diff options
| -rw-r--r-- | README.txt | 90 | ||||
| -rwxr-xr-x | bin/release | 22 | ||||
| -rw-r--r-- | release_docs/HISTORY-1_10.txt | 1257 | ||||
| -rw-r--r-- | release_docs/INSTALL | 335 | ||||
| -rw-r--r-- | release_docs/INSTALL_parallel | 16 | ||||
| -rw-r--r-- | release_docs/RELEASE.txt | 927 |
6 files changed, 1461 insertions, 1186 deletions
@@ -1,38 +1,80 @@ HDF5 version 1.10.3-snap0 currently under development + +------------------------------------------------------------------------------ Please refer to the release_docs/INSTALL file for installation instructions. ------------------------------------------------------------------------------ +THE HDF GROUP +--------------- + +The HDF Group is the developer of HDF5®, a high-performance software library and +data format that has been adopted across multiple industries and has become a +de facto standard in scientific and research communities. + +More information about The HDF Group, the HDF5 Community and the HDF5 software +project, tools and services can be found at the Group's website. + + https://www.hdfgroup.org/ + + +DOCUMENTATION +------------- This release is fully functional for the API described in the documentation. -See the RELEASE.txt file in the release_docs/ directory for information -specific to this release of the library. Several INSTALL* files can also be -found in the release_docs/ directory: INSTALL contains instructions for -compiling and installing the library; INSTALL_parallel contains instructions -for installing the parallel version of the library; similarly-named files -contain instructions for several environments on MS Windows systems. + https://portal.hdfgroup.org/display/HDF5/The+HDF5+API + +Full Documentation and Programming Resources for this release can be found at + https://portal.hdfgroup.org/display/HDF5 + +See the RELEASE.txt file in the release_docs/ directory for information specific +to the features and updates included in this release of the library. + +Several more files are located within the release_docs/ directory with specific +details for several common platforms and configurations. + + INSTALL - Start Here. General instructions for compiling and installing the library + INSTALL_CMAKE - instructions for building with CMake (Kitware.com) + INSTALL_parallel - instructions for building and configuring Parallel HDF5 + INSTALL_Windows and INSTALL_Cygwin - MS Windows installations. + + + +HELP AND SUPPORT +---------------- +Information regarding Help Desk and Support services is available at + + https://portal.hdfgroup.org/display/support/The+HDF+Help+Desk + + -Documentation for this release can be found at the following URL: - http://www.hdfgroup.org/HDF5/doc/. +FORUM and NEWS +-------------- +The following public forums are provided for public announcements and discussions +of interest to the general HDF5 Community. -The following mailing lists are currently set up for HDF5 Library users: + Homepage of the Forum + https://forum.hdfgroup.org - news - For announcements of HDF5 related developments, - not a discussion list. + News and Announcement + https://forum.hdfgroup.org/c/news-and-announcements-from-the-hdf-group - hdf-forum - For general discussion of the HDF5 library with - other users. + HDF5 and HDF4 Topics + https://forum.hdfgroup.org/c/hdf5 + +These forums are provided as an open and public service for searching and reading. +Posting requires completing a simple registration and allows one to join in the +conversation. Please read the following instructions pertaining to the Forum's +use and configuration + https://forum.hdfgroup.org/t/quickstart-guide-welcome-to-the-new-hdf-forum -To subscribe to a list, send mail to "<list>-subscribe@lists.hdfgroup.org". -where <list> is the name of the list. For example, send a request -to subscribe to the 'news' mail list to the following address: - news-subscribe@lists.hdfgroup.org -Messages sent to the list should be addressed to "<list>@lists.hdfgroup.org". +SNAPSHOTS, PREVIOUS RELEASES AND SOURCE CODE +-------------------------------------------- +Periodically development code snapshots are provided at the following URL: + https://gamma.hdfgroup.org/ftp/pub/outgoing/hdf5/snapshots/ -Periodic code snapshots are provided at the following URL: - ftp://ftp.hdfgroup.uiuc.edu/pub/outgoing/hdf5/snapshots -Please read the README.txt file in that directory before working with a -library snapshot. +Source packages for current and previous releases are located at: + https://portal.hdfgroup.org/display/support/Downloads -The HDF5 website is located at http://hdfgroup.org/HDF5/ +Development code is available at our BitBucket Server: + https://bitbucket.hdfgroup.org/projects/HDFFV/repos/hdf5/browse -Bugs should be reported to help@hdfgroup.org. diff --git a/bin/release b/bin/release index 040711a..3f75a00 100755 --- a/bin/release +++ b/bin/release @@ -213,17 +213,18 @@ tar2cmakezip() return 1 fi - # step 2: add batch file for building CMake on window - cp /mnt/scr1/pre-release/hdf5/CMake/build-VS2013-32.bat $cmziptmpdir - cp /mnt/scr1/pre-release/hdf5/CMake/build-VS2013-64.bat $cmziptmpdir - cp /mnt/scr1/pre-release/hdf5/CMake/build-VS2015-32.bat $cmziptmpdir - cp /mnt/scr1/pre-release/hdf5/CMake/build-VS2015-64.bat $cmziptmpdir - cp /mnt/scr1/pre-release/hdf5/CMake/build-VS2017-32.bat $cmziptmpdir - cp /mnt/scr1/pre-release/hdf5/CMake/build-VS2017-64.bat $cmziptmpdir + # step 2: add batch files for building CMake on windows + cp /mnt/scr1/pre-release/hdf5/CMake/HDF5_1_10/build-VS2013-32.bat $cmziptmpdir + cp /mnt/scr1/pre-release/hdf5/CMake/HDF5_1_10/build-VS2013-64.bat $cmziptmpdir + cp /mnt/scr1/pre-release/hdf5/CMake/HDF5_1_10/build-VS2015-32.bat $cmziptmpdir + cp /mnt/scr1/pre-release/hdf5/CMake/HDF5_1_10/build-VS2015-64.bat $cmziptmpdir + cp /mnt/scr1/pre-release/hdf5/CMake/HDF5_1_10/build-VS2017-32.bat $cmziptmpdir + cp /mnt/scr1/pre-release/hdf5/CMake/HDF5_1_10/build-VS2017-64.bat $cmziptmpdir # step 3: add SZIP.tar.gz, ZLib.tar.gz and cmake files cp /mnt/scr1/pre-release/hdf5/CMake/SZip.tar.gz $cmziptmpdir cp /mnt/scr1/pre-release/hdf5/CMake/ZLib.tar.gz $cmziptmpdir + cp /mnt/scr1/pre-release/hdf5/CMake/HDF5Examples-1.10.7-Source.tar.gz $cmziptmpdir cp $cmziptmpdir/$version/config/cmake/scripts/CTestScript.cmake $cmziptmpdir cp $cmziptmpdir/$version/config/cmake/scripts/HDF5config.cmake $cmziptmpdir cp $cmziptmpdir/$version/config/cmake/scripts/HDF5options.cmake $cmziptmpdir @@ -240,6 +241,10 @@ tar2cmakezip() unix2dos -q -k $inf; \ fi\ done + + + mkdir $cmziptmpdir/CMake-$HDF5_VERS + mv $cmziptmpdir/* $cmziptmpdir/CMake-$HDF5_VERS # step 3: make zipball # -9 maximum compression # -y Store symbolic links as such in the zip archive @@ -316,9 +321,12 @@ tar2cmaketgz() # step 3: add SZIP.tar.gz, ZLib.tar.gz and cmake files cp /mnt/scr1/pre-release/hdf5/CMake/SZip.tar.gz $cmgztmpdir cp /mnt/scr1/pre-release/hdf5/CMake/ZLib.tar.gz $cmgztmpdir + cp /mnt/scr1/pre-release/hdf5/CMake/HDF5Examples-1.10.7-Source.tar.gz $cmgztmpdir cp $cmgztmpdir/$version/config/cmake/scripts/CTestScript.cmake $cmgztmpdir cp $cmgztmpdir/$version/config/cmake/scripts/HDF5config.cmake $cmgztmpdir cp $cmgztmpdir/$version/config/cmake/scripts/HDF5options.cmake $cmgztmpdir + mkdir $cmgztmpdir/CMake-$HDF5_VERS + mv $cmgztmpdir/* $cmgztmpdir/CMake-$HDF5_VERS tar czf $DEST/CMake-$HDF5_VERS.tar.gz -C $cmgztmpdir . || exit 1 # cleanup diff --git a/release_docs/HISTORY-1_10.txt b/release_docs/HISTORY-1_10.txt index 52eb273..62e3f08 100644 --- a/release_docs/HISTORY-1_10.txt +++ b/release_docs/HISTORY-1_10.txt @@ -3,12 +3,1269 @@ HDF5 History This file contains development history of the HDF5 1.10 branch +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.] +%%%%1.10.2%%%% + +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 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 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. 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) + + - 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 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 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 unecessary 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 diff --git a/release_docs/INSTALL b/release_docs/INSTALL index 3709a58..baad559 100644 --- a/release_docs/INSTALL +++ b/release_docs/INSTALL @@ -3,10 +3,11 @@ Instructions for the Installation of HDF5 Software ================================================== This file provides instructions for installing the HDF5 software. -If you have any problems with the installation, please see The HDF Group's -support page at the following location: - http://www.hdfgroup.org/services/support.html +For help with installing, questions can be posted to the HDF Forum or sent to the HDF Helpdesk: + + HDF Forum: https://forum.hdfgroup.org/ + HDF Helpdesk: https://portal.hdfgroup.org/display/support/The+HDF+Help+Desk CONTENTS -------- @@ -31,59 +32,34 @@ CONTENTS 4.3. Configuring 4.3.1. Specifying the installation directories 4.3.2. Using an alternate C compiler - 4.3.3. Configuring for 64-bit support - 4.3.4. Additional compilation flags - 4.3.5. Compiling HDF5 wrapper libraries - 4.3.6. Specifying other programs - 4.3.7. Specifying other libraries and headers - 4.3.8. Static versus shared linking - 4.3.9. Optimization versus symbolic debugging - 4.3.10. Parallel versus serial library - 4.3.11. Threadsafe capability - 4.3.12. Backward compatibility + 4.3.3. Additional compilation flags + 4.3.4. Compiling HDF5 wrapper libraries + 4.3.5. Specifying other programs + 4.3.6. Specifying other libraries and headers + 4.3.7. Static versus shared linking + 4.3.8. Optimization versus symbolic debugging + 4.3.9. Parallel versus serial library + 4.3.10. Threadsafe capability + 4.3.11. Backward compatibility 4.4. Building 4.5. Testing 4.6. Installing HDF5 5. Using the Library - 6. Support - - A. Warnings about compilers - A.1. GNU (Intel platforms) - A.2. DEC - A.3. SGI (Irix64 6.2) - A.4. Windows/NT - - B. Large (>2GB) versus small (<2GB) file capability - - C. Building and testing with other compilers - C.1. Building and testing with Intel compilers - C.2. Building and testing with PGI compilers ***************************************************************************** 1. Obtaining HDF5 The latest supported public release of HDF5 is available from - ftp://ftp.hdfgroup.org/HDF5/current/src. For Unix and UNIX-like + https://www.hdfgroup.org/downloads/hdf5/. For Unix and UNIX-like platforms, it is available in tar format compressed with gzip. For Microsoft Windows, it is in ZIP format. - The HDF team also makes snapshots of the source code available on - a regular basis. These snapshots are unsupported (that is, the - HDF team will not release a bug-fix on a particular snapshot; - rather any bug fixes will be rolled into the next snapshot). - Furthermore, the snapshots have only been tested on a few - machines and may not test correctly for parallel applications. - Snapshots, in a limited number of formats, can be found on THG's - development FTP server: - - ftp://ftp.hdfgroup.uiuc.edu/pub/outgoing/hdf5/snapshots - 2. Quick installation For those who don't like to read ;-) the following steps can be used - to configure, build, test, and install the HDF5 Library, header files, + to configure, build, test, and install the HDF5 library, header files, and support programs. For example, to install HDF5 version X.Y.Z at location /usr/local/hdf5, use the following steps. @@ -125,28 +101,30 @@ CONTENTS 3. HDF5 dependencies 3.1. Zlib - The HDF5 Library includes a predefined compression filter that + The HDF5 library includes a predefined compression filter that uses the "deflate" method for chunked datasets. If zlib-1.1.2 or later is found, HDF5 will use it. Otherwise, HDF5's predefined compression method will degenerate to a no-op; the compression filter will succeed but the data will not be compressed. 3.2. Szip (optional) - The HDF5 Library includes a predefined compression filter that + The HDF5 library includes a predefined compression filter that uses the extended-Rice lossless compression algorithm for chunked - datasets. For more information about Szip compression and license - terms, see http://hdfgroup.org/doc_resource/SZIP/. + datasets. For information on Szip compression, license terms, + and obtaining the Szip source code, see: + + https://portal.hdfgroup.org/display/HDF5/Szip+Compression+in+HDF+Products - The Szip source code can be obtained from the HDF5 Download page - http://www.hdfgroup.org/HDF5/release/obtain5.html#extlibs. Building - instructions are available with the Szip source code. + Building instructions are available with the Szip source code. The HDF Group does not distribute separate Szip precompiled libraries, - but the HDF5 binaries available from - http://www.hdfgroup.org/HDF5/release/obtain5.html include - the Szip encoder enabled binary for the corresponding platform. + but the HDF5 pre-built