EVOLUTION-MANAGER

Edit File: RELEASE.txt

HDF5 version 1.8.12 released on 2013-11-21 ================================================================================ INTRODUCTION ============ This document describes the differences between HDF5-1.8.11 and HDF5-1.8.12, and contains information on the platforms tested and known problems in HDF5-1.8.12. For more details, see the files HISTORY-1_0-1_8_0_rc3.txt and HISTORY-1_8.txt in the release_docs/ directory of the HDF5 source. Links to the HDF5 1.8.12 source code, documentation, and additional materials can be found on the HDF5 web page at: http://www.hdfgroup.org/products/hdf5/ The HDF5 1.8.12 release can be obtained from: http://www.hdfgroup.org/HDF5/release/obtain5.html User documentation for 1.8.12 can be accessed directly at this location: http://www.hdfgroup.org/HDF5/doc/ New features in the HDF5-1.8.x release series, including brief general descriptions of some new and modified APIs, are described in the "What's New in 1.8.0?" document: http://www.hdfgroup.org/HDF5/doc/ADGuide/WhatsNew180.html All new and modified APIs are listed in detail in the "HDF5 Software Changes from Release to Release" document, in the section "Release 1.8.12 (current release) versus Release 1.8.11": http://www.hdfgroup.org/HDF5/doc/ADGuide/Changes.html 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, Languages, and Compilers - Bug Fixes since HDF5-1.8.11 - Supported Platforms - Supported Configuration Features Summary - More Tested Platforms - Known Problems New Features ============ Configuration ------------- - Added a configuration option to change the default plugin path. The configure option is --with-default-plugindir=location. The cmake option is -DH5_DEFAULT_PLUGINDIR:PATH=location. HDFFV-8513. (ADB 2013/09/04) - Renamed FFLAGS to FCFLAGS in configure. (ADB 2013/08/13) - CMake can now package a compressed examples file, the default for Windows binaries from HDF Group. (ADB - 2013/07/22) Library ------- - None Parallel Library ---------------- - None Tools ----- - h5repack: Added the ability to use plugin filters to read and write files. The option uses the filter number. HDFFV-8345 (ADB - 2013/09/04). - h5dump: Added the option -N --any_path, which searches the file for paths that match the search path. HDFFV-7989 (ADB - 2013/08/12). - h5dump: Added the optional arg 0 to -A, which excludes attributes from display. HDFFV-8134 (ADB - 2013/08/01). High-Level APIs --------------- - None Fortran API ----------- - None C++ API ------- - Added tutorial examples to C++/examples. They can be installed by "make install-examples" and, in the installed directory, they can be executed by running the script file run-c++-ex.sh. (BMR - 2013/09/28) - A new class, H5::H5Location, is added to represent the location concept in the C library. It is a base class to H5::H5File and H5::H5Ojbect, whose member functions are moved into H5::H5Location. H5::H5File can now inherent those functions. As a result, an H5::H5File object can have an attribute. (BMR - 2013/09/27) - Added wrappers for H5Rget_obj_type2 to retrieve the type of the object that an object reference points to. (BMR - 2013/09/27) H5O_type_t H5Location::getRefObjType(void *ref, H5R_type_t ref_type) - Added wrappers for H5Aexist to check whether an attribute exists given a name. (BMR - 2013/09/27) bool H5::H5Location::attrExists(const char* name) bool H5::H5Location::attrExists(const H5std_string& name) - Added a number of overloaded functions for convenience. (BMR - 2013/09/27) Support for New Platforms, Languages, and Compilers =================================================== - None Bug Fixes since HDF5-1.8.11 =========================== Configuration ------------- - 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) - HDF5 rpaths are no longer encoded in the library files when configured with --disable-sharedlib-rpath. (LRK-2013-09-23 - HDFFV-8276) CMake ----- - Fix installation problem for Mac OS X reported on FORUM. (ADB - 2013/11/20) Library ------- - Added const qualifier to source buffer parameters in H5Dgather and H5D_scatter_func_t (H5Dscatter callback). (NAF - 2013/7/09) - CMake now creates *.so.