up the debug socket. To resolve this problem,
- check to see whether there are many old /tmp/s.pedb.* files staying around.
- These are sockets used by the poe command and left behind due to failed
- commands. First, ask your system administrator to clean them out.
- Lastly, request IBM to provide a means to run poe without the debug socket.
-
-* The --enable-static-exec configure flag fails to compile for Solaris
- platforms. This is due to the fact that not all of the system libraries on
- Solaris are available in a static format.
-
- The --enable-static-exec configure flag also fails to correctly compile
- on IBM SP2 platforms for serial mode. The parallel mode works fine with
- this option.
-
- It is suggested that you do not use this option on these platforms
- during configuration.
-
-* There is also a configure error on Altix machines that incorrectly reports
- when a version of Szip without an encoder is being used.
-
-* Information about building with PGI and Intel compilers is available in
- the INSTALL file sections 4.7 and 4.8.
-
-
-%%%%1.8.2%%%%
-
-
-HDF5 version 1.8.2 released on Mon Nov 10 15:43:09 CST 2008
-================================================================================
-
-INTRODUCTION
-============
-
-This document describes the differences between HDF5-1.8.1 and HDF5 1.8.2,
-and contains information on the platforms tested and known problems in
-HDF5-1.8.2. For more details, see the files HISTORY-1_0-1_8_0_rc3.txt
-and HISTORY-1_8.txt in the release_docs/ directory of the HDF5 source.
-
-Links to the HDF5 1.8.2 source code, documentation, and additional materials
-can be found on the HDF5 web page at:
-
- http://www.hdfgroup.org/products/hdf5/
-
-The HDF5 1.8.2 release can be obtained from:
-
- http://www.hdfgroup.org/HDF5/release/obtain5.html
-
-User documentation for 1.8.2 can be accessed directly at this location:
-
- http://www.hdfgroup.org/HDF5/doc/
-
-New features in the HDF5-1.8.x release series, including brief general
-descriptions of some new and modified APIs, are described in the "What's New
-in 1.8.0?" document:
-
- http://www.hdfgroup.org/HDF5/doc/ADGuide/WhatsNew180.html
-
-All new and modified APIs are listed in detail in the "HDF5 Software Changes
-from Release to Release" document, in the section "Release 1.8.2 (current
-release) versus Release 1.8.1":
-
- http://www.hdfgroup.org/HDF5/doc/ADGuide/Changes.html
-
-If you have any questions or comments, please send them to the HDF Help Desk:
-
- help@hdfgroup.org
-
-
-CONTENTS
-========
-
-- New Features
-- Support for new platforms and languages
-- Bug Fixes since HDF5-1.8.1
-- Platforms Tested
-- Supported Configuration Features Summary
-- Known Problems
-
-
-New Features
-============
-
- Configuration
- -------------
- - Upgraded libtool to version 2.2.6a. (MAM - 2008/10/15).
-
- Library
- -------
- - Added two new public routines: H5Pget_elink_fapl() and
- H5Pset_elink_fapl(). (see bug #1247) (VC - 2008/10/13)
- - Improved free space tracking in file to be faster. (QAK - 2008/10/06)
- - Added 'mounted' field to H5G_info_t struct. (QAK - 2008/07/15)
-
- Parallel Library
- ----------------
- - None
-
- Tools
- -----
- - h5repack: added new options -u and -b to add a userblock to an HDF5
- file during the repack. (PVN - 2008/08/26)
- - h5repack: added options -t and -a to call H5Pset_alignment while
- creating a repacked file. (PVN - 2008/08/29)
- - h5ls: added capability to traverse through external links when the -r
- (recursive) flag is given. (NAF - 2008/09/16)
- - h5ls: added -E option to enable traversal of external links.
- h5ls will not traverse external links without this flag being set.
- (NAF - 2008/10/06)
- - h5dump: when -b flag is used without a keyword after it, binary
- output defaults to NATIVE. MEMORY keyword was deprecated
- and replaced by NATIVE keyword. (PVN - 2008/10/30)
- - h5diff: returns 1 when file graphs differ by any object.
- Error return code was changed to 2 from -1. (PVN - 2008/10/30)
- - h5import: TEXTFPE (scientific format) was deprecated. Use TEXTFP
- instead (PVN - 2008/10/30)
-
-
-
- F90 API
- ------
- - Added optional parameter 'mounted' to H5Gget_info_f,
- H5Gget_info_by_idx_f, H5Gget_info_by_name_f (MSB - 2008/09/24)
- - Added H5Tget_native_type_f (MSB - 2008/09/30)
-
-
- C++ API
- ------
- - These member functions were added as wrapper for H5Rdereference to
- replace the incorrect IdComponent::dereference().
- void H5Object::dereference(H5Object& obj, void* ref,
- H5R_type_t ref_type=H5R_OBJECT)
- void H5Object::dereference(H5File& h5file, void* ref,
- H5R_type_t ref_type=H5R_OBJECT)
- void H5Object::dereference(Attribute& obj, void* ref,
- H5R_type_t ref_type=H5R_OBJECT)
-
- In addition, these constructors were added to create the associated
- objects by way of dereference:
- DataSet(H5Object& obj, void* ref, H5R_type_t ref_type=H5R_OBJECT)
- DataSet(H5File& file, void* ref, H5R_type_t ref_type=H5R_OBJECT)
- DataSet(Attribute& attr, void* ref, H5R_type_t ref_type=H5R_OBJECT)
- Group(H5Object& obj, void* ref, H5R_type_t ref_type=H5R_OBJECT)
- Group(H5File& obj, void* ref, H5R_type_t ref_type=H5R_OBJECT)
- Group(Attribute& attr, void* ref, H5R_type_t ref_type=H5R_OBJECT)
- DataType(H5Object& obj, void* ref, H5R_type_t ref_type=H5R_OBJECT)
- DataType(H5File& file, void* ref, H5R_type_t ref_type=H5R_OBJECT)
- DataType(Attribute& attr, void* ref, H5R_type_t ref_type=H5R_OBJECT)
- (BMR - 2008/10/29)
-
-
-Support for New Platforms, Languages, and Compilers
-===================================================
- - Intel 10.1 is supported on Mac OS X 10.5.4.
- Note:
- When Fortran is enabled, configure automatically
- disables the build of shared libraries (i.e., only
- static C and C++ HDF5 libraries will be built
- along with the static HDF5 Fortran library).
- Intel 10.1 C and C++ compilers require
- "-no-multibyte-chars" compilation flag due to the known
- bug in the compilers.
- (EIP - 2008/10/30)
-
-
-Bug Fixes since HDF5-1.8.1
-==========================
-
- Configuration
- -------------
- - Fixed error with 'make check install' failing due to h5dump
- needing other tools built first. (MAM - 2008/10/15).
- - When using shared szip, it is no longer necessary to specify
- the path to the shared szip libraries in LD_LIBRARY_PATH.
- (MAM - 2008/10/15).
- - The file libhdf5_fortran.settings is not installed since its content
- is included in libhdf5.settings now. (AKC - 2008/10/21)
- - "make DESTDIR=xxx install" failed to install some tools and files
- (e.g., h5cc and fortran modules). Fixed. (AKC - 2008/10/8).
-
- Library
- -------
- - H5Ovisit and H5Ovisit_by_name will now properly terminate when the
- callback function returns a positive value on the starting object.
- (NAF - 2008/11/03)
- - Fixed an error where a null message could be created that was larger
- than could be written to the file. (NAF - 2008/10/23)
- - Corrected error with family/split/multi VFD not updating driver info
- when "latest" version of the file format used. (QAK - 2008/10/14)
- - Corrected alignment+threshold errors to work correctly when metadata
- aggregation is enabled. (QAK - 2008/10/06)
- - Changed H5Fget_obj_count and H5Fget_obj_ids to ignore objects
- registered by the library for internal library use.
- (NAF - 2008/10/06)
- - Fixed potential memory leak during compound conversion.
- (NAF - 2008/10/06)
- - Changed the return value of H5Fget_obj_count from INT to SSIZE_T.
- Also changed the return value of H5Fget_obj_ids from HERR_T to
- SSIZE_T and the type of the parameter MAX_OBJS from INT to SIZE_T.
- (SLU - 2008/09/26)
- - Fixed an issue that could cause data to be improperly overwritten
- during compound type conversion. (NAF - 2008/09/19)
- - Fixed pointer alignment violations that could occur during vlen
- conversion. (NAF - 2008/09/16)
- - Fixed problem where library could cause a segmentation fault when
- an invalid location ID was given to H5Giterate(). (QAK - 2008/08/19)
- - Fixed improper shutdown when objects have reference count > 1. The
- library now tracks reference count due to the application separately
- from that due to internal library routines. (NAF - 2008/08/19)
- - Fixed assertion failure caused by incorrect array datatype version.
- (NAF - 2008/08/08)
- - Fixed an issue where mount point traversal would fail when using
- multiple handles for the child. (NAF - 2008/08/07)
- - Fixed an issue where mount points were inaccessible when using
- multiple file handles for the parent. The mount table is now in
- the shared file structure (the parent pointer is still in the
- top structure). (NAF - 2008/08/07)
- - Fixed assertion failure caused by incorrect array datatype version.
- (NAF - 2008/08/04)
- - Fixed issue where a group could have a file mounted on it twice.
- (QAK - 2008/07/15)
- - When an attribute was opened twice and data was written with
- one of the handles, the file didn't have the data. It happened
- because each handle had its own object structure, and the empty
- one overwrote the data with fill value. This is fixed by making
- some attribute information like the data be shared in the
- attribute structure. (SLU - 2008/07/07)
- - Fixed a Windows-specific issue in the ohdr test which was causing
- users in some timezones to get false errors. This a deficiency in
- the Windows mktime() function, and has been handled properly.
- (SJW - 2008/06/19)
-
- Parallel Library
- ----------------
- - None
-
- Tools
- -----
- - h5dump now checks for uniqueness of committed datatypes.
- (NAF - 2008/10/15)
- - Fixed unnecessary indentation of committed datatypes in h5dump.
- (NAF - 2008/10/15)
- - Fixed bugs in h5stat: segmemtation fault when printing groups and
- print warning message when traversal of objects is unsuccessful.
- (see bug #1253) (VC- 2008/10/13)
- - Fixed bug in h5ls that prevented relative group listings (like
- "h5ls foo.h5/bar") from working correctly (QAK - 2008/06/03)
- - h5dump: when doing binary output (-b), the stdout printing of
- attributes was done incorrectly. Removed printing of attributes
- when doing binary output. (PVN - 2008/06/05)
-
-
- F90 API
- ------
- - h5sselect_elements_f: Added additional operators H5S_SELECT_APPEND
- and H5S_SELECT_PREPEND (MSB - 2008/09/30)
- - h5sget_select_elem_pointlist: Fixed list of returned points by
- rearranging the point list correctly by accounting for C
- conventions. (MSB - 2008/09/30)
- - h5sget_select_hyper_blocklist_f: Fixed error in transposed dimension
- of arrays.(MSB - 2008/9/30)
- - h5sget_select_bounds_f: Swapped array bounds to account for C and
- Fortran reversed array notation (MSB - 2008/9/30)
- - Changed to initializing string to a blank character instead of a
- null type in tH5P.f90 to fix compiling error using AIX 5.3.0
- (MSB - 2008/7/29)
- - Fixed missing commas in H5test_kind.f90 detected by NAG compiler
- (MSB - 2008/7/29)
- - Fixed passing and array to a scalar in tH5A_1_8.f90 detected by
- NAG compiler (MSB - 2008/7/29)
- - Added the ability of the test programs to use the status of
- HDF5_NOCLEANUP to determine if the *.h5 files should be removed
- or not after the tests are completed (MSB - 2008/10/1)
- - In nh5tget_offset_c: (MSB 9/12/2008)
- If offset was equal to 0 it returned the error code of -1,
- this was changed to return an error code of -1 when the offset
- value is < 0.