binaries provided on The HDF Group download page + include the Szip library with the encoder enabled. These can be found + here: - To configure the HDF5 Library with the Szip compression filter, use + https://www.hdfgroup.org/downloads/hdf5/ + + To configure the HDF5 library with the Szip compression filter, use the '--with-szlib=/PATH_TO_SZIP' flag. For more information, see section 4.3.7, "Specifying other libraries and headers." @@ -204,20 +182,6 @@ CONTENTS $ cd build-fortran $ ../hdf5-X.Y.Z/configure --enable-fortran ... - Unfortunately, this does not work on recent Irix platforms (6.5? - and later) because that `make' does not understand the VPATH variable. - However, HDF5 also supports Irix `pmake' which has a .PATH target - which serves a similar purpose. Here's what the Irix man pages say - about VPATH, the facility used by HDF5 makefiles for this feature: - - The VPATH facility is a derivation of the undocumented - VPATH feature in the System V Release 3 version of make. - System V Release 4 has a new VPATH implementation, much - like the pmake(1) .PATH feature. This new feature is also - undocumented in the standard System V Release 4 manual - pages. For this reason it is not available in the IRIX - version of make. The VPATH facility should not be used - with the new parallel make option. 4.3. Configuring HDF5 uses the GNU autoconf system for configuration, which @@ -243,7 +207,7 @@ CONTENTS 4.3.1. Specifying the installation directories The default installation location is the HDF5 directory created in the build directory. Typing `make install' will install the HDF5 - Library, header files, examples, and support programs in hdf5/lib, + library, header files, examples, and support programs in hdf5/lib, hdf5/include, hdf5/doc/hdf5/examples, and hdf5/bin. To use a path other than hdf5, specify the path with the `--prefix=PATH' switch: @@ -275,45 +239,24 @@ CONTENTS $ CC=/usr/local/mpi/bin/mpicc ./configure -4.3.3. Configuring for 64-bit support - Several machine architectures support 32-bit or 64-bit binaries. - The options below describe how to enable support for different options. - - On Irix64, the default compiler is `cc'. To use an alternate compiler, - specify it with the CC variable: - - $ CC='cc -n32' ./configure - - Similarly, users compiling on a Solaris machine and desiring to - build the distribution with 64-bit support should specify the - correct flags with the CC variable: - - $ CC='cc -m64' ./configure - - To configure AIX 64-bit support including the Fortran and C++ APIs, - (Note: need to set $AR to 'ar -X 64'.) - Serial: - $ CFLAGS=-q64 FCFLAGS=-q64 CXXFLAGS=-q64 AR='ar -X 64'\ - ./configure --enable-fortran - Parallel: (C++ not supported with parallel) - $ CFLAGS=-q64 FCFLAGS=-q64 AR='ar -X 64'\ - ./configure --enable-fortran -4.3.4. Additional compilation flags - If addtional flags must be passed to the compilation commands, +4.3.3. Additional compilation flags + If additional flags must be passed to the compilation commands, specify those flags with the CFLAGS variable. For instance, to enable symbolic debugging of a production version of HDF5, one might say: $ CFLAGS=-g ./configure --enable-build-mode=production -4.3.5. Compiling HDF5 wrapper libraries - One can optionally build the Fortran and/or C++ interfaces to the - HDF5 C library. By default, both options are disabled. To build - them, specify `--enable-fortran' and `--enable-cxx', respectively. +4.3.4. Compiling HDF5 wrapper libraries + One can optionally build the Fortran, C++, and Java interfaces to + the HDF5 C library. By default, these options are disabled. To build + them, specify '--enable-fortran', '--enable-cxx', or '--enable-java', + respectively. $ ./configure --enable-fortran $ ./configure --enable-cxx + $ ./configure --enable-java Configuration will halt if a working Fortran 90 or 95 compiler or C++ compiler is not found. Currently, the Fortran configure tests @@ -322,15 +265,8 @@ CONTENTS $ FC=/usr/local/bin/g95 ./configure --enable-fortran - Note: The Fortran and C++ interfaces are not supported on all the - platforms the main HDF5 Library supports. Also, the Fortran - interface supports parallel HDF5 while the C++ interface does - not. - Note: See sections 4.7 and 4.8 for building the Fortran library with - Intel or PGI