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diff --git a/release_docs/HISTORY-1_10.txt b/release_docs/HISTORY-1_10.txt new file mode 100644 index 0000000..03d0e3e --- /dev/null +++ b/release_docs/HISTORY-1_10.txt @@ -0,0 +1,1367 @@ +HDF5 History +============ + +This file contains development history of the HDF5 1.10 branch + +02. Release Information for hdf5-1.10.0-patch1 +01. Release Information for hdf5-1.10.0 + +[Search on the string '%%%%' for section breaks of each release.] + +%%%%1.10.0-patch1%%%% + + +HDF5 version 1.10.0-patch1 released on 2016-05-23 +================================================================================ + +INTRODUCTION + +This document describes the differences between HDF5-1.8 series and +HDF5 1.10.0 releases, and contains information on the platforms +tested. + +Links to HDF5 1.10.0 source code can be found on The HDF Group's +development FTP server at the following location: + + https://www.hdfgroup.org/HDF5/release/obtain5110.html + +User documentation can be accessed directly at this location: + + https://www.hdfgroup.org/HDF5/docNewFeatures/ + +For more information, see the HDF5 home page: + + https://www.hdfgroup.org/HDF5/ + +If you have any questions or comments, please send them to the HDF +Help Desk: + + help@hdfgroup.org + + + +CONTENTS + +- New Features +- Issues Addressed in this Release +- Supported Platforms +- Tested Configuration Features Summary +- More Tested Platforms +- Known Problems and Limitations + + + +New Features +============ +This release supports the following features: + + Configuration + ------------- + - API Compatibility with HDF5 1.8 Flag Was Added + + The 1.10 version of the HDF5 Library can be configured to operate + identically to the 1.8 library with the --with-default-api-version=v18 + configure flag. This allows existing code to be compiled with the 1.10 + library without requiring immediate changes to the application source + code. For addtional configuration options and other details, see + "API Compatibility Macros in HDF5" at + https://www.hdfgroup.org/HDF5/doc/RM/APICompatMacros.html. + + - Autotools Configuration Has Been Extensively Reworked + + The autotools configuration options have been updated to allow more + fine-grained control of the build options and to correct some bugs. + See configure --help for comprehensive information on each option. + + Specific changes: + + * --enable-debug and --enable-production are no longer accepted. + Use --enable-build-mode=(debug | production) instead. These set + appropriate defaults for symbols, optimizations, and other + configuration options. These defaults can be overridden by the + user. + + * Extra debug output messages are no longer enabled with + --enable-debug=<package list>. Use --enable-internal-debug=<pkg list> + instead. + + * A new --enable-symbols option allows symbols to be generated + independently of the build mode. --disable-symbols can be used + to strip symbols from the binary. + + * A new --enable-asserts option sets/unsets NDEBUG. This is + independent of the build mode. This also enables some extra + low-overhead debug checks in the library. + + * A new --enable-profiling option sets profiling flags. This is + independent of the build mode. + + * A new --enable-optimization option sets the optimization level. + This is independent of the build mode. + + * Many of these options can take a flags string that will be used + to build the library. This can be useful for specifying custom + optimization flags such as -Os and -Ofast. + + * gnu C++ and Fortran use configure sub-files that update the + build flags and turn on warnings. The increase in warnings when + building these wrapper libraries is due to these flag changes + and not to a decrease in code quality. + + * The option to clear file buffers has been removed. Any buffer that + will eventually be written to disk will now always be memset + to zero. This prevents the previous contents of the buffer from + being written to the disk if the buffer contents are not + completely overwritten, which has security implications. + + - LFS Changes + + The way the autotools handle large file support (LFS) has been + overhauled in this release. + + * We assume ftello and fseeko exist + + * We no longer explicitly use the *64 I/O functions. Instead, we + rely on a mapping provided by _FILE_OFFSET_BITS or its equivalent. + + * _LARGEFILE(64)_SOURCE is no longer exported via AM_CPPFLAGS. + + + + Parallel Library + ----------------- + - Collective Metadata I/O + + Calls for HDF5 metadata can result in many small reads and writes. + On metadata reads, collective metadata I/O can improve performance + by allowing the library to perform optimizations when reading the + metadata by having one rank read the data and broadcasting it to + all other ranks. + + Collective metadata I/O improves metadata write performance through + the construction of an MPI derived datatype that is then written + collectively in a single call. For more information, see + https://www.hdfgroup.org/HDF5/docNewFeatures/NewFeaturesCollectiveMetadataIoDocs.html. + + + + Library + -------- + - Concurrent Access to HDF5 Files - Single Writer/ Multple Reader (SWMR) + + The Single Writer/ Multiple Reader or SWMR feature enables users to + read data concurrently while writing it. Communications between the + processes and file locking are not required. The processes can run + on the same or on different platforms as long as they share a common + file system that is POSIX compliant. For more information, see the + Single-Writer/Multiple-Reader (SWMR) documentation at + https://www.hdfgroup.org/HDF5/docNewFeatures/NewFeaturesSwmrDocs.html. + + - Virtual Dataset (VDS) + + The VDS feature enables data to be accessed across HDF5 files + using standard HDF5 objects such as groups and datasets without + rewriting or rearranging the data. An HDF5 virtual dataset (VDS) + is an HDF5 dataset that is composed of source HDF5 datasets in + a