{lt_version} files with the same version as configure. (ADB - 2013/06/05 HDFFV-8437) Parallel Library ---------------- - None Performance ------------- - None Tools ----- - h5dump: Added the option -N --any_path, which searches the file for paths that match the search path. HDFFV-7989 (ADB - 2013/08/12). - h5dump: Added the optional arg 0 to -A, which excludes attributes from display. HDFFV-8134 (ADB - 2013/08/01). - h5dump correctly exports subsetted data to a file, using the --output option. (ADB - 2013/06/07 HDFFV-8447) - h5cc and other compile scripts now default to linking shared libraries when HDF5 is configured with the --disable-static option. (LRK - 2013-09-23 - HDFFV-8141) F90 API ------- - None C++ API ------ - None High-Level APIs: ------ - None Fortran High-Level APIs: ------ - None Testing ------- - test/big sometimes failed with the message of "file selection+offset not within extent". This has been fixed. (AKC - 2013/09/28 HDFFV-8271). - 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 are no code changes. Fixed. (AKC - 2013/07/19 HDFFV-8392) 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 5.3 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 4.8.1 PGI C, Fortran, C++ Compilers for 32-bit applications; Version 13.7-0 Intel(R) C, C++, Fortran Compiler for 32-bit applications; Version 13.1.3 (Build 20130607) Linux 2.6.18-308.16.1.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 4.8.1 PGI C, Fortran, C++ for 64-bit target on x86-64; Version 13.7-0 Intel(R) C, C++, Fortran Compilers for applications running on Intel(R) 64; Version 13.1.3 (Build 20130607) Linux 2.6.32-358.18.1.el6 GNU C (gcc), Fortran (gfortran), C++ (g++) #1 SMP x86_64 GNU/Linux compilers: (platypus) Version 4.4.7 20120313 Version 4.8.1 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 13.1.3 (Build 20130607) Linux 2.6.32-358.18.1.el6.ppc64 gcc (GCC) 4.4.7 20120313 (Red Hat 4.4.7-3) #1 SMP ppc64 GNU/Linux g++ (GCC) 4.4.7 20120313 (Red Hat 4.4.7-3) (ostrich) GNU Fortran (GCC) 4.4.7 20120313 (Red Hat 4.4.7-3) IBM XL C/C++ V11.1 IBM XL Fortran V13.1 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 w/ Intel Fortran 11 (cmake) Visual Studio 2010 w/ Intel Fortran 12 (cmake) Visual Studio 2012 w/ Intel Fortran 13 (cmake) Cygwin(CYGWIN_NT-6.1 1.7.15(0.260/5/3) gcc(4.5.3) compiler and gfortran) (cmake and autotools) Windows 7 x64 Visual Studio 2008 w/ Intel Fortran 11 (cmake) Visual Studio 2010 w/ Intel Fortran 12 (cmake) Visual Studio 2012 w/ Intel Fortran 13 (cmake) Windows 8.1 Visual Studio 2012 w/ Intel Fortran 13 (cmake) Windows 8.1 x64 Visual Studio 2012 w/ Intel Fortran 13 (cmake) Mac OS X Snow Leopard 10.6.8 gcc i686-apple-darwin11-llvm-gcc-4.2 (GCC) 4.2.1 from Xcode 3.2.6 Darwin Kernel Version 10.8.0 g++ i686-apple-darwin11-llvm-g++-4.2 (GCC) 4.2.1 from Xcode 3.2.6 64-bit gfortran GNU Fortran (GCC) 4.6.2 (fred) Intel C (icc), Fortran (ifort), C++ (icpc) 12.1 Build 20120928 Mac OS X Lion 10.7.3 Apple clang/clang++ version 3.0 from Xcode 4.6.1 64-bit gfortran GNU Fortran (GCC) 4.6.2 (duck) Intel icc/icpc/ifort version 13.0.3 Mac OS X Mountain Lion 10.8.1 Apple clang/clang++ version 4.2 from Xcode 4.6.1 64-bit gfortran GNU Fortran (GCC) 4.6.2 (wren) Intel icc/icpc/ifort version 13.0.3 OpenVMS IA64 V8.4 HP C V7.3-018 HP Fortran V8.2-104939-50H96 HP C++ V7.4-004 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/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/n n y y y Windows 8.1 n y/y n y y y Windows 8.1 x64 n y/y n y y y Mac OS X Snow Leopard 10.6.8 64-bit n y/y n y y y 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 AIX 5.3 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 y y/y y y y y CentOS 5.9 Linux 2.6.18 x86_64 Intel n y/y n y y y CentOS 5.9 Linux 2.6.18 x86_64 PGI n y/y n y y y CentOS 6.4 Linux 2.6.32 x86_64 GNU n y/y n y y y CentOS 6.4 Linux 2.6.32 x86_64 Intel n y/y n y y y Linux 2.6.32-358.2.1.el6.ppc64 n y/n n y y y OpenVMS IA64 V8.4 n y/n n y y n 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 8.1 y y y y Windows 8.1 x64 y y y y Mac OS X Snow Leopard 10.6.8 64-bit y n y n 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 AIX 5.3 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 5.9 Linux 2.6.18 x86_64 PGI 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 Linux 2.6.32-358.2.1.el6.ppc64 y y y n OpenVMS IA64 V8.4 n n n 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 mpich2-1.4.1p1 compiled with #1 SMP i686 i686 i386 gcc 4.1.2 and gfortran 4.1.2 (jam) g95 (GCC 4.0.3 (g95 0.94!) Linux 2.6.18-308.16.1.el5 MPICH mpich2-1.4.1p1 compiled with #1 SMP x86_64 GNU/Linux gcc 4.1.2 and gfortran 4.1.2 (koala) g95 (GCC 4.0.3 (g95 0.94!) FreeBSD 8.2-STABLE i386 gcc 4.5.4 [FreeBSD] 