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diff --git a/release_docs/RELEASE.txt b/release_docs/RELEASE.txt index 0c3873b..8f3c434 100755 --- a/release_docs/RELEASE.txt +++ b/release_docs/RELEASE.txt @@ -1,15 +1,15 @@ -HDF5 version 1.10.2 released on 2018-03-29 +HDF5 version 1.10.3 released on 2018-08-21 ================================================================================ INTRODUCTION -This document describes the differences between this release and the previous -HDF5 release. It contains information on the platforms tested and known -problems in this release. For more details check the HISTORY*.txt files in the +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 +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: @@ -33,575 +33,306 @@ If you have any questions or comments, please send them to the HDF Help Desk: 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 - Known Problems +- CMake vs. Autotools installations 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. + Library + ------- + - Moved the H5DOread/write_chunk() API calls to H5Dread/write_chunk() + + The functionality of the direct chunk I/O calls in the high-level + library has been moved to the H5D package in the main library. This + will allow using those functions without building the high-level + library. The parameters and functionality of the H5D calls are + identical to the H5DO calls. + + The original H5DO high-level API calls have been retained, though + they are now just wrappers for the H5D calls. They are marked as + deprecated and are only available when the library is built with + deprecated functions. New code should use the H5D calls for this + reason. + + As a part of this work, the following symbols from H5Dpublic.h are no + longer used: + + H5D_XFER_DIRECT_CHUNK_WRITE_FLAG_NAME + H5D_XFER_DIRECT_CHUNK_WRITE_FILTERS_NAME + H5D_XFER_DIRECT_CHUNK_WRITE_OFFSET_NAME + H5D_XFER_DIRECT_CHUNK_WRITE_DATASIZE_NAME + H5D_XFER_DIRECT_CHUNK_READ_FLAG_NAME + H5D_XFER_DIRECT_CHUNK_READ_OFFSET_NAME + H5D_XFER_DIRECT_CHUNK_READ_FILTERS_NAME + + And properties with these names are no longer stored in the dataset + transfer property lists. The symbols are still defined in H5Dpublic.h, + but only when the library is built with deprecated symbols. + + (DER - 2018/05/04) + + Configuration: + ------------- + - Add missing USE_110_API_DEFAULT option. - 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. + Option USE_110_API_DEFAULT sets the default version of + versioned APIs. The bin/makevers perl script did not set + the maxidx variable correctly when the 1.10 branch was + created. This caused the versioning process to always use + the latest version of any API. - (JRM - 2018/03/29) + (ADB - 2018/08/17, HDFFV-10552) - - Optimized parallel open/location of the HDF5 super-block. + - Added configuration checks for the following MPI functions: - 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. + MPI_Mprobe - Used for the Parallel Compression feature + MPI_Imrecv - Used for the Parallel Compression feature - 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(). + MPI_Get_elements_x - Used for the "big Parallel I/O" feature + MPI_Type_size_x - Used for the "big Parallel I/O" feature - 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. + (JTH - 2018/08/02, HDFFV-10512) - (RAW - 2017/10/10, HDFFV-10294) + - Added section to the libhdf5.settings file to indicate + the status of the Parallel Compression and "big Parallel I/O" + features. - - Added large (>2GB) MPI-IO transfers. + (JTH - 2018/08/02, HDFFV-10512) - 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. + - Add option to execute swmr shell scripts from CMake. - 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. + Option TEST_SHELL_SCRIPTS redirects processing into a + separate ShellTests.cmake file for UNIX types. The tests + execute the shell scripts if a SH program is found. - (RAW - 2017/09/10, HDFFV-8839) + (ADB - 2018/07/16) 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. + - New wrappers - + 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) + Added the following items: - Note: additional parameter is added to previous