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diff --git a/doc/html/ADGuide/RELEASE.txt b/doc/html/ADGuide/RELEASE.txt new file mode 100644 index 0000000..59d0aab --- /dev/null +++ b/doc/html/ADGuide/RELEASE.txt @@ -0,0 +1,435 @@ + + + HDF5 Release 1.4-Beta3 + + +INTRODUCTION + +This document describes the differences between HDF5-1.2.0 and +HDF5-1.4-Beta3, and contains information on the platforms tested and +known problems in HDF5-1.4-Beta3. For more details check the HISTORY +file in the HDF5 source. + +The HDF5 documentation can be found on the NCSA ftp server +(ftp.ncsa.uiuc.edu) in the directory: + + /HDF/HDF5/docs/ + +For more information look at the HDF5 home page at: + + http://hdf.ncsa.uiuc.edu/HDF5/ + +If you have any questions or comments, please send them to: + + hdfhelp@ncsa.uiuc.edu + + +CONTENTS + +- New Features +- h4toh5 Utility +- F90 Support +- C++ Support +- Bug Fixes since HDF5-1.2.0 +- Bug Fixes since HDF5-1.4.0-beta2 +- Platforms Tested +- Known Problems + +New Features +============ + * The Virtual File Layer, VFL, was added to replace the old file + drivers. It also provides an API for user defined file drivers. + * New features added to snapshots. Use 'snapshot help' to see a + complete list of features. + * Improved configure to detect if MPIO routines are available when + parallel mode is requested. + * Added Thread-Safe support. Phase I implemented. + * Added data sieve buffering to raw data I/O path. This is enabled + for all VFL drivers except the mpio & core drivers. Setting the + sieve buffer size is controlled with the new API function, + H5Pset_sieve_buf_size(), and retrieved with H5Pget_sieve_buf_size(). + * Added new Virtual File Driver, Stream VFD, to send/receive entire + HDF5 files via socket connections. + * As parts of VFL, HDF-GASS and HDF-SRB are also added to this + release. To find out details, please read INSTALL_VFL file. + * Increased maximum number of dimensions for a dataset (H5S_MAX_RANK) + from 31 to 32 to align with HDF4 & netCDF. + * Added 'query' function to VFL drivers. Also added 'type' parameter to + VFL 'read' & 'write' calls, so they are aware of the type of data + being accessed in the file. Updated the VFL document also. + * A new h4toh5 uitlity, to convert HDF4 files to analogous HDF5 files. + * Added a new array datatype to the datatypes which can be created. Removed + "array fields" from compound datatypes (use an array datatype instead). + * Parallel HDF5 works correctly with mpich-1.2.1 on Solaris, SGI, Linux. + +h4toh5 Utility +============== + + The h4toh5 utility is a new utility that converts an HDF4 file to an + HDF5 file. For details, see the document, "Mapping HDF4 Objects to + HDF5 Objects": + http://hdf.ncsa.uiuc.edu/HDF5/papers/H4-H5MappingGuidelines.pdf + + Known Limitations of the h4toh5 beta release + --------------------------------------------- + + 1. Error Handling + + Error reporting is minimal. + + 2. String Datatype + + HDF4 has no 'string' type. String valued data are usually defined as + an array of 'char' in HDF4. The h4toh5 utility will generally map + these to HDF5 'String' types rather than array of char, with the + following additional rules: + + * For the data of an HDF4 SDS, image, and palette, if the data is + declared 'DFNT_CHAR8' it will be assumed to be integer and + will be an H5T_INTEGER type. + * For attributes of any HDF4 object, data of type 'DFNT_CHAR8' + will be converted to an HDF5 'H5T_STRING' type. + * For an HDF4 Vdata, it is difficult to determine whether data + of type 'DFNT_CHAR8' is intended to be bytes or characters. + The h4toh5 utility will consider them to be C characters, and + will convert them to an HDF5 'H5T_STRING' type. + + + 3. Compression, Chunking and External Storage + + Chunking is supported, but compression and external storage is not. + + An HDF4 object that uses chunking will be converted to an HDF5 file + with analogous chunked storage. + + An HDF4 object that uses compression will be converted to an + uncompressed HDF5 object. + + An HDF4 object that uses external storage will be converted to an + HDF5 object without external storage. + + 4. Memory Use + + The beta version of the h4toh5 utility copies data from HDF4 objects + in a single read followed by a single write to