predefined mapping. VDS can be used with the SWMR feature. For + documentation, check + https://www.hdfgroup.org/HDF5/docNewFeatures/NewFeaturesVirtualDatasetDocs.html. + + - Persistent Free File Space Tracking + + Usage patterns when working with an HDF5 file sometimes result in + wasted space within the file. This can also impair access times + when working with the resulting files. The new file space management + feature provides strategies for managing space in a file to improve + performance in both of these areas. For more information, see + https://www.hdfgroup.org/HDF5/docNewFeatures/NewFeaturesFileSpaceMgmtDocs.html. + + - Version 3 Metadata Cache + + The version 3 metadata cache moves management of metadata I/O from + the clients to the metadata cache proper. This change is essential for + SWMR and other features that have yet to be released. + + + + C++ Library + ------------ + - New Member Function Added to H5::ArrayType + + The assignment operator ArrayType::operator= was added because + ArrayType has pointer data members. + + (BMR - 2016/03/07, HDFFV-9562) + + + + Tools + ------ + - h5watch + + The h5watch tool allows users to output new records appended to + a dataset under SWMR access as it grows. The functionality is + similar to the Unix user command "tail" with the follow option, + which outputs appended data as the file grows. For more + information, see + https://www.hdfgroup.org/HDF5/docNewFeatures/NewFeaturesSwmrDocs.html#Tools. + + - h5format_convert + + The h5format_convert tool allows users to convert the indexing + type of a chunked dataset made with a 1.10.x version of the HDF5 + Library when the latest file format is used to the 1.8.x version 1 B-tree indexing + type. For example, datasets created using SWMR access, can be + converted to be accessed by the HDF5 1.18 library and tools. The + tool does not rewrite raw data, but it does rewrite HDF5 metadata. + + + + High-Level APIs + ---------------- + - H5DOappend + + The function appends data to a dataset along a specified dimension. + + + C Packet Table API + ------------------ + - Replacement of a Public Function with H5PTcreate + + The existing function H5PTcreate_fl limits applications so they + can use the deflate compression only. The public function + H5PTcreate has been added to replace H5PTcreate_fl. H5PTcreate + takes a property list identifier to provide flexibility on + creation properties. + + (BMR - 2016/03/04, HDFFV-8623) + + - New Public Functions: H5PTget_dataset and H5PTget_type + + Two accessor functions have been added. H5PTget_dataset returns + the identifier of the dataset associated with the packet table, + and H5PTget_type returns the identifier of the datatype used by + the packet table. + + (BMR, 2016/03/04, HDFFV-8623) + + - Regarding #ifdef VLPT_REMOVED + + The #ifdef VLPT_REMOVED blocks have been removed from the packet + table (PT) library source except for the following functions: + + H5PTis_varlen() has been made available again + + H5PTfree_vlen_readbuff() is now H5PTfree_vlen_buff() + + (BMR - 2016/03/04, HDFFV-442) + + C++ Packet Table API + -------------------- + - New Constructor Added to FL_PacketTable + + An overloaded constructor has been added to FL_PacketTable and + takes a property list identifier to provide flexibility on + creation properties. + + (BMR - 2016/03/08, HDFFV-8623) + + - New Public Functions + + Two accessor wrappers are added to class PacketTable. + PacketTable::GetDataset() returns the identifier of the dataset + associated with the packet table, and PacketTable::GetDatatype() + returns the identifier of the datatype that the packet table uses. + + (BMR - 2016/03/04, HDFFV-8623) + + - Member Functions with "char*" as an Argument + + Overloaded functions were added to provide the "const char*" + argument; the existing version will be deprecated in future + releases. + + (BMR - 2016/03/04, HDFFV-8623) + + - Regarding #ifdef VLPT_REMOVED + + The #ifdef VLPT_REMOVED blocks have been removed from the packet + table library source code except for the following functions: + + VL_PacketTable::IsVariableLength() was moved to PacketTable + + VL_PacketTable::FreeReadBuff() is now PacketTable::FreeBuff() + + (BMR - 2016/03/04, HDFFV-442) + + + + Java Wrapper Library + -------------------- + + The Java HDF5 JNI library has been integrated into the HDF5 repository. + The configure option is "--enable-java", and the CMake option is + HDF5_BUILD_JAVA:BOOL=ON. The package hierarchy has changed from the + HDF5 1.8 JNI, which was "ncsa.hdf.hdflib.hdf5", to HDF5 1.10, + "hdf.hdflib.hdf5". + + A number of new APIs were added including some for VDS and SWMR. + + + + Other Important Changes + ----------------------- + + The hid_t type was changed from 32-bit to a 64-bit value. + + + +Issues Addressed in this Release Since 1.10.0 +============================================= + + - h5diff would return from a compare attributes abnormally if one of the datatypes + was a vlen. This resulted in a memory leak as well as an incorrect report of + attribute comparison. + + Fixed. + (ADB - 2016/04/26, HDFFV-9784) + + - The JUnit-interface test may fail on Solaris platforms. The result of + a test for verifying the content of the error stack to stdout is + in a different order on Solaris then other platforms. + + This test is skipped on Solaris + (ADB - 2016/04/21, HDFFV-9734) + + - When building HDF5 with Java using CMake and specifying Debug for CMAKE_BUILD_TYPE, + there was a missing command argument for the tests of the examples. + + Fixed. + (ADB - 2016/04/21, HDFFV-9743) + + - Changed h5diff to print a warning when a dataset is virtual, enabling + the data to be compared. In addition h5repack failed to copy the data + of a virtual dataset to the new file. Function H5D__get_space_status changed + to correctly determine the H5D_space_status_t allocation value. + + CMake added the Fixed Array indexing tests that were only in the autotools + test scripts. + + Fixed and tests added for vds