- - Uses intrinsic Fortran function SIZEOF if available when detecting
- type of INTEGERs and REALs in H5test_kind.f90 (MSB - 2008/9/3)
- - Put the DOUBLE PRECISION interfaces in a separate module and
- added a USE statement for the module. The interfaces are
- included/excluded depending on the state of FORTRAN_DEFAULT_REAL
- is DBLE_F which detects if the default REAL is DOUBLE PRECISION.
- This allows the library to be compiled with -r8 Fortran flag
- without the user needing to edit the source code.
- (MSB - 200/8/27)
- - Enable building shared library for fortran by adding the flag -fPIC
- to the compile flags for versions of Intel Fortran compiler >=9
- (MSB - 2008/8/26)
-
- C++ API
- ------
- - Fixed a design bug which allowed an Attribute object to create/modify
- attributes (bugzilla #1068). The API class hierarchy was revised
- to address the problem. Classes AbstractDS and Attribute are moved
- out of H5Object. Class Attribute now multiply inherits from
- IdComponent and AbstractDs and class DataSet from H5Object and
- AbstractDs. In addition, the data member IdComponent::id was
- moved into subclasses: Attribute, DataSet, DataSpace, DataType,
- H5File, Group, and PropList. (BMR - 2008/05/20)
- - IdComponent::dereference was incorrect and replaced as described
- in "New Features" section.
- (BMR - 2008/10/29)
-
-
-Platforms Tested
-================
-The following platforms and compilers have been tested for this release.
-
- AIX 5.3 xlc 7.0.0.8
- xlf 09.01.0000.0008
- xlC 7.0.0.8
- mpcc_r 7.0.0.8
- mpxlf_r 09.01.0000.0008
-
- Cray XT3 (2.0.41) cc (pgcc) 7.1-4
- (red storm) ftn (pgf90) 7.1-4
- CC (pgCC) 7.1-4
-
- FreeBSD 6.3-STABLE i386 gcc 3.4.6 [FreeBSD] 20060305
- (duty) g++ 3.4.6 [FreeBSD] 20060305
- gcc 4.2.5 20080702
- g++ 4.2.5 20080702
- gfortran 4.2.5 20080702
-
- FreeBSD 6.3-STABLE amd64 gcc 3.4.6 [FreeBSD] 20060305
- (liberty) g++ 3.4.6 [FreeBSD] 20060305
- gcc 4.2.5 20080702
- g++ 4.2.5 20080702
- gfortran 4.2.5 20080702
-
- IRIX64 6.5 (64 & n32) MIPSpro cc 7.4.4m
- F90 MIPSpro 7.4.4m
- C++ MIPSpro cc 7.4.4m
-
- Linux 2.6.9-42.0.10.ELsmp #1 gcc (GCC) 3.4.6
- SMP i686 i386 G95 (GCC 4.0.3 (g95 0.92!) April 18 2007)
- (kagiso) PGI C, Fortran, C++ 7.2-1 32-bit
- Intel(R) C Compiler for 32-bit
- applications, Version 10.1
- Intel(R) C++ Compiler for 32-bit
- applications, Version 10.1
- Intel(R) Fortran Compiler for 32-bit
- applications, Version 10.1
- Absoft 32-bit Fortran 95 10.0.4
- MPICH mpich-1.2.7 compiled with
- gcc 3.4.6 and G95 (GCC 4.0.3 (g95 0.92!)
- MPICH mpich2-1.0.6p1 compiled with
- gcc 3.4.6 and G95 (GCC 4.0.3 (g95 0.92!)
-
- Linux 2.6.16.46-0.14-smp #1 Intel(R) C++ for Intel(R) EM64T
- SMP x86_64 GNU/Linux Ver. 10.1.013
- (smirom) Intel(R) Fortran Intel(R) EM64T
- Ver. 10.1.013
- PGI C, Fortran, C++ Version 7.2-1
- for 64-bit target on x86-64
- MPICH mpich-1.2.7 compiled with
- gcc 4.1.2 and G95 (GCC 4.0.3 (g95 0.92!)
- MPICH mpich2-1.0.7 compiled with
- gcc 4.1.2 and G95 (GCC 4.0.3 (g95 0.92!)
- tested for both 32- and 64-bit binaries
-
- Linux 2.6.16.54-0.2.5 #1 Intel(R) C++ Version 10.1.017
- Altix SMP ia64 Intel(R) Fortran Itanium(R) Version 10.1.017
- (cobalt) SGI MPI 1.16
-
- SunOS 5.10 32- and 64-bit Sun WorkShop 6 update 2 C 5.8
- (linew) Sun WorkShop 6 update 2 Fortran 95 8.2
- Sun WorkShop 6 update 2 C++ 5.8
- Patch 121019-06
-
- Xeon Linux 2.6.9-42.0.10.EL_lustre-1.4.10.1smp
- (abe) Intel(R) C++ Version 10.0.026
- Intel(R) Fortran Compiler Version 10.0.026
- Open MPI 1.2.2
- MVAPICH2-0.9.8p28p2patched-intel-ofed-1.2
- compiled with icc v10.0.026 and
- ifort 10.0.026
-
- IA-64 Linux 2.4.21-309.tg1 #1 SMP
- ia64 gcc (GCC) 3.2.2
- (NCSA tg-login) Intel(R) C++ Version 8.1.037
- Intel(R) Fortran Compiler Version 8.1.033
- mpich-gm-1.2.7p1..16-intel-8.1.037-r1
-
- Intel 64 Linux 2.6.9-42.0.10.EL_lustre-1.4.10.1smp
- (abe) gcc 3.4.6 20060404
- Intel(R) C++ Version 10.0
- Intel (R) Fortran Compiler Version 10.0
- mvapich2-0.9.8p2patched-intel-ofed-1.2
-
- Windows XP Visual Studio .NET
- Visual Studio 2005 w/ Intel Fortran 9.1
- Cygwin(native gcc compiler and g95)
-
- Windows XP x64 Visual Studio 2005 w/ Intel Fortran 9.1
-
- Windows Vista Visual Studio 2005
-
- MAC OS 10.5.4 (Intel) i686-apple-darwin9-gcc-4.0.1 (GCC) 4.0.1
- GNU Fortran (GCC) 4.3.0 20070810
- G95 (GCC 4.0.3 (g95 0.91!) Apr 24 2008)
- Intel C, C++ and Fortran compilers 10.1
-
-
-Supported Configuration Features Summary
-========================================
-
- In the tables below
- y = tested and supported
- n = not supported or not tested in this release
- x = not working in this release
- dna = does not apply
- ( ) = footnote appears below second table
- <blank> = testing incomplete on this feature or platform
-
-Platform C F90 F90 C++ zlib SZIP
- parallel parallel
-Solaris2.10 32-bit n y n y y y
-Solaris2.10 64-bit n y n y y y
-IRIX64_6.5 32-bit n n n n y y
-IRIX64_6.5 64-bit n y y y y y
-Windows XP n y(15) n(15) y y y
-Windows XP x64 n y(15) n(15) y y y
-Windows Vista n n n y y y
-Mac OS X 10.5 Intel n y n y y y
-AIX 5.3 32- and 64-bit n y n y y n
-FreeBSD 6.3-STABLE
-32&64 bit n y n y y y
-RedHat EL4 (3) W y(1) y(10) y(1) y y y
-RedHat EL4 Intel (3) W n y n y y n
-RedHat EL4 PGI (3) W n y n y y n
-SuSe x86_64 gcc(3,12) W y(2) y(11) y(2) y y y
-SuSe x86_64 Int(3,12) W n y(13) n y y n
-SuSe x86_64 PGI(3,12) W n y(8) n y y y
-Linux 2.6 SuSE ia64 C
- Intel (3,7) y y y y y n
-Linux 2.6 SGI Altix
- ia64 Intel (3) y y y y y y
-Linux 2.6 RHEL C
- Lustre Intel (5) y(4) y y(4) y y n
-Cray XT3 2.0.41 y y y y y n
-
-
-Platform Shared Shared Shared Thread-
- C libs F90 libs C++ libs safe
-Solaris2.10 32-bit y y y y
-Solaris2.10 64-bit y y y y
-IRIX64_6.5 32-bit y dna y y
-IRIX64_6.5 64-bit y y n y
-Windows XP y y(15) y y
-Windows XP x64 y y(15) y y
-Windows Vista y n n y
-Mac OS X 10.5 y n y n
-AIX 5.3 32- and 64-bit n n n n
-FreeBSD 6.2 32&64 bit y n y y
-RedHat EL4 (3) W y y(10) y y
-RedHat EL4 Intel (3) W y y y n
-RedHat EL4 PGI (3) W y y y n
-SuSe x86_64 GNU(3,12) W y y y y
-SuSe x86_64 Int(3,12) W y y y n
-SuSe x86_64 PGI(3,12) W y y y n
-Linux 2.4 SuSE C
- ia64 C Intel (7) y y y n
-Linux 2.4 SGI Altix C
- ia64 Intel y n
-Linux 2.6 RHEL C
- Lustre Intel (5) y y y n
-Cray XT3 2.0.41 n n n n
-
- Notes: (1) Using mpich2 1.0.6.
- (2) Using mpich2 1.0.7.
- (3) Linux 2.6 with GNU, Intel, and PGI compilers, as indicated.
- W or C indicates workstation or cluster, respectively.
- (4) Using mvapich2 0.9.8.
- (5) Linux 2.6.9-42.0.10. Xeon cluster with ELsmp_perfctr_lustre
- and Intel compilers
- (6) Linux 2.4.21-32.0.1. Xeon cluster with ELsmp_perfctr_lustre
- and Intel compilers
- (7) Linux 2.4.21, SuSE_292.till. Ia64 cluster with Intel compilers
- (8) pgf90
- (9) With Compaq Visual Fortran 6.6c compiler.
- (10) With PGI and Absoft compilers.
- (11) PGI and Intel compilers for both C and Fortran
- (12) AMD Opteron x86_64
- (13) ifort
- (14) Yes with C and Fortran, but not with C++
- (15) Using Visual Studio 2005 or Cygwin
- (16) Not tested for this release.
- Compiler versions for each platform are listed in the preceding
- "Platforms Tested" table.
-
-
-Known Problems
-==============
-* For Red Storm, a Cray XT3 system, the tools/h5ls/testh5ls.sh and
- tools/h5copy/testh5copy.sh will fail some of its sub-tests. These sub-tests
- are expected to fail and should exit with a non-zero code but the yod
- command does not propagate the exit code of the executables. Yod always
- returns 0 if it can launch the executable. The test suite shell expects
- a non-zero for this particular test, therefore it concludes the test has
- failed when it receives 0 from yod. Skip all the "failing" test for now
- by changing them as following.
