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diff --git a/release_docs/HISTORY-1_8_0-1_10_0.txt b/release_docs/HISTORY-1_8_0-1_10_0.txt new file mode 100644 index 0000000..a364274 --- /dev/null +++ b/release_docs/HISTORY-1_8_0-1_10_0.txt @@ -0,0 +1,1742 @@ +HDF5 HISTORY +============= + + +INTRODUCTION + +This document describes the development history between the HDF5-1.8.0 and +HDF5 1.10.0 releases. For more iformation see the SVN log. + +Information about supported and tested platforms is provided for historical +reasons only and may not be accurate. + + +For more information, see the HDF5 home page: + + http://www.hdfgroup.org/HDF5/ + +If you have any questions or comments, please send them to the HDF Help Desk: + + help@hdfgroup.org + + +CONTENTS + +- New Features +- Support for new platforms and languages +- Bug Fixes since HDF5-1.8.0 +- Supported Platforms +- Tested Configuration Features Summary +- More Tested Platforms +- Known Problems + + +New Features +============ + + Configuration: + ------------- + - Java JNI library API wrappers and supporting files added as HDF_JAVA language + option. Both configure and CMake disable this option by default. + HDFFV-9552 (ADB 2016/02.28) + - CMake minimum is now 3.1.0. (ADB 2015/11/14) + - cmakehdf5: configure options added to enable or disable the building of + different API's and testings. See "cmakehdf5 --help" for details. + (AKC - 2014/12/09 HDFFV-8932) + - Autotools: Automake updated to 1.14.1 (ADB - 2014/04/08) + - CMake: Moved minimum CMake version to 2.8.11 which enables better library + include processing. (ADB - 2014/03/26) + - New configuration option added to change the default plugin path. + configure option is --with-default-plugin=location + cmake option is -DH5_DEFAULT_PLUGINDIR:PATH=location + HDFFV-8513. (ADB 2013/09/04) + - Rename FFLAGS to FCFLAGS in configure (ADB 2013/08/13) + - CMake minimum is now 2.8.10. (ADB 2013/01/14) + - A new tool, cmakehdf5, which is a build command script similar to + buildhdf5 is added and is available in the bin directory. + (AKC - 2012/12/12) + - Fixed AIX Fortran compiler flags to use appropriate settings for + debugging, profiling, optimization situations. HDFFV-8069. (AKC + 2012/09/27) + - Updated to latest autotools and changed all hard *.sh scripts to + configure managed *.sh.in files. Removed overloading of autotools + TESTS variable by examples and tests. Renamed configure.in to + configure.ac. (ADB - 2012/08/23 - HDFFV-8129) + - Added code to display the version information of XL fortran and C++ + in the summary of configure. (AKC - 2012/02/28 - HDFFV-7793) + - Configure now generates Makefiles that build in "silent make mode" + by default in which compile and link lines are significantly + simplified for clarity. To override this and view actual compile and + link lines during building, the --disable-silent-rules flag can be used + at configure time, or the 'make' command can be followed by V=1, to + indicate a "verbose" make. (MAM - 2011/4/14). + - Added mpicc and mpif90 as the default C and Fortran compilers for Linux + systems when --enable-parallel is specified but no $CC or $FC is defined. + (AKC - 2011/2/7) + - Added a new configure option, "--enable-unsupported", which can + be used to stop configure from preventing the use of unsupported + configure option combinations, such as c++ in parallel or parallel + HDF5 with threadsafe. Use at your own risk, as it may result in a + library that won't compile or run as expected! + (MAM - 2010/11/17 - Bug 2061) + - PHDF5 changed to use "mpiexec", instead of mpirun, as the default MPI + applications startup command as defined in the MPI-2 definition, section + 4.1. (AKC - 2010/6/11 - Bug 1921) + - Configure now adds appropriate defines for supporting large (64-bit) + files on all systems, where supported, by default, instead of only linux. + This largefile support is controllable with the --enable-largefile + configure option. This is replacing the linux-specific --enable-linux-lfs + option, which has been removed from configure. + (MAM - 2010/05/05 - 1772/1434) + - Upgraded versions of autotools used to generate configuration suite. + We now use Automake 1.11.1, Autoconf 2.65, and Libtool 2.2.6b. + MAM 2010/04/15. + - Added the xlc-* and mpcc_r-* BASENAME patterns to be recognized as IBM + compilers so that the ibm compiler options can be added properly. This + allows non-system-default compiler command names (e.g. xlc-m.n.k.l) be + recognized. AKC 2009/11/26. + - Configuration suite now uses Automake 1.11 and Autoconf 2.64. + MAM 2009/08/11. + - Changed default Gnu fortran compiler from g95 to gfortran since + gfortran is more likely installed with gcc now. -AKC 2009/07/19- + - Added libtool version numbers to generated c++, fortran, and + hl libraries. MAM 2009/04/19. + - Regenerated Makefile.ins using Automake 1.10.2. MAM 2009/04/19. + - Added a Make target of check-all-install to test the correctness of + installing via the prefix= or $DESTDIR options. AKC - 2009/04/14 + - Configuration suite now uses Libtool 2.2.6a. MAM 2008/10/24 + + - Configuration suite now uses Autoconf 2.61, Automake 1.10.1. + MAM 2008/05/05. + + - The new configure option "--disable-sharedlib-rpath" disables + embedding the '-Wl,-rpath' information into executables when + shared libraries are produced, and instead solely relies on the + information in LD_LIBRARY_PATH. (MAM - 2008/05/15) + + Library: + -------- + + - Virtual Dataset feature was added + (NAF - 2015-10-05, VDS-193) + + - H5F_ACC_DEBUG labeled "deprecated" + + The symbol was originally used to emit some extra debugging + informationi in the multi VFD. The underlying functionality + was removed due to disuse in HDF5 1.8.16 though the symbol + remained defined since it was visible in H5Fpublic.h. + + In this release, the symbol has been labeled deprecated and will + not be defined when H5_NO_DEPRECATED_SYMBOLS is defined. + + (DER - 2015-04-30, HDFFV-1074) + + - The library can load filter libraries dynamically during runtime. Users + can set the search path through environment variable HDF5_PLUGIN_PATH + and call H5Pset_filter to enable a dynamic filter. (SLU - 2013/04/08) + - Added new API functions H5Dscatter and H5Dgather to scatter data to and + and gather data from a selection within a memory buffer. + (NAF - 2013/02/05) + - The library now supports the data conversion from enumeration to numeric + (integer and floating-point number) datatypes. See Issue 8221. + (SLU - 2012/10/23) + - The data sieve buffer size was for all the datasets in the file. It + could waste memory if any dataset size is smaller than the sieve buffer + size. Now the library picks the smaller one between the dataset size + and the sieve buffer size from the file access property. See Issue 7934. + (SLU - 2012/4/2) + - I added a new parameter of object access property list to the function + H5Rdereference (Issue 2763). It's called H5Rdereference2 now. The former + H5Rdereference function has been deprecated to H5Rdereference1. (SLU - + 2011/7/18) + - H5Tcreate now supports string type (fixed-length and variable-length). + (SLU - 2011/05/20) + - Added ability to cache files opened through external links. Added new + public functions H5Pset_elink_file_cache_size(), + H5Pget_elink_file_cache_size(), and H5Fclear_elink_file_cache(). + (NAF - 2011/02/17) + - Removed all old code for Metraowerks compilers, bracketed by + __MWERKS__). Metraowerks compiler is long gone. (AKC - 2010/11/17) + - Added support for threadsafety on windows using the windows threads + library. Use the HDF5_ENABLE_THREADSAFE option in CMake while on a + windows platform to enable this functionality. This is supported on + Windows Vista and newer Windows operating systems. (MAM - 2010/09/10) + - When a mandatory filter failed to write data chunks, the dataset + couldn't close (bug 1260). The fix releases all resources and closes + the dataset but returns a failure. (SLU - 2010/9/8) + - H5Tset_order and H5Tget_order now support all data types. A new byte + order H5T_ORDER_MIXED has been added specifically for compound datatype + and its derived type. Please see bug #1934. (SLU - 2010/8/23) + - Improved performance of the chunk cache by avoiding unnecessary b-tree + lookups of chunks already in cache. (NAF - 2010/06/15) + - Greatly improved performance of extending a dataset with early + allocation. (NAF - 2010/03/24 - 1637) + - Added support for filtering densely stored groups. Many of the API + functions related to filters have been extended to support dense groups + as well as datasets. Pipeline messages can now be stored in a group's + object header. (NAF/QAK - 2009/10/8) + - The embedded library information is displayed by H5check_version() if a + version mismatch is detected. Also changed H5check_version() to + suppress the warning message totally if $HDF5_DISABLE_VERSION_CHECK is 2 + or higher. (Old behavior treated 3 or higher the same as 1, that is + print a warning and allows the program to continue. (AKC - 2009/9/28) + - If a user does not care for the extra library information insert + in the executables, he may turn it off by --disable-embedded-libinfo + during configure. (AKC - 2009/9/15) + - Corrected problem where library would re-write the superblock in a file + opened for R/W access, even when no changes were made to the file. + (QAK - 2009/08/20, Bz#1473) + - Separated "factory" free list class from block free lists. These free + lists are dynamically created and manage blocks of a fixed size. + H5set_free_list_limits() will use the same settings specified for block + free lists for factory free lists. (NAF - 2009/04/08) + - Added support for dense attributes to H5Ocopy. (XCao/NAF - 2009/01/29) + - Added H5Pset_elink_cb and H5Pget_elink_cb functions to support a + user-defined callback function for external link traversal. + (NAF - 2009/01/08) + - Added H5Pset_elink_acc_flags and H5Pget_elink_acc_flags functions to + allow the user to specify the file access flags used to open the target + file of an external link. (NAF - 2009/01/08) + - Added H5Pset_chunk_cache() and H5Pget_chunk_cache() functions to allow + individual rdcc configuration for each dataset. Added + H5Dget_access_plist() function to retrieve a dataset access property + list from a dataset. (NAF - 2008/11/12) + - Added H5Iis_valid() function to check if an id is valid without producing + an error message. (NAF - 2008/11/5) + - Added two new public routines: H5Pget_elink_fapl() and + H5Pset_elink_fapl(). (see bug #1247) (VC - 2008/10/13) + - Improved free space tracking in file to be faster. (QAK - 2008/10/06) + - Added 'mounted' field to H5G_info_t