issues. + (ADB,NAF - 2016/04/21, HDFFV-9756) + + - CMake added the h5format_convert tool and tests that were only in the autotools + build and test scripts. The autotools test script was reworked to allow CMake + to execute the test suite in parallel. + + Also, h5clear tool and tests were added to the misc folder. + + Fixed. + (ADB - 2016/04/21, HDFFV-9766) + + - CMake added the h5watch tool and argument tests that were only in the autotools + build and test scripts. The POSIX only tests were not added to CMake. + + CMake HL tools files were refactored to move the CMake test scripts into each tool folder. + + Fixed. + (ADB - 2016/04/21, HDFFV-9770) + + - Configure fails to detect valid real KINDs on FreeBSD 9.3 (i386) with Fortran enabled. + + Fixed. Added the exponential option to SELECTED_REAL_KIND to distinguish + KINDs of same precision + (MSB - 2016/05/14,HDFFV-9912) + + + - Corrected the f90 H5AWRITE_F integer interface's buf to be INTENT(IN). + (MSB - 2016/05/14) + + - Configure fails in sed command on FreeBSD 9.3 (i386) with Fortran enabled. + + Fixed. + (MSB - 2016/05/14,HDFFV-9912) + + - Compile time error in H5f90global.F90 with IBM XL Fortran 14.1.0.13 on BG/Q with Fortran + enabled. + + Fixed. + (MSB - 2016/05/16,HDFFV-9917) + + - A cmake build with Fortran enabled does not install module h5fortkit + + Fixed. + (MSB - 2016/05/23,HDFFV-9923) + + +Issues Addressed in this Release Since alpha1 +============================================= + + - H5Pget_virtual_printf_gap, H5Pget_virtual_view, H5Pget_efile_prefix + + The correct access property list settings from the + H5Pget_virtual_printf_gap, H5Pget_virtual_view, and + H5Pget_efile_prefix function calls could not be retrieved + using H5Dget_access_plist(). + + Fixed. + + (DER and NAF - 2016/03/14, HDFFV-9716) + + - h5dump + + When h5dump was provided with the name of a non-existing file or + when optional arguments were the last option on the command line, + h5dump would segfault. + + Fixed. + + (ADB 2016/02/28 HDFFV-9639, HDFFV-9684) + + - No Error Message for Corrupt Metadata + + The HDF5 Library did not propagate an error when it encountered + corrupt metadata in an HDF5 file. The issue was fixed for a + specific file provided by a user. If you still see the problem, + please contact help@hdfgroup.org + + Fixed. + + (MC - 2016/02/18, HDFFV-9670) + + - Problem Reading Chunked Datasets with a String Datatype Larger + Than the Chunk Size in Bytes + + When the latest file format was used and when a chunked dataset + was created with a datatype with the size bigger than a chunk + size, the data could not be read back. The issue was reported + for chunked datasets with a string datatype and was confirmed + for other datatypes with the sizes bigger than the chunk size in + bytes. + + Fixed. + + (JM - 2016/02/13, HDFFV-9672) + + - Control over the Location of External Files + + Users were unable to specify the locations of external files. + + Two APIs - H5Pget_efile_prefix and H5Pset_efile_prefix - were + added so that users could specify the locations of external files. + + (DER - 2016/02/04, HDFFV-8740) + + + +Issues Addressed in this Release Since alpha0 +============================================= + - h5format_convert + + The h5format_convert tool did not downgrade the version of the + superblock. + + Fixed. The tool now will downgrade the version of the superblock. + + (EIP 2016/01/11) + + - Crashes with multiple threads: invalid pointers + + It was reported that alpha0 crashed when used with multiple + threads. The issue exists in the HDF5 Library versions 1.8 and + 1.9. The problem is related to a shared file pointer used in some + miscellaneous data structures. The thread-safe library exposed + paths in the library where a file pointer became invalid. + + The alpha1 release contains the fixes for the specific use case + as described in HDFFV-9643. We will keep working on identifying + and fixing other paths in the library with similar problems. + + (EIP - 2016/01/15, HDFFV-9643) + + + +Supported Platforms +=================== +The following platforms are supported and have been tested for this release. +They are built with the configure process unless specified otherwise. + + AIX 6.1 xlc/xlc_r 10.1.0.5 + (NASA G-ADA) xlC/xlC_r 10.1.0.5 + xlf90/xlf90_r 12.1.0.6 + + Linux 2.6.32-573.22.1.el6 GNU C (gcc), Fortran (gfortran), C++ (g++) + #1 SMP x86_64 GNU/Linux compilers: + (mayll/platypus) Version 4.4.7 20120313 (Red Hat 4.4.7-16) + Version 4.9.3, Version 5.2.0 + PGI C, Fortran, C++ for 64-bit target on + x86-64; + Version 15.7-0 + Intel(R) C (icc), C++ (icpc), Fortran (icc) + compilers: + Version 15.0.3.187 Build 20150407 + MPICH 3.1.4 compiled with GCC 4.9.3 + + Linux 2.6.32-573.18.1.el6.ppc64 gcc (GCC) 4.4.7 20120313 (Red Hat 4.4.7-11) + #1 SMP ppc64 GNU/Linux g++ (GCC) 4.4.7 20120313 (Red Hat 4.4.7-11) + (ostrich) GNU Fortran (GCC) 4.4.7 20120313 (Red Hat 4.4.7-11) + IBM XL C/C++ V13.1 + IBM XL Fortran V15.1 + + Linux 3.10.0-327.10.1.el7 GNU C (gcc), Fortran (gfortran), C++ (g++) + #1 SMP x86_64 GNU/Linux compilers: + (kituo/moohan) Version 4.8.5 20150623 (Red Hat 4.8.5-4) + Version 4.9.3, Version 5.2.0 + Intel(R) C (icc), C++ (icpc), Fortran (icc) + compilers: + Version 15.0.3.187 Build 20150407 + MPICH 3.1.4 compiled with GCC 4.9.3 + + SunOS 5.11 32- and 64-bit Sun C 5.12 SunOS_sparc + (emu) Sun Fortran 95 8.6 SunOS_sparc + Sun C++ 5.12 SunOS_sparc + + Windows 7 Visual Studio 2012 w/ Intel Fortran 15 (cmake) + Visual Studio 2013 w/ Intel Fortran 15 (cmake) + Visual Studio 2015 w/ Intel Fortran 16 (cmake) + Cygwin(CYGWIN_NT-6.1 2.2.1(0.289/5/3) gcc(4.9.3) compiler and gfortran) + (cmake and autotools) + + Windows 7 x64 Visual Studio 2012 w/ Intel Fortran 15 (cmake) + Visual Studio 2013 w/ Intel Fortran 15 (cmake) + Visual Studio 2015 w/ Intel Fortran 16 (cmake) + + Windows 8.1 Visual Studio 2012 w/ Intel Fortran 15 (cmake) + Visual Studio 2013 w/ Intel Fortran 15 (cmake) + + Windows 8.1 x64 Visual Studio 2012 w/ Intel