-
- ======== Original tools/h5ls/testh5ls.sh =========
- TOOLTEST tgroup-1.ls 1 -w80 -r -g tgroup.h5
- ======== Change to ===============================
- echo SKIP TOOLTEST tgroup-1.ls 1 -w80 -r -g tgroup.h5
- ==================================================
-
- ======== Original tools/h5copy/testh5copy.sh =========
- TOOLTEST_FAIL -i $TESTFILE -o $FILEOUT -v -s grp_dsets -d grp_rename
- TOOLTEST_FAIL -i $TESTFILE -o $FILEOUT -v -s grp_dsets -d /grp_rename/grp_dsets
- TOOLTEST_FAIL -i $TESTFILE -o $FILEOUT -vp -s /grp_dsets -d /E/F/grp_dsets
- TOOLTEST_FAIL -i $TESTFILE -o $FILEOUT -vp -s /grp_nested -d /G/H/grp_nested
- H5LSTEST $FILEOUT
- ======== Change to ===============================
- echo SKIP TOOLTEST_FAIL -i $TESTFILE -o $FILEOUT -v -s grp_dsets -d grp_rename
- echo SKIP TOOLTEST_FAIL -i $TESTFILE -o $FILEOUT -v -s grp_dsets -d /grp_rename/grp_dsets
- echo SKIP TOOLTEST_FAIL -i $TESTFILE -o $FILEOUT -vp -s /grp_dsets -d /E/F/grp_dsets
- echo SKIP TOOLTEST_FAIL -i $TESTFILE -o $FILEOUT -vp -s /grp_nested -d /G/H/grp_nested
- echo SKIP H5LSTEST $FILEOUT
- ==================================================
- AKC - 2008/11/10
-
-* For Red Storm, a Cray XT3 system, the yod command sometimes gives the
- message, "yod allocation delayed for node recovery". This interferes with
- test suites that do not expect seeing this message. See the section of "Red
- Storm" in file INSTALL_parallel for a way to deal with this problem.
- AKC - 2008/05/28
-
-* We have discovered two problems when running collective IO parallel HDF5
- tests with chunking storage on the ChaMPIon MPI compiler on tungsten, a
- Linux cluster at NCSA.
-
- Under some complex selection cases:
- 1) MPI_Get_element returns the wrong value.
- 2) MPI_Type_struct also generates the wrong derived datatype and corrupt
- data may be generated.
- These issues arise only when turning on collective IO with chunking storage
- with some complex selections. We have not found these problems on other
- MPI-IO compilers. If you encounter these problems, you may use independent
- IO instead.
-
- To avoid this behavior, change the following line in your code
- H5Pset_dxpl_mpio(xfer_plist, H5FD_MPIO_COLLECTIVE);
- to
- H5Pset_dxpl_mpio(xfer_plist, H5FD_MPIO_INDEPENDENT);
-
- KY - 2007/08/24
-
-* On Intel 64 Linux cluster (RH 4, Linux 2.6.9) with Intel 10.0 compilers,
- use -mp -O1 compilation flags to build the libraries. A higher level of
- optimization causes failures in several HDF5 library tests.
-
-* For LLNL, uP: both serial and parallel tests pass.
- Zeus: Serial tests pass but parallel tests fail with a known problem in MPI.
- ubgl: Serial tests pass but parallel tests fail.
-
-* On mpich 1.2.5 and 1.2.6, if more than two processes contribute no IO and
- the application asks to do collective IO, we have found that when using 4
- processors, a simple collective write will sometimes be hung. This can be
- verified with t_mpi test under testpar.
-
-* On IRIX6.5, when the C compiler version is greater than 7.4, complicated
- MPI derived datatype code will work. However, the user should increase
- the value of the MPI_TYPE_MAX environment variable to some appropriate value
- to use collective irregular selection code. For example, the current
- parallel HDF5 test needs to raise MPI_TYPE_MAX to 200,000 to pass the test.
-
-* A dataset created or rewritten with a v1.6.3 library or after cannot be read
- with the v1.6.2 library or before when the Fletcher32 EDC filter is enabled.
- There was a bug in the calculation of the Fletcher32 checksum in the
- library before v1.6.3; the checksum value was not consistent between big-
- endian and little-endian systems. This bug was fixed in Release 1.6.3.
- However, after fixing the bug, the checksum value was no longer the same as
- before on little-endian system. Library releases after 1.6.4 can still read
- datasets created or rewritten with an HDF5 library of v1.6.2 or before.
- SLU - 2005/6/30
-
-* On IBM AIX systems, parallel HDF5 mode will fail some tests with error
- messages like "INFO: 0031-XXX ...". This is from the command `poe'.
- Set the environment variable MP_INFOLEVEL to 0 to minimize the messages
- and run the tests again.
-
- The tests may fail with messages like "The socket name is already in use",
- but HDF5 does not use sockets. This failure is due to problems with the
- poe command trying to set up the debug socket. To resolve this problem,
- check to see whether there are many old /tmp/s.pedb.* files staying around.
- These are sockets used by the poe command and left behind due to failed
- commands. First, ask your system administrator to clean them out.
- Lastly, request IBM to provide a means to run poe without the debug socket.
-
-* The --enable-static-exec configure flag fails to compile for Solaris
- platforms. This is due to the fact that not all of the system libraries on
- Solaris are available in a static format.
-
- The --enable-static-exec configure flag also fails to correctly compile
- on IBM SP2 platforms for serial mode. The parallel mode works fine with
- this option.
-
- It is suggested that you do not use this option on these platforms
- during configuration.
-
-* There is also a configure error on Altix machines that incorrectly reports
- when a version of Szip without an encoder is being used.
-
-* Information about building with PGI and Intel compilers is available in
- the INSTALL file sections 4.7 and 4.8.
-
-
-
-
-%%%%1.8.1%%%%
-
-
-HDF5 version 1.8.1 released on Thu May 29 15:28:55 CDT 2008
-================================================================================
-
-INTRODUCTION
-============
-
-This document describes the differences between the HDF5-1.8.1 release
-and HDF5 1.8.0, and contains information on the platforms tested and known
-problems in HDF5-1.8.1. For more details, see the files
-HISTORY-1_0-1_8_0_rc3.txt and HISTORY-1_8.txt in the release_docs/ directory
-of the HDF5 source.
-
-Links to the HDF5 1.8.1 source code, documentation, and additional materials
-can be found on the HDF5 web page at:
-
- http://www.hdfgroup.org/products/hdf5/
-
-The HDF5 1.8.1 release can be obtained from:
-
- http://www.hdfgroup.org/HDF5/release/obtain5.html
-
-User documentation for 1.8.1 can be accessed directly at this location:
-
- http://www.hdfgroup.org/HDF5/doc/
-
-New features in the HDF5-1.8.x release series, including brief general
-descriptions of some new and modified APIs, are described in the "What's New
-in 1.8.0?" document:
-
- http://www.hdfgroup.org/HDF5/doc/ADGuide/WhatsNew180.html
-
-All new and modified APIs are listed in detail in the "HDF5 Software Changes
-from Release to Release" document, in the section "Release 1.8.1 (current
-release) versus Release 1.8.0":
-
- http://www.hdfgroup.org/HDF5/doc/ADGuide/Changes.html
-
-If you have any questions or comments, please send them to the HDF Help Desk:
-
- help@hdfgroup.org
-
-
-CONTENTS
-========
-
-- New Features
-- Support for new platforms and languages
-- Bug Fixes since HDF5-1.8.0
-- Platforms Tested
-- Supported Configuration Features Summary
-- Known Problems
-
-
-New Features
-============
-
- Configuration
- -------------
- - The lib/libhdf5.settings file contains much more configure
- information. (AKC - 2008/05/18)
-
- - The new configure option "--disable-sharedlib-rpath" disables
- embedding the '-Wl,-rpath' information into executables when
- shared libraries are produced, and instead solely relies on the
- information in LD_LIBRARY_PATH. (MAM - 2008/05/15)
-
- - Configuration suite now uses Autoconf 2.61, Automake 1.10.1, and
- Libtool 2.2.2 (MAM - 2008/05/01)
-
- Source code distribution
- ========================
-
- Library
- -------
- - None
-
- Parallel Library
- ----------------
- - None
-
- Tools
- -----
- - h5repack: Reinstated the -i and -o command line flags to specify
- input and output files. h5repack now understands both the old
- syntax (with -i and -o) and the new syntax introduced in Release
- 1.8.0. (PVN - 2008/05/23)
- - h5dump: Added support for external links, displaying the object that
- an external link points to. (PVN - 2008/05/12)
- - h5dump: Added an option, -m, to allow user-defined formatting in the
- output of floating point numbers. (PVN - 2008/05/06)
- - h5dump, in output of the -p option: Added effective data compression
- ratio to the dataset storage layout output when a compression filter
- has been applied to a dataset. (PVN - 2008/05/01)
-
- F90 API
- ------
- - New H5A, H5G, H5L, H5O, and H5P APIs to enable 1.8 features were
- added. See "Release 1.8.1 (current release) versus Release 1.8.0" in
- the document "HDF5 Software Changes from Release to Release"
- (http://hdfgroup.org/HDF5/doc/ADGuide/Changes.html) for the
- complete list of the new APIs.
-
- C++ API
- ------
- - None
-
-
-Support for New Platforms, Languages, and Compilers
-===================================================
- - Both serial and parallel HDF5 are supported for the Red Storm machine
- which is a Cray XT3 system.
-
- - The Fortran library will work correctly if compiled with the -i8
- flag. This has been tested with the g95, PGI and Intel Fortran
- compilers.
-
-
-Bug Fixes since HDF5-1.8.0
-==========================
-
- Configuration
- -------------
- - None
-
- Source code distribution
- ========================
-
- Library
- -------
- - Chunking: Chunks greater than 4GB are disallowed.
- (QAK - 2008/05/16)
- - Fixed the problem with searching for a target file when following
- an external link. The search pattern will depend on whether the
- target file's pathname is an absolute or a relative path.
- Please see the H5Lcreate_external description in the "HDF5
- Reference Manual" (http://hdfgroup.org/HDF5/doc/RM/RM_H5L.html).
- (VC - 2008/04/08)
- - Fixed possible file corruption bug when encoding datatype
- descriptions for compound datatypes whose size was between
- 256 and 511 bytes and the file was opened with the "use the
- latest format" property enabled (with H5Pset_libver_bounds).
- (QAK - 2008/03/13)
- - Fixed bug in H5Aget_num_attrs() routine to correctly handle an
- invalid location identifier. (QAK - 2008/03/11)
-
- Parallel Library
- ----------------
- - None
-
- Tools
- -----
- - Fixed bug in h5diff that prevented datasets and attributes with
- variable-length string elements from comparing correctly.
- (QAK - 2008/02/28)
- - Fixed bug in h5dump that caused binary output to be made only for
- the first dataset, when several datasets were requested.
- (PVN - 2008/04/07)
-
- F90 API
- ------
- - The h5tset(get)_fields subroutines were missing the parameter to
- specify a sign position; fixed. (EIP - 2008/05/23)
- - Many APIs were fixed to work with the 8-byte integers in Fortran vs.
- 4-byte integers in C. This change is transparent to user applications.
-
- C++ API
- ------
- - The class hierarchy was revised to address the problem reported
- in bugzilla #1068, Attribute should not be derived from base
- class H5Object. Classes AbstractDS was moved out of H5Object.