H5Location::unlink. + + Class DSetAccPropList for the dataset access property list. - + H5Tencode and H5Tdecode: - // Creates a binary object description of this datatype. - void DataType::encode() - C API H5Tencode() + + Wrapper for H5Dget_access_plist to class DataSet + // Gets the access property list of this dataset. + DSetAccPropList getAccessPlist() const; - // 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() + + Wrappers for H5Pset_chunk_cache and H5Pget_chunk_cache to class DSetAccPropList + // Sets the raw data chunk cache parameters. + void setChunkCache(size_t rdcc_nslots, size_t rdcc_nbytes, double rdcc_w0) - + H5Lget_info: - // Returns the information of the named link. - H5L_info_t getLinkInfo(const H5std_string& link_name,...) + // Retrieves the raw data chunk cache parameters. + void getChunkCache(size_t &rdcc_nslots, size_t &rdcc_nbytes, double &rdcc_w0) - (BMR - 2018/03/11, HDFFV-10149) + + New operator!= to class DataType (HDFFV-10472) + // Determines whether two datatypes are not the same. + bool operator!=(const DataType& compared_type) - - Added class LinkCreatPropList for link create property list. + + Wrappers for H5Oget_info2, H5Oget_info_by_name2, and H5Oget_info_by_idx2 + (HDFFV-10458) - (BMR - 2018/03/11, HDFFV-10149) + // Retrieves information about an HDF5 object. + void getObjinfo(H5O_info_t& objinfo, unsigned fields = H5O_INFO_BASIC) const; - - 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) + // Retrieves information about an HDF5 object, given its name. + void getObjinfo(const char* name, H5O_info_t& objinfo, + unsigned fields = H5O_INFO_BASIC, + const LinkAccPropList& lapl = LinkAccPropList::DEFAULT) const; + void getObjinfo(const H5std_string& name, H5O_info_t& objinfo, + unsigned fields = H5O_INFO_BASIC, + const LinkAccPropList& lapl = LinkAccPropList::DEFAULT) const; - (BMR - 2018/03/11, HDFFV-10149) + // Retrieves information about an HDF5 object, given its index. + void getObjinfo(const char* grp_name, H5_index_t idx_type, + H5_iter_order_t order, hsize_t idx, H5O_info_t& objinfo, + unsigned fields = H5O_INFO_BASIC, + const LinkAccPropList& lapl = LinkAccPropList::DEFAULT) const; + void getObjinfo(const H5std_string& grp_name, H5_index_t idx_type, + H5_iter_order_t order, hsize_t idx, H5O_info_t& objinfo, + unsigned fields = H5O_INFO_BASIC, + const LinkAccPropList& lapl = LinkAccPropList::DEFAULT) const; - - 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) + (BMR - 2018/07/22, HDFFV-10150, HDFFV-10458, HDFFV-1047) 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. + - Java HDFLibraryException class - See the C library section, above, for further information. + Change parent class from Exception to RuntimeException. - (HDFFV-10252, DER, 2017/04/05) + (ADB - 2018/07/30, HDFFV-10534) + - JNI Read and Write - Tools: - ------ - - h5diff has a new option to display error stack. + Refactored variable-length functions, H5DreadVL and H5AreadVL, + to correct dataset and attribute reads. New write functions, + H5DwriteVL and H5AwriteVL, are under construction. - 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 - 2018/06/02, HDFFV-10519) - (ADB - 2017/08/30, HDFFV-9774) - -Support for new platforms, languages and compilers. -======================================= - - None - -Bug Fixes since HDF5-1.10.1 release +Bug Fixes since HDF5-1.10.2 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) + - Performance issue with H5Oget_info - - Freeing of object header after failed checksum verification. + H5Oget_info family of routines retrieves information for an object such + as object type, access time, number of attributes, and storage space etc. + Retrieving all such information regardless is an overkill and causes + performance issue when doing so for many objects. - 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. + Add an additional parameter "fields" to the the H5Oget_info family of routines + indicating the type of information to be retrieved. The same is done to + the H5Ovisit family of routines which recursively visits an object + returning object information in a callback function. Both sets of routines + are versioned and the corresponding compatibility