struct. (QAK - 2008/07/15) + + Parallel Library: + ----------------- + - Add H5Pget_mpio_no_collective_cause() function that retrive reasons + why the collective I/O was broken during read/write IO access. + (JKM - 2012/08/30 HDFFV-8143) + - Special Collective IO (IO when some processes do not contribute to the + IO) and Complex Derived Datatype MPI functionalities are no longer + conditionally enabled in the library by configure. They are always + enabled in order to take advantage of performance boosts from these + behaviors. Older MPI implementations that do not allow for these + functionalities can no longer by used by HDF5. (MAM - 2011/07/08). + - Modified parallel tests to run with arbitrary number of processes. The + modified tests are testphdf5 (parallel dataset access), t_chunk_alloc + (chunk allocation), and t_posix_compliant (posix compliance). The rest of + the parallel tests already use in the code the number of processes + available in the communicator. (CMC - 2009/04/28) + + Fortran Library: + ---------------- + + - Added parallel routine H5Pget_mpio_actual_io_mode_f (MSB - 2012/09/27) + + - Added for the C API the Fortran wrapper: + h5ocopy_f (MSB - 2012/03/22) + + + HDF5 Fortran library was enhanced to support Fortran 2003 standard. + The following features are available when the HDF5 library is configured + using --enable-fortran --enable-fortran2003 configure flags AND + if fortran compiler is Fortran2003 compliant: + + - Subroutines overloaded with the C_PTR derived type: + h5pget_f + h5pget_fill_value_f + h5pinsert_f + h5pregister_f + h5pset_f + h5pset_fill_value_f + h5rcreate_f + h5rderefrence_f + h5rget_name_f + h5rget_obj_type_f + - Subroutines overloaded with the C_PTR derived type + and simplified signatures: + h5aread_f + h5awrite_f + h5dread_f + h5dwrite_f + - New subroutines + h5dvlen_reclaim_f + h5literate_by_name_f + h5literate_f + h5ovisit_f + h5tconvert_f + + - Subroutines with additional optional parameters: + h5pcreate_class_f + (EIP - 2011/10/14) + + - Added for the C APIs the Fortran wrappers: + h5dget_access_plist_f + h5iis_valid_f + h5pset_chunk_cache_f + h5pget_chunk_cache_f + (MSB - 2009/04/17) + + + + C++ Library: + ------------ + - New member function added + + The assignment operator ArrayType::operator= is added because ArrayType + has pointer data members. + + (BMR, 2016/03/07, HDFFV-9562) + + - New member functions + + Overloaded CommonFG::getObjnameByIdx to take char* for name + + Overloaded CommonFG::getObjTypeByIdx to return type name as a char*. + (BMR - 2010/05/02) + + DataSet::getInMemDataSize() to simplify getting the dataset's + data size in memory. (BMR - 2009/07/26) + - These member functions were added as wrapper for H5Rdereference to + replace the incorrect IdComponent::dereference(). + void H5Object::dereference(H5File& h5file, void* ref) + void H5Object::dereference(H5Object& obj, void* ref) + In addition, these constructors were added to create the associated + objects by way of dereference: + Attribute(H5Object& obj, void* ref); + Attribute(H5File& file, void* ref); + DataSet(H5Object& obj, void* ref); + DataSet(H5File& file, void* ref); + DataType(H5Object& obj, void* ref); + DataType(H5File& file, void* ref); + Group(H5Object& obj, void* ref); + Group(H5File& obj, void* ref); + (BMR - 2008/08/10) + + + + Tools: + ------ + - h5repack: Added ability to use plugin filters. HDFFV-8345 (ADB - 2013/09/04). + - h5dump: Added option -N --any_path, which searches the file for paths that + match the search path. HDFFV-7989 (ADB - 2013/08/12). + - h5dump: Added optional arg 0 to -A, which excludes attributes from display. + HDFFV-8134 (ADB - 2013/08/01). + - h5dump: Fixed displaying compression ratio for unknown or user-defined + filters. HDFFV-8344 (XCAO 2013/03/19) + - h5dump: Changed UNKNOWN_FILTER to USER_DEFINED_FILTER for user defined filter. + HDFFV-8346 (XCAO 2013/03/19) + - h5dump: Added capability for "-a" option to show attributes containing "/" + by using an escape character. For example, for a dataset "/dset" + containing attribute "speed(m/h)", use "h5dump -a "/dset/speed(\/h)" + to show the content of the attribute. See details at HDFFV-7523 + (PC -- 2012/03/12) + - h5dump: Added ability to apply command options across multiple files using a + wildcard in the filename. Example; "h5dump -H -d Dataset1 tarr*.h5". + HDFFV-7876 (ADB - 2012/03/12). + - h5repack: Improved performance for big chunked datasets (size > 128MB) + when used with layout (-l) or compression (-f) option. + It would perform much better prior to the improvement, + especially for cases that chunk dimentions looks like + "1024x5x1" (compare to "1x5x1024"). When bigger numbers + are toward front and smaller number is toward back in chunk + dimentions. HDFFV-7862 (JKM - 2012/03/01) + - h5dump: Added new option --no-compact-subset. This option will not + interpret the '[' character as starting the compact form of + subsetting. This is useful when the "h5dump error: unable to + open dataset "datset_name"" message is output because a dataset + name contains a '[' character. HDFFV-7689 (ADB - 2012/01/31) + - h5dump: Corrected schema location: + <hdf5:HDF5-File + xmlns:hdf5="http://hdfgroup.org/HDF5/XML/schema/HDF5-File" + xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" + xsi:schemaLocation="http://hdfgroup.org/HDF5/XML/schema/HDF5-File + http://www.hdfgroup.org/HDF5/XML/schema/HDF5-File.xsd"> + (ADB - 2011/08/10) + - h5diff: Added new level for -v (verbose) option. The new levels are + 1 and 2. So -v1 and -v2 can be specified to view more + information about attributes differences. + Bug#2121 (JKM 2011/3/23) + - h5dump: Added new option --enable-error-stack. This option will display + error stack information in the output stream. This is useful + when the "h5dump: Unable to print data" message is output. + (ADB - 2011/02/24) + - h5diff: Add a new flag --exclude-path. Specified path to an object will + be excluded from comparing the two files or two groups. If group + is specified all the member objects will be excluded. + (JKM - 2010/09/16). + - h5ls: Add new flag --no-dangling-links. (refer to --help for details) + (JKM - 2010/06/15) + - h5ls: Add new flag --follow-symlinks. (refer to --help for details) + (JKM - 2010/05/25) + - h5diff: Add new flag --no-dangling-links. (refer to --help for details) + (JKM - 2010/02/10) + - h5diff: Add new flag --follow-symlinks. (refer to --help for details) + (JKM - 2010/01/25) + - h5diff: fix for displaying garbage value on LE machine for BE data. + (JKM - 2009/11/20) + - h5dump: subsetting now allows default for count. Also trailing ; in short form + can be omitted after last specified value. + (ADB - 2009/09/04) + - h5dump/h5ls: now can display data in region references + using new -R, --region flag. + (ADB - 2009/09/04) + - h5diff: new flag, -c, --compare, list objects that are not comparable. + (PVN - 2009/4/10 - 1368) + - h5diff new flag, -N, --nan, avoids NaNs detection. (PVN - 2009/4/10) + - h5dump correctly specifies XML dtd / schema urls (ADB - 2009/4/3 - 1519) + - h5repack now handles group creation order. (PVN - 2009/4/2 - 1402) + - h5dump: added a printing of the compression ratio of uncompressed and compressed + sizes for cases where compression filters are present. (PVN - 2008/05/01) + - h5dump: added an option to allow a user defined formatting string for printf + regarding floating point numbers. (PVN - 2008/05/06) + - h5dump: support for external links, display the object that the external link + points to. (PVN - 2008/05/12) + - h5repack: add a userblock to an HDF5 file during the repack. (PVN - 2008/08/26) + - h5repack: add 2 options that call H5Pset_alignment in the repacked file. (PVN - 2008/08/29) + - h5ls: added capability to traverse through external links when the -r + (recursive) flag is given. (NAF - 2008/09/16) + - h5ls: added -E option to enable traversal of external links. h5ls will + not traverse external links without this flag being set. + (NAF - 2008/10/06) + - h5diff: added support for long double (PVN - 2008/10/28) + - h5dump: binary output defaults to NATIVE with -b optionally accepting + the form of binary output (NATIVE, FILE, BE, LE). (PVN - 2008/10/30) + - h5diff: return 1 for file differences when both file graphs differ by any object. + Error return code was changed to 2 from -1. (PVN - 2008/10/30) + - h5import: TEXTFPE (scientific format) was deprecated. Use TEXTFP + instead (PVN - 2008/10/30) + - h5repack: When user doesn't specify a chunk size, h5repack now defines a default + chunk size as the same size of the size of the hyperslab used to read the chunks. + The size of the hyperslabs are defined as the size of each dimension or a + predefined constant, whatever is smaller. This assures that the chunk + read fits in the chunk cache. (PVN - 2008/11/21) + - h5diff: h5diff treats two INFINITY values different. Fixed by checking (value==expect) + before call ABS(...) at h5diff_array.c This will make that (INF==INF) is true + (INF is treated as an number instead of NaN) (PC -- 2009/07/28) + - h5diff: add option "--use-system-epsilon" to print difference if (|a-b| > EPSILON) + Change default to use strict equality (PC -- 2009/09/12) + + + High-Level APIs: + --------------- + + C Packet Table API + ------------------ + - Replacement of a public function + + The existing function H5PTcreate_fl limits applications to deflate + compression only. The public function H5PTcreate is added to replace + H5PTcreate_fl. H5PTcreate takes a property list ID to provide + flexibility on creation properties. + + hid_t H5PTcreate(hid_t loc_id, const char *dset_name, + hid_t dtype_id, hsize_t chunk_size, hid_t plist_id); + (BMR, 2016/03/04, HDFFV-8623) + + - New public functions + + Two accessor functions were added per HDFFV-8623/patch 003. + /* Returns the ID of the dataset associated with the packet table */ + hid_t H5PTget_dataset(hid_t table_id); + + /* Returns the ID of the datatype the packet table uses */ + hid_t H5PTget_type(hid_t table_id); + (BMR, 2016/03/04, HDFFV-8623) + + - Regarding #ifdef VLPT_REMOVED + + The #ifdef VLPT_REMOVED blocks are removed from the PT library source + except the following cases: + + H5PTis_varlen() is made available again. + + H5PTfree_vlen_readbuff() now became H5PTfree_vlen_buff() + (BMR, 2016/03/04, HDFFV-442) + + C++ Packet Table API + -------------------- + - New constructor + + An overloaded constructor is added to FL_PacketTable and takes a property + list ID to provide flexibility on creation properties. + + FL_PacketTable(hid_t fileID, hid_t plist_id, const char* name, hid_t dtypeID, hsize_t chunkSize); + (BMR, 2016/03/08, HDFFV-8623) + + - New