- Class Attribute now multiply inherits from IdComponent and
- AbstractDs and class DataSet from H5Object and AbstractDs.
- In addition, data member IdComponent::id was moved into subclasses:
- Attribute, DataSet, DataSpace, DataType, H5File, Group, and PropList.
- (BMR - 2008/05/20)
- - IdComponent::dereference was incorrect; it was changed from:
- void IdComponent::dereference(IdComponent& obj, void* ref)
- to:
- void H5Object::dereference(H5File& h5file, void* ref)
- void H5Object::dereference(H5Object& obj, void* ref)
- (BMR - 2008/05/20)
- - Revised Attribute::write and Attribute::read wrappers to handle
- memory allocation/deallocation properly. (bugzilla 1045)
- (BMR - 2008/05/20)
-
-
-Platforms Tested
-================
-The following platforms and compilers have been tested for this release.
-
- Cray XT3 (2.0.41) cc (pgcc) 7.1-4
- (red storm) ftn (pgf90) 7.1-4
- CC (pgCC) 7.1-4
- mpicc 1.0.2
- mpif90 1.0.2
-
- FreeBSD 6.2-STABLE i386 gcc 3.4.6 [FreeBSD] 20060305
- (duty) g++ 3.4.6 [FreeBSD] 20060305
- gcc 4.2.1 20080123
- g++ 4.2.1 20080123
- gfortran 4.2.1 20070620
-
- FreeBSD 6.2-STABLE amd64 gcc 3.4.6 [FreeBSD] 20060305
- (liberty) g++ 3.4.6 [FreeBSD] 20060305
- gcc 4.2.1 20080123
- g++ 4.2.1 20080123
- gfortran 4.2.1 20080123
-
- IRIX64 6.5 (64 & n32) MIPSpro cc 7.4.4m
- F90 MIPSpro 7.4.4m
- C++ MIPSpro cc 7.4.4m
-
- Linux 2.6.9 (RHEL4) Intel 10.0 compilers
- (abe.ncsa.uiuc.edu)
-
- Linux 2.4.21-47 gcc 3.2.3 20030502
- (osage)
-
- Linux 2.6.9-42.0.10 gcc,g++ 3.4.6 20060404, G95 (GCC 4.0.3)
- (kagiso) PGI 7.1-6 (pgcc, pgf90, pgCC)
- Intel 9.1 (icc, ifort, icpc)
-
- Linux 2.6.16.27 x86_64 AMD gcc 4.1.0 (SuSE Linux), g++ 4.1.0,
- (smirom) g95 (GCC 4.0.3)
- PGI 7.1-6 (pgcc, pgf90, pgCC)
- Intel 9.1 (icc, ifort, icpc)
-
- Linux 2.6.5-7.252.1-rtgfx #1 Intel(R) C++ Version 9.0
- SMP ia64 Intel(R) Fortran Itanium(R) Version 9.0
- (cobalt) SGI MPI
-
- SunOS 5.8 32,46 Sun WorkShop 6 update 2 C 5.3
- (Solaris 2.8) Sun WorkShop 6 update 2 Fortran 95 6.2
- Sun WorkShop 6 update 2 C++ 5.3
-
- SunOS 5.10 cc: Sun C 5.8
- (linew) f90: Sun Fortran 95 8.2
- CC: Sun C++ 5.8
-
- Xeon Linux 2.4.21-32.0.1.ELsmp-perfctr-lustre
- (tungsten) gcc 3.2.2 20030222
- Intel(R) C++ Version 9.0
- Intel(R) Fortran Compiler Version 9.0
-
- IA-64 Linux 2.4.21.SuSE_309.tg1 ia64
- (NCSA tg-login) gcc 3.2.2
- Intel(R) C++ Version 8.1
- Intel(R) Fortran Compiler Version 8.1
- mpich-gm-1.2.6..14b-intel-r2
-
- Intel 64 Linux 2.6.9-42.0.10.EL_lustre-1.4.10.1smp
- (abe) gcc 3.4.6 20060404
- Intel(R) C++ Version 10.0
- Intel (R) Fortran Compiler Version 10.0
- mvapich2-0.9.8p2patched-intel-ofed-1.2
-
- Windows XP Visual Studio .NET
- Visual Studio 2005 w/ Intel Fortran 9.1
- Cygwin(native gcc compiler and g95)
- MinGW(native gcc compiler and g95)
-
- Windows XP x64 Visual Studio 2005 w/ Intel Fortran 9.1
-
- Windows Vista Visual Studio 2005
-
- MAC OS 10.5.2 (Intel) i686-apple-darwin9-gcc-4.0.1 (GCC) 4.0.1
- GNU Fortran (GCC) 4.3.0 20070810
- G95 (GCC 4.0.3 (g95 0.91!) Apr 24 2008)
-
-
-Supported Configuration Features Summary
-========================================
-
- In the tables below
- y = tested and supported
- n = not supported or not tested in this release
- x = not working in this release
- dna = does not apply
- ( ) = footnote appears below second table
- <blank> = testing incomplete on this feature or platform
-
-Platform C F90 F90 C++ zlib SZIP
- parallel parallel
-SunOS5.10 64-bit n y n y y y
-SunOS5.10 32-bit n y n y y y
-IRIX64_6.5 64-bit n y y y y y
-IRIX64_6.5 32-bit n n n n y y
-Windows XP n y(15) n(15) y y y
-Windows XP x64 n y(15) n(15) y y y
-Windows Vista n n n y y y
-Mac OS X 10.5 Intel n y n y y y
-FreeBSD 4.11 n n n y y y
-RedHat EL3 W (3) y(1) y(10) y(1) y y y
-RedHat EL3 W Intel (3) n y n y y n
-RedHat EL3 W PGI (3) n y n y y n
-SuSe x86_64 gcc (3,12) y(2) y(11) y(2) y y y
-SuSe x86_64 Int (3,12) n y(13) n y y n
-SuSe x86_64 PGI (3,12) n y(8) n y y y
-Linux 2.4 Xeon C
- Lustre Intel (3,6) n y n y y n
-Linux 2.6 SuSE ia64 C
- Intel (3,7) y y y y y n
-Linux 2.6 SGI Altix
- ia64 Intel (3) y y y y y y
-Linux 2.6 RHEL C
- Lustre Intel (5) y(4) y y(4) y y n
-Cray XT3 2.0.41 y y y y y n
-
-
-Platform Shared Shared Shared Thread-
- C libs F90 libs C++ libs safe
-Solaris2.10 64-bit y y y y
-Solaris2.10 32-bit y y y y
-IRIX64_6.5 64-bit y y n y
-IRIX64_6.5 32-bit y dna y y
-Windows XP y y(15) y y
-Windows XP x64 y y(15) y y
-Windows Vista y n n y
-Mac OS X 10.3 y n
-FreeBSD 4.11 y n y y
-RedHat EL3 W (3) y y(10) y y
-RedHat EL3 W Intel (3) y y y n
-RedHat EL3 W PGI (3) y y y n
-SuSe x86_64 W GNU (3,12) y y y y
-SuSe x86_64 W Int (3,12) y y y n
-SuSe x86_64 W PGI (3,12) y y y n
-Linux 2.4 Xeon C
- Lustre Intel (6) y y y n
-Linux 2.4 SuSE
- ia64 C Intel (7) y y y n
-Linux 2.4 SGI Altix
- ia64 Intel y n
-Linux 2.6 RHEL C
- Lustre Intel (5) y y y n
-Cray XT3 2.0.41 n n n n n
-
- Notes: (1) Using mpich2 1.0.6.
- (2) Using mpich2 1.0.7.
- (3) Linux 2.6 with GNU, Intel, and PGI compilers, as indicated.
- W or C indicates workstation or cluster, respectively.
- (4) Using mvapich2 0.9.8.
- (5) Linux 2.6.9-42.0.10. Xeon cluster with ELsmp_perfctr_lustre
- and Intel compilers
- (6) Linux 2.4.21-32.0.1. Xeon cluster with ELsmp_perfctr_lustre
- and Intel compilers
- (7) Linux 2.4.21, SuSE_292.till. Ia64 cluster with Intel compilers
- (8) pgf90
- (9) With Compaq Visual Fortran 6.6c compiler.
- (10) With PGI and Absoft compilers.
- (11) PGI and Intel compilers for both C and Fortran
- (12) AMD Opteron x86_64
- (13) ifort
- (14) Yes with C and Fortran, but not with C++
- (15) Using Visual Studio 2005 or Cygwin
- (16) Not tested for this release.
- Compiler versions for each platform are listed in the preceding
- "Platforms Tested" table.
-
-
-Known Problems
-==============
-* For Red Storm, a Cray XT3 system, the yod command sometimes gives the
- message, "yod allocation delayed for node recovery". This interferes with
- test suites that do not expect seeing this message. See the section of "Red
- Storm" in file INSTALL_parallel for a way to deal with this problem.
- AKC - 2008/05/28
-
-* For Red Storm, a Cray XT3 system, the tools/h5ls/testh5ls.sh will fail on
- the test "Testing h5ls -w80 -r -g tgroup.h5" fails. This test is
- expected to fail and exit with a non-zero code but the yod command does
- not propagate the exit code of the executables. Yod always returns 0 if it
- can launch the executable. The test suite shell expects a non-zero for
- this particular test, therefore it concludes the test has failed when it
- receives 0 from yod. To bypass this problem for now, change the following
- lines in the tools/h5ls/testh5ls.sh.
- ======== Original =========
- # The following combination of arguments is expected to return an error message
- # and return value 1
- TOOLTEST tgroup-1.ls 1 -w80 -r -g tgroup.h5
- ======== Skip the test =========
- echo SKIP TOOLTEST tgroup-1.ls 1 -w80 -r -g tgroup.h5
- ======== end of bypass ========
- AKC - 2008/05/28
-
-* We have discovered two problems when running collective IO parallel HDF5
- tests with chunking storage on the ChaMPIon MPI compiler on tungsten, a
- Linux cluster at NCSA.
-
- Under some complex selection cases:
- 1) MPI_Get_element returns the wrong value.
- 2) MPI_Type_struct also generates the wrong derived datatype and corrupt
- data may be generated.
- These issues arise only when turning on collective IO with chunking storage
- with some complex selections. We have not found these problems on other
- MPI-IO compilers. If you encounter these problems, you may use independent
- IO instead.
-
- To avoid this behavior, change the following line in your code
- H5Pset_dxpl_mpio(xfer_plist, H5FD_MPIO_COLLECTIVE);
- to
- H5Pset_dxpl_mpio(xfer_plist, H5FD_MPIO_INDEPENDENT);
-
- KY - 2007/08/24
-
-* For SNL, spirit/liberty/thunderbird: The serial tests pass but parallel
- tests failed with MPI-IO file locking message. AKC - 2007/6/25
-
-* On Intel 64 Linux cluster (RH 4, Linux 2.6.9) with Intel 10.0 compilers,
- use -mp -O1 compilation flags to build the libraries. A higher level of
- optimization causes failures in several HDF5 library tests.
-
-* For LLNL, uP: both serial and parallel tests pass.
- Zeus: Serial tests pass but parallel tests fail with a known problem in MPI.
- ubgl: Serial tests pass but parallel tests fail.