Fortran 15 (cmake) + Visual Studio 2013 w/ Intel Fortran 15 (cmake) + + Mac OS X Mt. Lion 10.8.5 Apple clang/clang++ version 5.1 from Xcode 5.1 + 64-bit gfortran GNU Fortran (GCC) 4.8.2 + (swallow/kite) Intel icc/icpc/ifort version 15.0.3 + + Mac OS X Mavericks 10.9.5 Apple clang/clang++ version 6.0 from Xcode 6.2 + 64-bit gfortran GNU Fortran (GCC) 4.9.2 + (wren/quail) Intel icc/icpc/ifort version 15.0.3 + + Mac OS X Yosemite 10.10.5 Apple clang/clang++ version 6.0 from Xcode 7.0 + 64-bit gfortran GNU Fortran (GCC) 4.9.2 + (osx1010dev/osx1010test) Intel icc/icpc/ifort version 15.0.3 + + Mac OS X El Capitan 10.11.4 Apple clang/clang++ version 7.3.0 from Xcode 7.3 + 64-bit gfortran GNU Fortran (GCC) 5.2.0 + (osx1010dev/osx1010test) Intel icc/icpc/ifort version 15.0.3 + + + +Tested Configuration Features Summary +===================================== + + In the tables below + y = tested + n = not tested in this release + C = Cluster + W = Workstation + x = not working in this release + dna = does not apply + ( ) = footnote appears below second table + <blank> = testing incomplete on this feature or platform + +Platform C F90/ F90 C++ zlib SZIP + parallel F2003 parallel +SunOS 5.11 32-bit n y/y n y y y +SunOS 5.11 64-bit n y/y n y y y +Windows 7 y y/y n y y y +Windows 7 x64 y y/y n y y y +Windows 7 Cygwin n y/y n y y n +Windows 8.1 n y/y n y y y +Windows 8.1 x64 n y/y n y y y +Mac OS X Mountain Lion 10.8.5 64-bit n y/y n y y y +Mac OS X Mavericks 10.9.5 64-bit n y/y n y y y +Mac OS X Yosemeti 10.10.5 64-bit n y/y n y y y +AIX 6.1 32- and 64-bit n y/n n y y y +CentOS 6.7 Linux 2.6.32 x86_64 GNU y y/y y y y y +CentOS 6.7 Linux 2.6.32 x86_64 Intel n y/y n y y y +CentOS 6.7 Linux 2.6.32 x86_64 PGI n y/y n y y y +CentOS 7.1 Linux 3.10.0 x86_64 GNU y y/y y y y y +CentOS 7.1 Linux 3.10.0 x86_64 Intel n y/y n y y y +Linux 2.6.32-431.11.2.el6.ppc64 n y/n n y y y + +Platform Shared Shared Shared Thread- + C libs F90 libs C++ libs safe +SunOS 5.11 32-bit y y y y +SunOS 5.11 64-bit y y y y +Windows 7 y y y y +Windows 7 x64 y y y y +Windows 7 Cygwin n n n y +Windows 8.1 y y y y +Windows 8.1 x64 y y y y +Mac OS X Mountain Lion 10.8.5 64-bit y n y y +Mac OS X Mavericks 10.9.5 64-bit y n y y +Mac OS X Yosemeti 10.10.5 64-bit y n y y +AIX 6.1 32- and 64-bit y n n y +CentOS 6.7 Linux 2.6.32 x86_64 GNU y y y y +CentOS 6.7 Linux 2.6.32 x86_64 Intel y y y y +CentOS 6.7 Linux 2.6.32 x86_64 PGI y y y y +CentOS 7.1 Linux 3.10.0 x86_64 GNU y y y y +CentOS 7.1 Linux 3.10.0 x86_64 Intel y y y y +Linux 2.6.32-431.11.2.el6.ppc64 y y y y + +Compiler versions for each platform are listed in the preceding +"Supported Platforms" table. + + + +More Tested Platforms +===================== +The following platforms are not supported but have been tested for this release. + + Linux 2.6.18-431.11.2.el6 g95 (GCC 4.0.3 (g95 0.94!) + #1 SMP x86_64 GNU/Linux + (platypus) + + Windows 7 Visual Studio 2008 (cmake) + + Windows 7 x64 Visual Studio 2008 (cmake) + + Windows 7 x64 Visual Studio 2010 (cmake) with SWMR using GPFS + + Windows 10 Visual Studio 2013 w/ Intel Fortran 15 (cmake) + + Windows 10 x64 Visual Studio 2013 w/ Intel Fortran 15 (cmake) + + Debian7.5.0 3.2.0-4-amd64 #1 SMP Debian 3.2.51-1 x86_64 GNU/Linux + gcc (Debian 4.7.2-5) 4.7.2 + GNU Fortran (Debian 4.7.2-5) 4.7.2 + (cmake and autotools) + + Fedora20 3.15.3-200.fc20.x86_64 #1 SMP x86_64 x86_64 x86_64 GNU/Linux + gcc (GCC) 4.8.3 20140624 (Red Hat 4.8.3-1) + GNU Fortran (GCC) 4.8.3 20140624 (Red Hat 4.8.3-1) + (cmake and autotools) + + SUSE 13.1 3.11.10-17-desktop #1 SMP PREEMPT x86_64 x86_64 x86_64 GNU/Linux + gcc (SUSE Linux) 4.8.1 + GNU Fortran (SUSE Linux) 4.8.1 + (cmake and autotools) + + Ubuntu 14.04 3.13.0-35-generic #62-Ubuntu SMP x86_64 GNU/Linux + gcc (Ubuntu/Linaro 4.9.1-0ubuntu1) 4.9.1 + GNU Fortran (Ubuntu/Linaro 4.9.1-0ubuntu1) 4.9.1 + (cmake and autotools) + + hopper.nersc.gov PrgEnv-gnu/5.2.40 + gcc (GCC) 4.9.2 20141030 (Cray Inc.) + GNU Fortran (GCC) 4.9.2 20141030 (Cray Inc.) + g++ (GCC) 4.9.2 20141030 (Cray Inc.) + + + +Known Problems and Limitations +============================== +This section contains the list of known problems and limitations introduced +in this release of HDF5. + +Note: this list is not exhaustive of all known issues discovered in HDF5 +software to date. For a list of significant problems and known workarounds +identified in past releases, please refer to: + +https://www.hdfgroup.org/HDF5/release/known_problems/ + +The HDF Group also maintains a JIRA issue-tracking database which is used to +capture all known issues which are too numerous to reasonably list in this +document. The HDF Group is taking steps to make our JIRA issue database +open to the public, and this section will refer to that database in a future +release. In the meantime, please contact help@hdfgroup.org if you come across +an issue not listed here or at the link above, and we will provide any +information about known workarounds that we have or add it to our list of +known issues if it is a new issue. + + - The flush/refresh test occasionally fails on OS X platforms. This is + being investigated but no fix or workaround is available at this time. + (DER - 2016/03/22, HDFFV-9731) + + - The VDS/SWMR test will fail with a segmentation fault if the library + is built with --enable-using-memchecker. The is due to a VDS shutdown + procedure freeing a shared resource too early when the memory + checker changes are built. This problem does not arise when the + memory checker changes are not used since the internal library free + lists behave differently. The memory checker configure option should + normally only be used under special circumstances so this should not + affect most users. Users should be aware that the --enable-using-memchecker + + VDS combination may cause a segfault, however, so Valgrind et al. may + have to be used with an HDF5 library built without the feature if this + proves to be a problem. + (DER - 2016/03/21, HDFFV-9732) + + - SWMR feature limitations + The SWMR feature will only work if an HDF5 file under SWMR access resides + on a file system that obeys POSIX write() ordering semantics. Because of + this, SWMR will not work on network file systems such as NFS or SMB/Windows + file shares since those systems do not guarantee write odering. SWMR + regression tests are likely to fail if run on a network file system. SWMR + is currently not tested on Windows though it can be tested manually + (some of the SWMR test programs are built by CMake), and there are no + obvious reasons for it to not work on NTFS or GPFS. + (EIP - 2016/03/20, HDFFV-9733) + + - VDS feature limitation + Currently, the path to a VDS source file is interpreted as relative to the + directory where the executable program runs and not to the HDF5 file with + the VDS dataset unless a full path to the source file is specified during + the mapping. + (EIP - 2016/03/20, HDFFV-9724) + + - The H5Lexists API changed behavior in HDF5-1.10 when used with a file handle + and root group name ("/"): + + H5Lexists(fileid, "/") + + In HDF5-1.8 it returns false (0) and in HDF5-1.10 it returns true (1). + The documentation will be updated with information regarding this change. + (LRK - 2016/03/30, HDFFV-8746) + + +%%%%1.10.0%%%% + +HDF5 version 1.10.0 released on 2016-03-30 +================================================================================ + + + +INTRODUCTION + +This document describes the differences between HDF5-1.8 series and +HDF5 1.10.0 releases, and contains information on the platforms +tested. + +Links to HDF5 1.10.0 source code can be found on The HDF Group's +development FTP server at the following location: + + https://www.hdfgroup.org/HDF5/release/obtain5110.html + +User documentation can be accessed directly at this location: + + https://www.hdfgroup.org/HDF5/docNewFeatures/ + +For more information, see the HDF5 home page: + + https://www.hdfgroup.org/HDF5/ + +If you have any questions or comments, please send them to the HDF +Help Desk: + + help@hdfgroup.org + + + +CONTENTS + +- New Features +- Issues Addressed in this Release +- Supported Platforms +- Tested Configuration Features Summary +- More Tested Platforms +- Known Problems and Limitations + + + +New Features +============ +This release supports the following features: + + Configuration + ------------- + - API Compatibility with HDF5 1.8 Flag Was Added + + The 1.10 version of the HDF5 Library can be configured to operate + identically to the 1.8 library with the --with-default-api-version=v18 + configure flag. This allows existing code to be compiled with the 1.10 + library without requiring immediate changes to the application source + code. For addtional configuration options and other details, see + "API Compatibility Macros in HDF5" at + https://www.hdfgroup.org/HDF5/doc/RM/APICompatMacros.html. + + - Autotools Configuration Has Been Extensively Reworked + + The autotools configuration options have been updated to allow more + fine-grained control of the build options and to correct some bugs. + See configure --help for comprehensive information on each option. + + Specific changes: + + * --enable-debug and --enable-production are no longer accepted. + Use --enable-build-mode=(debug | production) instead. These set + appropriate defaults for symbols, optimizations, and other + configuration options. These defaults can be overridden by the + user. + + * Extra debug output messages are no longer enabled with + --enable-debug=<package list>. Use --enable-internal-debug=<pkg list> + instead. + + * A new --enable-symbols option allows symbols to be generated + independently of the build mode. --disable-symbols can be used + to strip symbols from the binary. + + * A new --enable-asserts option sets/unsets NDEBUG. This is + independent of the build mode. This also enables some extra + low-overhead debug checks in the library. + + * A new --enable-profiling option sets profiling flags. This is + independent of the build mode. + + * A new --enable-optimization option sets the optimization level. + This is independent of the build mode. + + * Many of these options can take a flags string that will be used + to build the library. This can be useful for specifying custom + optimization flags such as -Os and -Ofast. + + * gnu C++ and Fortran use configure sub-files that update the + build flags and turn on warnings. The increase in warnings when + building these wrapper libraries is due to these flag changes + and not to a decrease in code quality. + + * The option to clear file buffers has been removed. Any buffer that + will eventually be written to disk will now always be memset + to zero. This prevents the previous contents of the buffer from + being written to the disk if the buffer contents are not + completely overwritten, which has security implications. + + - LFS Changes + + The way the autotools handle large file support (LFS) has been + overhauled in this release. + + * We assume ftello and fseeko exist + + * We no longer explicitly use the *64 I/O functions. Instead, we + rely on a mapping provided by _FILE_OFFSET_BITS or its equivalent. + + * _LARGEFILE(64)_SOURCE is no longer exported via AM_CPPFLAGS. + + + + Parallel Library + ----------------- + - Collective Metadata I/O + + Calls for HDF5 metadata can result in many small reads and writes. + On metadata reads, collective metadata I/O can improve performance + by allowing the library to perform optimizations when reading the + metadata by having one rank read the data and broadcasting it to + all other ranks. + + Collective metadata I/O improves metadata write performance through + the construction of an MPI derived datatype that is then written + collectively in a single call. For more information, see + https://www.hdfgroup.org/HDF5/docNewFeatures/NewFeaturesCollectiveMetadataIoDocs.html. + + + + Library + -------- + - Concurrent Access to HDF5 Files - Single Writer/ Multple Reader (SWMR) + + The Single Writer/ Multiple Reader or SWMR feature