public functions + + Two accessor wrappers to class PacketTable, per HDFFV-8623/patch 004. + /* Returns the ID of the dataset associated with the packet table */ + hid_t PacketTable::GetDataset() + + /* Returns the ID of the datatype the packet table uses */ + hid_t PacketTable::GetDataset() + (BMR, 2016/03/04, HDFFV-8623) + + - Member functions having "char*" as an argument + + Overloaded functions were added to provide "const char*" argument, the + existing version will be deprecated. + (BMR, 2016/03/04) + + - Regarding #ifdef VLPT_REMOVED + + The #ifdef VLPT_REMOVED blocks are removed from the PT library source + except the following cases: + + VL_PacketTable::IsVariableLength() is moved to PacketTable + + VL_PacketTable::FreeReadBuff() now became PacketTable::FreeBuff() + + (BMR, 2016/03/04, HDFFV-442) + + + Internal header file + -------------------- + - A new API function H5DOwrite_chunk. It writes a data chunk directly + into a file bypassing hyperslab selection, data conversion, and + filter pipeline. The user must be careful with the function and + clearly understand the I/O process of the library. + (SLU - 2013/2/11) + - New API: h5ltpath_valid (Fortran: h5ltpath_valid_f) which checks + if a path is correct and determines if a link resolves to a valid + object and checks that the link does not dangle. (MSB- 2012/3/15) + + - Added Fortran wrappers for Dimension Scale APIs. HDFFV-3797 + h5dsset_scale_f + h5dsattach_scale_f + h5dsdetach_scale_f + h5dsis_attached_f + h5dsis_scale_f + h5dsset_label_f + h5dsget_label_f + h5dsget_scale_name_f + h5dsget_num_scales_f + (EIP for SB - 2011/10/13) + + - Table: In version 3.0 of Table, "NROWS" (used to store number of records) was + deprecated (PVN - 2008/11/24) + + Documentation + ------------- + +Support for new platforms, languages and compilers. +======================================= + - Intel V11.1 uses now -O3 optimization in production mode (EIP - 2010/10/08) + - PathScale compilers are recognized and can build the HDF5 library + properly. AKC - 2009/7/28 - + - SunOS 5.11 (emu) 32-bit and 64-bit with Sun C/C++ 5.12 compiler and + Sun Fortran 95 8.6 compiler. (SLU - 2013/04/15) + +Bug Fixes since HDF5-1.8.0 release +================================== + + Library + ------- + - Incorrect usage of list in CMake COMPILE_DEFINITIONS set_property + + The CMake command, set_property with COMPILE_DEFINITIONS property + needs a quoted semi-colon separated list of values. CMake will + transform the list to a series of -D{value} for the compile. + + (ADB - 2014/12/09, HDFV-9041) + + - H5Z.c: H5Zfilter_avail(H5Z_filter_t id) + Added else block if the call to the internal H5Z_filter_avail(id) does not + fail and returns FALSE. This block calls the H5PL_load(H5PL_TYPE_FILTER, (int)id) + function to attempt to dynamically load the filter plugin. + (ADB - 2014/03/03 HDFFV-8629) + - Added const qualifier to source buffer parameters in H5Dgather and + H5D_scatter_func_t (H5Dscatter callback). (NAF - 2013/7/02) + - Fixed an error involving failure to write fill values to the user's + buffer when reading unallocated chunks from datasets that have a + fill value set to H5D_FILL_VALUE_DEFAULT. A consequence of this + was the reporting of spurious data values in h5dump and h5diff + output. + (HDFFV-8247; JP - 2013/05/03) + - Fixed an error that could occur when calling H5Ocopy within an + H5Literate callback (and possibly other situations). + (NAF - 2012/7/25 - HDFFV-5853) + - Fixed an error that would occur when copying an object with attribute + creation order tracked and indexed. (NAF - 2012/3/28 - HDFFV-7762) + - Fixed a bug in H5Ocopy(): When copying an opened object, call the + object's flush class action to ensure that cached data is flushed + so that H5Ocopy will get the correct data. + (VC - 2012/3/27 - HDFFV-7853) + - When an application tries to write or read many small data chunks and + runs out of memory, the library had a seg fault. The fix is to + return the error stack with proper information. (SLU - 2012/3/23. + Issue 7785) + - H5Pset_data_transform had seg fault in some cases like x*-100. It + works correctly now and handles other cases like 100-x or 2/x. + (SLU - 2012/3/15. Issue 7922) + - Fixed rare corruption bugs that could occur when using the new object + header format. (NAF - 2012/3/15 - HDFFV-7879) + - Creating a dataset in a read-only file caused seg fault when the file + is closed. It's fixed. The attemp to create a dataset will fail + with the error stack indicating the file is read-only. (SLU - + 2012/1/25. Issue 7756) + - Fixed a seg fault that could occur when shrinking a dataset with chunks + larger than 1 MB. (NAF - 2011/11/30 - HDFFV-7833) + - Fixed a bug that could cause file corruption when copying named + datatypes to a file using shared messages. (NAF - 2011/11/14) + - Fixed a bug that could cause H5Oget_info to return the wrong address + after copying a named datatype. (NAF - 2011/11/14) + - The library allowed the conversion of strings between ASCII and UTF8 + (Issue 7582). We have corrected it to report an error under this + situation. (SLU - 2011/11/8) + - The library had seg fault when it tried to shrink the size of compound type + through H5Tset_size immediately after the type was created (Issue + 7618). It's fixed now. (SLU - 2011/10/26) + - Fixed a bug that occurred when using H5Ocopy on a committed datatype + containing an attribute using that committed datatype. + (NAF - 2011/10/13 - Issue 5854) + - #ifdef _WIN32 instances changed to #ifdef H5_HAVE_WIN32_API and added + H5_HAVE_VISUAL_STUDIO checks where necessary. CMake only as configure + never set _WIN32. + - CLANG compiler with the options -fcatch-undefined-behavior and -ftrapv + discovered 3 problems in tests and tools' library (Issue 7674): + 1. In dsets.c, left shifting an unsigned int for 32 bits or more + caused undefined behavior. + 2. In dt_arith.c, the INIT_INTEGER macro definition has an overflow + when the value is negative minimal and is being subtracted one. + 3. In tools/lib/h5tools_str.c, right shifting an int value for 32 bits + or more caused undefined behavior. + All the problems have been corrected. (SLU - 2011/9/2) + - In v1.6 library, there was EOA for the whole MULTI file saved in the + super block. We took it out in v1.8 library because it's meaningless + for the MULTI file. v1.8 library saves the EOA for the metadata file, + instead. But this caused some backward compatibility problem. + v1.8 library couldn't open the file created with v1.6 library. We + fixed the problem by checking the EOA value to detect the file + created with v1.6 library. (SLU - 2011/6/22) + - When a dataset had filters and reading data failed, the error message + didn't say which filter isn't registered. It's fixed now. + (SLU - 2011/6/3) + - The datatype handler created with H5Tencode/decode used to have the + reference count 0 (zero). I have fixed it. It is 1 (one) now. + (SLU - 2011/2/18) + - Fixed a bug that caused big endian machines to generate corrupt files + when using the scale-offset filter with floating point data or + fill values. Note that such datasets will no longer be readable + by any machine after this patch. (NAF - 2010/02/02 - Bug 2131) + - Retrieving a link's name by index in the case where the link is + external and the file that the link refers to doesn't exist will + now fail gracefully rather than cause a segmentation fault. + (MAM - 2010/11/17) + - Modified library to always cache symbol table information. Libraries + version 1.6.3 have a bug which causes them to require this + information for some operations. (NAF - 2010/09/21 - 1864) + - Fixed a bug that could occur when getting information for a new-style + group that was previously opened through a file handle that was + later closed. (NAF - 2010/09/15) + - Added define check in H5public.h if stdint.h is supported by the C++ + compiler. This define is only available on Windows with VS2010 and + using CMake to build the library. (ADB - 2010/09/13 - Bug 1938) + - H5Eset_current_stack now also closes the error stack to be set as the + default. This is to avoid a potential problem (Bug 1799). + (SLU - 2010/9/7) + - Fixed the bug in the filter's public CAN_APPLY function. The return + value should be htri_t not herr_t (Bug #1239). (SLU - 2010/8/5) + - Fixed a bug in the direct I/O driver that could render files with + certain kinds of unaligned data unreadable or corrupt them. + (NAF - 2010/07/28) + - valgrind reported an error of copying data to itself when a new attribute + is written (Bug #1956). I fixed it by taking out the memcpy step in + the attribute code. (SLU - 2010/07/28) + - Fixed a bug that could cause file corruption when using non-default + sizes of addresses and/or lengths. This bug could also cause + uncorrupted files with this property to be unreadable. This bug + was introduced in 1.8.5. (NAF - 2010/07/16 - 1951) + - Fixed a file corruption bug that could happen when shrinking a + compressed dataset. (NAF - 2010/05/20) + - Fixed some memory leaks in VL datatype conversion when strings are + used as fill values. (MAM - 2010/05/12 - BZ# 1826) + - Fixed a bug when copying objects with NULL references with the + H5O_COPY_EXPAND_REFERENCE_FLAG flag set. (NAF - 2010/04/08 - 1815) + - Files can now be concurrently opened more than once using the core file + driver, as long as the backing store is used. (NAF - 2010/03/09) + - Added support for H5O_COPY_EXPAND_EXT_LINK_FLAG to H5Ocopy. External + links will now be expanded if this flag is set. + (NAF - 2010/03/05 - 1733) + - Fixed a bug where the library, when traversing an external link, would + reopen the source file if nothing else worked. (NAF - 2010/03/05) + - Fixed an intermittent bug in the b-tree code which could be triggered + by expanding and shrinking chunked datasets in certain ways. + (NAF - 2010/02/16) + - H5Tdetect_class said a VL string is a string type. But when it's + in a compound type, it said it's a VL type (Bug #1584). I fixed it + to be consistent. It always return string type. (SLU - 2009/12/10) + - Fixed a bug where writing and deleting many global heap objects (i.e. + variable length data) would render the file unreadable. Previously + created files exhibiting this problem should now be readable. + (NAF - 2009/10/27 - 1483) + - Fixed incorrect return value for H5Pget_preserve. (AKC - 2009/10/08 - 1628) + - Fixed an assertion failure that occurred when H5Ocopy was called on a + dataset using a vlen inside a compound. (NAF - 2009/10/02 - 1597) + - Fixed incorrect return value for H5Pget_filter_by_id1/2 in H5Ppublic.h. + (NAF - 2009/09/25 - 1620) + - Fixed a bug where properties