-
-* Configuring with --enable-debug=all produces compiler errors on most
- platforms: Users who want to run HDF5 in debug mode should use
- --enable-debug rather than --enable-debug=all to enable debugging
- information on most modules.
-
-* On Mac OS 10.4, test/dt_arith.c has some errors in conversion from long
- double to (unsigned) long long and from (unsigned) long long to long double.
-
-* On Altix SGI with Intel 9.0, testmeta.c would not compile with -O3
- optimization flag.
-
-* On VAX, the Scaleoffset filter is not supported. The Scaleoffset filter
- supports only the IEEE standard for floating-point data; it cannot be applied
- to HDF5 data generated on VAX.
-
-* On Cray X1, a lone colon on the command line of h5dump --xml (as in
- the testh5dumpxml.sh script) is misinterpereted by the operating system
- and causes an error.
-
-* On mpich 1.2.5 and 1.2.6, if more than two processes contribute no IO and
- the application asks to do collective IO, we have found that when using 4
- processors, a simple collective write will sometimes be hung. This can be
- verified with t_mpi test under testpar.
-
-* On IRIX6.5, when the C compiler version is greater than 7.4, complicated
- MPI derived datatype code will work. However, the user should increase
- the value of the MPI_TYPE_MAX environment variable to some appropriate value
- to use collective irregular selection code. For example, the current
- parallel HDF5 test needs to raise MPI_TYPE_MAX to 200,000 to pass the test.
-
-* A dataset created or rewritten with a v1.6.3 library or after cannot be read
- with the v1.6.2 library or before when the Fletcher32 EDC filter is enabled.
- There was a bug in the calculation of the Fletcher32 checksum in the
- library before v1.6.3; the checksum value was not consistent between big-
- endian and little-endian systems. This bug was fixed in Release 1.6.3.
- However, after fixing the bug, the checksum value was no longer the same as
- before on little-endian system. Library releases after 1.6.4 can still read
- datasets created or rewritten with an HDF5 library of v1.6.2 or before.
- SLU - 2005/6/30
-
-* For version 6 (6.02 and 6.04) of the Portland Group compiler on the AMD
- Opteron processor, there is a bug in the compiler for optimization(-O2).
- The library failed in several tests, all related to the MULTI driver.
- The problem has been reported to the vendor.
-
-* On IBM AIX systems, parallel HDF5 mode will fail some tests with error
- messages like "INFO: 0031-XXX ...". This is from the command `poe'.
- Set the environment variable MP_INFOLEVEL to 0 to minimize the messages
- and run the tests again.
-
- The tests may fail with messages like "The socket name is already in use",
- but HDF5 does not use sockets. This failure is due to problems with the
- poe command trying to set up the debug socket. To resolve this problem,
- check to see whether there are many old /tmp/s.pedb.* files staying around.
- These are sockets used by the poe command and left behind due to failed
- commands. First, ask your system administrator to clean them out.
- Lastly, request IBM to provide a means to run poe without the debug socket.
-
-* The --enable-static-exec configure flag fails to compile for Solaris
- platforms. This is due to the fact that not all of the system libraries on
- Solaris are available in a static format.
-
- The --enable-static-exec configure flag also fails to correctly compile
- on IBM SP2 platforms for serial mode. The parallel mode works fine with
- this option.
-
- It is suggested that you do not use this option on these platforms
- during configuration.
-
-* With the gcc 2.95.2 compiler, HDF5 uses the `-ansi' flag during
- compilation. The ANSI version of the compiler complains about not being
- able to handle the `long long' datatype with the warning:
-
- warning: ANSI C does not support `long long'
-
- This warning is innocuous and can be safely ignored.
-
-* The ./dsets tests fail on the TFLOPS machine if the test program,
- dsets.c, is compiled with the -O option. The HDF5 library still works
- correctly with the -O option. The test program works fine if it is
- compiled with -O1 or -O0. Only -O (same as -O2) causes the test
- program to fail.
-
-* Not all platforms behave correctly with Szip's shared libraries. Szip is
- disabled in these cases, and a message is relayed at configure time. Static
- libraries should be working on all systems that support Szip and should be
- used when shared libraries are unavailable.
-
- There is also a configure error on Altix machines that incorrectly reports
- when a version of Szip without an encoder is being used.
-
-* On some platforms that use Intel and Absoft compilers to build the HDF5
- Fortran library, compilation may fail for fortranlib_test.f90, fflush1.f90
- and fflush2.f90 complaining about the exit subroutine. Comment out the line
- IF (total_error .ne. 0) CALL exit (total_error).
-
-* Information about building with PGI and Intel compilers is available in
- the INSTALL file sections 4.7 and 4.8.
-
-* On at least one system, SDSC DataStar, the scheduler (in this case
- LoadLeveler) sends job status updates to standard error when you run
- any executable that was compiled with the parallel compilers.
-
- This causes problems when running "make check" on parallel builds, as
- many of the tool tests function by saving the output from test runs,
- and comparing it to an exemplar.
-
- The best solution is to reconfigure the target system so it no longer
- inserts the extra text. However, this may not be practical.
-
- In such cases, one solution is to "setenv HDF5_Make_Ignore yes" prior to
- the configure and build. This will cause "make check" to continue after
- detecting errors in the tool tests. However, in the case of SDSC DataStar,
- it also leaves you with some 150 "failed" tests to examine by hand.
-
- A second solution is to write a script to run serial tests and filter
- out the text added by the scheduler. A sample script used on SDSC
- DataStar is given below, but you will probably have to customize it
- for your installation.
-
- Observe that the basic idea is to insert the script as the first item
- on the command line which executes the the test. The script then
- executes the test and filters out the offending text before passing
- it on.
-
- #!/bin/csh
-
- set STDOUT_FILE=~/bin/serial_filter.stdout
- set STDERR_FILE=~/bin/serial_filter.stderr
-
- rm -f $STDOUT_FILE $STDERR_FILE
-
- ($* > $STDOUT_FILE) >& $STDERR_FILE
-
- set RETURN_VALUE=$status
-
- cat $STDOUT_FILE
-
- tail +3 $STDERR_FILE
-
- exit $RETURN_VALUE
-
- You get the HDF5 make files and test scripts to execute your filter script
- by setting the environment variable "RUNSERIAL" to the full path of the
- script prior to running configure for parallel builds. Remember to
- "unsetenv RUNSERIAL" before running configure for a serial build.
-
- Note that the RUNSERIAL environment variable exists so that we can
- prefix serial runs as necessary on the target system. On DataStar,
- no prefix is necessary. However on an MPICH system, the prefix might
- have to be set to something like "/usr/local/mpi/bin/mpirun -np 1" to
- get the serial tests to run at all.
-
- In such cases, you will have to include the regular prefix in your
- filter script.
-
-* H5Ocopy() does not copy reg_ref attributes correctly when shared-message
- is turn on. The value of the reference in the destination attriubte is
- wrong. This H5Ocopy problem will affect the h5copy tool.
-
-* In the C++ API, it appears that there are bugs in Attribute::write/read
- and DataSet::write/read for fixed- and variable-len strings. The problems
- are being worked on and a patch will be provided when the fixes are
- available.
-
-
-%%%%1.8.0%%%%
-
-
-HDF5 version 1.8.0 released on Tue Feb 12 20:41:19 CST 2008
-================================================================================
-
-INTRODUCTION
-============
-
-This document describes the differences between the HDF5-1.6.x release series
-and HDF5 1.8.0, and contains information on the platforms tested and known
-problems in HDF5-1.8.0. For more details, see the HISTORY-1_0-1_8_0_rc3.txt
-file in the
-release_docs/ directory of the HDF5 source.
-
-Links to the HDF5 1.8.0 source code, documentation, and additional materials
-can be found on the HDF5 web page at:
-
- http://www.hdfgroup.org/products/hdf5/
-
-The HDF5 1.8.0 release can be obtained from:
-
- http://www.hdfgroup.org/HDF5/release/obtain5.html
-
-User documentation for 1.8.0 can be accessed directly at this location:
-
- http://www.hdfgroup.org/HDF5/doc/
-
-New features in 1.8.0, including brief general descriptions of some new
-and modified APIs, are described in the "What's New in 1.8.0?" document:
-
- http://www.hdfgroup.org/HDF5/doc/ADGuide/WhatsNew180.html
-
-All new and modified APIs are listed in detail in the "HDF5 Software Changes
-from Release to Release" document, in the section "Release 1.8.0 (current
-release) versus Release 1.6.x":
-
- http://www.hdfgroup.org/HDF5/doc/ADGuide/Changes.html
-
-If you have any questions or comments, please send them to the HDF Help Desk:
-
- help@hdfgroup.org
-
-
-CONTENTS
-========
-
-- New Features
-- Removed Feature
-- Support for new platforms and languages
-- Bug Fixes since HDF5-1.6.0
-- Platforms Tested
-- Supported Configuration Features Summary
-- Known Problems
-
-
-New Features
-============
-
- HDF5 Release 1.8.0 is a major release with many changes and new features.
-
- New format and interface features discussed in the "What's New in
- HDF5 1.8.0" document include the following:
-
- Enhanced group object management
- Enhanced attribute management and more efficient meta data handling
- Expanded datatype features
- Creation order tracking and indexing
- Improved meta data caching and cache control
- UTF-8 encoding
- New I/O filters: n-bit and scale+offset compression
- New link (H5L) and object (H5O) interfaces and features
- External and user-defined links
- New high-level APIs:
- HDF5 Packet Table (H5PT) and HDF5 Dimension Scale (H5DS)
- C++ and Fortran interfaces for older high-level APIs:
- H5Lite (H5LT), H5Image (H5IM), and H5Table (H5TB)
- New and improved tools
- And more...
-
- http://hdfgroup.org/HDF5/doc/ADGuide/WhatsNew180.html
-
-
- New APIs associated with these features, other interface changes
- (e.g., ENUM and struct definitions), and new library configuration flags
- are listed in the "Release 1.8.0 (current release) versus Release 1.6.x"
- section of "HDF5 Software Changes from Release to Release."
-
- http://hdfgroup.org/HDF5/doc/ADGuide/Changes.html
-
-Compatibility
--------------
- Many HDF5 users and user communities have existing applications that
- they may wish to port to Release 1.8.0. Alternatively, some users may
- wish to take advantage of Release 1.8.0's improved performance without
- having to port such applications. To facilitate managing application
- compatibility and porting applications from release to release, the HDF
- Team has implemented the following features:
- Individually-configurable macros that selectively map common
- interface names to the old and new interfaces
- Library configuration options to configure the macro mappings
-
- Two related documents accompany this release:
- "API Compatibility Macros in HDF5" discusses the specifics of the
- new individually-configurable macros and library configuration
- options.
- http://hdfgroup.org/HDF5/doc/RM/APICompatMacros.html
-
- "New Features in HDF5 Release 1.8.0 and Backward/Forward Format
- Compatibility Issues" discusses each new feature with regard to
- its impact on format compatibility.
