From 6d7917d341e0c2a1a96e55f94f6d14c65e0266e9 Mon Sep 17 00:00:00 2001 From: Elena Pourmal Date: Thu, 5 Jul 2001 10:51:25 -0500 Subject: [svn-r4112] Purpose: Maintenance Description: Source directory has been rearranged. INSTALL*, HISTORY.txt and RELEASE.txt were moved to the release_docs directory. *.zip files were moved to the windows directory. README file was renamed to README.txt MANIFEST was updated to reflect those changes. --- HISTORY.txt | 1751 -------------------------------------- INSTALL | 538 ------------ INSTALL_TFLOPS | 163 ---- INSTALL_VFL | 130 --- INSTALL_Windows.txt | 916 -------------------- INSTALL_parallel | 177 ---- MANIFEST | 25 +- README | 44 - README.txt | 44 + RELEASE.txt | 144 ---- all.zip | Bin 205910 -> 0 bytes all_withf90.zip | Bin 212986 -> 0 bytes all_withhdf4.zip | Bin 217014 -> 0 bytes release_docs/HISTORY.txt | 1751 ++++++++++++++++++++++++++++++++++++++ release_docs/INSTALL | 538 ++++++++++++ release_docs/INSTALL_TFLOPS | 163 ++++ release_docs/INSTALL_VFL | 130 +++ release_docs/INSTALL_Windows.txt | 916 ++++++++++++++++++++ release_docs/INSTALL_parallel | 177 ++++ release_docs/RELEASE.txt | 144 ++++ windows/all.zip | Bin 0 -> 205910 bytes windows/all_withf90.zip | Bin 0 -> 212986 bytes windows/all_withhdf4.zip | Bin 0 -> 217014 bytes 23 files changed, 3877 insertions(+), 3874 deletions(-) delete mode 100644 HISTORY.txt delete mode 100644 INSTALL delete mode 100644 INSTALL_TFLOPS delete mode 100644 INSTALL_VFL delete mode 100644 INSTALL_Windows.txt delete mode 100644 INSTALL_parallel delete mode 100644 README create mode 100644 README.txt delete mode 100644 RELEASE.txt delete mode 100644 all.zip delete mode 100644 all_withf90.zip delete mode 100644 all_withhdf4.zip create mode 100644 release_docs/HISTORY.txt create mode 100644 release_docs/INSTALL create mode 100644 release_docs/INSTALL_TFLOPS create mode 100644 release_docs/INSTALL_VFL create mode 100644 release_docs/INSTALL_Windows.txt create mode 100644 release_docs/INSTALL_parallel create mode 100644 release_docs/RELEASE.txt create mode 100755 windows/all.zip create mode 100755 windows/all_withf90.zip create mode 100644 windows/all_withhdf4.zip diff --git a/HISTORY.txt b/HISTORY.txt deleted file mode 100644 index ebf460a..0000000 --- a/HISTORY.txt +++ /dev/null @@ -1,1751 +0,0 @@ -HDF5 HISTORY -============ - -CONTENTS -I. Release Information for hdf5-1.4.1 -II. Release Information for hdf5-1.4.0 -III. Release Information for hdf5-1.2.2 -IV. Release Information for hdf5-1.2.1 -V. Release Information for hdf5-1.2.0 - A. Platforms Supported - B. Known Problems - C. Changes Since Version 1.0.1 - 1. Documentation - 2. Configuration - 3. Debugging - 4. Datatypes - 5. Dataspaces - 6. Persistent Pointers - 7. Parallel Support - 8. New API Functions - a. Property List Interface - b. Dataset Interface - c. Dataspace Interface - d. Datatype Interface - e. Identifier Interface - f. Reference Interface - g. Ragged Arrays - 9. Tools - -VI. Changes from Release 1.0.0 to Release 1.0.1 -VII. Changes from the Beta 1.0.0 Release to Release 1.0.0 -VIII. Changes from the Second Alpha 1.0.0 Release to the Beta 1.0.0 Release -IX. 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.] - ------------------------------------------------------------------------ - - -%%%%1.4.1%%%% Release Information for hdf5-1.4.1 (April/01) - - - - - HDF5 Release 1.4.1 - - -INTRODUCTION - -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 -(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 -- Bug Fixes since HDF5-1.4.0 -- Documentation -- Platforms Tested -- Supported Configuration Features -- Known Problems - - -New Features -============ - - * 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 - - The XML output is suitable for use with other tools, including the - Java Tools: - - http://hdf.ncsa.uiuc.edu/java-hdf5-html - - -Bug Fixes since HDF5-1.4.0 Release -================================== - - * h4toh5 utility: conversion of images is fixed - - 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 - - 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 - - * 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 - * The RCSID string in H5public.h was causing the C++ compiling problem - because when it was included multiple times, C++ did not like - multiple definitions of the same static variable. All occurance of - RCSID definition are removed since we have not used it consistently - before. - - -Documentation -============= - - PDF and Postscript versions of the following documents are available - for this release: - Document Filename - -------- -------- - Introduction to HDF5 H5-R141-Introduction.pdf - HDF5 Reference Manual H5-R141-RefManual.pdf - C++ APIs to HDF5 documents H5-R141-Cplusplus.pdf - Fortran90 APIs to HDF5 documents H5-R141-Fortran90.pdf - - PDF and Postscript files containing H5-R141-DocSet.pdf - all of the above H5-R141-DocSet.ps - - These files are not included in this distribution, but are available - via the Web or FTP at the following locations: - http://hdf.ncsa.uiuc.edu/HDF5/doc/PSandPDF/ - ftp://ftp.ncsa.uiuc.edu/HDF/HDF5/docs/ - - While these documents are labeled Release 1.4.1, they describe - Release 1.4.0 as well. - - -Platforms Tested -================ - -Due to the nature of this release only C, C++ libraries and tools were tested. - - AIX 4.3.3.0 (IBM SP powerpc) xlc 3.6.6 - mpcc_r 3.6.6 - Cray T3E sn6711 2.0.5.47 Cray Standard C Version 6.5.0.0 - Cray SV1 10.0.0.8 Cray Standard C Version 6.5.0.0 - FreeBSD 4.3 gcc 