weren't being compared with the registered + compare callback. (NAF - 2009/09/25 - 1555) + - Fixed a bug where H5Pget_fitler_by_id would succeed when called for a + filter that wasn't present. (NAF - 2009/06/25 - 1250) + - Fixed an issue with committed compound datatypes containing a vlen. + Also fixed memory leaks involving committed datatypes. + (NAF - 2009/06/10 - 1593) + - Added versioning to H5Z_class_t struct to allow compatibility with 1.6 + API. (NAF - 2009/04/20 - 1533) + - Fixed a problem with using data transforms with non-native types in the + file. (NAF - 2009/04/20 - 1548) + - Added direct.h include file to windows section of H5private.h + to fix _getcwd() warning. (ADB - 2009/04/14 - 1536) + - Fixed a bug that prevented external links from working after calling + H5close(). (NAF - 2009/04/10 - 1539) + - Modified library to write cached symbol table information to the + superblock, to allow library versions 1.3.0 to 1.6.3 to read files + created by this version. (NAF - 2009/04/08 - 1423) + - Changed skip lists to use a deterministic algorithm. The library should + now never call rand() or srand(). (NAF - 2009/04/08 - 503) + - Fixed a bug where H5Lcopy and H5Lmove wouldn't create intermediate + groups when that property was set. (NAF - 2009/04/07 - 1526) + - Fixed a bug that caused files with a user block to grow by the size of + the user block every time they were opened. + (NAF - 2009/03/26 - 1499) + - Fixed a rare problem that could occur with files using the old (pre 1.4) + array datatype. (NAF - 2009/03/23) + - Modified library to be able to open files with corrupt root group symbol + table messages, and correct these errors if they are found. Such + files can only be successfully opened with write access. + (NAF - 2009/03/23 - 1189) + - Removed the long_long #define and replaced all instances with + "long long". This caused problems with third party products. All + currently supported compliers support the type. (ADB - 2009/03/05) + - Fixed various bugs that could prevent the fill value from being written + in certain rare cases. (NAF - 2009/02/26 - 1469) + - Fixed a bug that prevented more than one dataset chunk from being cached + at a time. (NAF - 2009/02/12 - 1015) + - Fixed an assertion failure caused by opening an attribute multiple times + through multiple file handles. (NAF - 2009/02/12 - 1420) + - Fixed a problem that could prevent the user from adding attributes (or + any object header message) in some circumstances. + (NAF - 2009/02/12 - 1427) + - Fixed a bug that could cause problems when an attribute was added to a + committed datatype using the committed datatype's datatype. + (NAF - 2009/02/12) + - Fixed a bug that could cause problems when copying an object with a + shared message in its own object header. (NAF - 2009/01/29) + - Changed H5Tset_order to properly reject H5T_ORDER_NONE for most + datatypes. (NAF - 2009/01/27 - 1443) + - Fixed a bug where H5Tpack wouldn't remove trailing space from an + otherwise packed compound type. (NAF - 2009/01/14) + - Fixed up some old v2 btree assertions that get run in debug mode that + were previously failing on compilation, and removed some of the + more heavily outdated and non-rewritable ones. (MAM - 2008/12/15) + - Fixed a bug that could cause problems when "automatically" unmounting + multiple files. (NAF - 2008/11/17) + - H5Ovisit and H5Ovisit_by_name will now properly terminate when the + callback function returns a positive value on the starting object. + (NAF - 2008/11/03) + - Fixed an error where a null message could be created that was larger + than could be written to the file. (NAF - 2008/10/23) + - Corrected error with family/split/multi VFD not updating driver info + when "latest" version of the file format used. (QAK - 2008/10/14) + - Corrected alignment+threshold errors to work correctly when metadata + aggregation is enabled. (QAK - 2008/10/06) + - Changed H5Fget_obj_count and H5Fget_obj_ids to ignore objects registered + by the library for internal library use. (NAF - 2008/10/06) + - Fixed potential memory leak during compound conversion. + (NAF - 2008/10/06) + - Changed the return value of H5Fget_obj_count from INT to SSIZE_T. Also + changed the return value of H5Fget_obj_ids from HERR_T to SSIZE_T and + the type of the parameter MAX_OBJS from INT to SIZE_T. (SLU - 2008/09/26) + - Fixed an issue that could cause data to be improperly overwritten + during compound type conversion. (NAF - 2008/09/19) + - Fixed pointer alignment violations that could occur during vlen + conversion. (NAF - 2008/09/16) + - Fixed problem where library could cause a segmentation fault when + an invalid location ID was given to H5Giterate(). (QAK - 2008/08/19) + - Fixed improper shutdown when objects have reference count > 1. The + library now tracks reference count due to the application separately + from that due to internal library routines. (NAF - 2008/08/19) + - Fixed assertion failure caused by incorrect array datatype version. + (NAF - 2008/08/08) + - Fixed an issue where mount point traversal would fail when using + multiple handles for the child. (NAF - 2008/08/07) + - Fixed an issue where mount points were inaccessible when using multiple + file handles for the parent. The mount table is now in the shared + file structure (the parent pointer is still in the top structure). + (NAF - 2008/08/07) + - when an attribute was opened twice and data was written with one of the handles, + the file didn't have the data. It happened because each handle had its own + object structure, and the empty one overwrote the data with fill value. This is + fixed by making some attribute information like the data be shared in the + attribute structure. SLU - 2008/07/22 + - Fixed issue where a group could have a file mounted on it twice. + (QAK - 2008/07/15) + - Fixed a Windows-specific issue in the ohdr test which was causing users + in some timezones to get false errors. This a deficiency in the Windows + mktime() function, and has been handled properly. SJW - 2008/06/19 + - Fixed the problem with the searching of target file for H5Lcreate_external(). + The searching pattern will depend on whether the target file's + pathname is an absolute or a relative path. Please see the description + in the RM for H5Lcreate_external(). (VC - 2008/04/08) + - Fixed possible file corruption bug when encoding datatype + descriptions for compound datatypes whose size was between + 256 & 511 bytes and the file was opened with the "use the + latest format" property enabled (with H5Pset_libver_bounds). + (QAK - 2008/03/13) + - Fixed bug in H5Aget_num_attrs() routine to handle invalid location + ID correctly. (QAK - 2008/03/11) + - H5Dset_extent: when shrinking dimensions, some chunks were not deleted. + (PVN - 2009/01/8) + - Added code to maintain a min_clean_fraction in the metadata cache when + in serial mode. (MAM - 2009/01/9) + + + + Configuration + ------------- + - CMake: When CMake commands are executed individually on the command line + and the external filters are being built, the CMAKE_BUILD_TYPE define + must be set to the same value as the configuration + (-DCMAKE_BUILD_TYPE:STRING=Release if using -C Release). This is needed + by the the szip and zlib filter build commands. (ADB - HDFFV-8695) + - CMake: Remove use of XLATE_UTILITY program. (ADB - 2014/03/28 HDFFV-8640) + - CMake: Added missing quotes in setting the CMAKE_EXE_LINKER_FLAGS for the + MPI option. (ADB - 2014/02/27 HDFFV-8674) + - Modified H5detect.c to scan floating point types for padding bits before + analyzing the type further. This should fix problems with gcc 4.8 + (NAF - 2013/09/19 - HDFFV-8523/HDFFV-8500) + - Fixed Makefile issue in which "-Wl," was not properly specified + prior to -rpath when building parallel fortran libraries with + an Intel compiler. (MAM - 2012/03/26) + - Makefiles generated by other packages using h5cc as the compiler + no longer error when 'make' is invoked more than once in order + to 'rebuild' after changes to source. (MAM - 2012/03/26) + - Added --enable-fortran2003 flag to enable Fortran2003 support + in the HDF5 Fortran library. The flag should be used along with the + --enable-fortran flag and takes affect only when Fortran compiler + is Fortran2003 compliant. (EIP - 2011/11/14) + + - In Windows platform, the default VFD, was Windows VFD, is restored back + to the SEC2, aka POSIX, VFD. The Windows VFD is deprecated. HDFFV-7740 + (AKC 2011/09/26) + - Removed config/ibm-aix6.x. All IBM-AIX settings are in one file, + ibm-aix. (AKC - 2011/4/14) + - Shared C libraries are no longer disabled on Mac when Fortran + is enabled. Shared Fortran libraries are still not supported on Mac, + so configure will disable them by default, but this is overridable + with the new --enable-unsupported configure option. The configure + summary has been updated to reflect the fact that the shared-ness of + the C++/Fortran wrapper libraries may not align with the C library. + (MAM - 04/11/2011 - HDFFV-4353). + - Removed recognition of the parallel compilers of LAM(hcc) and + ChMPIon(cmpicc) since we have no access to these two MPI implementations + and cannot verify their correctness. (AKC - 2010/7/14 - Bug 1921) + - Removed the following config files, as we no longer support them: + config/dec-osf*, config/hpux11.00, config/irix5.x, + config/powerpc-ibm-aix4.x config/rs6000-ibm-aix5.x config/unicos* + MAM - 2009/10/08 + - Modified configure and make process to properly preserve user's CFLAGS + (and company) environment variables. Build will now properly use + automake's AM_CFLAGS for any compiler flags set by the configure + process. Configure will no longer modify CFLAGS directly, nor will + setting CFLAGS during make completely replace what configure has set up. + MAM - 2009/10/08 + - Support for TFLOPS, config/intel-osf1, is removed since the TFLOPS + machine has long retired. AKC - 2009/10/06. + - Added $(EXEEXT) extension to H5detect when it's executed in the + src/Makfile to generate H5Tinit.c so it works correctly on platforms + that require the full extension when running executables. + MAM - 2009/10/01 - BZ #1613 + - Configure will now set FC and CXX to "no" when fortran and c++ + are not being compiled, respectively, so configure will not run + some of the compiler tests for these languages when they are not + being used. MAM - 2009/10/01 + - The PathScale compiler (v3.2) was mistaken as gcc v4.2.0 but it fails to + recognize some gcc options. Fixed. (see bug 1301). AKC - 2009/7/28 - + - The --enable-static-exec flag will now properly place the -static flag + on the link line of all installed executables. This will force the + executable to