- http://hdfgroup.org/HDF5/doc/ADGuide/CompatFormat180.html
-
-Referenced documents
---------------------
- http://hdfgroup.org/HDF5/doc/ADGuide/WhatsNew180.html
- "What's New in HDF5 1.8.0"
-
- http://hdfgroup.org/HDF5/doc/ADGuide/Changes.html
- The "Release 1.8.0 (current release) versus Release 1.6.x "
- section in "HDF5 Software Changes from Release to Release"
-
- http://hdfgroup.org/HDF5/doc/RM/APICompatMacros.html
- "API Compatibility Macros in HDF5"
-
- http://hdfgroup.org/HDF5/doc/ADGuide/CompatFormat180.html
- "New Features in HDF5 Release 1.8.0 and Backward/Forward Format
- Compatibility Issues"
-
-
-Removed Feature
-===============
-The stream virtual file driver (H5FD_STREAM) have been removed in this
-release. This affects the functions H5Pset_fapl_stream and H5Pget_fapl_stream
-and the constant H5FD_STREAM.
-
-This virtual file driver will be available at
-http://hdf5-addons.origo.ethz.ch/. Note that at the time of this release,
-the transition is still in progress; the necessary integration tools may
-not be available when HDF5 Release 1.8.0 first comes out.
-
-
-Support for New Platforms, Languages, and Compilers
-===================================================
- - Support for Open VMS 7.3 was added.
-
-
-Bug Fixes since HDF5-1.6.0
-==========================
- This release contains numerous bug fixes. For details, see the
- "Changes from 1.6.0 to 1.8.0-rc3" section of the HISTORY.txt file for
- this release.
-
-
-Platforms Tested
-================
-The following platforms and compilers have been tested for for this release.
-
- AIX 5.2 (32/64 bit) xlc 8.0.0.11
- xlC 8.0
- xlf 10.01.0000.0
- mpcc_r 6.0.0.8
- mpxlf_r 8.1.1.7
-
- FreeBSD 6.2-STABLE i386 gcc 3.4.6 [FreeBSD] 20060305
- (duty) g++ 3.4.6 [FreeBSD] 20060305
- gcc 4.2.1 20080123
- g++ 4.2.1 20080123
- gfortran 4.2.1 20070620
-
- FreeBSD 6.2-STABLE amd64 gcc 3.4.6 [FreeBSD] 20060305
- (liberty) g++ 3.4.6 [FreeBSD] 20060305
- gcc 4.2.1 20080123
- g++ 4.2.1 20080123
- gfortran 4.2.1 20080123
-
- IRIX64 6.5 (64 & n32) MIPSpro cc 7.4.4m
- F90 MIPSpro 7.4.4m
- C++ MIPSpro cc 7.4.4m
-
- Linux 2.6.9 (RHEL4) Intel 10.0 compilers
- (abe.ncsa.uiuc.edu)
-
- Linux 2.4.21-47 gcc 3.2.3 20030502
- (osage)
-
- Linux 2.6.9-42.0.10 gcc 3.4.6 20060404
- (kagiso) PGI 7.0-7 (pgcc, pgf90, pgCC)
- Intel 9.1 (icc, ifort, icpc)
-
- Linux 2.6.16.27 x86_64 AMD gcc 4.1.0 (SuSE Linux), g++ 4.1.0,
- (smirom) g95 (GCC 4.0.3)
- PGI 6.2-5 (pgcc, pgf90, pgCC)
- Intel 9.1 (icc, iort, icpc)
-
- Linux 2.6.5-7.252.1-rtgfx #1 Intel(R) C++ Version 9.0
- SMP ia64 Intel(R) Fortran Itanium(R) Version 9.0
- (cobalt) SGI MPI
-
- SunOS 5.8 32,46 Sun WorkShop 6 update 2 C 5.3
- (Solaris 2.8) Sun WorkShop 6 update 2 Fortran 95 6.2
- Sun WorkShop 6 update 2 C++ 5.3
-
- SunOS 5.10 cc: Sun C 5.8
- (linew) f90: Sun Fortran 95 8.2
- CC: Sun C++ 5.8
-
- Xeon Linux 2.4.21-32.0.1.ELsmp-perfctr-lustre
- (tungsten) gcc 3.2.2 20030222
- Intel(R) C++ Version 9.0
- Intel(R) Fortran Compiler Version 9.0
-
- IA-64 Linux 2.4.21.SuSE_292.til1 ia64
- (NCSA tg-login) gcc 3.2.2
- Intel(R) C++ Version 8.1
- Intel(R) Fortran Compiler Version 8.1
- mpich-gm-1.2.5..10-intel-r2
-
- Windows XP Visual Studio .NET
- Visual Studio 2005 w/ Intel Fortran 9.1
- Cygwin(native gcc compiler and g95)
- MinGW(native gcc compiler and g95)
-
- Windows XP x64 Visual Studio 2005 w/ Intel Fortran 9.1
-
- Windows Vista Visual Studio 2005
-
- MAC OS 10.4 (Intel) gcc i686-apple-darwin8-gcc-4.0.1 (GCC) 4.0.1
- G95 (GCC 4.0.3 (g95 0.91!) Nov 21 2006)
-
- Alpha Open VMS 7.3 Compaq C V6.5-001-48BCD
- HP Fortran V7.6-3276
- Compaq C++ V6.5-004
-
-
-Supported Configuration Features Summary
-========================================
-
- In the tables below
- y = tested and supported
- n = not supported or not tested in this release
- x = not working in this release
- dna = does not apply
- ( ) = footnote appears below second table
- <blank> = testing incomplete on this feature or platform
-
-Platform C F90 F90 C++ zlib SZIP
- parallel parallel
-SunOS5.8 64-bit n y n y y y
-SunOS5.8 32-bit n y n y y y
-SunOS5.10 64-bit y(1) y n y y y
-SunOS5.10 32-bit y(1) y n y y y
-IRIX64_6.5 64-bit n y y y y y
-IRIX64_6.5 32-bit n n n n y y
-AIX-5.2 32-bit y y y y y y
-AIX-5.2 64-bit y y y y y y
-Windows XP n y(15) n(15) y y y
-Windows XP x64 n y(15) n(15) y y y
-Windows Vista n n n y y y
-Mac OS X 10.4 PowerPC n n
-Mac OS X 10.4 Intel n y n y y y
-FreeBSD 4.11 n n n y y y
-RedHat EL3 W (3) y(1a) y(10) y(1a) y y y
-RedHat EL3 W Intel (3) n y n y y n
-RedHat EL3 W PGI (3) n y n y y n
-SuSe x86_64 gcc (3,12) y(1a) y(11) n y y y
-SuSe x86_64 Int (3,12) n y(13) n y y n
-SuSe x86_64 PGI (3,12) n y(8) n y y y
-Linux 2.4 Xeon C
- Lustre Intel (3,6) n y n y y n
-Linux 2.6 SuSE ia64 C
- Intel (3,7) y y y y y n
-Linux 2.6 SGI Altix
- ia64 Intel (3) y y y y y y
-Alpha OpenVMS 7.3.2 n y n y n n
-
-
-
-Platform Shared Shared Shared static- Thread-
- C libs F90 libs C++ libs exec safe
-Solaris2.8 64-bit y y y x y
-Solaris2.8 32-bit y y y x y
-Solaris2.10 64-bit y x y
-Solaris2.10 32-bit y x y
-IRIX64_6.5 64-bit y y n y y
-IRIX64_6.5 32-bit y dna y y y
-AIX-5.2 & 5.3 32-bit n n n y n
-AIX-5.2 & 5.3 64-bit n n n y n
-Windows XP y y(15) y y y
-Windows XP x64 y y(15) y y y
-Windows Vista y n n y y
-Mac OS X 10.3 y y n
-FreeBSD 4.11 y n y y y
-RedHat EL3 W (3) y y(10) y y y
-RedHat EL3 W Intel (3) y y y y n
-RedHat EL3 W PGI (3) y y y y n
-SuSe x86_64 W GNU (3,12) y y y y y
-SuSe x86_64 W Int (3,12) y y y y(14) n
-SuSe x86_64 W PGI (3,12) y y y y(14) n
-Linux 2.4 Xeon C
- Lustre Intel (6) y y y y n
-Linux 2.4 SuSE
- ia64 C Intel (7) y y y y n
-Linux 2.4 SGI Altix
- ia64 Intel y y n
-Alpha OpenVMS 7.3.2 n n n y n
-
- Notes: (1) Using mpich 1.2.6.
- (1a) Using mpich2 1.0.6.
- (2) Using mpt and mpich 1.2.6.
- (3) Linux 2.6 with GNU, Intel, and PGI compilers, as indicated.
- W or C indicates workstation or cluster, respectively.
-
- (6) Linux 2.4.21-32.0.1. Xeon cluster with ELsmp_perfctr_lustre
- and Intel compilers
- (7) Linux 2.4.21, SuSE_292.till. Ia64 cluster with Intel
-compilers
- (8) pgf90
- (9) With Compaq Visual Fortran 6.6c compiler.
- (10) With PGI and Absoft compilers.
- (11) PGI and Intel compilers for both C and Fortran
- (12) AMD Opteron x86_64
- (13) ifort
- (14) Yes with C and Fortran, but not with C++
- (15) Using Visual Studio 2005 or Cygwin
- (16) Not tested for this release.
- Compiler versions for each platform are listed in the preceding
- "Platforms Tested" table.
-
-
-Known Problems
-==============
-* We have discovered two problems when running collective IO parallel HDF5
- tests with chunking storage on the ChaMPIon MPI compiler on tungsten, a
- Linux cluster at NCSA.
-
- Under some complex selection cases:
- 1) MPI_Get_element returns the wrong value.
- 2) MPI_Type_struct also generates the wrong derived datatype and corrupt
- data may be generated.
- These issues arise only when turning on collective IO with chunking storage
- with some complex selections. We have not found these problems on other
- MPI-IO compilers. If you encounter these problems, you may use independent
- IO instead.
-
- To avoid this behavior, change the following line in your code
- H5Pset_dxpl_mpio(xfer_plist, H5FD_MPIO_COLLECTIVE);
-
- to
- H5Pset_dxpl_mpio(xfer_plist, H5FD_MPIO_INDEPENDENT);
-
- KY - 2007/08/24
-
-* For SNL, spirit/liberty/thunderbird: The serial tests pass but parallel
- tests failed with MPI-IO file locking message. AKC - 2007/6/25
-
-* On Intel 64 Linux cluster (RH 4, Linux 2.6.9) with Intel 10.0 compilers,
- use -mp -O1 compilation flags to build the libraries. A higher level of
- optimization causes failures in several HDF5 library tests.
-
-* For SNL, Red Storm: Only parallel HDF5 is supported. The serial tests pass
- when run against the parallel library; the parallel tests also pass, but
- with lots of non-fatal error messages.
-
-* For LLNL, uP: both serial and parallel tests pass.
- Zeus: Serial tests pass but parallel tests fail with a known problem in MPI.
- ubgl: Serial tests pass but parallel tests fail.
-
-* On SUN 5.10 C++, testing fails in the "Testing Shared Datatypes with
- Attributes" test.
-
-* Configuring with --enable-debug=all produces compiler errors on most
- platforms: Users who want to run HDF5 in debug mode should use
- --enable-debug rather than --enable-debug=all to enable debugging
- information on most modules.
-
-* On Mac OS 10.4, test/dt_arith.c has some errors in conversion from long
- double to (unsigned) long long and from (unsigned) long long to long double.
-
-* On Altix SGI with Intel 9.0, testmeta.c would not compile with -O3
- optimization flag.