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.11.01.20 - IRIX 6.5 MIPSpro cc 7.30 - IRIX64 6.5 (64 & n32) MIPSpro cc 7.3.1m - Linux 2.2.18smp gcc-2.95.2 - g++ 2.95.2 - 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) - - SunOS 5.7 WorkShop Compilers 5.0 98/12/15 C 5.0 - (Solaris 2.7) Workshop Compilers 5.0 98/12/15 C++ 5.0 - 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 -======================================== - - * See "Supported Configuration Features Summary" section for the HDF5 - 1.4.0 release in the HISTORY.txt file. - -Known Problems -============== - - * The h5dump tests may fail to match the expected output in some - platforms (e.g. SP2 parallel, Windows) where the error messages - directed to "stderr" do not appear in the "right order" with output - from stdout. This is not an error. - - * The --enable-static-exec configure flag fails to compile for HP-UX - 11.00 platforms. - - * The executable are always dynamic on IRIX64 6.5(64 and n32) and - IRIX 6.5 even if they are configured with --enable-static-exec. - - * The shared library failed compilation on IRIX 6.5. - - * After "make install" or "make install-doc" one may need to reload the source - from the tar file before doing another build. - - * See "Known problems" section for the HDF5 1.4.0 release in the - HISTORY.txt file. - -%%%%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) - -II. Release Information for hdf5-1.2.2 - -INTRODUCTION - -This document describes the differences between HDF5-1.2.1 and -HDF5-1.2.2, and contains information on the platforms where HDF5-1.2.2 -was tested and known problems in HDF5-1.2.2. - -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 - -- Features Added since HDF5-1.2.1 -- Bug Fixes since HDF5-1.2.1 -- Known Problems -- Platforms Tested - - -Features Added since HDF5-1.2.1 -=============================== - * Added internal free-lists to reduce memory required by the library and - H5garbage_collect API function. - * h5dump displays opaque and bitfield types. - * 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. - -Bug Fixes since HDF5-1.2.1 -========================== - * h5dump correctly displays compound datatypes, including simple and - nested compound types. - * h5dump correctly displays the committed copy of predefined types. - * Corrected an error in h5toh4 which did not convert the 32-bit - int from HDF5 to HDF4 correctly for the T3E platform. - * Corrected a floating point number conversion error for the - Cray J90 platform. The error did not convert the value 0.0 - correctly. - * 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 caused 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 without the same dimension being unlimited. - * Improved metadata hashing & caching algorithms to avoid - many hash flushes and also removed some redundant I/O when moving metadata - blocks in the file. - * The libhdf5.settings file shows the correct machine byte-sex. - * 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. - -Known Problems -============== - -o SunOS 5.6 with C WorkShop Compilers 4.2: hyperslab selections will - fail if library is compiled using optimization of any level. -o TFLOPS: dsets test fails if compiled with optimization turned on. -o J90: tools fail to dispay data for the datasets with a compound datatype. - -Platforms Tested -================ - - AIX 4.3.3 (IBM SP) 3.6.6 | binaries - mpicc using mpich 1.1.2 | are not - mpicc_r using IBM MPI-IO prototype | available - AIX 4.3.2.0 (IBM SP) xlc 5.0.1.0 - Cray J90 10.0.0.7 cc 6.3.0.2 - Cray T3E 2.0.5.29 cc 6.3.0.2 - mpt.1.3 - FreeBSD 4.0 gcc 2.95.2 - HP-UX B.10.20 HP C HP92453-01 A.10.32 - HP-UX B.11.00 HP92453-01 A.11.00.13 HP C Compiler - (static library only, h5toh4 tool is not available) - IRIX 6.5 MIPSpro cc 7.30 - IRIX64 6.5 (64 & n32) MIPSpro cc 7.3.1m - mpt.1.4 - - Linux 2.2.10 SMP gcc 2.95.1 - mpicc(gcc-2.95.1) - gcc (egcs-2.91.66) - mpicc (egcs-2.91.66) - Linux 2.2.16 (RedHat 6.2) gcc 2.95.2 - - OSF1 V4.0 DEC-V5.2-040 - SunOS 5.6 cc WorkShop Compilers 5.0 no optimization - SunOS 5.7 cc WorkShop Compilers 5.0 - SolarisX86 SunOS 5.5.1 gcc version 2.7.2 with --disable-hsizet - TFLOPS 3.2.1 pgcc Rel 3.1-3i - mpich-1.1.2 with local changes - Windows NT4.0 sp5 MSVC++ 6.0 - Windows 98 MSVC++ 6.0 - Windows 2000 MSVC++ 6.0 - - - -%%%%1.2.1%%%% Release Information for hdf5-1.2.1 - -III. Release Information for hdf5-1.2.1 - -Bug fixes since HDF5-1.2.0 -========================== - -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. - -Library -------- - - * Error was fixed which was not allowing dataset region references to have - their regions retrieved correctly. - * 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. - -Tests ------- - - * Added additional tests for group and attribute iteration. - * Added additional test for staggered hyperslab iteration. - * Added additional test for random 5-D hyperslab selection. - -Tools ------- - - * 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. - -Documentation -------------- - - * User's Guide and Reference Manual were updated. - See doc/html/PSandPDF/index.html for more details. - - -Platforms Tested: -================ -Note: Due to the nature of bug fixes, only static versions of the library and tools were tested. - - - AIX 4.3.2 (IBM SP) 3.6.6 - Cray T3E 2.0.4.81 cc 6.3.0.1 - mpt.1.3 - FreeBSD 3.3-STABLE gcc 2.95.2 - HP-UX B.10.20 HP C HP92453-01 A.10.32 - IRIX 6.5 MIPSpro cc 7.30 - IRIX64 6.5 (64 & n32) MIPSpro cc 7.3.1m - mpt.1.3 (SGI MPI 3.2.0.0) - - Linux 2.2.10 SuSE egcs-2.91.66 configured with - (i686-pc-linux-gnu) --disable-hsizet - mpich-1.2.0 egcs-2.91.66 19990314/Linux - - OSF1 V4.0 DEC-V5.2-040 - SunOS 5.6 cc WorkShop Compilers 4.2 no optimization - SunOS 5.7 cc WorkShop Compilers 5.0 - TFLOPS 2.8 cicc (pgcc Rel 3.0-5i) - mpich-1.1.2 with local changes - Windows NT4.0 sp5 MSVC++ 6.0 - -Known Problems: -============== - -o SunOS 5.6 with C WorkShop Compilers 4.2: Hyperslab selections will - fail if library is compiled using optimization of any level. - - - -%%%%1.2.0%%%% Release Information for hdf5-1.2.0 - -IV. Release Information for hdf5-1.2.0 - -A. Platforms Supported - ------------------- - -Operating systems listed below with compiler information and MPI library, if -applicable, are systems that HDF5 1.2.0 was tested on. - - Compiler & libraries - Platform Information Comment - -------- ---------- -------- - - AIX 4.3.2 (IBM SP) 3.6.6 - - Cray J90 10.0.0.6 cc 6.3.0.0 - - Cray T3E 2.0.4.61 cc 6.2.1.0 - mpt.1.3 - - FreeBSD 3.2 gcc 2.95.1 - - HP-UX B.10.20 HP C HP92453-01 A.10.32 - gcc 2.8.1 - - IRIX 6.5 MIPSpro cc 7.30 - - IRIX64 6.5 (64 & n32) MIPSpro cc 7.3.1m - mpt.1.3 (SGI MPI 3.2.0.0) - - Linux 2.2.10 egcs-2.91.66 configured with - --disable-hsizet - lbraries: glibc2 - - OSF1 V4.0 DEC-V5.2-040 - - SunOS 5.6 cc WorkShop Compilers 4.2 - no optimization - gcc 2.8.1 - - SunOS 5.7 cc WorkShop Compilers 5.0 - gcc 2.8.1 - - TFLOPS 2.7.1 cicc (pgcc Rel 3.0-4i) - mpich-1.1.2 with local changes - - Windows NT4.0 intel MSVC++ 5.0 and 6.0 - - Windows NT alpha 4.0 MSVC++ 5.0 - - Windows 98 MSVC++ 5.0 - - -B. Known Problems - -------------- - -* NT alpha 4.0 - Dumper utiliy h5dump fails if linked with DLL. - -* SunOS 5.6 with C WorkShop Compilers 4.2 - Hyperslab selections will fail if library is compiled using optimization - of any level. - - -C. Changes Since Version 1.0.1 - --------------------------- - -1. Documentation - ------------- - -* More examples - -* Updated user guide, reference manual, and format specification. - -* Self-contained documentation for installations isolated from the - Internet. - -* HDF5 Tutorial was added to the documentation - -2. Configuration - ------------- - -* Better detection and support for MPI-IO. - -* Recognition of compilers with known code generation problems. - -* Support for various compilers on a single architecture (e.g., the - native compiler and the GNU compilers). - -* Ability to build from read-only media and with different compilers - and/or options concurrently. - -* Added a libhdf5.settings file which summarizes the configuration - information and is installed along with the library. - -* Builds a shared library on most systems that support it. - -* Support for Cray T3E, J90 and Windows/NT. - -3. Debugging - --------- - -* Improved control and redirection of debugging and tracing messages. - -4. Datatypes - --------- - -* Optimizations to compound datatype conversions and I/O operations. - -* Added nearly 100 optimized conversion functions for native datatypes - including support for non-aligned data. - -* Added support for bitfield, opaque, and enumeration types. - -* Added distinctions between signed and unsigned char types to the - list of predefined native hdf5 datatypes. - -* Added HDF5 type definitions for C9x types like int32_t. - -* Application-defined type conversion functions can handle non-packed - data. - -* Changed the H5Tunregister() function to use wildcards when matching - conversion functions. H5Tregister_hard() and H5Tregister_soft() - were combined into H5Tregister(). - -* Support for variable-length datatypes (arrays of varying length per - dataset element). Variable length strings currently supported only - as variable length arrays of 1-byte integers. - -5. Dataspaces - ---------- - -* New query functions for selections. - -* I/O operations bypass the stripmining loop and go directly to - storage for certain contiguous selections in the absense of type - conversions. In other cases the stripmining buffers are used more - effectively. - -* Reduced the number of I/O requests under certain circumstances, - improving performance on systems with high I/O latency. - -6. Persistent Pointers - ------------------- - -* Object (serial and parallel) and dataset region (serial only) - references are implemented. - -7. Parallel Support - ---------------- - -* Improved parallel I/O performance. - -* Supported new platforms: Cray T3E, Linux, DEC Cluster. - -* Use vendor supported version of MPIO on SGI O2K and Cray platforms. - -* Improved the algorithm that translates an HDF5 hyperslab selection - into an MPI type for better collective I/O performance. - -8. New API functions - ----------------- - - a. Property List Interface: - ------------------------ - - H5Pset_xfer - set data transfer properties - H5Pset_preserve - set dataset transfer property list status - H5Pget_preserve - get dataset transfer property list status - H5Pset_hyper_cache - indicates whether to cache hyperslab blocks during I/O - H5Pget_hyper_cache - returns information regarding the caching of - hyperslab blocks during I/O - H5Pget_btree_ratios - sets B-tree split ratios for a dataset - transfer property list - H5Pset_btree_ratios - gets B-tree split ratios for a dataset - transfer property list - H5Pset_vlen_mem_manager - sets the memory manager for variable-length - datatype allocation - H5Pget_vlen_mem_manager - sets the memory manager for variable-length - datatype allocation - - b. Dataset Interface: - ------------------ - - H5Diterate - iterate over all selected elements in a dataspace - H5Dget_storage_size - return the amount of storage required for a dataset - H5Dvlen_reclaim - reclaim VL datatype memory buffers - - c. Dataspace Interface: - -------------------- - H5Sget_select_hyper_nblocks - get number of hyperslab blocks - H5Sget_select_hyper_blocklist - get the list of hyperslab blocks - currently selected - H5Sget_select_elem_npoints - get the number of element points - in the current selection - H5Sget_select_elem_pointlist - get the list of element points - currently selected - H5Sget_select_bounds - gets the bounding box containing - the current selection - - d. Datatype Interface: - ------------------- - H5Tget_super - return the base datatype from which a - datatype is derived - H5Tvlen_create - creates a new variable-length dataype - H5Tenum_create - creates a new enumeration datatype - H5Tenum_insert - inserts a new enumeration datatype member - H5Tenum_nameof - returns the symbol name corresponding to a - specified member of an enumeration datatype - H5Tvalueof - return the value corresponding to a - specified member of an enumeration datatype - H5Tget_member_value - return the value of an enumeration datatype member - H5Tset_tag - tags an opaque datatype - H5Tget_tag - gets the tag associated with an opaque datatype - - e. Identifier Interface: - --------------------- - H5Iget_type - retrieve the type of an object - - f. Reference Interface: - -------------------- - H5Rcreate - creates a reference - H5Rdereference - open the HDF5 object referenced - H5Rget_region - retrieve a dataspace with the specified region selected - H5Rget_object_type - retrieve the type of object that an - object reference points to - - g. Ragged Arrays (alpha) (names of those API functions were changed): - ------------------------------------------------------------------ - H5RAcreate - create a new ragged array (old name was H5Rcreate) - H5RAopen - open an existing array (old name was H5Ropen) - H5RAclose - close a ragged array (old name was H5Rclose) - H5RAwrite - write to an array (old name was H5Rwrite) - H5RAread - read from an array (old name was H5Rread) - - -9. Tools - ----- - -* Enhancements to the h5ls tool including the ability to list objects - from more than one file, to display raw hexadecimal data, to - show file addresses for raw data, to format output more reasonably, - to show object attributes, and to perform a recursive listing, - -* Enhancements to h5dump: support new data types added since previous - versions. - -* h5toh4: An hdf5 to hdf4 converter. - - - -%%%%1.0.1%%%% Release Information for hdf5-1.0.1 - -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. - -* [Bug-Fix]: Configure failed for all IRIX versions other than 6.3. - It now configures correctly for all IRIX 6.x version. - -* Released Parallel HDF5 - - Supported Features: - ------------------ - - HDF5 files are accessed according to the communicator and INFO - object defined in the property list set by H5Pset_mpi. - - Independent read and write accesses to fixed and extendable dimension - datasets. - - Collective read and write accesses to fixed dimension datasets. - - Supported Platforms: - ------------------- - - Intel Red - IBM SP2 - SGI Origin 2000 - - Changes In This Release: - ----------------------- - - o Support of Access to Extendable Dimension Datasets. - Extendable dimension datasets must use chunked storage methods. - A new function, H5Dextend, is created to extend the current - dimensions of a dataset. The current release requires the - MPI application must make a collective call to extend the - dimensions of an extendable dataset before writing to the - newly extended area. (The serial does not require the - call of H5Dextend. The dimensions of an extendable - dataset is increased when data is written to beyond the - current dimensions but within the maximum dimensions.) - The required collective call of H5Dextend may be relaxed - in future release. - - This release only support independent read and write accesses - to extendable datasets. Collective accesses to extendable - datasets will be implemented in future releases. - - o Collective access to fixed dimension datasets. - Collective access to a dataset can be specified in the transfer - property list argument in H5Dread and H5Dwrite. The current - release supports collective access to fixed dimension datasets. - Collective access to extendable datasets will be implemented in - future releases. - - o HDF5 files are opened according to Communicator and INFO object. - H5Dopen now records the communicator and INFO setup by H5Pset_mmpi - and pass them to the corresponding MPIO open file calls for - processing. - - o This release has been tested on IBM SP2, Intel Red and SGI Origin 2000 - systems. It uses the ROMIO version of MPIO interface for parallel - I/O supports. - - - -%%%%1.0.0%%%% Release Information for hdf5-1.0.0 - -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 - entire dataset when the dataset is created. This will be remedied - in a future version. Chunked datasets using fill values do not - incur any additional overhead. See H5Pset_fill_value(). - -* Multiple hdf5 files can be "mounted" on one another to create a - larger virtual file. See H5Fmount(). - -* Object names can be removed or changed but objects are never - actually removed from the file yet. See H5Gunlink() and H5Gmove(). - -* Added a tuning mechanism for B-trees to insure that sequential - writes to chunked datasets use less overhead. See H5Pset_btree_ratios(). - -* Various optimizations and bug fixes. - - - -%%%%1.0.0 