20110526 (loyalty) gcc 4.6.1 20110527 g++ 4.6.1 20110527 gfortran 4.6.1 20110527 FreeBSD 8.2-STABLE amd64 gcc 4.5.4 [FreeBSD] 20110526 (freedom) gcc 4.6.1 20110527 g++ 4.6.1 20110527 gfortran 4.6.1 20110527 Debian7.1.0 3.2.0-4-amd64 #1 SMP Debian 3.2.46-1 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) Fedora19 3.11.1-200.fc19.x86_64 #1 SMP x86_64 x86_64 x86_64 GNU/Linux gcc (GCC) 4.8.1 20130603 (Red Hat 4.8.1-1) GNU Fortran (GCC) 4.8.1 20130603 (Red Hat 4.8.1-1) (cmake and autotools) SUSE 12.3 3.7.10-1.16-desktop #1 SMP PREEMPT x86_64 x86_64 x86_64 GNU/Linux gcc (SUSE Linux) 4.7.2 GNU Fortran (SUSE Linux) 4.7.2 (cmake and autotools) Ubuntu 13.04 3.8.0-30-generic #44-Ubuntu SMP x86_64 GNU/Linux gcc (Ubuntu/Linaro 4.7.3-1ubuntu1) 4.7.3 GNU Fortran (Ubuntu/Linaro 4.7.3-1ubuntu1) 4.7.3 (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 ============== * Several HDF5 command-line tools and tests leave behind generated files that are not cleaned up with "make clean" or "make distclean" when software is built in place. The issue will be addressed in the 1.8.13 release. We recommend to use build directory to compile and test HDF5 as described in the INSTALL file, section 4.2. * Source directory names with spaces in them will cause failures in configure or make on Mac (HDFFV-8152), Linux, and probably all other platforms. If a configure command with a space is run from a build directory, it will exit with an error message: "checking whether build environment is sane... configure: error: unsafe srcdir value: '/scr/lrknox/hdf5 v1.8.12'". If configure is run inside or below the directory with the space in the name, libtool will get the directory path from the system, put the part of the path before the space in the libdir variable in .../src/libhdf5.la, and then fail to find the nonexistent directory. This is a known libtool issue and the suggested workaround is to rename the directory without spaces. (LRK - 2013/10/22) * 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 (HDFFV-8147). This issue will be addressed in the next release. (SLU - 2013/10/16) * Running make check for the tools can fail in the tools tests if make was not run prior. The tests for the tools use other tools in the tests, therefore all the tools should be built before testing the tools. (ADB - 2013/10/09) * Make provided by Solaris fails in "make check". Solaris users should use gmake to build and install HDF5 software. (AKC - 2013/10/08 - HDFFV-8534) * On OpenVMS, two soft conversion functions (H5T__conv_i_f and H5T__conv_f_i) have bugs. They convert data between floating-point numbers and integers. But the library's default is hard conversion. The user should avoid explicitly enabling soft conversion between floating-point numbers and integers. (Issue VMS-8; SLU - 2013/09/19) * On OpenVMS, ZLIB 1.2.8 library doesn't work properly. ZLIB 1.2.5 works fine. So please use ZLIB 1.2.5 to build HDF5 library. (Issue VMS-5; SLU 2013/09/19) * When building using the Cray compilers on Cray machines, HDF5 configure mistakenly thinks the compiler is an intel compiler and sets the -std=c99 flag which breaks configure on Cray. To build HDF5 properly on a Cray machine, please consult with the instructions in INSTALL_parallel for building on Hopper. (MSC - 2013/04/26 - HDFFV-8429) * The h5dump and h5diff utilities occasionally produce different output between Linux and Windows systems. This is caused by lower-level library routines that fail 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. Due to platform differences the return of spurious data values has only been encountered on Windows 32-bit systems. (Issue HDFFV-8247; JP - 2013/03/27) * 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 Sun's 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 following h5dump test case fails in BG/P machines (and potentially other machines that use a command script to launch executables): h5dump --no-compact-subset -d "AHFINDERDIRECT::ah_centroid_t[0] it=0 tl=0" tno-subset.h5 This is due to the embedded spaces in the dataset name being interpreted by the command script launcher as meta-characters, thus passing three arguments to h5dump's -d flag. The command passes if run by hand, just not via the test script. (AKC - 2012/05/03) * On hopper, the build failed when RUNSERIAL and RUNPARALLEL are set to aprun -np X, because the H5lib_settings.c file was not generated properly. Not setting those environment variables