-
-* On VAX, the Scaleoffset filter is not supported. The filter cannot be
- applied to HDF5 data generated on VAX. The Scaleoffset filter only supports
- the IEEE standard for floating-point data.
-
-* On Cray X1, a lone colon on the command line of h5dump --xml (as in
- the testh5dumpxml.sh script) is misinterpereted by the operating system
- and causes an error.
-
-* On mpich 1.2.5 and 1.2.6, if more than two processes contribute no IO and
- the application asks to do collective IO, we have found that when using 4
- processors, a simple collective write will sometimes be hung. This can be
- verified with t_mpi test under testpar.
-
-* On IRIX6.5, when the C compiler version is greater than 7.4, complicated
- MPI derived datatype code will work. However, the user should increase
- the value of the MPI_TYPE_MAX environment variable to some appropriate value
- to use collective irregular selection code. For example, the current
- parallel HDF5 test needs to raise MPI_TYPE_MAX to 200,000 to pass the test.
-
-* A dataset created or rewritten with a v1.6.3 library or after cannot be read
- with the v1.6.2 library or before when the Fletcher32 EDC filter is enabled.
- There was a bug in the calculating code of the Fletcher32 checksum in the
- library before v1.6.3; the checksum value was not consistent between big-
- endian and little-endian systems. This bug was fixed in Release 1.6.3.
- However, after fixing the bug, the checksum value was no longer the same as
- before on little-endian system. Library releases after 1.6.4 can still read
- datasets created or rewritten with an HDF5 library of v1.6.2 or before.
- SLU - 2005/6/30
-
-* For version 6 (6.02 and 6.04) of the Portland Group compiler on the AMD
- Opteron processor, there is a bug in the compiler for optimization(-O2).
- The library failed in several tests, all related to the MULTI driver.
- The problem has been reported to the vendor.
-
-* On IBM AIX systems, parallel HDF5 mode will fail some tests with error
- messages like "INFO: 0031-XXX ...". This is from the command `poe'.
- Set the environment variable MP_INFOLEVEL to 0 to minimize the messages
- and run the tests again.
-
- The tests may fail with messages like "The socket name is already in use",
- but HDF5 does not use sockets. This failure is due to problems with the
- poe command trying to set up the debug socket. To resolve this problem,
- check to see whether there are many old /tmp/s.pedb.* files staying around.
- These are sockets used by the poe command and left behind due to failed
- commands. First, ask your system administrator to clean them out.
- Lastly, request IBM to provide a means to run poe without the debug socket.
-
-* The --enable-static-exec configure flag fails to compile for Solaris
- platforms. This is due to the fact that not all of the system libraries on
- Solaris are available in a static format.
-
- The --enable-static-exec configure flag also fails to correctly compile
- on IBM SP2 platform for the serial mode. The parallel mode works fine with
- this option.
-
- It is suggested that you do not use this option on these platforms
- during configuration.
-
-* With the gcc 2.95.2 compiler, HDF5 uses the `-ansi' flag during
- compilation. The ANSI version of the compiler complains about not being
- able to handle the `long long' datatype with the warning:
-
- warning: ANSI C does not support `long long'
-
- This warning is innocuous and can be safely ignored.
-
-* The ./dsets tests fail on the TFLOPS machine if the test program,
- dsets.c, is compiled with the -O option. The HDF5 library still works
- correctly with the -O option. The test program works fine if it is
- compiled with -O1 or -O0. Only -O (same as -O2) causes the test
- program to fail.
-
-* Not all platforms behave correctly with Szip's shared libraries. Szip is
- disabled in these cases, and a message is relayed at configure time. Static
- libraries should be working on all systems that support Szip and should be
- used when shared libraries are unavailable.
-
- There is also a configure error on Altix machines that incorrectly reports
- when a version of Szip without an encoder is being used.
-
-* On some platforms that use Intel and Absoft compilers to build the HDF5
- Fortran library, compilation may fail for fortranlib_test.f90, fflush1.f90
- and fflush2.f90 complaining about the exit subroutine. Comment out the line
- IF (total_error .ne. 0) CALL exit (total_error).
-
-* Information about building with PGI and Intel compilers is available in
- the INSTALL file sections 4.7 and 4.8.
-
-* On at least one system, SDSC DataStar, the scheduler (in this case
- LoadLeveler) sends job status updates to standard error when you run
- any executable that was compiled with the parallel compilers.
-
- This causes problems when running "make check" on parallel builds, as
- many of the tool tests function by saving the output from test runs,
- and comparing it to an exemplar.
-
- The best solution is to reconfigure the target system so it no longer
- inserts the extra text. However, this may not be practical.
-
- In such cases, one solution is to "setenv HDF5_Make_Ignore yes" prior to
- the configure and build. This will cause "make check" to continue after
- detecting errors in the tool tests. However, in the case of SDSC DataStar,
- it also leaves you with some 150 "failed" tests to examine by hand.
-
- A second solution is to write a script to run serial tests and filter
- out the text added by the scheduler. A sample script used on SDSC
- DataStar is given below, but you will probably have to customize it
- for your installation.
-
- Observe that the basic idea is to insert the script as the first item
- on the command line which executes the the test. The script then
- executes the test and filters out the offending text before passing
- it on.
-
- #!/bin/csh
-
- set STDOUT_FILE=~/bin/serial_filter.stdout
- set STDERR_FILE=~/bin/serial_filter.stderr
-
- rm -f $STDOUT_FILE $STDERR_FILE
-
- ($* > $STDOUT_FILE) >& $STDERR_FILE
-
- set RETURN_VALUE=$status
-
- cat $STDOUT_FILE
-
- tail +3 $STDERR_FILE
-
- exit $RETURN_VALUE
-
- You get the HDF5 make files and test scripts to execute your filter script
- by setting the environment variable "RUNSERIAL" to the full path of the
- script prior to running configure for parallel builds. Remember to
- "unsetenv RUNSERIAL" before running configure for a serial build.
-
- Note that the RUNSERIAL environment variable exists so that we can
- can prefix serial runs as necessary on the target system. On DataStar,
- no prefix is necessary. However on an MPICH system, the prefix might
- have to be set to something like "/usr/local/mpi/bin/mpirun -np 1" to
- get the serial tests to run at all.
-
- In such cases, you will have to include the regular prefix in your
- filter script.
-
-* H5Ocopy() does not copy reg_ref attributes correctly when shared-message
- is turn on. The value of the reference in the destination attriubte is
- wrong. This H5Ocopy problem will affect the h5copy tool.
-
diff --git a/release_docs/NEWSLETTER.txt b/release_docs/NEWSLETTER.txt
new file mode 100644
index 0000000..f03f710
--- /dev/null
+++ b/release_docs/NEWSLETTER.txt
@@ -0,0 +1,25 @@
+INTRODUCTION
+============
+
+This purpose of this document is to contain entries that can be used to quickly
+produce a release newsletter. When something is added to the library that is
+"newsletter worthy" (i.e., new feature, CVE fix, etc.) a summary note should
+be added here.
+
+The format should look like this:
+
+* SUMMARY OF NEWSLETTER-WORTHY THING
+
+ Here is where you describe the summary. Summarize the feature, fix, or
+ change in general language. Remember, RELEASE.txt is for communicating
+ technical specifics. Text entered here is more like advertising.
+
+ (GitHub #123, #125)
+
+The GitHub #s could be relevant issues or PRs. They will probably not appear
+in the final newsletter, but are so that the person writing the newsletter
+has easy access to context if they have questions.
+
+Every entry in RELEASE.txt does NOT require an entry here. The newsletter is
+for communicating major changes that are of interest to anyone. Minor bugfixes,
+memory leak fixes, etc. do not require entries.
diff --git a/release_docs/README.md b/release_docs/README.md
new file mode 100644
index 0000000..1532f1a
--- /dev/null
+++ b/release_docs/README.md
@@ -0,0 +1,102 @@
+# The `release_docs` directory
+
+## Intro
+
+This directory contains instructions for building and using the library as
+well as the HDF5 history files.
+
+## HISTORY files
+
+The `HISTORY` files contain the history of this branch of HDF5. They fall into
+three categories.
+
+### HISTORY-\[VERSION 1\]-\[VERSION 2\].txt
+
+These files are created when we release a new major version and include all
+the changes that were made to the `develop` branch while creating a major release.
+
+### HISTORY-\[VERSION\].txt
+
+This file contains the changes that were made to a maintenance branch since
+it split off from `develop`. It will also be found in the `develop` branch
+when experimental releases have been created.
+
+### RELEASE.txt
+
+This is the changelog for the current version of the library.
+
+For a MAJOR release (or in `develop`) this files lists all the changes since the
+last major version. For a MINOR release (or in a maintenance branch), this file
+lists all the changes since the last release in the maintenance branch.
+
+Examples:
+
+* The file for HDF5 1.14.0 includes all the changes since HDF5 1.12.0
+* The file for HDF5 1.10.9 includes all the changes since HDF5 1.10.8
+* The file in `develop` includes all the changes since the last major release
+* The file in `hdf5_1_14` includes all the changes since the last minor HDF5 1.14 release
+
+Note that we make no effort to bring maintenance branch `HISTORY` files back to
+develop. If you want to compare, say, 1.10.4 with 1.12.3, you'd have to get
+the history files from those releases and compare them by hand.
+
+## Creating new releases
+
+### MAJOR release
+
+* If there were experimental releases, merge the experimental `HISTORY` file
+ and the current `RELEASE.txt` by category to create a separate, unified
+ file that ignores the experimental releases. Don't check this in yet or
+ clobber any existing `HISTORY`/`RELEASE` files, but put it someplace handy for
+ use in later steps.
+
+* Create the new maintenance branch
+
+In develop:
+* Create the new `HISTORY-\[VERSION 1\]-\[VERSION 2\].txt` file
+ * If there is an experimental `HISTORY` file, add `RELEASE.txt` to the beginning of it and use that
+ * Otherwise, start with `RELEASE.txt`
+ * Add the introduction boilerplate like in the other `HISTORY` files (TOC, etc.)
+* Delete any experimental `HISTORY` file
+* Clear out `RELEASE.txt`
+
+Note that we're KEEPING any experimental release history information in the
+`HISTORY-\[VERSION 1\]-\[VERSION 2\].txt` file, so do NOT use the merged file in
+the above steps!
+
+In the new maintenance branch:
+* Create the new `HISTORY-\[VERSION\].txt` file
+ * If there is an experimental `HISTORY` file use the combined file you created earlier
+ * Otherwise, start with `RELEASE.txt`
+ * Add the introduction boilerplate like in the other `HISTORY` files (TOC, etc.)
+* Delete any experimental `HISTORY` file
+* Clear out `RELEASE.txt`
+
+* Create the new release branch
+
+In the new release branch:
+* If there were experimental releases, use the combined file you created earlier as `RELEASE.txt`
+* Otherwise the `RELEASE.txt` will be used as-is
+
+### MINOR release
+
+* Create the release branch
+
+In the maintenance branch:
+* Add the contents of `RELEASE.txt` to the beginnnig of `HISTORY-\[VERSION\].txt`
+* Clear out `RELEASE.txt`
+
+### EXPERIMENTAL release
+
+* Add the contents of `RELEASE.txt` to the beginnnig of `HISTORY-\[VERSION\].txt`
+* Clear out `RELEASE.txt`
+
+## INSTALL files
+
+These files include instructions for building and installing HDF5 on various
+platforms.
