HDF5 version 1.8.11-snap4 currently under development ================================================================================ INTRODUCTION ============ This document describes the differences between HDF5-1.8.10 and HDF5 1.8.11-*, and contains information on the platforms tested and known problems in HDF5-1.8.11-*. 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 1.8.11 source code, documentation, and additional materials can be found on the HDF5 web page at: http://www.hdfgroup.org/products/hdf5/ The HDF5 1.8.11 release can be obtained from: http://www.hdfgroup.org/HDF5/release/obtain5.html User documentation for 1.8.11 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 1.8.11 (current release) versus Release 1.8.10": 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 HDF5-1.8.10 - Supported Platforms - Supported Configuration Features Summary - More Tested Platforms - Known Problems New Features ============ Configuration ------------- - None Library ------- - The library now supports the data conversion from enumeration to numeric (integer and floating-point number) datatypes. See Issue 8221. (SLU - 2012/10/23) Parallel Library ---------------- - None Tools ----- - None High-Level APIs --------------- - None Fortran API ----------- C++ API ------- - None Support for New Platforms, Languages, and Compilers =================================================== - None Bug Fixes since HDF5-1.8.10 ========================== Configuration ------------- - None Library ------- - None Parallel Library ---------------- - None Performance ------------- - None Tools ----- - The following h5stat test case failed in BG/P machines (and potentially other machines that display extra output if an MPI task returns with a non-zero code.) Testing h5stat notexist.h5 The test script was fixed to ignore the extra output. HDFFV-8233 (AKC - 2012/11/30) - 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) F90 API ------- - None C++ API ------ - None High-Level APIs: ------ - None Fortran High-Level APIs: ------ - None Supported Platforms =================== 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 4.1.2-52) Version 4.6.3 PGI C, Fortran, C++ Compilers for 32-bit applications; Version 11.9-0 Intel(R) C, C++, Fortran Compiler for 32-bit applications; Version 12.1 MPICH mpich2-1.4.1p1 compiled with gcc 4.1.2 and gfortran 4.1.2 Linux 2.6.18-308.16.1.el5 GNU C (gcc), Fortran (gfortran), C++ (g++) #1 SMP x86_64 GNU/Linux compilers for 32-bit applications; (koala) Version 4.1.2 20080704 (Red Hat 4.1.2-52) Version 4.6.3 PGI C, Fortran, C++ for 64-bit target on x86-64; Version 11.9-0 Version 12.5-0 Intel(R) C, C++, Fortran Compilers for applications running on Intel(R) 64; Version 12.1 (Build 20110811) Version 12.1 (Build 20120212) MPICH mpich2-1.4.1p1 compiled with gcc 4.1.2 and gfortran 4.1.2 Linux 2.6.32-220.7.1.el6.ppc64 gcc (GCC) 4.4.6 20120305 (Red Hat 4.4.6-4) #1 SMP ppc64 GNU/Linux g++ (GCC) 4.4.6 20120305 (Red Hat 4.4.6-4) (ostrich) GNU Fortran (GCC) 4.4.6 20120305 (Red Hat 4.4.6-4) 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 5.10 32- and 64-bit Sun C 5.9 Sun OS_sparc Patch 124867-16 (linew) Sun Fortran 95 8.3 Sun OS_sparc Patch 127000-13 Sun C++ 5.9 Sun OS_sparc Patch 124863-26 Sun C 5.11 SunOS_sparc Sun Fortran 95 8.5 SunOS_sparc Sun C++ 5.11 SunOS_sparc Windows XP Visual Studio 2008 w/ Intel Fortran 10.1 (project files) Windows XP x64 Visual Studio 2008 w/ Intel Fortran 10.1 (project files) Windows 7 Visual Studio 2008 w/ Intel Fortran 11.1 (cmake) Visual Studio 2010 w/ Intel Fortran 12 (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 11.1 (cmake) Visual Studio 2010 w/ Intel Fortran 12 (cmake) Cygwin(CYGWIN_NT-6.1 1.7.15(0.260/5/3) gcc(4.5.3) compiler and gfortran) (cmake and autotools) 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 (fred) gfortran GNU Fortran (GCC) 4.6.2 Intel C (icc), Fortran (ifort), C++ (icpc) 12.1.0.038 Build 20110811 