enables users to + read data concurrently while writing it. Communications between the + processes and file locking are not required. The processes can run + on the same or on different platforms as long as they share a common + file system that is POSIX compliant. For more information, see the + Single-Writer/Multiple-Reader (SWMR) documentation at + https://www.hdfgroup.org/HDF5/docNewFeatures/NewFeaturesSwmrDocs.html. + + - Virtual Dataset (VDS) + + The VDS feature enables data to be accessed across HDF5 files + using standard HDF5 objects such as groups and datasets without + rewriting or rearranging the data. An HDF5 virtual dataset (VDS) + is an HDF5 dataset that is composed of source HDF5 datasets in + a predefined mapping. VDS can be used with the SWMR feature. For + documentation, check + https://www.hdfgroup.org/HDF5/docNewFeatures/NewFeaturesVirtualDatasetDocs.html. + + - Persistent Free File Space Tracking + + Usage patterns when working with an HDF5 file sometimes result in + wasted space within the file. This can also impair access times + when working with the resulting files. The new file space management + feature provides strategies for managing space in a file to improve + performance in both of these areas. For more information, see + https://www.hdfgroup.org/HDF5/docNewFeatures/NewFeaturesFileSpaceMgmtDocs.html. + + - Version 3 Metadata Cache + + The version 3 metadata cache moves management of metadata I/O from + the clients to the metadata cache proper. This change is essential for + SWMR and other features that have yet to be released. + + + + C++ Library + ------------ + - New Member Function Added to H5::ArrayType + + The assignment operator ArrayType::operator= was added because + ArrayType has pointer data members. + + (BMR - 2016/03/07, HDFFV-9562) + + + + Tools + ------ + - h5watch + + The h5watch tool allows users to output new records appended to + a dataset under SWMR access as it grows. The functionality is + similar to the Unix user command "tail" with the follow option, + which outputs appended data as the file grows. For more + information, see + https://www.hdfgroup.org/HDF5/docNewFeatures/NewFeaturesSwmrDocs.html#Tools. + + - h5format_convert + + The h5format_convert tool allows users to convert the indexing + type of a chunked dataset made with a 1.10.x version of the HDF5 + Library when the latest file format is used to the 1.8.x version 1 B-tree indexing + type. For example, datasets created using SWMR access, can be + converted to be accessed by the HDF5 1.18 library and tools. The + tool does not rewrite raw data, but it does rewrite HDF5 metadata. + + + + High-Level APIs + ---------------- + - H5DOappend + + The function appends data to a dataset along a specified dimension. + + + C Packet Table API + ------------------ + - Replacement of a Public Function with H5PTcreate + + The existing function H5PTcreate_fl limits applications so they + can use the deflate compression only. The public function + H5PTcreate has been added to replace H5PTcreate_fl. H5PTcreate + takes a property list identifier to provide flexibility on + creation properties. + + (BMR - 2016/03/04, HDFFV-8623) + + - New Public Functions: H5PTget_dataset and H5PTget_type + + Two accessor functions have been added. H5PTget_dataset returns + the identifier of the dataset associated with the packet table, + and H5PTget_type returns the identifier of the datatype used by + the packet table. + + (BMR, 2016/03/04, HDFFV-8623) + + - Regarding #ifdef VLPT_REMOVED + + The #ifdef VLPT_REMOVED blocks have been removed from the packet + table (PT) library source except for the following functions: + + H5PTis_varlen() has been made available again + + H5PTfree_vlen_readbuff() is now H5PTfree_vlen_buff() + + (BMR - 2016/03/04, HDFFV-442) + + C++ Packet Table API + -------------------- + - New Constructor Added to FL_PacketTable + + An overloaded constructor has been added to FL_PacketTable and + takes a property list identifier to provide flexibility on + creation properties. + + (BMR - 2016/03/08, HDFFV-8623) + + - New Public Functions + + Two accessor wrappers are added to class PacketTable. + PacketTable::GetDataset() returns the identifier of the dataset + associated with the packet table, and PacketTable::GetDatatype() + returns the identifier of the datatype that the packet table uses. + + (BMR - 2016/03/04, HDFFV-8623) + + - Member Functions with "char*" as an Argument + + Overloaded functions were added to provide the "const char*" + argument; the existing version will be deprecated in future + releases. + + (BMR - 2016/03/04, HDFFV-8623) + + - Regarding #ifdef VLPT_REMOVED + + The #ifdef VLPT_REMOVED blocks have been removed from the packet + table library source code except for the following functions: + + VL_PacketTable::IsVariableLength() was moved to PacketTable + + VL_PacketTable::FreeReadBuff() is now PacketTable::FreeBuff() + + (BMR - 2016/03/04, HDFFV-442) + + + + Java Wrapper Library + -------------------- + + The Java HDF5 JNI library has been integrated into the HDF5 repository. + The configure option is "--enable-java", and the CMake option is + HDF5_BUILD_JAVA:BOOL=ON. The package hierarchy has changed from the + HDF5 1.8 JNI, which was "ncsa.hdf.hdflib.hdf5", to HDF5 1.10, + "hdf.hdflib.hdf5". + + A number of new APIs were added including some for VDS and SWMR. + + + + Other Important Changes + ----------------------- + + The hid_t type was changed from 32-bit to a 64-bit value. + + + +Issues Addressed in this Release Since alpha1 +============================================= + + - H5Pget_virtual_printf_gap, H5Pget_virtual_view, H5Pget_efile_prefix + + The correct access property list settings from the + H5Pget_virtual_printf_gap, H5Pget_virtual_view, and + H5Pget_efile_prefix function calls could not be retrieved + using H5Dget_access_plist(). + + Fixed. + + (DER and NAF - 2016/03/14, HDFFV-9716) + + - h5dump + + When h5dump was provided with the name of a non-existing