compilers. - -4.3.6. Specifying other programs +4.3.5. Specifying other programs The build system has been tuned for use with GNU make but also works with other versions of make. If the `make' command runs a non-GNU version but a GNU version is available under a different @@ -346,7 +282,7 @@ CONTENTS the `ar' and `ranlib' (or `:') commands to override values detected by configure. - The HDF5 Library, include files, and utilities are installed + The HDF5 library, include files, and utilities are installed during `make install' (described below) with a BSD-compatible install program detected automatically by configure. If none is found, the shell script bin/install-sh is used. Configure does not @@ -364,7 +300,7 @@ CONTENTS because the HDF5 makefiles also use the install program to change file ownership and/or access permissions. -4.3.7. Specifying other libraries and headers +4.3.6. Specifying other libraries and headers Configure searches the standard places (those places known by the systems compiler) for include files and header files. However, additional directories can be specified by using the CPPFLAGS @@ -389,12 +325,12 @@ CONTENTS ./configure HDF5 includes Szip as a predefined compression method (see 3.2). - To enable Szip compression, the HDF5 Library must be configured - and built using the Szip Library: + To enable Szip compression, the HDF5 library must be configured + and built using the Szip library: $ ./configure --with-szlib=/Szip_Install_Directory -4.3.8. Static versus shared linking +4.3.7. Static versus shared linking The build process will create static libraries on all systems and shared libraries on systems that support dynamic linking to a sufficient degree. Either form of the library may be suppressed by @@ -410,7 +346,7 @@ CONTENTS $ ./configure --enable-static-exec -4.3.9. Optimization versus symbolic debugging +4.3.8. Optimization versus symbolic debugging The library can be compiled to provide symbolic debugging support so it can be debugged with gdb, dbx, ddd, etc., or it can be compiled with various optimizations. To compile for symbolic @@ -430,9 +366,7 @@ CONTENTS (such as type conversion execution times and extensive invariant condition checking). To enable this debugging, supply a comma-separated list of package names to the `--enable-internal-debug' - switch. See "Debugging HDF5 Applications" for a list of package names: - - http://www.hdfgroup.org/HDF5/doc/H5.user/Debugging.html + switch. Debugging can be disabled by saying `--disable-internal-debug'. The default debugging level for snapshots is a subset of the @@ -448,39 +382,39 @@ CONTENTS arguments, and the return values. To enable or disable the ability to trace the API say `--enable-trace' (the default for snapthots) or `--disable-trace' (the default for public releases). - The tracing must also be enabled at runtime to see any output - (see "Debugging HDF5 Applications," reference above). + The tracing must also be enabled at runtime to see any output. -4.3.10. Parallel versus serial library - The HDF5 Library can be configured to use MPI and MPI-IO for +4.3.9. Parallel versus serial library + The HDF5 library can be configured to use MPI and MPI-IO for parallelism on a distributed multi-processor system. Read the - file INSTALL_parallel for detailed explanations. + file INSTALL_parallel for detailed information. -4.3.11. Threadsafe capability - The HDF5 Library can be configured to be thread-safe (on a very +4.3.10. Threadsafe capability + The HDF5 library can be configured to be thread-safe (on a very large scale) with the `--enable-threadsafe' flag to the configure script. Some platforms may also require the '-with-pthread=INC,LIB' (or '--with-pthread=DIR') flag to the configure script. - For further details, see "HDF5 Thread Safe Library": + For further information, see: + + https://portal.hdfgroup.org/display/knowledge/Questions+about+thread-safety+and+concurrent+access - http://www.hdfgroup.org/HDF5/doc/TechNotes/ThreadSafeLibrary.html -4.3.12. Backward compatibility - The 1.10 version of the HDF5 Library can be configured to operate +4.3.11. Backward compatibility + The 1.10 version of the HDF5 library can be configured to operate identically to the v1.8 library with the --with-default-api-version=v18 configure flag, or identically to the v1.6 library