+
+## USING files
+
+These files document how to build HDF5 applications with an installed HDF5
+library.
diff --git a/release_docs/RELEASE.txt b/release_docs/RELEASE.txt
index c8637f0..b4d8cb2 100644
--- a/release_docs/RELEASE.txt
+++ b/release_docs/RELEASE.txt
@@ -21,7 +21,7 @@ The official HDF5 releases can be obtained from:
https://www.hdfgroup.org/downloads/hdf5/
-Changes from Release to Release and New Features in the HDF5-1.13.x release series
+Changes from Release to Release and New Features in the HDF5-1.16.x release series
can be found at:
https://portal.hdfgroup.org/display/HDF5/Release+Specific+Information
@@ -36,7 +36,7 @@ CONTENTS
- New Features
- Support for new platforms and languages
-- Bug Fixes since HDF5-1.13.3
+- Bug Fixes since HDF5-1.14.0
- Platforms Tested
- Known Problems
- CMake vs. Autotools installations
@@ -72,45 +72,6 @@ New Features
(ADB - 2023/02/21)
- - Removal of MPE support
-
- The ability to build with MPE instrumentation has been removed along with
- the following configure options:
-
- Autotools:
- --with-mpe=
-
- CMake has never supported building with MPE support.
-
- (DER - 2022/11/08)
-
- - Removal of dmalloc support
-
- The ability to build with dmalloc support has been removed along with
- the following configure options:
-
- Autotools:
- --with-dmalloc=
-
- CMake:
- HDF5_ENABLE_USING_DMALLOC
-
- (DER - 2022/11/08)
-
- - Removal of memory allocation sanity checks configure options
-
- With the removal of the memory allocation sanity checks feature, the
- following configure options are no longer necessary and have been
- removed:
-
- Autotools:
- --enable-memory-alloc-sanity-check
-
- CMake:
- HDF5_MEMORY_ALLOC_SANITY_CHECK
- HDF5_ENABLE_MEMORY_STATS
-
- (DER - 2022/11/03)
Library:
--------
@@ -126,66 +87,6 @@ New Features
(JTH - 2023/02/22)
- - Overhauled the Virtual Object Layer (VOL)
-
- The virtual object layer (VOL) was added in HDF5 1.12.0 but the initial
- implementation required API-breaking changes to better support optional
- operations and pass-through VOL connectors. The original VOL API is
- now considered deprecated and VOL users and connector authors should
- target the 1.14 VOL API.
-
- The specific changes are too extensive to document in a release note, so
- VOL users and connector authors should consult the updated VOL connector
- author's guide and the 1.12-1.14 VOL migration guide.
-
- (DER - 2022/12/28)
-
- - H5VLquery_optional() signature change
-
- The last parameter of this API call has changed from a pointer to hbool_t
- to a pointer to uint64_t. Due to the changes in how optional operations
- are handled in the 1.14 VOL API, we cannot make the old API call work
- with the new scheme, so there is no API compatibility macro for it.
-
- (DER - 2022/12/28)
-
- - H5I_free_t callback signature change
-
- In order to support asynchronous operations and future IDs, the signature
- of the H5I_free_t callback has been modified to take a second 'request'
- parameter. Due to the nature of the internal library changes, no API
- compatibility macro is available for this change.
-
- (DER - 2022/12/28)
-
- - Fix for CVE-2019-8396
-
- Malformed HDF5 files may have truncated content which does not match
- the expected size. When H5O__pline_decode() attempts to decode these it
- may read past the end of the allocated space leading to heap overflows
- as bounds checking is incomplete.
-
- The fix ensures each element is within bounds before reading.
-
- (2022/11/09 - HDFFV-10712, CVE-2019-8396, GitHub #2209)
-
- - Removal of memory allocation sanity checks feature
-
- This feature added heap canaries and statistics tracking for internal
- library memory operations. Unfortunately, the heap canaries caused
- problems when library memory operations were mixed with standard C
- library memory operations (such as in the filter pipeline, where
- buffers may have to be reallocated). Since any platform with a C
- compiler also usually has much more sophisticated memory sanity
- checking tools than the HDF5 library provided (e.g., valgrind), we
- have decided to to remove the feature entirely.
-
- In addition to the configure changes described above, this also removes
- the following from the public API:
- H5get_alloc_stats()
- H5_alloc_stats_t
-
- (DER - 2022/11/03)
Parallel Library:
-----------------
@@ -229,11 +130,7 @@ New Features
Documentation:
--------------
- - Ported the existing VOL Connector Author Guide document to doxygen.
-
- Added new dox file, VOLConnGuide.dox.
-
- (ADB - 2022/12/20)
+ -
Support for new platforms, languages and compilers
@@ -292,128 +189,6 @@ Bug Fixes since HDF5-1.13.3 release
(JTH - 2023/02/16, GH #2433)
- - Seg fault on file close
-
- h5debug fails at file close with core dump on a file that has an
- illegal file size in its cache image. In H5F_dest(), the library
- performs all the closing operations for the file and keeps track of
- the error encountered when reading the file cache image.
- At the end of the routine, it frees the file's file structure and
- returns error. Due to the error return, the file object is not removed
- from the ID node table. This eventually causes assertion failure in
- H5VL__native_file_close() when the library finally exits and tries to
- access that file object in the table for closing.
-
- The closing routine, H5F_dest(), will not free the file structure if
- there is error, keeping a valid file structure in the ID node table.
- It will be freed later in H5VL__native_file_close() when the
- library exits and terminates the file package.
-
- (VC - 2022/12/14, HDFFV-11052, CVE-2020-10812)
-
- - Fix CVE-2018-13867 / GHSA-j8jr-chrh-qfrf
-
- Validate location (offset) of the accumulated metadata when comparing.
-
- Initially, the accumulated metadata location is initialized to HADDR_UNDEF
- - the highest available address. Bogus input files may provide a location
- or size matching this value. Comparing this address against such bogus
- values may provide false positives. Thus make sure, the value has been
- initialized or fail the comparison early and let other parts of the
- code deal with the bogus address/size.
- Note: To avoid unnecessary checks, it is assumed that if the 'dirty'
- member in the same structure is true the location is valid.
-
- (EFE - 2022/10/10 GH-2230)
-
- - Fix CVE-2018-16438 / GHSA-9xmm-cpf8-rgmx
-
- Make sure info block for external links has at least 3 bytes.
-
- According to the specification, the information block for external links
- contains 1 byte of version/flag information and two 0 terminated strings
- for the object linked to and the full path.
- Although not very useful, the minimum string length for each (with
- terminating 0) would be one byte.
- Checking this helps to avoid SEGVs triggered by bogus files.
-
- (EFE - 2022/10/09 GH-2233)
-
- - CVE-2021-46244 / GHSA-vrxh-5gxg-rmhm
-
- Compound datatypes may not have members of size 0
-
- A member size of 0 may lead to an FPE later on as reported in
- CVE-2021-46244. To avoid this, check for this as soon as the
- member is decoded.
-
- (EFE - 2022/10/05 GEH-2242)
-
-
- - Fix CVE-2021-45830 / GHSA-5h2h-fjjr-x9m2
-
- Make H5O__fsinfo_decode() more resilient to out-of-bound reads.
-
- When decoding a file space info message in H5O__fsinfo_decode() make
- sure each element to be decoded is still within the message. Malformed
- hdf5 files may have trunkated content which does not match the
- expected size. Checking this will prevent attempting to decode
- unrelated data and heap overflows. So far, only free space manager
- address data was checked before decoding.
-
- (EFE - 2022/10/05 GH-2228)
-
- - Fix CVE-2021-46242 / GHSA-x9pw-hh7v-wjpf
-
- When evicting driver info block, NULL the corresponding entry.
-
- Since H5C_expunge_entry() called (from H5AC_expunge_entry()) sets the flag
- H5C__FLUSH_INVALIDATE_FLAG, the driver info block will be freed. NULLing
- the pointer in f->shared->drvinfo will prevent use-after-free when it is
- used in other functions (like H5F__dest()) - as other places will check
- whether the pointer is initialized before using its value.
-
- (EFE - 2022/09/29 GH-2254)
-
- - Fix CVE-2021-45833 / GHSA-x57p-jwp6-4v79
-
- Report error if dimensions of chunked storage in data layout < 2
-
- For Data Layout Messages version 1 & 2 the specification state
- that the value stored in the data field is 1 greater than the
- number of dimensions in the dataspace. For version 3 this is
- not explicitly stated but the implementation suggests it to be
- the case.
- Thus the set value needs to be at least 2. For dimensionality
- < 2 an out-of-bounds access occurs.
-
- (EFE - 2022/09/28 GH-2240)
-
- - Fix CVE-2018-14031 / GHSA-2xc7-724c-r36j
-
- Parent of enum datatype message must have the same size as the
- enum datatype message itself.
- Functions accessing the enumeration values use the size of the
- enumeration datatype to determine the size of each element and
- how much data to copy.
- Thus the size of the enumeration and its parent need to match.
- Check in H5O_dtype_decode_helper() to avoid unpleasant surprises
- later.
-
- (EFE - 2022/09/28 GH-2236)
-
- - Fix CVE-2018-17439 / GHSA-vcxv-vp43-rch7
-
- H5IMget_image_info(): Make sure to not exceed local array size
-
- Malformed hdf5 files may provide more dimensions than the array dim[] in
- H5IMget_image_info() is able to hold. Check number of elements first by calling
- H5Sget_simple_extent_dims() with NULL for both 'dims' and 'maxdims' arguments.
- This will cause the function to return only the number of dimensions.
- The fix addresses a stack overflow on write.
-
- (EFE - 2022/09/27 HDFFV-10589, GH-2226)
-
Java Library
------------
@@ -435,49 +210,10 @@ Bug Fixes since HDF5-1.13.3 release
(ADB - 2023/02/16 GH-1546,GH-2259)
- - Remove Javadoc generation
-
- The use of doxygen now supersedes the requirement to build javadocs. We do not
- have the resources to continue to support two documentation methods and have
- chosen doxygen as our standard.
-
- (ADB - 2022/12/19)
-
- - Change the default for building the high-level tools
-
- The gif2hdf5 and hdf2gif high-level tools are deprecated and will be removed
- in a future release. The default build setting for them have been changed from enabled
- to disabled. A user can enable the build of these tools if needed.
- autotools: --enable-hlgiftools
- cmake: HDF5_BUILD_HL_GIF_TOOLS=ON
-
- (ADB - 2022/12/16)
-
- - Change the settings of the *pc files to use the correct format
-
- The pkg-config files generated by CMake uses incorrect syntax for the 'Requires'
- settings. Changing the set to use 'lib-name = version' instead 'lib-name-version'
- fixes the issue
-
- (ADB - 2022/12/06 HDFFV-11355)
-
- - Move MPI libraries link from PRIVATE to PUBLIC
-
- The install dependencies were not including the need for MPI libraries when
- an application or library was built with the C library. Also updated the
- CMake target link command to use the newer style MPI::MPI_C link variable.
-
- (ADB - 2022/10/27)
-
Tools
-----
- - Fix h5repack to only print output when verbose option is selected
-
- When timing option was added to h5repack, the check for verbose was
- incorrectly implemented.
-
- (ADB - 2022/12/02, GH #2270)
+ -
Performance