macros are added. - Freed the object header that failed the chksum verification only - after the new object header is reloaded, deserialized and set up. + The version 2 names of the two sets of routines are: + (1) H5Oget_info2, H5Oget_info_by_idx2, H5Oget_info_by_name2 + (2) H5Ovisit2, H5Ovisit_by_name2 - (VC - 2018/03/14, HDFFV-10209) + (VC - 2018/08/15, HDFFV-10180) - - Updated H5Pset_evict_on_close in H5Pfapl.c + - Test failure due to metadata size in test/vds.c - Changed the minor error number from H5E_CANTSET to H5E_UNSUPPORTED for - parallel library. + The size of metadata from test_api_get_ex_dcpl() in test/vds.c is not as expected + because the latest format should be used when encoding the layout for VDS. - (ADB - 2018/03/06, HDFFV-10414) + Set the latest format in a temporary fapl and pass the setting to the routines that + encode the dataset selection for VDS. - - Fixed the problems with the utility function that could not handle lowercase - Windows drive letters. + (VC - 2018/08/14 HDFFV-10469) - Added call to upper function for drive letter. + - Java HDF5LibraryException class - (ADB - 2017/12/18, HDFFV-10307) + The error minor and major values would be lost after the + constructor executed. - - Fixed H5Sencode() bug when the number of elements selected was > 2^32. + Created two local class variables to hold the values obtained during + execution of the constructor. Refactored the class functions to retrieve + the class values rather then calling the native functions. + The native functions were renamed and called only during execution + of the constructor. + Added error checking to calling class constructors in JNI classes. - 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. + (ADB - 2018/08/06, HDFFV-10544) - 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. + - Added checks of the defined MPI_VERSION to guard against usage of + MPI-3 functions in the Parallel Compression and "big Parallel I/O" + features when HDF5 is built with MPI-2. Previously, the configure + step would pass but the build itself would fail when it could not + locate the MPI-3 functions used. - (VC - 2017/11/28, HDFFV-9947) + As a result of these new checks, HDF5 can again be built with MPI-2, + but the Parallel Compression feature will be disabled as it relies + on the MPI-3 functions used. - - Fixed filter plugin handling in H5PL.c and H5Z.c to not require i availability of - dependent libraries (e.g., szip or zlib). + (JTH - 2018/08/02, HDFFV-10512) - It was discovered that the dynamic loading process used by - filter plugins had issues with library dependencies. + - User's patches: CVEs - 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) + The following patches have been applied: - - Fixed rare object header corruption bug. + CVE-2018-11202 - NULL pointer dereference was discovered in + H5S_hyper_make_spans in H5Shyper.c (HDFFV-10476) + https://security-tracker.debian.org/tracker/CVE-2018-11202 + https://cve.mitre.org/cgi-bin/cvename.cgi?name=3DCVE-2018-11202 - 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. + CVE-2018-11203 - A division by zero was discovered in + H5D__btree_decode_key in H5Dbtree.c (HDFFV-10477) + https://security-tracker.debian.org/tracker/CVE-2018-11203 + https://cve.mitre.org/cgi-bin/cvename.cgi?name=3DCVE-2018-11203 - (NAF - 2017/11/14, HDFFV-10274) + CVE-2018-11204 - A NULL pointer dereference was discovered in + H5O__chunk_deserialize in H5Ocache.c (HDFFV-10478) + https://security-tracker.debian.org/tracker/CVE-2018-11204 + https://cve.mitre.org/cgi-bin/cvename.cgi?name=3DCVE-2018-11204 - - Updated H5Zfilter_avail in H5Z.c. + CVE-2018-11206 - An out of bound read was discovered in + H5O_fill_new_decode and H5O_fill_old_decode in H5Ofill.c + (HDFFV-10480) + https://security-tracker.debian.org/tracker/CVE-2018-11206 + https://cve.mitre.org/cgi-bin/cvename.cgi?name=3DCVE-2018-11206 - The public function checked for plugins, while the private - function did not. + CVE-2018-11207 - A division by zero was discovered in + H5D__chunk_init in H5Dchunk.c (HDFFV-10481) + https://security-tracker.debian.org/tracker/CVE-2018-11207 + https://cve.mitre.org/cgi-bin/cvename.cgi?name=3DCVE-2018-11207 - 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. + (BMR - 2018/7/22, PR#s: 1134 and 1139, + HDFFV-10476, HDFFV-10477, HDFFV-10478, HDFFV-10480, HDFFV-10481) - (ADB - 2017/10/10, HDFFV-10297, HDFFV-10319) + - H5Adelete - - h5dump produced SEGFAULT when dumping corrypted file. - - The behavior was due to the error in the internal function H5HL_offset_into(). + H5Adelete failed when deleting the last "large" attribute that + is stored densely via fractal heap/v2 b-tree. - (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. + After removing the attribute, update the ainfo message. If the + number of attributes goes to zero, remove the message. - (VC - 2017/08/30, HDFFV-10216) + (VC - 2018/07/20, HDFFV-9277) - - Fixes for paged aggregation feature. + - A bug was discovered in the parallel library which caused partial + parallel reads of filtered datasets to return incorrect data. The + library used the incorrect dataspace for each chunk read, causing + the selection used in each chunk to be wrong. - Skip test in test/fheap.c when: - (1) multi/split drivers and - (2) persisting free-space or using paged aggregation strategy + The bug was not caught during testing because all of the current + tests which do parallel reads of filtered data read all of the data + using an H5S_ALL selection. Several tests were added which exercise + partial parallel reads. - (VC, 2017/07/10) + (JTH - 2018/07/16, HDFFV-10467) - 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 + - A bug was discovered in the parallel library which caused parallel + writes of filtered datasets to trigger an assertion failure in the + file free space manager. - (VC - 2017/06/09) + This occurred when the filter used caused chunks to repeatedly shrink + and grow over the course of several dataset writes. The previous chunk + information, such as the size of the chunk and the offset in the file, + was being cached and not updated after each write, causing the next write + to the chunk to retrieve the incorrect cached information and run into + issues when reallocating space in the file for the chunk. - - Fixed for infinite loop in H5VM_power2up(). + (JTH - 2018/07/16, HDFFV-10509) - 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. + - A bug was discovered in the parallel library which caused the + H5D__mpio_array_gatherv() function to allocate too much memory. - The fix ensures that the function checks for n >= 2^63 - and returns 0. + When the function is called with the 'allgather' parameter set + to a non-true value, the function will receive data from all MPI + ranks and gather it to the single rank specied by the 'root' + parameter. However, the bug in the function caused memory for + the received data to be allocated on all MPI ranks, not just the + singular rank specified as the receiver. In some circumstances, + this would cause an application to fail due to the large amounts + of memory being allocated. - (VC - 2017/07/10, HDFFV-10217) + (JTH - 2018/07/16, HDFFV-10467) - - Fixed for H5Ocopy doesn't work with open identifiers. + - Error checks in h5stat and when decoding messages - 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. + h5stat exited with seg fault/core dumped when + errors are encountered in the internal library. - (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. + Add error checks and --enable-error-stack option to h5stat. + Add range checks when decoding messages: old fill value, old + layout and refcount. - 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) + (VC - 2018/07/11, HDFFV-10333) - If an HDF5 file contains a malformed compound datatype with a suitably large offset, the type conversion code can run off @@ -609,8 +340,6 @@ Bug Fixes since HDF5-1.10.1 release 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 @@ -625,448 +354,102 @@ Bug Fixes since HDF5-1.10.1 release (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 H5FDpublich.