From c65c1d25235dde13d5f544119f65d7d5470ff752 Mon Sep 17 00:00:00 2001 From: Elena Pourmal Date: Tue, 20 Mar 2001 14:18:01 -0500 Subject: [svn-r3675] Purpose: Update for hdf5 1.4.1 release Description: Information in HISTORY.txt and RELEASE.txt files should be updated for the upcoming hdf5 1.4.1 release. Solution: I created a new section for the HDF5 1.4.0 release in the HISTORY.txt file and copied RELEASE.txt into it. I updtaed RELEASE.txt to be the release file for HDF5 1.4.1. Platforms tested: --- HISTORY.txt | 629 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++-- RELEASE.txt | 530 +++----------------------------------------------- 2 files changed, 645 insertions(+), 514 deletions(-) diff --git a/HISTORY.txt b/HISTORY.txt index 79f5065..06cb61e 100644 --- a/HISTORY.txt +++ b/HISTORY.txt @@ -2,9 +2,10 @@ HDF5 HISTORY ============ CONTENTS -I. Release Information for hdf5-1.2.2 -II. Release Information for hdf5-1.2.1 -III. Release Information for hdf5-1.2.0 +I. Release Information for hdf5-1.4.0 +II. Release Information for hdf5-1.2.2 +III. Release Information for hdf5-1.2.1 +IV. Release Information for hdf5-1.2.0 A. Platforms Supported B. Known Problems C. Changes Since Version 1.0.1 @@ -25,10 +26,10 @@ III. Release Information for hdf5-1.2.0 g. Ragged Arrays 9. Tools -IV. Changes from Release 1.0.0 to Release 1.0.1 -V. Changes from the Beta 1.0.0 Release to Release 1.0.0 -VI. Changes from the Second Alpha 1.0.0 Release to the Beta 1.0.0 Release -VII. Changes from the First Alpha 1.0.0 Release to the +V. Changes from Release 1.0.0 to Release 1.0.1 +VI. Changes from the Beta 1.0.0 Release to Release 1.0.0 +VII. Changes from the Second Alpha 1.0.0 Release to the Beta 1.0.0 Release +VIII. Changes from the First Alpha 1.0.0 Release to the Second Alpha 1.0.0 Release [Search on the string '%%%%' for per-release section breaks.] @@ -37,9 +38,609 @@ VII. Changes from the First Alpha 1.0.0 Release to the +%%%%1.4.0%%%% Release Information for hdf5-1.4.0 (2/22/01) + +I. Release Information for hdf5-1.4.0 + + HDF5 Release 1.4.0 + + +INTRODUCTION + +This document describes the differences between HDF5-1.2.0 and +HDF5-1.4.0, and contains information on the platforms tested and +known problems in HDF5-1.4.0. For more details check the HISTORY.txt +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 +- Pablo Support +- Bug Fixes since HDF5-1.2.0 +- Bug Fixes since HDF5-1.4.0-beta2 +- Bug Fixes since HDF5-1.4.0 +- Documentation +- Platforms Tested +- Supported Configuration Features +- 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. See: + + http://hdf.ncsa.uiuc.edu/HDF5/papers/mthdf/MTHDFpaper.htm + + for more details. + * 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 utility, 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. + * You can now install the HDF5 documentation using the + ``make install-doc'' command. The documentation is installed in the + $(prefix)/doc directory where $(prefix) is the prefix specified by + the (optional) ``--prefix'' flag during configuration. + * HDF5 can operate correctly in the OpenMP environment in a limited way. + Check doc/html/TechNotes/openmp-hdf5.html for details. + + +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 Bugs: + + The h4toh5 utility produces images that do not correctly conform + to the HDF5 Image and Palette Specification. + + http://hdf.ncsa.uiuc.edu/HDF5/doc/ImageSpec.html + + Several required HDF5 attributes are omitted, and the dataspace + is reversed (i.e., the ht. and width of the image dataset is + incorrectly described.) For more information, please see: + + http://hdf.ncsa.uiuc.edu/HDF5/H5Image/ImageDetails.html + + This bug has been fixed for the snapshot of hdf5 1.4 release. March 12th,2001 + + Known Limitations of the h4toh5 release + --------------------------------------------- + + 1. Error handlings + + h4toh5 utility will print out an error message when an error occurs. + + 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 + + This 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 HDF5-1.4.0 and HDF4r1.4 + + h4toh5 utility has been tested on all platforms listed below (see + section "Platforms Tested") except TFLOPS. + + +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, SV1 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. + + +Pablo Support +============= + This version does not allow proper building of the Pablo-instrumented + version of the library. A version supporting the pablo build is + available on the Pablo Website at + www-pablo.cs.uiuc.edu/pub/Pablo.Release.5/HDFLibrary/hdf5_v1.4.tar.gz + + +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 correctly 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 :"). + * h5dump has a new feature "-o " which outputs the raw data + of the dataset into ascii text file . + * 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. + + +Bug Fixes since HDF5-1.4.0-beta2 +================================ + * Fixed a bug in the conversion from a little endian double to a big + endian float in some special cases. + * 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. + + +Bug Fixes since HDF5-1.4.0 Release +================================== + + * Fixed bug with contiguous hyperslabs not being detected, causing + slower I/O than necessary. + * Fixed bug where non-aligned hyperslab I/O on chunked datasets was + causing errors during I/O + * Implemented XML support in h5dump. + + +Documentation +============= + * A new document summarizing the changes in the library leading up to + the current release has been added: + HDF5 Software Changes from Release to Release + This document is in the Application Developer's Guide and is of + particular interest to developers who must keep an application + synchronized with the library. + * The documentation for the Fortran90 and C++ APIs is linked to the + opening page of the Reference Manual. Fortran90 functions are + individually referenced from the corresponding C functions through- + out the Reference Manual. + * User's Guide and Reference Manual were updated to reflect changed + function syntax and to fix reported bugs. + * Functions that are new at this release were added to the Reference + Manual. + * Functions that have been removed from the library were removed from + the User's Guide and the Reference Manual. + * PostScript and PDF versions of the Release 1.4 document set are + not available at the time of Release 1.4.0. + + +Platforms Tested +================ + AIX 4.3.3.0 (IBM SP powerpc) xlc 3.6.6 + mpcc_r 3.6.6 + Cray T3E sn6711 2.0.5.45 Cray Standard C Version 6.4.0.0 + Cray Fortran Version 3.4.0.2 + Cray SV1 sn9605 10.0.0.7 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 + mpich-1.2.1 + 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 + mpich-1.2.1 + 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 + mpich-1.2.1 + SunOS 5.5.1 gcc-2.7.2 + (Solaris 2.5.1 (x86)) + TFLOPS r1.0.4 v4.0 mpich-1.2.1 with local changes + Windows NT4.0, 2000 (NT5.0) MSVC++ 6.0 + Windows 98 MSVC++ 6.0 + + +Supported Configuration Features Summary +======================================== + In the tables below + y = tested and supported + n = not supported or not working in this release + ( ) = footnote appears below table + + Platform C C F90 F90 C++ Shared zlib Tools + parallel parallel libraries + Solaris2.6 y n y n y y y y + Solaris2.7 y y (1) y n y y y y + Solarisx86 y n n n n y y y + IRIX6.5 y y (1) n n n n y y + IRIX64_6.5 64 y y (2) y y n y y y + IRIX64_6.5 32 y y (2) n n n y y y + HPUX10.20 y n n n n y y y + DECOSF y n y n n y y y + T3E y y y y n n y y + SV1 y n y n n n y y + TFLOPS y y (1) n n n n y y (4) + AIX-4.3 y y n n n n y n + Win2000 y n n n n y y y + Win98 y n n n n y y y + WinNT y n n n n y y y + FreeBSD y n n n y y y y + Linux y y (1) y n y y y y + + + Platform 1.2 static- Thread- SRB GASS STREAM- + compatibility exec safe VFD + Solaris2.6 y n n n n y + Solaris2.7 y n y n n y + Solarisx86 y n n n n y + IRIX6.5 y n y n n y + IRIX64_6.5 64 y n n n n y + IRIX64_6.5 32 y n n n n y + HPUX10.20 y y n n n y + DECOSF y y n n n y + T3E y y n n n y + SV1 y y n n n y + TFLOPS y y n n n n + AIX-4.3 y y (3) n n n y + Win2000 y y n n n n + Win98 y y n n n n + WinNT y y n n n n + FreeBSD y y n n n y + Linux y n y n n y + + Footnotes: (1) Using mpich. + (2) Using mpt and mpich. + (3) When configured with static-exec enabled, tests fail + in serial mode. + (4) No HDF4-related tools. + + +Known Problems +============== + * The stream-vfd test uses ip port 10007 for testing. If another + application is already using that port address, the test will hang + indefinitely and has to be terminated by the kill command. To try the + test again, change the port address in test/stream_test.c to one not + being used in the host. + + * The --enable-static-exec configure flag 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. + + The --enable-static-exec configure flag also fails to correctly compile + on IBM SP2 platform for the serial mode. The parallel mode works fine + with this option. + + The compilation fails if configured with --enable-static-exec on IRIX 6.5. + + The executable files in hdf5/bin