with the --with-default-api-version=v16 configure flag. This allows existing code to be compiled with the v1.10 library without requiring immediate changes to the application - source code. For addtional configuration options and other details, - see "API Compatibility Macros in HDF5": + source code. For additional configuration options and other details, + see "API Compatibility Macros": - https://support.hdfgroup.org/HDF5/doc/RM/APICompatMacros.html + https://portal.hdfgroup.org/display/HDF5/API+Compatibility+Macros 4.4. Building The library, confidence tests, and programs can be built by - saying just: + specifying: $ make @@ -497,7 +431,7 @@ CONTENTS 4.5. Testing HDF5 comes with various test suites, all of which can be run by - saying + specifying: $ make check @@ -526,13 +460,13 @@ CONTENTS longer test, set HDF5TestExpress to 0. 1 is the default. 4.6. Installing HDF5 - The HDF5 Library, include files, and support programs can be - installed in a (semi-)public place by saying `make install'. The - files are installed under the directory specified with - `--prefix=DIR' (default is 'hdf5') in directories named `lib', - `include', and `bin'. The directories, if not existing, will be - created automatically, provided the mkdir command supports the -p - option. + The HDF5 library, include files, and support programs can be + installed by specifying `make install'. The files are installed under the + directory specified with `--prefix=DIR' (or if not specified, in 'hdf5' + in the top directory of the HDF5 source code). They will be + placed in directories named `lib', `include', and `bin'. The directories, + if not existing, will be created automatically, provided the mkdir command + supports the -p option. If `make install' fails because the install command at your site somehow fails, you may use the install-sh that comes with the @@ -589,134 +523,15 @@ CONTENTS 5. Using the Library - Please see the "HDF5 User's Guide" and the "HDF5 Reference Manual": - - http://www.hdfgroup.org/HDF5/doc/ - - Most programs will include <hdf5.h> and link with -lhdf5. - Additional libraries may also be necessary depending on whether - support for compression, etc., was compiled into the HDF5 Library. - - A summary of the HDF5 installation can be found in the - libhdf5.settings file in the same directory as the static and/or - shared HDF5 Libraries. - - -6. Support - Support is described in the README file. - - -***************************************************************************** - APPENDIX -***************************************************************************** - -A. Warnings about compilers - Output from the following compilers should be extremely suspected - when used to compile the HDF5 Library, especially if optimizations are - enabled. In all cases, HDF5 attempts to work around the compiler bugs. - -A.1. GNU (Intel platforms) - Versions before 2.8.1 have serious problems allocating registers - when functions contain operations on `long long' datatypes. - -A.2. COMPAQ/DEC - The V5.2-038 compiler (and possibly others) occasionally - generates incorrect code for memcpy() calls when optimizations - are enabled, resulting in unaligned access faults. HDF5 works - around the problem by casting the second argument to `char *'. - The Fortran module (5.4.1a) fails in compiling some Fortran - programs. Use 5.5.0 or higher. - -A.3. SGI (Irix64 6.2) - The Mongoose 7.00 compiler has serious optimization bugs and - should be upgraded to MIPSpro 7.2.1.2m. Patches are available - from SGI. - -A.4. Windows/NT - The Microsoft Win32 5.0 compiler is unable to cast unsigned long - long values to doubles. HDF5 works around this bug by first - casting to signed long long and then to double. - - A link warning: defaultlib "LIBC" conflicts with use of other libs - appears for debug version of VC++ 6.0. This warning will not affect - building and testing HDF5 Libraries. - - -B. Large (>2GB) versus small (<2GB) file capability - In order to read or write files that could potentially be larger - than 2GB, it is necessary to use the non-ANSI `long long' data - type on some platforms. However, some compilers (e.g., GNU gcc - versions before 2.8.1 on Intel platforms) are unable to produce - correct machine code for this datatype. - - -C. Building and testing with other