Beta%%%% Release Information for hdf5-1.0.0 Beta - -VII. Changes from the Second Alpha 1.0.0 Release to the Beta 1.0.0 Release - -* Strided hyperslab selections in dataspaces now working. - -* The compression API has been replaced with a more general filter - API. See doc/html/Filters.html for details. - -* Alpha-quality 2d ragged arrays are implemented as a layer built on - top of other hdf5 objects. The API and storage format will almost - certainly change. - -* More debugging support including API tracing. See Debugging.html. - -* C and Fortran style 8-bit fixed-length character string types are - supported with space or null padding or null termination and - translations between them. - -* Added function H5Fflush() to write all cached data immediately to - the file. - -* Datasets maintain a modification time which can be retrieved with - H5Gstat(). - -* The h5ls tool can display much more information, including all the - values of a dataset. - - - -%%%%1.0.0 Alpha 2%%%% Release Information for hdf5-1.0.0 Alpha 2 - -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 - renamed from `H5P' to `H5S' and the property list (template) API has - been renamed from `H5C' to `H5P'. - -* The new attribute API `H5A' has been added. An attribute is a small - dataset which can be attached to some other object (for instance, a - 4x4 transformation matrix attached to a 3-dimensional dataset, or an - English abstract attached to a group). - -* The error handling API `H5E' has been completed. By default, when an - API function returns failure an error stack is displayed on the - standard error stream. The H5Eset_auto() controls the automatic - printing and H5E_BEGIN_TRY/H5E_END_TRY macros can temporarily - disable the automatic error printing. - -* Support for large files and datasets (>2GB) has been added. There - is an html document that describes how it works. Some of the types - for function arguments have changed to support this: all arguments - pertaining to sizes of memory objects are `size_t' and all arguments - pertaining to file sizes are `hsize_t'. - -* More data type conversions have been added although none of them are - fine tuned for performance. There are new converters from integer - to integer and float to float, but not between integers and floating - points. A bug has been fixed in the converter between compound - types. - -* The numbered types have been removed from the API: int8, uint8, - int16, uint16, int32, uint32, int64, uint64, float32, and float64. - Use standard C types instead. Similarly, the numbered types were - removed from the H5T_NATIVE_* architecture; use unnumbered types - which correspond to the standard C types like H5T_NATIVE_INT. - -* More debugging support was added. If tracing is enabled at - configuration time (the default) and the HDF5_TRACE environment - variable is set to a file descriptor then all API calls will emit - the function name, argument names and values, and return value on - that file number. There is an html document that describes this. - If appropriate debugging options are enabled at configuration time, - some packages will display performance information on stderr. - -* Data types can be stored in the file as independent objects and - multiple datasets can share a data type. - -* The raw data I/O stream has been implemented and the application can - control meta and raw data caches, so I/O performance should be - improved from the first alpha release. - -* Group and attribute query functions have been implemented so it is - now possible to find out the contents of a file with no prior - knowledge. - -* External raw data storage allows datasets to be written by other - applications or I/O libraries and described and accessed through - HDF5. - -* Hard and soft (symbolic) links are implemented which allow groups to - share objects. Dangling and recursive symbolic links are supported. - -* User-defined data compression is implemented although we may - generalize the interface to allow arbitrary user-defined filters - which can be used for compression, checksums, encryption, - performance monitoring, etc. The publicly-available `deflate' - method is predefined if the GNU libz.a can be found at configuration - time. - -* The configuration scripts have been modified to make it easier to - build debugging vs. production versions of the library. - -* The library automatically checks that the application was compiled - with the correct version of header files. - - - Parallel HDF5 Changes - -* Parallel support for fixed dimension datasets with contiguous or - chunked storages. Also, support unlimited dimension datasets which - must use chunk storage. No parallel support for compressed datasets. - -* Collective data transfer for H5Dread/H5Dwrite. Collective access - support for datasets with contiguous storage only, thus only fixed - dimension datasets for now. - -* H5Pset_mpi and H5Pget_mpi no longer have the access_mode - argument. It is taken over by the data-transfer property list - of H5Dread/H5Dwrite. - -* New functions H5Pset_xfer and H5Pget_xfer to handle the - specification of independent or collective data transfer_mode - in the dataset transfer properties list. The properties - list can be used to specify data transfer mode in the H5Dwrite - and H5Dread function calls. - -* Added parallel support for datasets with chunked storage layout. - When a dataset is extend in a PHDF5 file, all processes that open - the file must collectively call H5Dextend with identical new dimension - sizes. - - - LIST