are dynamic-linked for IRIX64 6.5(64 and + n32 modes) and IRIX 6.5, even though they are compiled with static library. + + It is suggested that you don't use this option on these platforms + during configuration. + + * testhdf5 got bus error with configuration options --prefix and --with-hdf4 + on IRIX 6.5. + + * 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 will continue investigating this. + + * h5toh4 converter fails two cases(tstr.h5 and tmany.h5) for release dll + version on windows 2000 and NT. The reason is possibly due to Windows NT + DLL convention on freeing memory. It seems that memory cannot be freed + across library or DLL. It is still under investigation. + + * HDF-GASS testings and testhdf5 in the test directory will get bus error if + the configured with --with-gass. + + * HDF-SRB testing got segmentation error on Solaris 2.7. + + * 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 --enable-static'. + + * 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 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 SV1) + 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://ftp.ncsa.uiuc.edu/HDF/HDF5/hdf5-1.4.0/src/crayf90/ directory. + + * The h4toh5 utility produces images that do not correctly conform + to the HDF5 Image and Palette Specification. + + http://hdf.ncsa.uiuc.edu/HDF5/doc/ImageSpec.html + + Several required HDF5 attributes are omitted, and the dataspace + is reversed (i.e., the ht. and width of the image dataset is + incorrectly described.) For more information, please see: + + http://hdf.ncsa.uiuc.edu/HDF5/H5Image/ImageDetails.htm + %%%%1.2.2%%%% Release Information for hdf5-1.2.2 (6/23/00) -I. Release Information for hdf5-1.2.2 +II. Release Information for hdf5-1.2.2 INTRODUCTION @@ -157,7 +758,7 @@ Platforms Tested %%%%1.2.1%%%% Release Information for hdf5-1.2.1 -II. Release Information for hdf5-1.2.1 +III. Release Information for hdf5-1.2.1 Bug fixes since HDF5-1.2.0 ========================== @@ -247,7 +848,7 @@ o SunOS 5.6 with C WorkShop Compilers 4.2: Hyperslab selections will %%%%1.2.0%%%% Release Information for hdf5-1.2.0 -III. Release Information for hdf5-1.2.0 +IV. Release Information for hdf5-1.2.0 A. Platforms Supported ------------------- @@ -500,7 +1101,7 @@ C. Changes Since Version 1.0.1 %%%%1.0.1%%%% Release Information for hdf5-1.0.1 -IV. Changes from Release 1.0.0 to Release 1.0.1 +V. Changes from Release 1.0.0 to Release 1.0.1 * [Improvement]: configure sets up the Makefile in the parallel tests suit (testpar/) correctly. @@ -568,7 +1169,7 @@ IV. Changes from Release 1.0.0 to Release 1.0.1 %%%%1.0.0%%%% Release Information for hdf5-1.0.0 -V. Changes from the Beta 1.0.0 Release to Release 1.0.0 +VI. Changes from the Beta 1.0.0 Release to Release 1.0.0 * Added fill values for datasets. For contiguous datasets fill value performance may be quite poor since the fill value is written to the @@ -591,7 +1192,7 @@ V. Changes from the Beta 1.0.0 Release to Release 1.0.0 %%%%1.0.0 Beta%%%% Release Information for hdf5-1.0.0 Beta -VI. Changes from the Second Alpha 1.0.0 Release to the Beta 1.0.0 Release +VII. Changes from the Second Alpha 1.0.0 Release to the Beta 1.0.0 Release * Strided hyperslab selections in dataspaces now working. @@ -621,7 +1222,7 @@ VI. Changes from the Second Alpha 1.0.0 Release to the Beta 1.0.0 Release %%%%1.0.0 Alpha 2%%%% Release Information for hdf5-1.0.0 Alpha 2 -VII. Changes from the First Alpha 1.0.0 Release to +VIII. Changes from the First Alpha 1.0.0 Release to the Second Alpha 1.0.0 Release * Two of the packages have been renamed. The data space API has been diff --git a/RELEASE.txt b/RELEASE.txt index c846870..a135183 100644 --- a/RELEASE.txt +++ b/RELEASE.txt @@ -1,13 +1,13 @@ - HDF5 Release 1.4.0 + HDF5 Release 1.4.1 INTRODUCTION -This document describes the differences between HDF5-1.2.0 and -HDF5-1.4.0, and contains information on the platforms tested and -known problems in HDF5-1.4.0. For more details check the HISTORY.txt +This document describes the differences between HDF5-1.4.0 and +HDF5-1.4.1, and contains information on the platforms tested and +known problems in HDF5-1.4.1. For more details check the HISTORY.txt file in the HDF5 source. The HDF5 documentation can be found on the NCSA ftp server @@ -27,12 +27,6 @@ If you have any questions or comments, please send them to: CONTENTS - New Features -- h4toh5 Utility -- F90 Support -- C++ Support -- Pablo Support -- Bug Fixes since HDF5-1.2.0 -- Bug Fixes since HDF5-1.4.0-beta2 - Bug Fixes since HDF5-1.4.0 - Documentation - Platforms Tested @@ -42,373 +36,48 @@ CONTENTS 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. See: - http://hdf.ncsa.uiuc.edu/HDF5/papers/mthdf/MTHDFpaper.htm + * XML output option for h5dump utility + A new option --xml to output data in XML format has been added. + The XML output contains a complete description of the file, marked up in XML. + The XML conforms to the HDF5 Document Type Definition (DTD), + which is available at: + http://hdf.ncsa.uiuc.edu/DTDs/HDF5-File.dtd - for more details. - * 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 utility, 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. - * You can now install the HDF5 documentation using the - ``make install-doc'' command. The documentation is installed in the - $(prefix)/doc directory where $(prefix) is the prefix specified by - the (optional) ``--prefix'' flag during configuration. - * HDF5 can operate correctly in the OpenMP environment in a limited way. - Check doc/html/TechNotes/openmp-hdf5.html for details. + The XML output is suitable for use with other tools, including the + Java Tools: + http://hdf.ncsa.uiuc.edu/java-hdf5-html -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 Bugs: - - The h4toh5 utility produces images that do not correctly conform - to the HDF5 Image and Palette Specification. - - http://hdf.ncsa.uiuc.edu/HDF5/doc/ImageSpec.html - - Several required HDF5 attributes are omitted, and the dataspace - is reversed (i.e., the ht. and width of the image dataset is - incorrectly described.) For more information, please see: - - http://hdf.ncsa.uiuc.edu/HDF5/H5Image/ImageDetails.html - - This bug has been fixed for the snapshot of hdf5 1.4 release. March 12th,2001 - - Known Limitations of the h4toh5 release - --------------------------------------------- - - 1. Error handlings - - h4toh5 utility will print out an error message when an error occurs. - - 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 - - This 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 HDF5-1.4.0 and HDF4r1.4 - - h4toh5 utility has been tested on all platforms listed below (see - section "Platforms Tested") except TFLOPS. - - -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, SV1 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. - - -Pablo Support -============= - This version does not allow proper building of the Pablo-instrumented - version of the library. A version supporting the pablo build is - available on the Pablo Website at - www-pablo.cs.uiuc.edu/pub/Pablo.Release.5/HDFLibrary/hdf5_v1.4.tar.gz - - -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 +Bug Fixes since HDF5-1.4.0 Release +================================== + * h4toh5 utility: conversion of images is fixed - 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 correctly 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 :"). - * h5dump has a new feature "-o " which outputs the raw data - of the dataset into ascii text file . - * 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. + Earlier releases of the h4toh5 utility produced images that did not + correctly conform to the HDF5 Image and Palette Specification. + http://hdf.ncsa.uiuc.edu/HDF5/doc/ImageSpec.html -Bug Fixes since HDF5-1.4.0-beta2 -================================ - * Fixed a bug in the conversion from a little endian double to a big - endian float in some special cases. - * 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. + Several required HDF5 attributes are omitted, and the dataspace + is reversed (i.e., the ht. and width of the image dataset is + incorrectly described.) For more information, please see: - -Bug Fixes since HDF5-1.4.0 Release -================================== + http://hdf.ncsa.uiuc.edu/HDF5/H5Image/ImageDetails.html * Fixed bug with contiguous hyperslabs not being detected, causing slower I/O than necessary. * Fixed bug where non-aligned hyperslab I/O on chunked datasets was causing errors during I/O - * Implemented XML support in h5dump. Documentation ============= - * A new document summarizing the changes in the library leading up to - the current release has been added: - HDF5 Software Changes from Release to Release - This document is in the Application Developer's Guide and is of - particular interest to developers who must keep an application - synchronized with the library. - * The documentation for the Fortran90 and C++ APIs is linked to the - opening page of the Reference Manual. Fortran90 functions are - individually referenced from the corresponding C functions through- - out the Reference Manual. - * User's Guide and Reference Manual were