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 Intel 32-bit gfortran GNU Fortran (GCC) 4.6.1 (tejeda) Intel C (icc), Fortran (ifort), C++ (icpc) 12.1.0.038 Build 20110811 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 = testing incomplete on this feature or platform Platform C F90/ F90 C++ zlib SZIP parallel F2003 parallel Solaris2.10 32-bit n y/y n y y y Solaris2.10 64-bit n y/n n y y y Windows 7 y y/n n y y y Windows 7 x64 y y/n n y y y Mac OS X Snow Leopard 10.6.8 32-bit n y/y n y y n Mac OS X Snow Leopard 10.6.8 64-bit n 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/n n y y n AIX 5.3 32- and 64-bit y y/n y y y y CentOS 5.5 Linux 2.6.18-308 i686 GNU y y/y y y y y CentOS 5.5 Linux 2.6.18-308 i686 Intel n y/y n y y y CentOS 5.5 Linux 2.6.18-308 i686 PGI n y/y n y y y CentOS 5.5 Linux 2.6.18 x86_64 GNU y y/y y y y y CentOS 5.5 Linux 2.6.18 x86_64 Intel n y/y n y y y CentOS 5.5 Linux 2.6.18 x86_64 PGI n y/y n y y y Linux 2.6.32-220.7.1.el6.ppc64 n y/n n y y y Platform Shared Shared Shared Thread- C libs F90 libs C++ libs safe Solaris2.10 32-bit y y y y Solaris2.10 64-bit n n n n Windows 7 y y y y Windows 7 x64 y y y y Mac OS X Snow Leopard 10.6.8 32-bit y n y n Mac OS X Snow Leopard 10.6.8 64-bit y n y n 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 AIX 5.3 32- and 64-bit n n n y CentOS 5.5 Linux 2.6.18-308 i686 GNU y y y y CentOS 5.5 Linux 2.6.18-308 i686 Intel y y y n CentOS 5.5 Linux 2.6.18-308 i686 PGI y y y n CentOS 5.5 Linux 2.6.18 x86_64 GNU y y y y CentOS 5.5 Linux 2.6.18 x86_64 Intel y y y n CentOS 5.5 Linux 2.6.18 x86_64 PGI y y y n Linux 2.6.32-220.7.1.el6.ppc64 y y y n Compiler versions for each platform are listed in the preceding "Supported Platforms" table. More Tested Platforms ===================== The following platforms are not supported but have been tested for this release. 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 Debian6.0.3 2.6.32-5-686 #1 SMP i686 GNU/Linux gcc (Debian 4.4.5-8) 4.4.5 GNU Fortran (Debian 4.4.5-8) 4.4.5 (cmake and autotools) Debian6.0.3 2.6.32-5-amd64 #1 SMP x86_64 GNU/Linux gcc (Debian 4.4.5-8) 4.4.5 GNU Fortran (Debian 4.4.5-8) 4.4.5 (cmake and autotools) Fedora17 3.5.2-1.fc17.i6866 #1 SMP i686 i686 i386 GNU/Linux gcc (GCC) 4.7.0 20120507 (Red Hat 4.7.0-5) GNU Fortran (GCC) 4.7.0 20120507 (Red Hat 4.7.0-5) (cmake and autotools) Fedora17 3.5.2-1.fc17.x86_64 #1 SMP x86_64 x86_64 x86_64 GNU/Linux gcc (GCC) 4.7.0 20120507 (Red Hat 4.7.0-5) GNU Fortran (GCC) 4.7.0 20120507 (Red Hat 4.7.0-5) (cmake and autotools) SUSE 12.2 3.4.6-2.10-desktop #1 SMP PREEMPT i686 i686 i386 GNU/Linux gcc (SUSE Linux) 4.7.1 GNU Fortran (SUSE Linux) 4.7.1 (cmake and autotools) SUSE 12.2 3.4.6-2.10-desktop #1 SMP PREEMPT x86_64 x86_64 x86_64 GNU/Linux gcc (SUSE Linux) 4.7.1 GNU Fortran (SUSE Linux) 4.7.1 (cmake and autotools) Ubuntu 12.04 3.2.0-29-generic #46-Ubuntu SMP i686 GNU/Linux gcc (Ubuntu/Linaro 4.6.3-1ubuntu5) 4.6.3 GNU Fortran (Ubuntu/Linaro 4.6.3-1ubuntu5) 4.6.3 (cmake and autotools) Ubuntu 12.04 3.2.0-29-generic #46-Ubuntu SMP x86_64 GNU/Linux gcc (Ubuntu/Linaro 4.6.3-1ubuntu5) 4.6.3 GNU Fortran (Ubuntu/Linaro 4.6.3-1ubuntu5) 4.6.3 (cmake and autotools) (Use optimization level -O1) 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 ============== * 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 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's 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 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 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) * 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) * The library's test dt_arith.c showed a compiler's rounding problem on Cygwin when converting from unsigned long long to long double. The library's own conversion works fine. We defined a macro for Cygwin to skip this test until we can solve the problem. (SLU - 2010/05/05 - HDFFV-1264) * 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)