link with static libraries over shared libraries, provided + the static libraries are available. MAM - 2009/08/31 - BZ #1583 + - The --includedir=DIR configuration option now works as intended, and can + be used to specify the location to install C header files. The default + location remains unchanged, residing at ${prefix}/include. + MAM - 2009/03/10 - BZ #1381 + - Configure no longer removes the '-g' flag from CFLAGS when in production + mode if it has been explicitly set in the CFLAGS environment variable + prior to configuration. MAM - 2009/03/09 - BZ #1401. + - Fixed error with 'make check install' failing due to h5dump + needing other tools built first. MAM - 2008/10/24. + - Wpen using shared szip, it is no longer necessary to specify + the path to the shared szip libraries in LD_LIBRARY_PATH. MAM - + 2008/10/24. + - The file libhdf5_fortran.settings is not installed since its content + is included in libhdf5.settings now. AKC - 2008/10/21 + - "make DESTDIR=xxx install" failed to install some tools and files + (e.g., h5cc and fortran modules). Fixed. AKC - 2008/10/8. + - Autotools: An export of LD_LIBRARY_PATH=<szip library location> was + removed from configure and make installcheck was revised to run + scripts installed in share/hdf5_examples to use the installed h5cc, etc. + to compile and run example source files also installed there. Make + installcheck will now fail when a shared szip or other external lib file + cannot be found in the same manner that executables compiled and linked + with h5cc will fail to run when those lib files cannot be found after + install. Make installcheck should pass after setting LD_LIBRARY_PATH to the + szip location. + (LRK - 2014/04/16) + + Performance + ------------- + - Removed program perform/benchpar from the enable-build-all list. The + program will be retired or moved to another location. HDFFV-8156 + (AKC 2012/10/01) + - Retired program perform/mpi-perf. Its purpose has been incorporated + into h5perf before. (AKC 2012/09/20) + - ifdefs added to tests around include unistd.h and function to simulate + getlogin() on Windows. + (ADB - 2011/08/15) + - perf_serial test added to Windows projects and check batch file. + (ADB - 2009/06/11) + Fortran + -------- + - Fixed a typo in return value of the nh5dread_f_c function ( was 1 + instead of 0 on success); fixed the return value to make it consistent + with other Fortran functions; cleaned the code from debug statements. + (EIP - 2012/06/23) + + - Fixed problem writing/reading control characters to a dataset; writing + a string containing: alerts, backspace, carriage_return, form_feed, + horizontal_tab, vertical_tab, new_line is now tested and working. + (MSB - 2012/09/01) + + - Corrected the integer type of H5S_UNLIMITED_F to HSIZE_T (MSB - 2012/09/01) + + - Corrected the number of continuation lines in the src files + to be less then 32 lines for F95 compliance. (MSB - 2012/10/01) + + Tools + ----- + - h5dump subsetting fixed for dims greater then two + When a dataset has more then two dimensions, subsetting would incorrectly + calculate the data that needed to be displayed. + Added in block and stride calculation that account for dimensions greater + then two. NOTE: lines that have line breaks inserted because of display + length calculations, may have index info that is incorrect until the next + dimension break. (ADB, 2016/03/04, HDFFV-9698) + - h5repack: h5repack would not attempt to remove UD filters. Added a + check to h5repack for UD filters that checks if the filter can + be dynamically loaded. This will require a change in the library to + add the H5PL_load() to the H5Zfilter_avail(). (ADB - 2014/03/03 HDFFV-8629) + - h5repack: Fixed failure for converting a layout of small chunked dataset + (size < 1K) to contiguous layout. HDFFV-8214 (JKM 2013/03/18) + - h5diff: Fixed to return correct exit code 1 when detect unique extra + attribute. Prior to this fix, h5diff returned exit code 0 indicating + two files are identical. HDFFV-7643 (JKM 2013/02/15) + - h5diff: Improved speed when comparing HDF5 files with lots of + attributes. Much slower performance was identified with release + version from 1.8.7 to 1.8.10 compared to 1.8.6. (JKM 2012/10/19) + - h5repack: "h5repack -f NONE file1.h5 out.h5" command failed if + source file contains chunked dataset and a chunk dim is bigger than + the dataset dim. Another issue is that the command changed max dims + if chunk dim is smaller than the dataset dim. + These issue occurred when dataset size is smaller than 64k (compact + size limit) Fixed both. + HDFFV-8012 (JKM 2012/09/24) + - h5diff: Fixed not to accumulate attribute difference to dataset + difference in verbose mode (-v, -r), which caused incorrect + difference between dataset and group/datatype object if attribute + exist with any differences. This also lead to fix inconsistent + format indicating difference between dataset and group/datatype + object. HDFFV-5919 (JKM 2012/09/05) + - h5diff: Fixed the incorrect result when comparing attribute data + values and the data type has same class but different size. + HDFFV-7942 (JKM 2012/08/15) + - ph5diff: Fixed intermittent hang issue on a certain operation in + parallel mode. It was detected by daily test for comparing + non-comparable objects, but it could have occurred in other + operations depend on machine condition. HDFFV-8003 (JKM 2012/08/01) + - h5diff: Fixed test failure for "make check" due to failure of + copying test files when performed in HDF5 source tree. Also applied + to other tools. + HDFFV-8107 (JKM 2012/08/01) + - h5diff: Fixed the Function COPY_TESTFILES_TO_TESTDIR() of + testh5diff.sh to better report when there is an error in the file + copying. HDFFV-8105 (AKC -2012/07/22) + - h5diff: Fixed not to check and display dangling link status without + --follow-symlinks option. This also improved performance when + comparing lots of external links without the --follow-symlinks + option. HDFFV-7998 (JKM 2012/04/26) + - h5unjam: Fixed sefgault when used -V (show version) option. + HDFFV-8001 (JKM 2012/04/19) + - h5repack: Fixed a failure when change the chunk size of a specified + chunked dataset with unlimited max dims. HDFFV-7993 (JKM 2012/04/11) + - h5diff: Fixed failure for comparing same named object with different + object types in comparing groups. Prior to the fix, h5diff resulted + in error. After the fix, h5diff detects such case as non-comparable + and display messages accordingly. HDFFV-7664 (JKM 2012/03/28) + - h5diff: If unique objects exists only in one file and try to exclude + the unique objects with --exclude-path option, h5diff missed + excluding some objects. + Fixed to exclude objects correctly in such case. + HDFFV-7837 (JKM 2012/03/20) + - h5dump: Added tools library error stack to properly catch error + information generated within the library. + HDFFV-7958 (ADB 2012/03/12) + - h5dump: Dangling links no longer throw error message, change process + when open link fails. + HDFFV-7839 (ADB 2012/03/12) + - h5diff: When two symbolic dangling links are compared with + --follow-symlinks option, the result should be same. It worked for + comparing two files, but didn't work for comparing two objects. + HDFFV-7835 (JKM 2012/03/09) + - h5dump: Refactored code to remove duplicated functions. Split XML + functions from DDL functions. Corrected indentation and formatting + errors. Also fixed subsetting counting overflow (HDFFV-5874). Verified + all tools call tools_init() in main. + HDFFV-7560 (ADB 2012/02/17) + - h5diff: fixed to prevent from displaying error stack message when + comparing the two dangling symlinks with follow-symlinks option. + HDFFV-7836 (JKM 2012/01/13) + - h5repack: fixed memory leak for handling variable length string in + attribute. HDFFV-7840 (JKM 2012/01/06) + - h5ls: fixed segfault when access region reference data in an + attribute. HDFFV-7838 (JKM 2011/12/29) + - h5diff: fixed segfault over non-comparable attribute with different + dimention or rank, along with '-c' option to display details. + HDFFV-7770 (JKM 2011/10/24) + - Fixed h5diff to display all the comparable object and attribute + regardless of non-comparables. HDFFV-7693 (JKM 2011/09/16) + - Fixed h5repack to update values of references(object and region) of + attributes in h5repack for 1) references, 2) ARRAY of references, + 3) VLEN of references, and 4) COMPOUND of references. + (JIRA HDF5 5932) PC -2011/09/14 + - h5diff: fixed segfault over dataset with container types + (array,lven) with multiple nested compound types. + (ex: compound->array->compound, compound->vlen->compound) + HDFFV-7712 JKM (2011/09/01) + - h5repack: added macro to handle failure in H5Dread/write when memory + allocation failed inside the library. (PC -- 2011/08/19) + - Fixed h5jam not to allow specifying an HDF5 formatted file as input + file for -u (user block file) option, because the original HDF5 file + will not be accessible if allows. HDFFV-5941 (JKM 2011/08/15) + - Revised command help pages of h5jam and h5unjam. The descriptions + were not up to date and some were missing. + HDFFV-7515 (JKM 2011/08/15) + - h5repack: h5repack failed to copy dataset if the layout is changed + from chunked with unlimited dims to contiguous. HDFFV-7649 + (PC -- 2011/07/15) + - h5diff: "--delta" option considers two NaN of the same type are + different, which is wrong based on h5diff description in Reference + Manual. HDFFV-7656 (PC -- 2011/07/15) + - Fixed h5diff to display instructive error message and exit with 1 + when mutually exclusive options (-d, -p and --use-system-epsilon) + are used together. HDFFV-7600 (JKM 2011/07/07) + - Fixed h5dump to display the first line of each element into correct + position for multiple dimention array type. + Before this fix, the first line of each element in array were + displayed after the last line of previous element without + moving to the next line (+indentation). + Bug #HDFFV-5878 (JKM 2011/06/15) + - Fixed h5dump to display correct value for H5T_STD_I8LE dataset + on a system (ppc64, linux, Big-Endian, clustering). + Bug #HDFFV-7594 (ABERT & JKM 2011/05/12) + - Fixed h5diff to compare file itself correctly. Previously h5diff + reported either different or not compatible in certain cases even + comparing file itself. This fix also improve performance when + comparing same target objects through verifying the obj&file + addresses before comparing the details in the objects (ex: datasets + or attributes) Bug #HDFFV-5928 (XCAO & JKM 2011/05/06) + - Updated h5dump test case script to prevent entire test failure upon + source directory is read-only. Bug# HDFFV-4342 (JKM 2011/4/12) + - Fixed h5dump displaying