updated to reflect changed - function syntax and to fix reported bugs. - * Functions that are new at this release were added to the Reference - Manual. - * Functions that have been removed from the library were removed from - the User's Guide and the Reference Manual. - * PostScript and PDF versions of the Release 1.4 document set are - not available at the time of Release 1.4.0. Platforms Tested ================ +Due to the nature of this release only C library and tools were tested. + AIX 4.3.3.0 (IBM SP powerpc) xlc 3.6.6 mpcc_r 3.6.6 Cray T3E sn6711 2.0.5.45 Cray Standard C Version 6.4.0.0 @@ -448,150 +117,11 @@ Platforms Tested Supported Configuration Features Summary ======================================== - In the tables below - y = tested and supported - n = not supported or not working in this release - ( ) = footnote appears below table - - Platform C C F90 F90 C++ Shared zlib Tools - parallel parallel libraries - Solaris2.6 y n y n y y y y - Solaris2.7 y y (1) y n y y y y - Solarisx86 y n n n n y y y - IRIX6.5 y y (1) n n n n y y - IRIX64_6.5 64 y y (2) y y n y y y - IRIX64_6.5 32 y y (2) n n n y y y - HPUX10.20 y n n n n y y y - DECOSF y n y n n y y y - T3E y y y y n n y y - SV1 y n y n n n y y - TFLOPS y y (1) n n n n y y (4) - AIX-4.3 y y n n n n y n - Win2000 y n n n n y y y - Win98 y n n n n y y y - WinNT y n n n n y y y - FreeBSD y n n n y y y y - Linux y y (1) y n y y y y - - - Platform 1.2 static- Thread- SRB GASS STREAM- - compatibility exec safe VFD - Solaris2.6 y n n n n y - Solaris2.7 y n y n n y - Solarisx86 y n n n n y - IRIX6.5 y n y n n y - IRIX64_6.5 64 y n n n n y - IRIX64_6.5 32 y n n n n y - HPUX10.20 y y n n n y - DECOSF y y n n n y - T3E y y n n n y - SV1 y y n n n y - TFLOPS y y n n n n - AIX-4.3 y y (3) n n n y - Win2000 y y n n n n - Win98 y y n n n n - WinNT y y n n n n - FreeBSD y y n n n y - Linux y n y n n y - - Footnotes: (1) Using mpich. - (2) Using mpt and mpich. - (3) When configured with static-exec enabled, tests fail - in serial mode. - (4) No HDF4-related tools. - + * See "Supported Configuration Features Summary" section for the HDF5 1.4.0 release + in the HISTORY.txt file. Known Problems ============== - * The stream-vfd test uses ip port 10007 for testing. If another - application is already using that port address, the test will hang - indefinitely and has to be terminated by the kill command. To try the - test again, change the port address in test/stream_test.c to one not - being used in the host. - - * The --enable-static-exec configure flag 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. - - The --enable-static-exec configure flag also fails to correctly compile - on IBM SP2 platform for the serial mode. The parallel mode works fine - with this option. - - The compilation fails if configured with --enable-static-exec on IRIX 6.5. - - The executable files in hdf5/bin are dynamic-linked for IRIX64 6.5(64 and - n32 modes) and IRIX 6.5, even though they are compiled with static library. - - It is suggested that you don't use this option on these platforms - during configuration. - - * testhdf5 got bus error with configuration options --prefix and --with-hdf4 - on IRIX 6.5. - - * 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 will continue investigating this. - - * h5toh4 converter fails two cases(tstr.h5 and tmany.h5) for release dll - version on windows 2000 and NT. The reason is possibly due to Windows NT - DLL convention on freeing memory. It seems that memory cannot be freed - across library or DLL. It is still under investigation. - - * HDF-GASS testings and testhdf5 in the test directory will get bus error if - the configured with --with-gass. - - * HDF-SRB testing got segmentation error on Solaris 2.7. - - * 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 --enable-static'. - - * 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 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 SV1) - 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://ftp.ncsa.uiuc.edu/HDF/HDF5/hdf5-1.4.0/src/crayf90/ directory. - - * The h4toh5 utility produces images that do not correctly conform - to the HDF5 Image and Palette Specification. - - http://hdf.ncsa.uiuc.edu/HDF5/doc/ImageSpec.html - - Several required HDF5 attributes are omitted, and the dataspace - is reversed (i.e., the ht. and width of the image dataset is - incorrectly described.) For more information, please see: - - http://hdf.ncsa.uiuc.edu/HDF5/H5Image/ImageDetails.htm + * See "Known problems" section for the HDF5 1.4.0 release in the HISTORY.txt + file. + -- cgit v0.12