file or + when optional arguments were the last option on the command line, + h5dump would segfault. + + Fixed. + + (ADB 2016/02/28 HDFFV-9639, HDFFV-9684) + + - No Error Message for Corrupt Metadata + + The HDF5 Library did not propagate an error when it encountered + corrupt metadata in an HDF5 file. The issue was fixed for a + specific file provided by a user. If you still see the problem, + please contact help@hdfgroup.org + + Fixed. + + (MC - 2016/02/18, HDFFV-9670) + + - Problem Reading Chunked Datasets with a String Datatype Larger + Than the Chunk Size in Bytes + + When the latest file format was used and when a chunked dataset + was created with a datatype with the size bigger than a chunk + size, the data could not be read back. The issue was reported + for chunked datasets with a string datatype and was confirmed + for other datatypes with the sizes bigger than the chunk size in + bytes. + + Fixed. + + (JM - 2016/02/13, HDFFV-9672) + + - Control over the Location of External Files + + Users were unable to specify the locations of external files. + + Two APIs - H5Pget_efile_prefix and H5Pset_efile_prefix - were + added so that users could specify the locations of external files. + + (DER - 2016/02/04, HDFFV-8740) + + + +Issues Addressed in this Release Since alpha0 +============================================= + - h5format_convert + + The h5format_convert tool did not downgrade the version of the + superblock. + + Fixed. The tool now will downgrade the version of the superblock. + + (EIP 2016/01/11) + + - Crashes with multiple threads: invalid pointers + + It was reported that alpha0 crashed when used with multiple + threads. The issue exists in the HDF5 Library versions 1.8 and + 1.9. The problem is related to a shared file pointer used in some + miscellaneous data structures. The thread-safe library exposed + paths in the library where a file pointer became invalid. + + The alpha1 release contains the fixes for the specific use case + as described in HDFFV-9643. We will keep working on identifying + and fixing other paths in the library with similar problems. + + (EIP - 2016/01/15, HDFFV-9643) + + + +Supported Platforms +=================== +The following platforms are supported and have been tested for this release. +They are built with the configure process unless specified otherwise. + + AIX 6.1 xlc/xlc_r 10.1.0.5 + (NASA G-ADA) xlC/xlC_r 10.1.0.5 + xlf90/xlf90_r 12.1.0.6 + + Linux 2.6.32-573.18.1.el6 GNU C (gcc), Fortran (gfortran), C++ (g++) + #1 SMP x86_64 GNU/Linux compilers: + (mayll/platypus) Version 4.4.7 20120313 (Red Hat 4.4.7-16) + Version 4.9.3, Version 5.2.0 + PGI C, Fortran, C++ for 64-bit target on + x86-64; + Version 15.7-0 + Intel(R) C (icc), C++ (icpc), Fortran (icc) + compilers: + Version 15.0.3.187 Build 20150407 + MPICH 3.1.4 compiled with GCC 4.9.3 + + Linux 2.6.32-504.8.1.el6.ppc64 gcc (GCC) 4.4.7 20120313 (Red Hat 4.4.7-11) + #1 SMP ppc64 GNU/Linux g++ (GCC) 4.4.7 20120313 (Red Hat 4.4.7-11) + (ostrich) GNU Fortran (GCC) 4.4.7 20120313 (Red Hat 4.4.7-11) + IBM XL C/C++ V13.1 + IBM XL Fortran V15.1 + + Linux 3.10.0-327.10.1.el7 GNU C (gcc), Fortran (gfortran), C++ (g++) + #1 SMP x86_64 GNU/Linux compilers: + (kituo/moohan) Version 4.8.5 20150623 (Red Hat 4.8.5-4) + Version 4.9.3, Version 5.2.0 + Intel(R) C (icc), C++ (icpc), Fortran (icc) + compilers: + Version 15.0.3.187 Build 20150407 + MPICH 3.1.4 compiled with GCC 4.9.3 + + SunOS 5.11 32- and 64-bit Sun C 5.12 SunOS_sparc + (emu) Sun Fortran 95 8.6 SunOS_sparc + Sun C++ 5.12 SunOS_sparc + + Windows 7 Visual Studio 2012 w/ Intel Fortran 15 (cmake) + Visual Studio 2013 w/ Intel Fortran 15 (cmake) + Visual Studio 2015 w/ Intel Fortran 16 (cmake) + Cygwin(CYGWIN_NT-6.1 2.2.1(0.289/5/3) gcc(4.9.3) compiler and gfortran) + (cmake and autotools) + + Windows 7 x64 Visual Studio 2012 w/ Intel Fortran 15 (cmake) + Visual Studio 2013 w/ Intel Fortran 15 (cmake) + Visual Studio 2015 w/ Intel Fortran 16 (cmake) + + Windows 8.1 Visual Studio 2012 w/ Intel Fortran 15 (cmake) + Visual Studio 2013 w/ Intel Fortran 15 (cmake) + + Windows 8.1 x64 Visual Studio 2012 w/ Intel Fortran 15 (cmake) + Visual Studio 2013 w/ Intel Fortran 15 (cmake) + + Mac OS X Mt. Lion 10.8.5 Apple clang/clang++ version 5.1 from Xcode 5.1 + 64-bit gfortran GNU Fortran (GCC) 4.8.2 + (swallow/kite) Intel icc/icpc/ifort version 15.0.3 + + Mac OS X Mavericks 10.9.5 Apple clang/clang++ version 6.0 from Xcode 6.2.0 + 64-bit gfortran GNU Fortran (GCC) 4.9.2 + (wren/quail) Intel icc/icpc/ifort version 15.0.3 + + Mac OS X Yosemite 10.10.5 Apple clang/clang++ version 6.0 from Xcode 7.0.0 + 64-bit gfortran GNU Fortran (GCC) 4.9.2 + (osx1010dev/osx1010test) Intel icc/icpc/ifort version 15.0.3 + + Mac OS X El Capitan 10.11.3 Apple clang/clang++ version 7.0.2 from Xcode 7.0.2 + 64-bit gfortran GNU Fortran (GCC) 5.2.0 + (osx1010dev/osx1010test) Intel icc/icpc/ifort version 15.0.3 + + + +Tested Configuration Features Summary +===================================== + + In the tables below + y = tested + n = not tested in this release + C = Cluster + W = Workstation + x = not working in this release + dna = does not apply + ( ) = footnote appears below second table + <blank> = testing incomplete on this feature or platform + +Platform C F90/ F90 C++ zlib SZIP + parallel F2003 parallel +SunOS 5.11 32-bit n y/y n y y y +SunOS 5.11 64-bit n y/y n y y y +Windows 7 y y/y n y y y +Windows 7 x64 y y/y n y y y +Windows 7 Cygwin n y/y n y y n +Windows 8.1 n y/y n y y y +Windows 8.1 x64 n y/y n y y y +Mac OS X Mountain Lion 10.8.5 64-bit n y/y n y y y +Mac OS X Mavericks 10.9.5 64-bit n y/y n y y y +Mac OS X Yosemeti 10.10.5 64-bit n y/y n y y y +AIX 6.1 32- and 64-bit n y/n n y y y +CentOS 6.7 Linux 2.6.32 x86_64 GNU y y/y y y y y +CentOS 6.7 Linux 2.6.32 x86_64 Intel n y/y n y y y +CentOS 6.7 Linux 2.6.32 x86_64 PGI n y/y n y y y +CentOS 7.1 Linux 3.10.0 x86_64 GNU y y/y y y y y +CentOS 7.1 Linux 3.10.0 x86_64 Intel n y/y n y y y +Linux 2.6.32-431.11.2.el6.ppc64 