the HDF5 object. For + large objects, this requires a very large amount of memory, which may + be extremely slow or fail on some platforms. + + Note that a dataset that has only been partly written will + be read completely, including uninitialized data, and all the + data will be written to the HDF5 object. + + 5. Platforms + + The h4toh5 utility requires HDF5.1.4 and HDF4r1.4 + + The beta h4toh5 utility has been tested on Solaris 2.6, Solaris 2.5, + Irix 6.5, HPUX 11.0, DEC Unix, FreeBSD, Windows 2000(NT5.0),Windows NT + and Windows 98. + +F90 Support +=========== + + This is the first release of the HDF5 Library with fully integrated + F90 API support. The Fortran Library is created when the + --enable-fortran flag is specified during configuration. + + Not all F90 subroutines are implemented. Please refer to the HDF5 + Reference Manual for more details. + + F90 APIs are available for the Solaris 2.6 and 2.7, Linux, DEC UNIX, + T3E, J90 and O2K (64 bit option only) platforms. The Parallel version of + the HDF5 F90 Library is supported on the O2K and T3E platforms. + + Changes since the last prototype release (July 2000) + ---------------------------------------------------- + + * h5open_f and h5close_f must be called instead of h5init_types and + h5close_types. + + * The following subroutines are no longer available: + h5pset_xfer_f + h5pget_xfer_f + h5pset_mpi_f + h5pget_mpi_f + h5pset_stdio_f + h5pget_stdio_f + h5pset_sec2_f + h5pget_sec2_f + h5pset_core_f + h5pget_core_f + h5pset_family_f + h5pget_family_f + + * The following functions have been added: + h5pset_fapl_mpio_f + h5pget_fapl_mpio_f + h5pset_dxpl_mpio_f + h5pget_dxpl_mpio_f + + * In the previous HDF5 F90 releases, the implementation of object + references and dataset region references was not portable. This + release introduces a portable implementation, but it also introduces + changes to the read/write APIs that handle references. If object or + dataset region references are written or read to/from an HDF5 file, + h5dwrite_f and h5dread_f must use the extra parameter, n, for the + buffer size: + + h5dwrite(read)_f(dset_id, mem_type_id, buf, n, hdferr, & + ^^^ + mem_space_id, file_space_id, xfer_prp) + + For other datatypes the APIs were not changed. + + +C++ Support +=========== + + This is the first release of the HDF5 Library with fully integrated + C++ API support. The HDF5 C++ library is built when the --enable-cxx + flag is specified during configuration. + + Check the HDF5 Reference Manual for available C++ documentation. + + C++ APIs are available for Solaris 2.6 and 2.7, Linux, and FreeBSD. + + +Bug Fixes since HDF5-1.2.0 +========================== + +Library +------- + + * The function H5Pset_mpi is renamed as H5Pset_fapl_mpio. + * Corrected a floating point number conversion error for the Cray J90 + platform. The error did not convert the value 0.0 correctly. + * Error was fixed which was not allowing dataset region references to + have their regions retrieved correctly. + * Corrected a bug that caused non-parallel file drivers to fail in + the parallel version. + * Added internal free-lists to reduce memory required by the library + and H5garbage_collect API function + * Fixed error in H5Giterate which was not updating the "index" + parameter correctly. + * Fixed error in hyperslab iteration which was not walking through the + correct sequence of array elements if hyperslabs were staggered in a + certain pattern + * Fixed several other problems in hyperslab iteration code. + * Fixed another H5Giterate bug which was causes groups with large + numbers of objects in them to misbehave when the callback function + returned non-zero values. + * Changed return type of H5Aiterate and H5A_operator_t typedef to be + herr_t, to align them with the dataset and group iterator functions. + * Changed H5Screate_simple and H5Sset_extent_simple to not allow + dimensions of size 0 with out the same dimension being unlimited. + * QAK - 4/19/00 - Improved metadata hashing & caching algorithms to + avoid many hash flushes and also remove some redundant I/O when + moving metadata blocks in the file. + * The "struct(opt)" type conversion function which gets invoked for + certain compound datatype conversions was fixed for nested compound + types. This required