works, because configure was able to automatically detect that it is a Cray system and used the proper launch commands when necessary. (MSC - 2012/04/18) * The data conversion test dt_arith.c fails in "long double" to integer conversion on Ubuntu 11.10 (3.0.0.13 kernel) with GCC 4.6.1 if the library is built with optimization -O3 or -O2. The older GCC (4.5) or newer kernel (3.2.2 on Fedora) do not have the problem. Users should lower the optimization level (-O1 or -O0) by defining CFLAGS in the command line of "configure" like: CFLAGS=-O1 ./configure This will overwrite the library's default optimization level. (SLU - 2012/02/07 - HDFFV-7829) This issue is no longer present on Ubuntu 12.10 (3.5.0 kernel) with gcc 4.7.2. * The STDIO VFD does not work on some architectures, possibly due to 32/64 bit or large file issues. The basic STDIO VFD test is known to fail on 64-bit SunOS 5.10 on SPARC when built with -m64 and 32-bit OS X/Darwin 10.7.0. The STDIO VFD test has been disabled while we investigate and a fix should appear in a future release. (DER - 2011/10/14 - HDFFV-8235) * h5diff can report inconsistent results when comparing datasets of enum type that contain invalid values. This is due to how enum types are handled in the library and will be addressed in a future release. (DER - 2011/10/14 - HDFFV-7527) * The links test can fail under the stdio VFD due to some issues with external links. This will be investigated and fixed in a future release. (DER - 2011/10/14 - HDFFV-7768) * After the shared library support was fixed for some bugs, it was discovered that "make prefix=XXX install" no longer works for shared libraries. It still works correctly for static libraries. Therefore, if you want to install the HDF5 shared libraries in a location such as /usr/local/hdf5, you need to specify the location via the --prefix option during configure time. E.g, ./configure --prefix=/usr/local/hdf5 ... (AKC - 2011/05/07 - HDFFV-7583) * The parallel test, t_shapesame, in testpar/, may run for a long time and may be terminated by the alarm signal. If that happens, one can increase the alarm seconds (default is 1200 seconds = 20 minutes) by setting the environment variable, $HDF5_ALARM_SECONDS, to a larger value such as 3600 (60 minutes). Note that the t_shapesame test may fail in some systems (see the "While working on the 1.8.6 release..." problem below). If it does, it will waste more time if $HDF5_ALARM_SECONDS is set to a larger value. (AKC - 2011/05/07) * The C++ and FORTRAN bindings are not currently working on FreeBSD. (QAK - 2011/04/26) * Shared Fortran libraries are not quite working on AIX. While they are generated when --enable-shared is specified, the fortran and hl/fortran tests fail. We are looking into the issue. HL and C++ shared libraries should now be working as intended, however. (MAM - 2011/04/20) * The --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 file systems. 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/ (NAF - 2011/01/19) * All the VFL drivers aren't backward compatible. In H5FDpublic.h, the structure H5FD_class_t changed in 1.8. There is new parameter added to get_eoa and set_eoa callback functions. A new callback function get_type_map was added in. The public function H5FDrealloc was taken out in 1.8. The problem only happens when users define their own driver for 1.6 and try to plug in 1.8 library. Because there's only one user complaining about it, we (Elena, Quincey, and I) decided to leave it as it is (see bug report #1279). Quincey will make a plan for 1.10. (SLU - 2010/02/02) * 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. (MAM - 2009/11/04) * 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) * On an Intel 64 Linux cluster (RH 4, Linux 2.6.9) with Intel 10.0 compilers, use -mp -O1 compilation flags to build the libraries. A higher level of optimization causes failures in several HDF5 library tests. * A dataset created or rewritten with a v1.6.3 library or after cannot be read with the v1.6.2 library or before when the Fletcher32 EDC filter is enabled. There was a bug in the calculation of the Fletcher32 checksum in the library before v1.6.3; the checksum value was not 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 was no longer the same as before on little-endian system. Library releases after 1.6.4 can still read datasets created or rewritten with an HDF5 library of v1.6.2 or before. (SLU - 2005/06/30)