OF API FUNCTIONS - -The following functions are implemented. Errors are returned if an -attempt is made to use some feature which is not implemented and -printing the error stack will show `not implemented yet'. - -Library - H5check - check that lib version matches header version - H5open - initialize library (happens automatically) - H5close - shut down the library (happens automatically) - H5dont_atexit - don't call H5close on exit - H5get_libversion - retrieve library version info - H5check_version - check for specific library version - -Property Lists - H5Pclose - release template resources - H5Pcopy - copy a template - H5Pcreate - create a new template - H5Pget_chunk - get chunked storage properties - H5Pset_chunk - set chunked storage properties - H5Pget_class - get template class - H5Pget_istore_k - get chunked storage properties - H5Pset_istore_k - set chunked storage properties - H5Pget_layout - get raw data layout class - H5Pset_layout - set raw data layout class - H5Pget_sizes - get address and size sizes - H5Pset_sizes - set address and size sizes - H5Pget_sym_k - get symbol table storage properties - H5Pset_sym_k - set symbol table storage properties - H5Pget_userblock - get user-block size - H5Pset_userblock - set user-block size - H5Pget_version - get file version numbers - H5Pget_alignment - get data alignment properties - H5Pset_alignment - set data alignment properties - H5Pget_external_count- get count of external data files - H5Pget_external - get information about an external data file - H5Pset_external - add a new external data file to the list - H5Pget_driver - get low-level file driver class - H5Pget_stdio - get properties for stdio low-level driver - H5Pset_stdio - set properties for stdio low-level driver - H5Pget_sec2 - get properties for sec2 low-level driver - H5Pset_sec2 - set properties for sec2 low-level driver - H5Pget_core - get properties for core low-level driver - H5Pset_core - set properties for core low-level driver - H5Pget_split - get properties for split low-level driver - H5Pset_split - set properties for split low-level driver - H5P_get_family - get properties for family low-level driver - H5P_set_family - set properties for family low-level driver - H5Pget_cache - get meta- and raw-data caching properties - H5Pset_cache - set meta- and raw-data caching properties - H5Pget_buffer - get raw-data I/O pipe buffer properties - H5Pset_buffer - set raw-data I/O pipe buffer properties - H5Pget_preserve - get type conversion preservation properties - H5Pset_preserve - set type conversion preservation properties - H5Pget_nfilters - get number of raw data filters - H5Pget_filter - get raw data filter properties - H5Pset_filter - set raw data filter properties - H5Pset_deflate - set deflate compression filter properties - H5Pget_mpi - get MPI-IO properties - H5Pset_mpi - set MPI-IO properties - H5Pget_xfer - get data transfer properties - + H5Pset_xfer - set data transfer properties - + H5Pset_preserve - set dataset transfer property list status - + H5Pget_preserve - get dataset transfer property list status - + H5Pset_hyper_cache - indicates whether to cache hyperslab blocks during I/O - + H5Pget_hyper_cache - returns information regarding the caching of - hyperslab blocks during I/O - + H5Pget_btree_ratios - sets B-tree split ratios for a dataset - transfer property list - + H5Pset_btree_ratios - gets B-tree split ratios for a dataset - transfer property list - + H5Pset_vlen_mem_manager - sets the memory manager for variable-length - datatype allocation - + H5Pget_vlen_mem_manager - sets the memory manager for variable-length - datatype allocation - -Datasets - H5Dclose - release dataset resources - H5Dcreate - create a new dataset - H5Dget_space - get data space - H5Dget_type - get data type - H5Dget_create_plist - get dataset creation properties - H5Dopen - open an existing dataset - H5Dread - read raw data - H5Dwrite - write raw data - H5Dextend - extend a dataset - + H5Diterate - iterate over all selected elements in a dataspace - + H5Dget_storage_size - return the amount of storage required for a dataset - + H5Dvlen_reclaim - reclaim VL datatype memory buffers - -Attributes - H5Acreate - create a new attribute - H5Aopen_name - open an attribute by name - H5Aopen_idx - open an attribute by number - H5Awrite - write values into an attribute - H5Aread - read values from an attribute - H5Aget_space - get attribute data space - H5Aget_type - get attribute data type - H5Aget_name - get attribute name - H5Anum_attrs - return the number of attributes for an object - H5Aiterate - iterate over an object's attributes - H5Adelete - delete an attribute - H5Aclose - close an attribute - -Errors - H5Eclear - clear the error stack - H5Eprint - print an error stack - H5Eget_auto - get automatic error reporting settings - H5Eset_auto - set automatic error reporting - H5Ewalk - iterate over the error stack - H5Ewalk_cb - the default error stack iterator function - H5Eget_major - get the message for the major error number - H5Eget_minor - get the message for the minor error number - -Files - H5Fclose - close a file and release resources - H5Fcreate - create a new file - H5Fget_create_plist - get file creation property list - H5Fget_access_plist - get file access property list - H5Fis_hdf5 - determine if a file is an hdf5 file - H5Fopen - open an existing file - H5Freopen - reopen an HDF5 file - H5Fmount - mount a file - H5Funmount - unmount a file - H5Fflush - flush all buffers associated with a file to disk - -Groups - H5Gclose - close a group and release resources - H5Gcreate - create a new group - H5Gopen - open an existing group - H5Giterate - iterate over the contents of a group - H5Gmove - change the name of some object - H5Glink - create a hard or soft link to an object - H5Gunlink - break the link between a name and an object - H5Gget_objinfo - get information about a group entry - H5Gget_linkval - get the value of a soft link - H5Gget_comment - get the comment string for an object - H5Gset_comment - set the comment string for an object - -Dataspaces - H5Screate - create a new data space - H5Scopy - copy a data space - H5Sclose - release data space - H5Screate_simple - create a new simple data space - H5Sset_space - set simple data space extents - H5Sis_simple - determine if data space is simple - H5Sset_extent_simple - set simple data space dimensionality and size - H5Sget_simple_extent_npoints - get number of points in simple extent - H5Sget_simple_extent_ndims - get simple data space dimensionality - H5Sget_simple_extent_dims - get simple data space size - H5Sget_simple_extent_type - get type of simple extent - H5Sset_extent_none - reset extent to be empty - H5Sextent_copy - copy the extent from one data space to another - H5Sget_select_npoints - get number of points selected for I/O - H5Sselect_hyperslab - set hyperslab dataspace selection - H5Sselect_elements - set element sequence dataspace selection - H5Sselect_all - select entire extent for I/O - H5Sselect_none - deselect all elements of extent - H5Soffset_simple - set selection offset - H5Sselect_valid - determine if selection is valid for extent - + H5Sget_select_hyper_nblocks - get number of hyperslab blocks - + H5Sget_select_hyper_blocklist - get the list of hyperslab blocks - currently selected - + H5Sget_select_elem_npoints - get the number of element points - in the current selection - + H5Sget_select_elem_pointlist - get the list of element points - currently selected - + H5Sget_select_bounds - gets the bounding box containing - the current selection - -Datatypes - H5Tclose - release data type resources - H5Topen - open a named data type - H5Tcommit - name a data type - H5Tcommitted - determine if a type is named - H5Tcopy - copy a data type - H5Tcreate - create a new data type - H5Tequal - compare two data types - H5Tlock - lock type to prevent changes - H5Tfind - find a data type conversion function - H5Tconvert - convert data from one type to another - H5Tregister - register a conversion function - H5Tunregister - remove a conversion function - H5Tget_overflow - get function that handles overflow conv. cases - H5Tset_overflow - set function to handle overflow conversion cases - H5Tget_class - get data type class - H5Tget_cset - get character set - H5Tget_ebias - get exponent bias - H5Tget_fields - get floating point fields - H5Tget_inpad - get inter-field padding - H5Tget_member_dims - get struct member dimensions - H5Tget_member_name - get struct member name - H5Tget_member_offset - get struct member byte offset - H5Tget_member_type - get struct member type - H5Tget_nmembers - get number of struct members - H5Tget_norm - get floating point normalization - H5Tget_offset - get bit offset within type - H5Tget_order - get byte order - H5Tget_pad - get padding type - H5Tget_precision - get precision in bits - H5Tget_sign - get integer sign type - H5Tget_size - get size in bytes - H5Tget_strpad - get string padding - H5Tinsert - insert scalar struct member - H5Tinsert_array - insert array struct member - H5Tpack - pack struct members - H5Tset_cset - set character set - H5Tset_ebias - set exponent bias - H5Tset_fields - set floating point fields - H5Tset_inpad - set inter-field padding - H5Tset_norm - set floating point normalization - H5Tset_offset - set bit offset within type - H5Tset_order - set byte order - H5Tset_pad - set padding type - H5Tset_precision - set precision in bits - H5Tset_sign - set integer sign type - H5Tset_size - set size in bytes - H5Tset_strpad - set string padding - + H5Tget_super - return the base datatype from which a - datatype is derived - + H5Tvlen_create - creates a new variable-length dataype - + H5Tenum_create - creates a new enumeration datatype - + H5Tenum_insert - inserts a new enumeration datatype member - + H5Tenum_nameof - returns the symbol name corresponding to a - specified member of an enumeration datatype - + H5Tvalueof - return the value corresponding to a - specified member of an enumeration datatype - + H5Tget_member_value - return the value of an enumeration datatype member - + H5Tset_tag - tags an opaque datatype - + H5Tget_tag - gets the tag associated with an opaque datatype - - - H5Tregister_hard - register specific type conversion function - - H5Tregister_soft - register general type conversion function - -Filters - H5Tregister - register a conversion function - -Compression - H5Zregister - register new compression and uncompression - functions for a method specified by a method number - -Identifiers - + H5Iget_type - retrieve the type of an object - -References - + H5Rcreate - creates a reference - + H5Rdereference - open the HDF5 object referenced - + H5Rget_region - retrieve a dataspace with the specified region selected - + H5Rget_object_type - retrieve the type of object that an - object reference points to - -Ragged Arrays (alpha) - H5RAcreate - create a new ragged array - H5RAopen - open an existing array - H5RAclose - close a ragged array - H5RAwrite - write to an array - H5RAread - read from an array - - diff --git a/INSTALL