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-rw-r--r--release_docs/RELEASE.txt927
1 files changed, 41 insertions, 886 deletions
diff --git a/release_docs/RELEASE.txt b/release_docs/RELEASE.txt
index 10c2978..ea8abb2 100644
--- a/release_docs/RELEASE.txt
+++ b/release_docs/RELEASE.txt
@@ -42,7 +42,7 @@ CONTENTS
- New Features
- Support for new platforms and languages
-- Bug Fixes since HDF5-1.10.1
+- Bug Fixes since HDF5-1.10.2
- Supported Platforms
- Tested Configuration Features Summary
- More Tested Platforms
@@ -54,320 +54,36 @@ 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)
-
- - 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.
-
- (HDFFV-9937, DER, 2017/05/31)
-
- - -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).
+ -
- (HDFFV-10226, DER, 2017/05/31)
Library:
--------
- - Add 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.
-
- Add 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)
-
- - Add 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 located 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.
-
- (HDFFV-10215, DER, 2017/05/31)
-
-
- - 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.
-
- (HDFFV-10214, DER, 2017/05/31)
-
- - The H5I_REFERENCE value in the H5I_type_t enum (defined in H5Ipublic.h)
- has been marked as deprectated.
-
- 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 branches.
-
- (HDFFV-10252, DER, 2017/04/05)
+ -
Parallel Library:
-----------------
- - Optimize 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. specifiying 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 independant collection of processes.
-
- (RAW - 2017/10/10, HDFFV-10294)
-
-
- - Large 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)
+ -
+
Fortran Library:
----------------
-
+
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 added for the following 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 deprectated.
-
- 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 branches.
-
- See the C library section, above, for further information.
-
- (HDFFV-10252, DER, 2017/04/05)
-
+ -
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)
+ -
High-Level APIs:
---------------
@@ -394,381 +110,11 @@ Bug Fixes since HDF5-1.10.1 release
Library
-------
- - The data read after a direct chunk write to a chunked dataset
- 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.
-
- Pass the dataset pointer to the insert callback for the chunk
- index in H5D__chunk_direct_write().
-
- (VC - 2018/03/20, HDFFV-10425)
-
- - Add public routine H5DOread_chunk to the high-level C library
-
- As we have H5DOwrite_chunk() to write an entire chunk to the file
- directly, the customer requested to add this public routine to
- read an entire chunk from the file directly.
-
- This public routine was added based on a patch from GE Healthcare.
-
- (VC - 2017/05/19, HDFFV-9934)
-
- - Freeing of object header in H5Ocache.c
-
- It was discovered that the object header was not released properly
- when the checksum verification failed and a re-load of the object
- header was needed.
-
- Free 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)
-
- - 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)
-
- - Utility function can not handle lowercase Windows drive letters
-
- Added call to toupper function for drive letter.
-
- (ADB - 2017/12/18, HDFFV-10307)
-
- - Fix H5Sencode() bug when the number of elements selected is > 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 because 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 > 32 bits when needed.
- See details in the RFC: H5Sencode/H5Secode Format Change.
-
- (VC - 2017/11/28, HDFFV-9947)
-
- - 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 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, 2017/08/30)
-
- - Fixes for paged aggregation
-
- 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)
-
- - Fixes for paged aggregation
-
- Changes made based on RFC review comments:
- (1) Add maximum value for file space page size
- (2) Drop check for page end metadata threshold
- (3) Remove "can_shrink" and "shrink" callbacks for small section class
-
- (VC, 2017/06/09)
-
- - Fix 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.
-
- (HDFFV-10217, VC, 2017/07/10)
-
- - Fix 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.
-
- (HDFFV-7853, VC, 2017/07/05)
-
- - 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)
-
- - 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)
-
- - Fix for 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.
-
- 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
-------------
- - 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)
-
- - 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)
-
- - 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.
-
- (HDFFV-10247, DER, 2017/07/05)
-
- - 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).
-
- (HDFFV-10248, DER, 2017/07/05)
-
- - 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)
+ -
Performance
-------------
@@ -776,205 +122,15 @@ Bug Fixes since HDF5-1.10.1 release
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.
-
- Add an option to the tool in setting the file's stored EOA in the
- superblock to the maximum of (EOA, EOF) + increment.
- Another option is 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 more then 9 chars for int conversion.
-
- User defined filter parameter conversions would fail for integers
- 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 also 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 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
-
- Add 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:
------
- - Fixed a bug in the H5DOwrite_chunk() API call where overwriting a chunk
- with no filters caused an assert to trip (with assertions enabled /
- debug builds) or additional chunks to be inserted instead of overwriting
- the data (without assertions enabled / production builds).
-
- (HDFFV-10187, DER, 2017/05/11)
+ -
Fortran High-Level APIs:
------
@@ -990,27 +146,18 @@ Bug Fixes since HDF5-1.10.1 release
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)
+ -
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)
+ 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
@@ -1020,7 +167,7 @@ Supported Platforms
Version 4.9.3, Version 5.2.0
Intel(R) C (icc), C++ (icpc), Fortran (icc)
compilers:
- Version 15.0.3.187 Build 20150407
+ 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
@@ -1047,14 +194,6 @@ Supported Platforms
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
@@ -1063,6 +202,9 @@ Supported Platforms
64-bit gfortran GNU Fortran (GCC) 5.2.0
(osx1010dev/osx1010test) 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
=====================================
@@ -1127,22 +269,29 @@ 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
+ Version 4.9.3, 5.3.0, 6.2.0
PGI C, Fortran, C++ for 64-bit target on
x86-64;
- Version 16.10-0
+ Version 17.10-0
Intel(R) C (icc), C++ (icpc), Fortran (icc)
compilers:
- Version 15.0.3.187 (Build 20150407)
+ 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)
+ (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 15.0.3.187 (Build 20150407)
+ Version 17.0.7.098 (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
@@ -1175,6 +324,12 @@ Known Problems
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.