compilers -C.1. Building and testing with Intel compilers - When Intel compilers are used (icc or ecc), you will need to modify - the generated "libtool" program after configuration is finished. - On or around line 104 of the libtool file, there are lines which - look like: - - # How to pass a linker flag through the compiler. - wl="" - - Change these lines to this: - - # How to pass a linker flag through the compiler. - wl="-Wl," - - UPDATE: This is now done automatically by the configure script. - However, if you still experience a problem, you may want to check this - line in the libtool file and make sure that it has the correct value. - - * To build the Fortran library using Intel compiler on Linux 2.4, - one has to perform the following steps: - x Use the -fpp -DDEC$=DEC_ -DMS$=MS_ compiler flags to disable - DEC and MS compiler directives in source files in the fortran/src, - fortran/test, and fortran/examples directories. - E.g., setenv F9X 'ifc -fpp -DDEC$=DEC_ -DMS$=MS_' - Do not use double quotes since $ is interpreted in them. - - x If Version 6.0 of Fortran compiler is used, the build fails in - the fortran/test directory and then in the fortran/examples - directory. To proceed, edit the work.pcl files in those - directories to contain two lines: - - work.pc - ../src/work.pc - - x Do the same in the fortran/examples directory. - - x A problem with work.pc files was resolved for the newest version - of the compiler (7.0). - - * To build the Fortran library on IA32, follow the steps described - above, except that the DEC and MS compiler directives should be - removed manually or use a patch from HDF FTP server: - - ftp://ftp.hdfgroup.org/HDF5/current/ - - -C.2. Building and testing with PGI compilers - When PGI C and C++ compilers are used (pgcc or pgCC), you will need to - modify the generated "libtool" program after configuration is finished. - On or around line 104 of the libtool file, there are lines which - look like this: - - # How to pass a linker flag through the compiler. - wl="" + + For information on using HDF5 see the documentation, tutorials and examples + found here: - Change these lines to this: + https://portal.hdfgroup.org/display/HDF5/HDF5 - # How to pass a linker flag through the compiler. - wl="-Wl," + A summary of the features included in the built HDF5 installation can be found + in the libhdf5.settings file in the same directory as the static and/or + shared HDF5 libraries. - UPDATE: This is now done automatically by the configure script. However, - if you still experience a problem, you may want to check this line in - the libtool file and make sure that it has the correct value. - To build the HDF5 C++ Library with pgCC (version 4.0 and later), set - the environment variable CXX to "pgCC -tlocal" - setenv CXX "pgCC -tlocal" - before running the configure script. diff --git a/release_docs/INSTALL_parallel b/release_docs/INSTALL_parallel index 5a8b603..f32fffc 100644 --- a/release_docs/INSTALL_parallel +++ b/release_docs/INSTALL_parallel @@ -40,9 +40,11 @@ and the parallel file system. 1.2. Further Help ----------------- -If you still have difficulties installing PHDF5 in your system, please send -mail to - help@hdfgroup.org + +For help with installing, questions can be posted to the HDF Forum or sent to the HDF Helpdesk: + + HDF Forum: https://forum.hdfgroup.org/ + HDF Helpdesk: https://portal.hdfgroup.org/display/support/The+HDF+Help+Desk In your mail, please include the output of "uname -a". If you have run the "configure" command, attach the output of the command and the content of @@ -87,12 +89,8 @@ The following steps are for building HDF5 for the Hopper compute nodes. They would probably work for other Cray systems but have not been verified. -Obtain a copy from the HDF ftp server: -http://www.hdfgroup.org/ftp/HDF5/current/src/ -(link might change, so always double check the HDF group website). - -$ wget http://www.hdfgroup.org/ftp/HDF5/current/src/hdf5-x.x.x.tar.gz -unpack the tarball +Obtain the HDF5 source code: + https://portal.hdfgroup.org/display/support/Downloads The entire build process should be done on a MOM node in an interactive allocation and on a file system accessible by all compute nodes. Request an interactive allocation with qsub: 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. |