incorrect values for H5T_STD_I8BE type data in + attribute on Big-Endian machine. H5T_STD_I8BE is unsigned 8bit type, + so h5dump is supposed to display -2 instead of 254. It worked + correctly on Little-Endian system , but not on Big-Endian system. + Bug #HDFFV-4358 (JKM 2011/04/08) + - Updated to unify option name to '--enable-error-stack' for printing + HDF5 error stack messages for HDF5 tools. h5ls and h5dump for now. + For h5ls, this replaces "-e/--errors" option, which is deprecated. + Bug#2182 (JKM 2011/3/30) + - Fix h5diff for --use-system-epsilon option: the calculation changed + from ( |a - b| / b ) to ( |a - b| ). This was decided for better + performance. Bug#2184 (JKM 2011/3/24) + - Fixed output for H5T_REFERENCE in h5dump. According to the BNF document + the output of a H5T_REFERENCE should be followed by the type; + <reference> ::= H5T_REFERENCE { <ref_type> } + <ref_type> ::= H5T_STD_REF_OBJECT | H5T_STD_REF_DSETREG + Previously this was only displayed if the -R option was used. + Bug#1725 (ADB 2011/3/28) + - Fix h5diff issues for #1: h5diff compared attributes correctly only + when two objects have the same number of attributes and attribute + names are identical, #2: didn't display useful information about + attribute difference. Bug#2121 (JKM 2011/3/17) + - Fixed memory leak for h5diff when accessing symbolic links with + --follow-symlink option. Bug#2214 (JKM 2011/3/18) + - Fixed memory leak for h5diff when access variable length string + data. Bug#2216 (JKM 2011/3/18) + - Fixed and improved help page for -a option of h5ls. + Bug#1904 (JKM 2011/3/11) + - Fixed h5dump not to include attribute values in the output file when + h5dump "-y -o output_file" options were used. The problem was introduced + in HDF5 1.8.6 by showing data pointed by region references. (XCAO 2011/3/9) + - Fixed h5copy to be able to copy any object into the same HDF5 file. + Previously h5copy displayed error message when target file is same + as source file. (XCAO 2011/3/8) + - Fixed h5dump for skipping some values for long array type dataset on + Windows. This issue only occurred on Windows due to the different + return behavior from _vsnprintf() funtion. Bug#2161 (JKM 2011/3/3) + - Fixed h5dump for skipping array indices every certain number + when the array type dataset is relatively big. The certain number + varies according to the size of array. Bug#2092 (JKM 2011/2/15). + - Fixed h5diff for the segfault when compares compound datasets + with combination of fixed length string types and vlen string types + in certain orders. bug#2089 (JKM 2010/12/28) + - Improve h5diff performance. 1) use HDmemcmp() before comparing each + elements. 2) replace expensive H5Tequals() calls 3) retrieve datatype + information at dataset level not each element level for compound + datasets + - Fixed h5ls to display nested compound type with curly bracket + when -S (--simple) option is used with -l (--label), so it shows + which member (in curly bracket) belong to which nested compound type + and make the output make sense. bug#1979 (JKM 2010/11/09) + - Fixed h5diff to handle variable-length strings in a compound dataset + correctly. (also variable-length string array in a compound dataset) + Garbage values were displayed when h5diff compared multiple + variable-length strings in a compound type dataset. + Bug#1989 (JKM 2010/10/28) + - Fixed h5copy to fail gracefully when copying object to non-exist + group without -p option. Bug#2040 (JKM 2010/10/18) + - Fixed to compare member objects and groups recursively when two + files or groups are specified to be compared. Bug#1975 + (JKM 2010/9/16) + - Make h5repack be able to convert a layout to COMPACT for small size + dataset as default. bug#1896 (JKM 2010/09/15) + - Change h5ls not to manipulate special characters in object name or + attribute name for smart display. bug#1784 (JKM 2010/06/28) + - Fixed h5ls to return exit code 1 (error) when non-existent file is + specified. bug#1793. (JKM 2010/04/27) + - h5copy failed to copy dangling link when the link is specified + directly. bug#1817. (JKM 2010/04/22) + - h5repack lost attributes from a dataset of reference type. bug#1726. + (JKM 2010/3/25) + - h5repack sets NULL for object reference value for group or + named datatype. bug#1814. (JKM 2010/03/19) + - h5diff: fixed incorrect behavior (hang) in parallel mode when + specify invalid options (ex: -v and -q) (JKM 2010/02/17) + - h5dump/h5ls display buffer resize fixed in tools library. + (ADB - 2009/07/21 - 1520) + - Fixed many problems that could occur when using h5repack with named + datatypes. (NAF - 2009/4/20 - 1516/1466) + - h5dump, h5diff, h5repack were not reading (by hyperslabs) datasets + that have a datatype datum size greater than H5TOOLS_BUFSIZE, a + constant defined as 1024Kb, such as array types with large + dimensions (PVN - 2009/4/1 - 1501) + - h5import: By selecting a compression type, a big endian byte order was being + selected (PVN - 2009/3/11 - 1462) + - zip_perf.c had missing argument on one of the open() calls. Fixed. + (AKC - 2008/12/9) + - h5dump now checks for uniqueness of committed datatypes. + (NAF - 2008/10/15) + - Fixed unnecessary indentation of committed datatypes in h5dump. + (NAF - 2008/10/15) + - Fixed bugs in h5stat:segmemtation fault when printing groups and + print warning message when traversal of objects is unsuccessful. + (see bug #1253) (VC- 2008/10/13) + - Fixed bug in h5ls that prevented relative group listings (like + "h5ls foo.h5/bar") from working correctly (QAK - 2008/06/03) + - Fixed bug in h5diff that prevented datasets & attributes with + variable-length string elements from comparing correctly. + (QAK - 2008/02/28) + - h5import bug on Windows w/binary datasets. fread in windows needs a + binary file to be open with 'rb' instead of 'r' otherwise it + terminates execution if an end of file character is found on the + input file. Besides that the binary file generated needs to be open + with 'wb' , otherwise an end of line character is read twice. + (PVN - 2008/02/19) + - Fixed bug in h5dump that caused binary output to be made only for the first + dataset, when several datasets were requested. (PVN - 2008/04/07) + - h5dump: when doing binary output (-b), the stdout printing of attributes + was done incorrectly. Removed printing of attributes when doing binary + output. PVN - 2008/06/05 + + + High-Level APIs: + ------ + - Packet Table is updated. + + In the Packet Table C API, there are changes with the following functions, + which had been ifdef'ed out with VLPT_REMOVED since 2006 + * H5PTcreate_vl, is removed from this release + * H5PTfree_vlen_readbuff, is renamed to H5PTfree_vlen_buff + * H5PTis_varlen, is made available again + + Various cleanup: replacing 0/-1 with SUCCEED/FAIL and H5I_BADID with + H5I_INVALID_HID. (BMR, 2016/03/04, HDFFV-442) + + - Fixed problem with H5DSget_scale_name including the NULL terminator in + the size calculation returned by the function. The API does not + include the NULL terminator in the size returned (MSB- 2013/2/10) + + - Fixed problem with H5TBdelete_record destroying all data following the deletion + of a row. (MSB- 2012/7/26) + + - Fixed H5LTget_attribute_string not closing an object identifier when an + error occurs. (MSB- 2012/7/21) + + - Fixed the H5LTdtype_to_text function. It had some memory problems when + dealing with some complicated data types. HDFFVI-7701 (SLU - 2011/10/19) + + - Fixed a bug in H5DSattach_scale, H5DSis_attached and H5DSdetach_scale + caused by using H5Tget_native_type function to determine the native + type for reading REFERENCE_LIST attribute. The bug was exposed + on Mac PPC. + (EIP - 2010/05/22 -1851) + - Fixed a bug in the H5DSdetach_scale function when 0 bytes + were allocated after the last reference to a dim. scale + was removed from the list of references in a VL element of the + DIMENSION_LIST attribute; modified the function to comply + with the Spec: DIMENSION_LIST attribute is deleted now when no + dimension scales left attached. + (EIP - 2010/05/14 -1822) + - Fixed a bug where the H5TB API would forget the order of fields when + added out of offset order. (NAF - 2009/10/27 - 1582) + - H5DSis_attached failed to account for different platform types. Added a + get native type call. (ADB - 2009/9/29 - 1562) + - Dimension scales: The scale index return value in H5DSiterate_scales was not always + incremented. (PVN - 2009/4/8 - 1538) + + Fortran High-Level APIs: + ------ + + - Lite: The h5ltget_attribute_string_f used to return the C NULL character in the + returned character buffer. The returned Fortran charactor buffer now does + not return the C NULL character. (MSB - 2012/3/23) + - Lite: The h5ltget_dataset_info_f function (gets information about a dataset) + was not correctly returning the dimension array. (PVN - 2009/3/23) + - Lite: the h5ltread_dataset_string_f and h5ltget_attribute_string_f functions + had memory problems with the g95 fortran compiler. (PVN � 5/13/2009) 1522 + + + + + + Documentation + ------------- + + + F90 APIs + -------- + - Modified the h5open_f and h5close_f subroutines to not to call H5open + and H5close correspodningly. While the H5open call just adds overhead, + the H5close call called by an Fortran application shuts down the HDF5 + library making it unaccessible to the application. + HDFFV-915 (EIP & SB - 2011/10/13) + + + C++ APIs + -------- + - The constructor PropList::PropList(id) was fixed to act properly + according to the nature of 'id'. When 'id' is a property class id, + a new property list will be created. When 'id' id a property list id, + a copy of the property list will be made. (BMR - 2010/5/9) + - The parameters 'size' and 'bufsize' in CommonFG::getLinkval and + CommonFG::getComment, respectively, now have default values for + user's convenience. (BMR - 2009/10/23) + - NULL pointer accessing was fixed, bugzilla 1061. (BMR - 2009/10/05) + - read/write methods of DataSet and Attribute classes were fixed + to handle string correctly. (BMR - 2009/07/26) + - Fixed bug that caused segfaults in Attribute::read. (BMR - 2008/04/20) + - Fixed bug in PropList::getClassName to use portable HDfree instead + of free. (BMR - 2008/04/20) + - Fixed a design bug which allowed an Attribute object to create/modify + attributes (bugzilla #1068). The API class hierarchy was revised + to address the problem. Classes AbstractDS and Attribute are moved + out of H5Object. Class Attribute now multiply inherits from + IdComponent and AbstractDs and class DataSet from H5Object and + AbstractDs. In addition, the data member IdComponent::id was + moved into subclasses: Attribute, DataSet, DataSpace, DataType, + H5File, Group, and