a small change in the datatype conversion + function API. + * Re-wrote lots of the hyperslab code to speed it up quite a bit. + * Added bounded garbage collection for the free lists when they run + out of memory and also added H5set_free_list_limits API call to + allow users to put an upper limit on the amount of memory used for + free lists. + * Checked for non-existent or deleted objects when dereferencing one + with object or region references and disallow dereference. + * "Time" datatypes (H5T_UNIX_D*) were not being stored and retrieved + from object headers correctly, fixed now. + * Fixed H5Dread or H5Dwrite calls with H5FD_MPIO_COLLECTIVE requests + that may hang because not all processes are transfer the same amount + of data. (A.K.A. prematured collective return when zero amount data + requested.) Collective calls that may cause hanging is done via the + corresponding MPI-IO independent calls. + * If configure with --enable-debug=all, couple functions would issue + warning messages to "stderr" that the operation is expensive time-wise. + This messed up applications (like testings) that did not expect the + extra output. It is changed so that the warning will be printed only + if the corresponding Debug key is set. + +Configuration +------------- + + * The hdf5.h include file was fixed to allow the HDF5 Library to be + compiled with other libraries/applications that use GNU autoconf. + * Configuration for parallel HDF5 was improved. Configure now attempts + to link with libmpi.a and/or libmpio.a as the MPI libraries by + default. It also uses "mpirun" to launch MPI tests by default. It + tests to link MPIO routines during the configuration stage, rather + than failing later as before. One can just do "./configure + --enable-parallel" if the MPI library is in the system library. + * Added support for pthread library and thread-safe option. + * The libhdf5.settings file shows the correct machine byte-sex. + * Added option "--enable-stream-vfd" to configure w/o the Stream VFD. + For Solaris, added -lsocket to the LIBS list of libraries. + +Tools +----- + * h5dump now accepts both short and long command-line parameters: + -h, --help Print a usage message and exit + -B, --bootblock Print the content of the boot block + -H, --header Print the header only; no data is displayed + -i, --object-ids Print the object ids + -V, --version Print version number and exit + -a P, --attribute=P Print the specified attribute + -d P, --dataset=P Print the specified dataset + -g P, --group=P Print the specified group and all members + -l P, --soft-link=P Print the value(s) of the specified soft link + -o F, --output=F Output raw data into file F + -t T, --datatype=T Print the specified named data type + -w #, --width=# Set the number of columns + + P - is the full path from the root group to the object. + T - is the name of the data type. + F - is a filename. + # - is an integer greater than 1. + * A change from the old way command line parameters were interpreted + is that multiple attributes, datasets, groups, soft-links, and + object-ids cannot be specified with just one flag but you have to + use a flag with each object. I.e., instead of doing this: + + h5dump -a /attr1 /attr2 foo.h5 + + do this: + + h5dump -a /attr1 -a /attr2 foo.h5 + + The cases are similar for the other object types. + * h5dump correctly displays compound datatypes. + * Corrected an error in h5toh4 which did not convert the 32bits + int from HDF5 to HDF4 corectly for the T3E platform. + * h5dump correctly displays the committed copy of predefined types + correctly. + * Added an option, -V, to show the version information of h5dump. + * Fixed a core dumping bug of h5toh4 when executed on platforms like + TFLOPS. + * The test script for h5toh4 used to not able to detect the hdp + dumper command was not valid. It now detects and reports the + failure of hdp execution. + * Merged the tools with the 1.2.2 branch. Required adding new + macros, VERSION12 and VERSION13, used in conditional compilation. + Updated the Windows project files for the tools. + * h5dump displays opaque and bitfield data correctly. + * h5dump and h5ls can browse files created with the Stream VFD + (eg. "h5ls <hostname>:<port>"). + * h5dump has a new feature "-o <filename>" which outputs