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=""). + - Applied patches to address Cywin build issues - 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. + There were three issues for Cygwin builds: + - Shared libs were not built. + - The -std=c99 flag caused a SIG_SETMASK undeclared error. + - Undefined errors when buildbing test shared libraries. - 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). + Patches to address these issues were received and incorporated in this version. - (DER - 2017/07/05, HDFFV-10248) + (LRK - 2018/07/18, HDFFV-10475) - - CMake + - The --enable-debug/production configure flags are listed as 'deprecated' + when they should really be listed as 'removed'. - Too many commands for POST_BUILD step caused command line to be - too big on windows. + In the autotools overhaul several years ago, we removed these flags and + implemented a new --enable-build-mode= flag. This was done because we + changed the semantics of the modes and didn't want users to silently + be exposed to them. The newer system is also more flexible and us to + add other modes (like 'clean'). - Changed foreach of copy command to use a custom command with the - use of the HDFTEST_COPY_FILE macro. + The --enable-debug/production flags are now listed as removed. - (ADB - 2017/07/12, HDFFV-10254) + (DER - 2018/05/31, HDFFV-10505) - - CMake test execution environment + - Moved the location of gcc attribute. - 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. + The gcc attribute(no_sanitize), named as the macro HDF_NO_UBSAN, + was located after the function name. Builds with GCC 7 did not + indicate any problem, but GCC 8 issued errors. Moved the + attribute before the function name, as required. - (RAW - 2017/11/03, HDFFV-10318) + (ADB - 2018/05/22, HDFFV-10473) - - Fortran compilation fails for xlf and CMake builds. + - Reworked java test suite into individual JUnit tests. - Fixed CMake shared library build for H5match_types and modules + Testing the whole suite of java unit tests in a single JUnit run + made it difficult to determine actual failures when tests would fail. + Running each file set of tests individually, allows individual failures + to be diagnosed easier. A side benefit is that tests for optional components + of the library can be disabled if not configured. - (MSB - 2017/12/19, HDFFV-10363) + (ADB - 2018/05/16, HDFFV-9739) - - Shared libraries fail test on OSX with Fortran enabled with CMake. + - Converted CMake global commands ADD_DEFINITIONS and INCLUDE_DIRECTORIES + to use target_* type commands. This change modernizes the CMake usage + in the HDF5 library. - Fixed by removing the F77 use of EQUIVALENCE and COMMON, replaced - using MODULES. Updated CMake. + In addition, there is the intention to convert to generator expressions, + where possible. The exception is Fortran FLAGS on Windows Visual Studio. + The HDF macros TARGET_C_PROPERTIES and TARGET_FORTRAN_PROPERTIES have + been removed with this change in usage. - (MSB - 2017/12/07, HDFFV-10223) + The additional language (C++ and Fortran) checks have also been localized + to only be checked when that language is enabled. - - The bin/trace script now emits an error code on problems and autogen.sh - will fail if bin/trace fails. + (ADB - 2018/05/08) - 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. + Performance + ------------- + - Revamped internal use of DXPLs, improving performance - (DER - 2017/11/15, HDFFV-10428) + (QAK - 2018/05/20) 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. + - Fixed issue with h5fget_obj_count_f and using a file id of H5F_OBJ_ALL_F not + returning the correct count. - 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. + (MSB - 2018/5/15, HDFFV-10405) - (ADB - 2018/01/18, HDFFV-10393) - - - h5repack - - h5repack failed to handle command line parameters for customer filters. - - User defined filter parameter conversions would fail whenintegers 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. + - Adding default arguments to existing functions - (BMR - 2018/03/12 - User's reported in email) + Added the following items: + + Two more property list arguments are added to H5Location::createDataSet: + const DSetAccPropList& dapl = DSetAccPropList::DEFAULT + const LinkCreatPropList& lcpl = LinkCreatPropList::DEFAULT - 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. + + One more property list argument is added to H5Location::openDataSet: + const DSetAccPropList& dapl = DSetAccPropList::DEFAULT - (LRK - 2018/03/12, HDFFV-10397) + (BMR - 2018/07/21, PR# 1146) - - Refactored the testpar/t_bigio.c test to include ALARM macros + - Improvement C++ documentation - 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. + Replaced the table in main page of the C++ documentation from mht to htm format + for portability. - (RAW - 2017/11/08, HDFFV-10301) + (BMR - 2018/07/17, PR# 1141) Supported Platforms @@ -1081,7 +464,7 @@ Supported Platforms 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, + Version 4.9.3, Version 5.2.0 Intel(R) C (icc), C++ (icpc), Fortran (icc) compilers: Version 17.0.0.098 Build 20160721 @@ -1091,25 +474,18 @@ Supported Platforms (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 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 Visual Studio 2015 w/ Intel Fortran 18 (cmake) - Windows 10 x64 Visual Studio 2015 w/ Intel Fortran 16 (cmake) + Windows 10 x64 Visual Studio 2015 w/ Intel Fortran 18 (cmake) + Visual Studio 2017 w/ Intel Fortran 18 (cmake) Mac OS X Yosemite 10.10.5 Apple clang/clang++ version 6.1 from Xcode 7.0 64-bit gfortran GNU Fortran (GCC) 4.9.2 @@ -1123,7 +499,6 @@ Supported Platforms 64-bit gfortran GNU Fortran (GCC) 7.1.0 (swallow/kite) Intel icc/icpc/ifort version 17.0.2 - Tested Configuration Features Summary ===================================== @@ -1147,10 +522,10 @@ 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 +Mac OS Sierra 10.12.6 64-bit n y/y n y y y CentOS 7.2 Linux 2.6.32 x86_64 PGI n y/y n y y y CentOS 7.2 Linux 2.6.32 x86_64 GNU y y/y y y y y CentOS 7.2 Linux 2.6.32 x86_64 Intel n y/y n y y y @@ -1167,10 +542,10 @@ 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 +Mac OS Sierra 10.12.6 64-bit y n y y CentOS 7.2 Linux 2.6.32 x86_64 PGI y y y n CentOS 7.2 Linux 2.6.32 x86_64 GNU y y y y CentOS 7.2 Linux 2.6.32 x86_64 Intel y y y n @@ -1190,19 +565,20 @@ The following platforms are not supported but have been tested for this release. 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 + Version 17.10-0 Intel(R) C (icc), C++ (icpc), Fortran (icc) compilers: - Version 17.0.4.196 Build 20170411 + 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 + OpenMPI 3.0.0-GCC-7.2.0-2.29, + 3.1.0-GCC-7.2.0-2.29 Intel(R) C (icc) and C++ (icpc) compilers - Version 17.0.0.098 Build 20160721 + 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 @@ -1251,3 +627,38 @@ Known Problems in the HDF5 source. Please report any new problems found to help@hdfgroup.org. + +CMake vs. Autotools installations +================================= +While both build systems produce similar results, there are differences. +Each system produces the same set of folders on linux (only CMake works +on standard Windows); bin, include, lib and share. Autotools places the +COPYING and RELEASE.txt file in the root folder, CMake places them in +the share folder. + +The bin folder contains the tools and the build scripts. Additionally, CMake +creates dynamic versions of the tools with the suffix "-shared". Autotools +installs one set of tools depending on the "--enable-shared" configuration +option. + build scripts + ------------- + Autotools: h5c++, h5cc, h5fc + CMake: h5c++, h5cc, h5hlc++, h5hlcc + +The include folder holds the header files and the fortran mod files. CMake +places the fortran mod files into separate shared and static subfolders, +while Autotools places one set of mod files into the include folder. Because +CMake produces a tools library, the header files for tools will appear in +the include folder. + +The lib folder contains the library files, and CMake adds the pkgconfig +subfolder with the hdf5*.pc files used by the bin/build scripts created by +the CMake build. CMake separates the C interface code from the fortran code by +creating C-stub libraries for each Fortran library. In addition, only CMake +installs the tools library. The names of the szip libraries are different +between the build systems. + +The share folder will have the most differences because CMake builds include +a number of CMake specific files for support of CMake's find_package and support +for the HDF5 Examples CMake project. + |