PropList. (BMR - 2008/08/10) + - IdComponent::dereference was incorrect and replaced as described + in "New Features" section. + (BMR - 2008/08/10) + + Testing + ------- + - tools/h5diff/testh5diff.sh is run in every "make check", even after it + has passed in the previous run. It should not run again if there is no + code changes. Fixed. (AKC - 2013/07/19 HDFFV-8392) + - In some Mac system, testlibinfo.sh failed with this error: + Check file ../src/.libs/libhdf5.7.dylib + strings: object: ../src/.libs/libhdf5.7.dylib malformed object \ + (unknown load command 15) + The strings command of Mac inspects library files and older + versions of strings may not know newer library format, resulting + in errors. Fixed by sending the library file as stdin to the strings + coommand to avoid this problem. (AKC - 2013/03/08 HDFFV-8305) + + - Fixed a typo in the ERROR macro in test/testhdf5.h. It segmentation + faulted when used before. (AKC - 2013/02/12 HDFFV-8267) + + +Supported Platforms +=================== + AIX 6.1 xlc 10.1.0.5 + (NASA G-ADA) xlC 10.1.0.5 + xlf90 12.1.0.6 + + Linux 2.6.18-308.13.1.el5PAE GNU C (gcc), Fortran (gfortran), C++ (g++) + #1 SMP i686 i686 i386 compilers for 32-bit applications; + (jam) Version 4.1.2 20080704 (Red Hat 4.1.2-54) + Version 4.8.2 + PGI C, Fortran, C++ Compilers for 32-bit + applications; + Version 13.7-0 + Intel(R) C, C++, Fortran Compiler for 32-bit + applications; + Version 14.0.2 (Build 20140120) + + Linux 2.6.18-371.6.1.el5 GNU C (gcc), Fortran (gfortran), C++ (g++) + #1 SMP x86_64 GNU/Linux compilers for 64-bit applications; + (koala) Version 4.1.2 20080704 (Red Hat 4.1.2-54) + Version 4.8.2 + Intel(R) C, C++, Fortran Compilers for + applications running on Intel(R) 64; + Version 14.0.2 (Build 20140120) + + Linux 2.6.32-431.11.2.el6 GNU C (gcc), Fortran (gfortran), C++ (g++) + #1 SMP x86_64 GNU/Linux compilers: + (platypus) Version 4.4.7 20120313 + Version 4.8.2 + PGI C, Fortran, C++ for 64-bit target on + x86-64; + Version 13.7-0 + Intel(R) C (icc), C++ (icpc), Fortran (icc) + compilers: + Version 14.0.2 (Build 20140120) + + Linux 2.6.32-431.29.2.el6.ppc64 gcc (GCC) 4.4.7 20120313 (Red Hat 4.4.7-4) + #1 SMP ppc64 GNU/Linux g++ (GCC) 4.4.7 20120313 (Red Hat 4.4.7-4) + (ostrich) GNU Fortran (GCC) 4.4.7 20120313 (Red Hat 4.4.7-4) + IBM XL C/C++ V13.1 + IBM XL Fortran V15.1 + + Linux 2.6.32-220.23.1.1chaos Intel C, C++, Fortran Compilers + ch5.x86_64 GNU/Linux Version 12.1.5.339 + (LLNL Aztec) + + IBM Blue Gene/P XL C for Blue Gene/P, bgxlc V9.0 + (LLNL uDawn) XL C++ for Blue Gene/P, bgxlC V9.0 + XL Fortran for Blue Gene/P, bgxlf90 V11.1 + + SunOS 5.11 32- and 64-bit Sun C 5.12 SunOS_sparc + (emu) Sun Fortran 95 8.6 SunOS_sparc + Sun C++ 5.12 SunOS_sparc + + Windows 7 Visual Studio 2008 (cmake) + Visual Studio 2010 w/ Intel Fortran 14 (cmake) + Visual Studio 2012 w/ Intel Fortran 15 (cmake) + Visual Studio 2013 w/ Intel Fortran 15 (cmake) + Visual Studio 2015 (cmake) + Cygwin(CYGWIN_NT-6.1 1.7.34(0.285/5/3) gcc(4.9.2) compiler and gfortran) + (cmake and autotools) + + Windows 7 x64 Visual Studio 2008 (cmake) + Visual Studio 2010 w/ Intel Fortran 14 (cmake) + Visual Studio 2012 w/ Intel Fortran 15 (cmake) + Visual Studio 2013 w/ Intel Fortran 15 (cmake) + Visual Studio 2015 (cmake) + + Windows 8.1 Visual Studio 2012 w/ Intel Fortran 15 (cmake) + Visual Studio 2013 w/ Intel Fortran 15 (cmake) + + Windows 8.1 x64 Visual Studio 2012 w/ Intel Fortran 15 (cmake) + Visual Studio 2013 w/ Intel Fortran 15 (cmake) + + Mac OS X Lion 10.7.3 gcc i686-apple-darwin11-llvm-gcc-4.2 (GCC) 4.2.1 from Xcode 4.2.1 + 32- and 64-bit g++ i686-apple-darwin11-llvm-g++-4.2 (GCC) 4.2.1 from Xcode 4.2.1 + (duck) gfortran GNU Fortran (GCC) 4.6.2 + + Mac OS X Mountain Lion 10.8.1 cc Apple clang version 4.0 from Xcode 4.5.1 + (owl) c++ Apple clang version 4.0 from Xcode 4.5.1 + gcc i686-apple-darwin11-llvm-gcc-4.2 (GCC) 4.2.1 from Xcode 4.5.1 + g++ i686-apple-darwin11-llvm-g++-4.2 (GCC) 4.2.1 from Xcode 4.5.1 + gfortran GNU Fortran (GCC) 4.6.2 + + +Tested Configuration Features Summary +===================================== + + In the tables below + y = tested + n = not tested in this release + C = Cluster + W = Workstation + x = not working in this release + dna = does not apply + ( ) = footnote appears below second table + <blank> = testing incomplete on this feature or platform + +Platform C F90/ F90 C++ zlib SZIP + parallel F2003 parallel +Solaris2.11 32-bit n y/y n y y y +Solaris2.11 64-bit n y/n n y y y +Windows 7 y y/y n y y y +Windows 7 x64 y y/y n y y y +Windows 7 Cygwin n y/n n y y y +Windows 7 x64 Cygwin n y/n n y y y +Windows 8 y y/y n y y y +Windows 8 x64 y y/y n y y y +Mac OS X Lion 10.7.3 32-bit n y/y n y y n +Mac OS X Lion 10.7.3 64-bit n y/y n y y y +Mac OS X Mountain Lion 10.8.1 64-bit n y/y n y y y +Mac OS X Mavericks 10.9.1 64-bit n y/y n y y ? +AIX 6.1 32- and 64-bit n y/n n y y y +CentOS 5.9 Linux 2.6.18-308 i686 GNU y y/y y y y y +CentOS 5.9 Linux 2.6.18-308 i686 Intel n y/y n y y y +CentOS 5.9 Linux 2.6.18-308 i686 PGI n y/y n y y y +CentOS 5.9 Linux 2.6.18 x86_64 GNU n y/y n y y y +CentOS 5.9 Linux 2.6.18 x86_64 Intel n y/y n y y y +CentOS 6.4 Linux 2.6.32 x86_64 GNU y y/y y y y y +CentOS 6.4 Linux 2.6.32 x86_64 Intel n y/y n y y y +CentOS 6.4 Linux 2.6.32 x86_64 PGI n y/y n y y y +Linux 2.6.32-431.11.2.el6.ppc64 n y/n n y y y + + +Platform Shared Shared Shared Thread- + C libs F90 libs C++ libs safe +Solaris2.11 32-bit y y y y +Solaris2.11 64-bit y y y y +Windows 7 y y y y +Windows 7 x64 y y y y +Windows 7 Cygwin n n n y +Windows 7 x64 Cygwin n n n y +Windows 8 y y y y +Windows 8 x64 y y y y +Mac OS X Lion 10.7.3 32-bit y n y y +Mac OS X Lion 10.7.3 64-bit y n y y +Mac OS X Mountain Lion 10.8.1 64-bit y n y y +Mac OS X Mavericks 10.9.1 64-bit y n y y +AIX 6.1 32- and 64-bit y n n y +CentOS 5.9 Linux 2.6.18-308 i686 GNU y y y y +CentOS 5.9 Linux 2.6.18-308 i686 Intel y y y n +CentOS 5.9 Linux 2.6.18-308 i686 PGI y y y n +CentOS 5.9 Linux 2.6.18 x86_64 GNU y y y y +CentOS 5.9 Linux 2.6.18 x86_64 Intel y y y n +CentOS 6.4 Linux 2.6.32 x86_64 GNU y y y n +CentOS 6.4 Linux 2.6.32 x86_64 Intel y y y n +CentOS 6.4 Linux 2.6.32 x86_64 PGI y y y n +Linux 2.6.32-431.11.2.el6.ppc64 y y y n + +Compiler versions for each platform are listed in the preceding +"Supported Platforms" table. + + +More Tested Platforms +===================== +The following platforms are not supported but have been tested for this release. + + Linux 2.6.18-308.13.1.el5PAE MPICH mpich 3.1.2 compiled with + #1 SMP i686 i686 i386 gcc 4.9.1 and gfortran 4.9.1 + (jam) g95 (GCC 4.0.3 (g95 0.94!) + + Linux 2.6.18-431.11.2.el6 MPICH mpich 3.1.2 compiled with + #1 SMP x86_64 GNU/Linux gcc 4.9.1 and gfortran 4.9.1 + (platypus) g95 (GCC 4.0.3 (g95 0.94!) + + FreeBSD 8.2-STABLE i386 gcc 4.2.1 [FreeBSD] 20070719 + (loyalty) gcc 4.6.1 20110422 + g++ 4.6.1 20110422 + gfortran 4.6.1 20110422 + + FreeBSD 8.2-STABLE amd64 gcc 4.2.1 [FreeBSD] 20070719 + (freedom) gcc 4.6.1 20110422 + g++ 4.6.1 20110422 + gfortran 4.6.1 20110422 + + Debian7.5.0 3.2.0-4-686 #1 SMP Debian 3.2.51-1 i686 GNU/Linux + gcc (Debian 4.7.2-5) 4.7.2 + GNU Fortran (Debian 4.7.2-5) 4.7.2 + (cmake and autotools) + + Debian7.5.0 3.2.0-4-amd64 #1 SMP Debian 3.2.51-1 x86_64 GNU/Linux + gcc (Debian 4.7.2-5) 4.7.2 + GNU Fortran (Debian 4.7.2-5) 4.7.2 + (cmake and autotools) + + Fedora20 3.15.3-200.fc20.i6866 #1 SMP i686 i686 i386 GNU/Linux + gcc (GCC) 4.8.3 20140624 (Red Hat 4.8.3-1) + GNU Fortran (GCC) 4.8.3 20140624 (Red Hat 4.8.3-1) + (cmake and autotools) + + Fedora20 3.15.3-200.fc20.x86_64 #1 SMP x86_64 x86_64 x86_64 GNU/Linux + gcc (GCC) 4.8.3 20140624 (Red Hat 4.8.3-1) + GNU Fortran (GCC) 4.8.3 20140624 (Red Hat 4.8.3-1) + (cmake and autotools) + + SUSE 13.1 3.11.10-17-desktop #1 SMP PREEMPT i686 athlon i386 GNU/Linux + gcc (SUSE Linux) 4.8.1 + GNU Fortran (SUSE Linux) 4.8.1 + (cmake and autotools) + + SUSE 13.1 3.11.10-17-desktop #1 SMP PREEMPT x86_64 x86_64 x86_64 GNU/Linux + gcc (SUSE Linux) 4.8.1 + GNU Fortran (SUSE Linux) 4.8.1 + (cmake and autotools) + + Ubuntu 14.04 3.13.0-35-generic #62-Ubuntu SMP i686 GNU/Linux + gcc (Ubuntu/Linaro 4.9.1-0ubuntu1) 4.9.1 + GNU Fortran (Ubuntu/Linaro 4.9.1-0ubuntu1) 4.9.1 + (cmake and autotools) + + Ubuntu 14.04 3.13.0-35-generic #62-Ubuntu SMP x86_64 GNU/Linux + gcc (Ubuntu/Linaro 4.9.1-0ubuntu1) 4.9.1 + GNU Fortran (Ubuntu/Linaro 4.9.1-0ubuntu1) 4.9.1 + (cmake and autotools) + + Cray Linux Environment (CLE) PrgEnv-pgi/4.0.46 + hopper.nersc.gov pgcc 12.5-0 64-bit target on x86-64 Linux -tp shanghai + pgf90 12.5-0 64-bit target on x86-64 Linux -tp shanghai + pgCC 12.5-0 64-bit target on x86-64 Linux -tp shanghai + + +Known Problems +============== +* "make check" fails on CYGWIN when building shared lib files is enabled. The + default on Cygwin has been changed to disable shared. It can be enabled with + the --enable-shared configure option but is likely to fail "make check" + with GCC compilers. (LK -2015/04/16) + +* CLANG compiler with the options -fcatch-undefined-behavior and -ftrapv + catches some undefined behavior in the alignment algorithm of the macro DETECT_I + in H5detect.c (Issue 8147). Since the algorithm is trying to detect the alignment + of integers, ideally the flag -fcatch-undefined-behavior shouldn't to be used for + H5detect.c. In the future, we can separate flags for H5detect.c from the rest of + the library. (SLU - 2013/10/16) + +* The 5.9 C++ compiler on Sun failed to compile a C++ test ttypes.cpp. It + complains with this message: + "/home/hdf5/src/H5Vprivate.h", line 130: Error: __func__ is not defined. + + The reason is that __func__ is a predefined identifier in C99 standard. The + HDF5 C library uses it in H5private.h. The test ttypes.cpp includes + H5private.h (H5Tpkg.h<-H5Fprivate.h<-H5Vprivate.h<-H5private.h). Sun's 5.9 + C++ compiler doesn't support __func__, thus fails to compile the C++ test. + But 5.11 C++ compiler does. To check whether your Sun C++ compiler knows this + identifier, try to compile the following simple C++ program: + #include<stdio.h> + + int main(void) + { + printf("%s\n", __func__); + return 0; + } + (SLU - 2012/11/5) + +* The C++ and FORTRAN bindings are not currently working on FreeBSD with the + native release 8.2 compilers (4.2.1), but are working with gcc 4.6 from the + ports (and probably gcc releases after that). + (QAK - 2012/10/19) + +* The data conversion test dt_arith.c has failures (segmentation fault) from + "long double" to other datatypes during hard conversion when the library + is built with the default GCC 4.2.1 on Mac Lion system. It only happens + with optimization (-O3, -O2, and -O1). Some newer versions of