n y/n n y y y + +Platform Shared Shared Shared Thread- + C libs F90 libs C++ libs safe +SunOS 5.11 32-bit y y y y +SunOS 5.11 64-bit y y y y +Windows 7 y y y y +Windows 7 x64 y y y y +Windows 7 Cygwin n n n y +Windows 8.1 y y y y +Windows 8.1 x64 y y y y +Mac OS X Mountain Lion 10.8.5 64-bit y n y y +Mac OS X Mavericks 10.9.5 64-bit y n y y +Mac OS X Yosemeti 10.10.5 64-bit y n y y +AIX 6.1 32- and 64-bit y n n y +CentOS 6.7 Linux 2.6.32 x86_64 GNU y y y y +CentOS 6.7 Linux 2.6.32 x86_64 Intel y y y y +CentOS 6.7 Linux 2.6.32 x86_64 PGI y y y y +CentOS 7.1 Linux 3.10.0 x86_64 GNU y y y y +CentOS 7.1 Linux 3.10.0 x86_64 Intel y y y y +Linux 2.6.32-431.11.2.el6.ppc64 y y y y + +Compiler versions for each platform are listed in the preceding +"Supported Platforms" table. + + + +More Tested Platforms +===================== +The following platforms are not supported but have been tested for this release. + + Linux 2.6.18-431.11.2.el6 g95 (GCC 4.0.3 (g95 0.94!) + #1 SMP x86_64 GNU/Linux + (platypus) + + Windows 7 Visual Studio 2008 (cmake) + + Windows 7 x64 Visual Studio 2008 (cmake) + + Windows 7 x64 Visual Studio 2010 (cmake) with SWMR using GPFS + + Windows 10 Visual Studio 2013 w/ Intel Fortran 15 (cmake) + + Windows 10 x64 Visual Studio 2013 w/ Intel Fortran 15 (cmake) + + Debian7.5.0 3.2.0-4-amd64 #1 SMP Debian 3.2.51-1 x86_64 GNU/Linux + gcc (Debian 4.7.2-5) 4.7.2 + GNU Fortran (Debian 4.7.2-5) 4.7.2 + (cmake and autotools) + + Fedora20 3.15.3-200.fc20.x86_64 #1 SMP x86_64 x86_64 x86_64 GNU/Linux + gcc (GCC) 4.8.3 20140624 (Red Hat 4.8.3-1) + GNU Fortran (GCC) 4.8.3 20140624 (Red Hat 4.8.3-1) + (cmake and autotools) + + SUSE 13.1 3.11.10-17-desktop #1 SMP PREEMPT x86_64 x86_64 x86_64 GNU/Linux + gcc (SUSE Linux) 4.8.1 + GNU Fortran (SUSE Linux) 4.8.1 + (cmake and autotools) + + Ubuntu 14.04 3.13.0-35-generic #62-Ubuntu SMP x86_64 GNU/Linux + gcc (Ubuntu/Linaro 4.9.1-0ubuntu1) 4.9.1 + GNU Fortran (Ubuntu/Linaro 4.9.1-0ubuntu1) 4.9.1 + (cmake and autotools) + + hopper.nersc.gov PrgEnv-gnu/5.2.40 + gcc (GCC) 4.9.2 20141030 (Cray Inc.) + GNU Fortran (GCC) 4.9.2 20141030 (Cray Inc.) + g++ (GCC) 4.9.2 20141030 (Cray Inc.) + + + +Known Problems and Limitations +============================== +This section contains the list of known problems and limitations introduced +in this release of HDF5. + +Note: this list is not exhaustive of all known issues discovered in HDF5 +software to date. For a list of significant problems and known workarounds +identified in past releases, please refer to: + +https://www.hdfgroup.org/HDF5/release/known_problems/ + +The HDF Group also maintains a JIRA issue-tracking database which is used to +capture all known issues which are too numerous to reasonably list in this +document. The HDF Group is taking steps to make our JIRA issue database +open to the public, and this section will refer to that database in a future +release. In the meantime, please contact help@hdfgroup.org if you come across +an issue not listed here or at the link above, and we will provide any +information about known workarounds that we have or add it to our list of +known issues if it is a new issue. + + - The JUnit-interface test may fail on Solaris platforms. The result of + a test for verifying the content of the error stack to stdout is + in a different order on Solaris then other platforms. Use make -i option + to test beyond the java/test folder. + (ADB - 2016/03/22, HDFFV-9734) + + - The flush/refresh test occasionally fails on OS X platforms. This is + being investigated but no fix or workaround is available at this time. + (DER - 2016/03/22, HDFFV-9731) + + - The VDS/SWMR test will fail with a segmentation fault if the library + is built with --enable-using-memchecker. The is due to a VDS shutdown + procedure freeing a shared resource too early when the memory + checker changes are built. This problem does not arise when the + memory checker changes are not used since the internal library free + lists behave differently. The memory checker configure option should + normally only be used under special circumstances so this should not + affect most users. Users should be aware that the --enable-using-memchecker + + VDS combination may cause a segfault, however, so Valgrind et al. may + have to be used with an HDF5 library built without the feature if this + proves to be a problem. + (DER - 2016/03/21, HDFFV-9732) + + - SWMR feature limitations + The SWMR feature will only work if an HDF5 file under SWMR access resides + on a file system that obeys POSIX write() ordering semantics. Because of + this, SWMR will not work on network file systems such as NFS or SMB/Windows + file shares since those systems do not guarantee write odering. SWMR + regression tests are likely to fail if run on a network file system. SWMR + is currently not tested on Windows though it can be tested manually + (some of the SWMR test programs are built by CMake), and there are no + obvious reasons for it to not work on NTFS or GPFS. + (EIP - 2016/03/20, HDFFV-9733) + + - VDS feature limitation + Currently, the path to a VDS source file is interpreted as relative to the + directory where the executable program runs and not to the HDF5 file with + the VDS dataset unless a full path to the source file is specified during + the mapping. + (EIP - 2016/03/20, HDFFV-9724) + + - When building HDF5 with Java using CMake and specifying Debug for CMAKE_BUILD_TYPE, + there is a missing command argument for the tests of the examples. + + This error can be avoided by not building Java with Debug, HDF5_BUILD_JAVA:BOOL=OFF, + or not building Examples, HDF5_BUILD_EXAMPLES:BOOL=OFF. + (LRK - 2016/03/30, HDFFV-9743) + + - The H5Lexists API changed behavior in HDF5-1.10 when used with a file handle + and root group name ("/"): + + H5Lexists(fileid, "/") + + In HDF5-1.8 it returns false (0) and in HDF5-1.10 it returns true (1). + The documentation will be updated with information regarding this change. + (LRK - 2016/03/30, HDFFV-8746) + |