the raw data + of the dataset into ascii text file <filename>. + * h5toh4 used to converts hdf5 strings type to hdf4 DFNT_INT8 type. + Corrected to produce hdf4 DFNT_CHAR type instead. + * h5dump and h5ls displays array data correctly. + +Documentation +------------- + + * User's Guide and Reference Manual were updated. + See doc/html/PSandPDF/index.html for more details. + + +Bug Fixes since HDF5-1.4.0-beta2 +================================ + + * Corrected configuration error which was not including compression support + correctly. + * Cleaned up lots of warnings. + * Changed a few h5dump command line switches and added long versions of + the switches. + * Changed parameters for H5Tconvert, H5Pset_bufer and H5Pget_buffer from + size_t to hsize_t + * Fixed fairly obscure bug in hyperslab I/O which could (in rare cases) + not copy all the data during a transfer. + * Removed ragged array code from library. + * F90 library and module files are installed properly now on all supported platforms. + +Platforms Tested +================ + + Note: Due to the nature of the bug fixes, only static versions of the + library and tools were tested. + + + AIX 4.3.2 (IBM SP) mpcc_r 3.6.6 + Cray T3E sn6711 2.0.5.43 Cray Standard C Version 6.4.0.0 + Cray Fortran Version 3.4.0.2 + FreeBSD 4.2 gcc 2.95.2 + g++ 2.95.2 + HP-UX B.10.20 HP C HP92453-01 A.10.32.30 + HP-UX B.11.00 HP C HP92453-01 A.11.00.13 + IRIX 6.5 MIPSpro cc 7.30 + IRIX64 6.5 (64 & n32) MIPSpro cc 7.3.1m + mpt.1.4.0.2 + mpich-1.2.1 + Linux 2.2.16-3smp gcc-2.95.2 + g++ 2.95.2 + pgf90 3.1-3 + OSF1 V4.0 DEC-V5.2-040 + Digital Fortran 90 V4.1-270 + SunOS 5.6 WorkShop Compilers 5.0 98/12/15 C 5.0 + (Solaris 2.6) WorkShop Compilers 5.0 99/10/25 Fortran 90 + 2.0 Patch 107356-04 + Workshop Compilers 5.0 98/12/15 C++ 5.0 + SunOS 5.7 WorkShop Compilers 5.0 98/12/15 C 5.0 + (Solaris 2.7) WorkShop Compilers 5.0 99/10/25 Fortran 90 + 2.0 Patch 107356-04 + Workshop Compilers 5.0 98/12/15 C++ 5.0 + TFLOPS 3.3 mpich-1.2.0 with local changes + Windows NT4.0, 2000 (NT5.0) MSVC++ 6.0 + Windows 98 MSVC++ 6.0 + +Known Problems +============== + +* The --enable-static-exec configure flag fails to compile for Solaris + platforms. This is due to the fact that not all of the system + libraries on Solaris are available in a static format. + + The --enable-static-exec configure flag also fails to correctly compile + on Linux platforms using the gcc-2.95.2 compiler. + + It is suggested that you don't use this option on these platforms + during configuration. + +* 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. + +* SunOS 5.6 with C WorkShop Compilers 4.2: Hyperslab selections will + fail if library is compiled using optimization of any level. + +* When building hdf5 tools and applications on windows platform, a linking +warning: defaultlib "LIBC" conflicts with use of other libs will appear +on debug version when running VC++6.0. This warning doesn't affect building +and testing hdf5 applications. We are investigating this now. +* The Stream VFD was not tested yet under Windows. + It is not supported in the TFLOPS machine. + +* Shared library option is broken for IBM SP and some Origin 2000 platforms. + One needs to run ./configure with '--disable-shared' + +* The ./dsets tests failed in the TFLOPS machine if the test program, + dsets.c, is compiled with the -O option. The hdf5 library still works + correctly with the -O option. The test program works fine if it is + compiled with -O1 or -O0. Only -O (same as -O2) causes the test + program to fail. + +* Certain platforms give false negatives when testing h5ls: + - Solaris x86 2.5.1, Cray T3E and Cray J90 give errors during testing + when displaying object references in certain files. These are benign + differences due to the difference in sizes of the objects created on + those platforms. h5ls appears to be dumping object references + correctly. + - Cray J90 (and Cray T3E?) 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. + +* Before building HDF5 F90 Library from source on Crays (T3E and J90) + replace H5Aff.f90, H5Dff.f90 and H5Pff.f90 files in the fortran/src subdirectory + in the top level directory with the Cray-specific files from the + ftp://hdf.ncsa.uiuc.edu/pub/ougoing/hdf5/hdf5-1.4.0-beta/F90_source_for_Crays + directory. |