GCC do not + have this problem. Users should disable optimization or try newer version + of GCC. (Issue 8017. SLU - 2012/6/12) + +* The data conversion test dt_arith.c fails in "long double" to integer + conversion on Ubuntu 11.10 (3.0.0.13 kernal) with GCC 4.6.1 if the library + is built with optimization -O3 or -O2. The older GCC (4.5) or newer kernal + (3.2.2 on Fedora) doesn't have the problem. Users should lower down the + optimization level (-O1 or -O0) by defining CFLAGS in the command line of + "configure" like: + + CFLAGS=-O1 ./configure + + It will overwrite the library's default optimization level. (Issue 7829. + SLU - 2012/2/7) + +* --with-mpe configure option does not work with Mpich2. AKC - 2011/03/10) + +* While working on the 1.8.6 release of HDF5, a bug was discovered that can + occur when reading from a dataset in parallel shortly after it has been + written to collectively. The issue was exposed by a new test in the parallel + HDF5 test suite, but had existed before that. We believe the problem lies with + certain MPI implementations and/or filesystems. + + We have provided a pure MPI test program, as well as a standalone HDF5 + program, that can be used to determine if this is an issue on your system. + They should be run across multiple nodes with a varying number of processes. + These programs can be found at: + http://www.hdfgroup.org/ftp/HDF5/examples/known_problems/ + +* Parallel mode in AIX will fail some of the testcheck_version.sh tests where + it treats "exit(134) the same as if process 0 had received an abort signal. + This is fixed and will be available in the next release. AKC - 2009/11/3 + +* The PathScale MPI implementation, accessing a Panasas file system, would + cause H5Fcreate() with H5F_ACC_EXCL to fail even when the file is not + existing. This is due to the MPI_File_open() call failing if the amode has + the MPI_MODE_EXCL bit set. (See bug 1468 for details.) AKC - 2009/8/11 + +* Parallel tests failed with 16 processes with data inconsistency at testphdf5 + / dataset_readAll. Parallel tests also failed with 32 and 64 processes with + collective abort of all ranks at t_posix_compliant / allwrite_allread_blocks + with MPI IO. (CMC - 2009/04/28) + +* For SNL, spirit/liberty/thunderbird: The serial tests pass but parallel + tests failed with MPI-IO file locking message. AKC - 2007/6/25. +* On Intel 64 Linux cluster (RH 4, Linux 2.6.9) with Intel 10.0 compilers use + -mp -O1 compilation flags to build the libraries. Higher level of optimization + causes failures in several HDF5 library tests. +* For HPUX 11.23 many tools tests failed for 64-bit version when linked to the + shared libraries (tested for 1.8.0-beta2) +* For SNL, Red Storm: only paralle HDF5 is supported. The serial tests pass + and the parallel tests also pass with lots of non-fatal error messages. +* on SUN 5.10 C++ test fails in the "Testing Shared Datatypes with Attributes" test +* configuring with --enable-debug=all produces compiler errors on most + platforms. Users who want to run HDF5 in debug mode should use + --enable-debug rather than --enable-debug=all to enable debugging + information on most modules. +* On Mac OS 10.4, test/dt_arith.c has some errors in conversion from long + double to (unsigned) long long and from (unsigned)long long to long double. +* On Altix SGI with Intel 9.0 testmeta.c would not compile with -O3 + optimization flag. +* On VAX, Scaleoffset filter isn't supported. The filter cannot be applied to + HDF5 data generated on VAX. Scaleoffset filter only supports IEEE standard + for floating-point data. +* On Cray X1, a lone colon on the command line of h5dump --xml (as in + the testh5dumpxml.sh script) is misinterpereted by the operating system + and causes an error. +* On mpich 1.2.5 and 1.2.6, we found that if more than two processes + contribute no IO and the application asks to do IO with collective, we found + that when using 4 processors, a simple collective write will be hung + sometimes. This can be verified with t_mpi test under testpar. +* The dataset created or rewritten with the v1.6.3 library or after can't + be read with the v1.6.2 library or before when Fletcher32 EDC(filter) is + enabled. There was a bug in the calculating code of the Fletcher32 + checksum in the library before v1.6.3. The checksum value wasn't consistent + between big-endian and little-endian systems. This bug was fixed in + Release 1.6.3. However, after fixing the bug, the checksum value is no + longer the same as before on little-endian system. The library release + after 1.6.4 can still read the dataset created or rewritten with the library + of v1.6.2 or before. SLU - 2005/6/30 +* For the version 6(6.02 and 6.04) of Portland Group compiler on AMD Opteron + processor, there's a bug in the compiler for optimization(-O2). The library + failed in several tests but all related to multi driver. The problem has + been reported to the vendor. +* On IBM AIX systems, parallel HDF5 mode will fail some tests with error + messages like "INFO: 0031-XXX ...". This is from the command poe. + Set the environment variable MP_INFOLEVEL to 0 to minimize the messages + and run the tests again. + The tests may fail with messages like "The socket name is already + in use". HDF5 does not use sockets (except for stream-VFD). This is + due to problems of the poe command trying to set up the debug socket. + Check if there are many old /tmp/s.pedb.* staying around. These are + sockets used by the poe command and left behind due to failed commands. + Ask your system administrator to clean them out. Lastly, request IBM + to provide a mean to run poe without the debug socket. + +* The C++ library's tests fails when compiling with PGI C++ compiler. The + workaround until the problem is correctly handled is to use the + flag "--instantiate=local" prior to the configure and build steps, as: + setenv CXX "pgCC --instantiate=local" for pgCC 5.02 and higher + + +* The stream-vfd test uses ip port 10007 for testing. If another + application is already using that port address, the test will hang + indefinitely and has to be terminated by the kill command. To try the + test again, change the port address in test/stream_test.c to one not + being used in the host. + +* The --enable-static-exec configure flag will only statically link libraries + if the static version of that library is present. If only the shared version + of a library exists (i.e., most system libraries on Solaris, AIX, and Mac, + for example, only have shared versions), the flag should still result in a + successful compilation, but note that the installed executables will not be + fully static. Thus, the only guarantee on these systems is that the + executable is statically linked with just the HDF5 library. + +* With the gcc 2.95.2 compiler, HDF 5 uses the `-ansi' flag during + compilation. The ANSI version of the compiler complains about not being + able to handle the `long long' datatype with the warning: + + warning: ANSI C does not support `long long' + + This warning is innocuous and can be safely ignored. + +* Certain platforms give false negatives when testing h5ls: + - Cray J90 and Cray T90IEEE give errors during testing when displaying + some floating-point values. These are benign differences due to + the different precision in the values displayed and h5ls appears to + be dumping floating-point numbers correctly. + +* Not all platforms behave correctly with szip's shared libraries. Szip is + disabled in these cases, and a message is relayed at configure time. Static + libraries should be working on all systems that support szip, and should be + used when shared libraries are unavailable. There is also a configure error + on Altix machines that incorrectly reports when a version of szip without + an encoder is being used. + +* On some platforms that use Intel and Absoft compilers to build HDF5 fortran library, + compilation may fail for fortranlib_test.f90, fflush1.f90 and fflush2.f90 + complaining about exit subroutine. Comment out the line + IF (total_error .ne. 0) CALL exit (total_error) + +* Information about building with PGI and Intel compilers is available in + INSTALL file sections 5.7 and 5.8 + +* On at least one system, (SDSC DataStar), the scheduler (in this case + LoadLeveler) sends job status updates to standard error when you run + any executable that was compiled with the parallel compilers. + + This causes problems when running "make check" on parallel builds, as + many of the tool tests function by saving the output from test runs, + and comparing it to an exemplar. + + The best solution is to reconfigure the target system so it no longer + inserts the extra text. However, this may not be practical. + + In such cases, one solution is to "setenv HDF5_Make_Ignore yes" prior to + the configure and build. This will cause "make check" to continue after + detecting errors in the tool tests. However, in the case of SDSC DataStar, + it also leaves you with some 150 "failed" tests to examine by hand. + + A second solution is to write a script to run serial tests and filter + out the text added by the scheduler. A sample script used on SDSC + DataStar is given below, but you will probably have to customize it + for your installation. + + Observe that the basic idea is to insert the script as the first item + on the command line which executes the the test. The script then + executes the test and filters out the offending text before passing + it on. + + #!/bin/csh + + set STDOUT_FILE=~/bin/serial_filter.stdout + set STDERR_FILE=~/bin/serial_filter.stderr + + rm -f $STDOUT_FILE $STDERR_FILE + + ($* > $STDOUT_FILE) >& $STDERR_FILE + + set RETURN_VALUE=$status + + cat $STDOUT_FILE + + tail +3 $STDERR_FILE + + exit $RETURN_VALUE + + You get the HDF make files and test scipts to execute your filter script + by setting the environment variable "RUNSERIAL" to the full path of the + script prior to running configure for parallel builds. Remember to + "unsetenv RUNSERIAL" before running configure for a serial build. + + Note that the RUNSERIAL environment variable exists so that we can + can prefix serial runs as necessary on the target system. On DataStar, + no prefix is necessary. However on an MPICH system, the prefix might + have to be set to something like "/usr/local/mpi/bin/mpirun -np 1" to + get the serial tests to run at all. + + In such cases, you will have to include the regular prefix in your + filter script. + +* H5Ocopy() does not copy reg_ref attributes correctly when shared-message + is turn on. The value of the reference in the destination attriubte is + wrong. This H5Ocopy problem will affect h5copy tool + |