b/INSTALL deleted file mode 100644 index 20ce060..0000000 --- a/INSTALL +++ /dev/null @@ -1,538 +0,0 @@ - - Instructions for the Installation of HDF5 Software - ================================================== - - CONTENTS - -------- - 1. Obtaining HDF5 - - 2. Warnings about compilers - 2.1. GNU (Intel platforms) - 2.2. DEC - 2.3. SGI (Irix64 6.2) - 2.4. Windows/NT - - 3. Quick installation - 3.1. TFLOPS - 3.2. Windows - 3.3. Certain Virtual File Layer(VFL) - - 4. HDF5 dependencies - 4.1. Zlib - 4.2. MPI and MPI-IO - - 5. Full installation instructions for source distributions - 5.1. Unpacking the distribution - 5.1.1. Non-compressed tar archive (*.tar) - 5.1.2. Compressed tar archive (*.tar.Z) - 5.1.3. Gzip'd tar archive (*.tar.gz) - 5.1.4. Bzip'd tar archive (*.tar.bz2) - 5.2. Source vs. Build Directories - 5.3. Configuring - 5.3.1. Specifying the installation directories - 5.3.2. Using an alternate C compiler - 5.3.3. Additional compilation flags - 5.3.4. Compiling HDF5 wrapper libraries - 5.3.5. Specifying other programs - 5.3.6. Specifying other libraries and headers - 5.3.7. Static versus shared linking - 5.3.8. Optimization versus symbolic debugging - 5.3.9. Large (>2GB) vs. small (<2GB) file capability - 5.3.10. Parallel vs. serial library - 5.4. Building - 5.5. Testing - 5.6. Installing - - 6. Using the Library - - 7. Support - -***************************************************************************** - -1. Obtaining HDF5 - The latest supported public release of HDF5 is available from - ftp://hdf.ncsa.uiuc.edu/pub/dist/HDF5. For Unix platforms, it is - available in tar format uncompressed or compressed with compress, - gzip, or bzip2. For Microsoft Windows, it is in ZIP format. - - The HDF team also makes snapshots of the source code available on - a regular basis. These snapshots are unsupported (that is, the - HDF team will not release a bug-fix on a particular snapshot; - rather any bug fixes will be rolled into the next snapshot). - Furthermore, the snapshots have only been tested on a few - machines and may not test correctly for parallel applications. - Snapshots can be found at - ftp://hdf.ncsa.uiuc.edu/pub/outgoing/hdf5/snapshots in a limited - number of formats. - -2. Warnings about compilers - OUTPUT FROM THE FOLLOWING COMPILERS SHOULD BE EXTREMELY SUSPECT - WHEN USED TO COMPILE THE HDF5 LIBRARY, ESPECIALLY IF - OPTIMIZATIONS ARE ENABLED. IN ALL CASES, HDF5 ATTEMPTS TO WORK - AROUND THE COMPILER BUGS BUT THE HDF5 DEVELOPMENT TEAM MAKES NO - GUARANTEES THAT THERE ARE OTHER CODE GENERATION PROBLEMS. - -2.1. GNU (Intel platforms) - Versions before 2.8.1 have serious problems allocating registers - when functions contain operations on `long long' data types. - Supplying the `--disable-hsizet' switch to configure (documented - below) will prevent hdf5 from using `long long' data types in - situations that are known not to work, but it limits the hdf5 - address space to 2GB. - -2.2. DEC - The V5.2-038 compiler (and possibly others) occasionally - generates incorrect code for memcpy() calls when optimizations - are enabled, resulting in unaligned access faults. HDF5 works - around the problem by casting the second argument to `char *'. - -2.3. SGI (Irix64 6.2) - The Mongoose 7.00 compiler has serious optimization bugs and - should be upgraded to MIPSpro 7.2.1.2m. Patches are available - from SGI. - -2.4. Windows/NT - The MicroSoft Win32 5.0 compiler is unable to cast unsigned long - long values to doubles. HDF5 works around this bug by first - casting to signed long long and then to double. - A link warning: defaultlib "LIBC" conflicts with use of other - libs appears for debug version of VC++ 6.0. This warning will - not affect building and testing hdf5 libraries. - - -3. Quick installation - For those that don't like to read ;-) the following steps can be - used to configure, build, test, and install the HDF5 library, - header files, and support programs. - - $ gunzip < hdf5-1.4.0.tar.gz | tar xf - - $ cd hdf5-1.4.0 - $ make check - $ make install - -3.1. TFLOPS - Users of the Intel TFLOPS machine, after reading this file, - should see the INSTALL_TFLOPS for more instructions. - -3.2. Windows - Users of Microsoft Windows should see the INSTALL_Windows for - detailed instructions. - -3.3. Certain Virtual File Layer(VFL) - If users want to install with special Virtual File Layer(VFL), - please go to read INSTALL_VFL file. SRB and Globus-GASS have - been documented. - - -4. HDF5 dependencies -4.1. Zlib - The HDF5 library has a predefined compression filter that uses - the "deflate" method for chunked datatsets. If zlib-1.1.2 or - later is found then HDF5 will use it, otherwise HDF5's predefined - compression method will degenerate to a no-op (the compression - filter will succeed but the data will not be compressed). - -4.2. MPI and MPI-IO - The parallel version of the library is built upon the foundation - provided by MPI and MPI-IO. If these libraries are not available - when HDF5 is configured then only a serial version of HDF5 can be - built. - -5. Full installation instructions for source distributions -5.1. Unpacking the distribution - The HDF5 source code is distributed in a variety of formats which - can be unpacked with the following commands, each of which - creates an `hdf5-1.2.0' directory. - -5.1.1. Non-compressed tar archive (*.tar) - - $ tar xf hdf5-1.4.0.tar - -5.1.2. Compressed tar archive (*.tar.Z) - - $ uncompress -c < hdf5-1.4.0.tar.Z | tar xf - - -5.1.3. Gzip'd tar archive (*.tar.gz) - - $ gunzip < hdf5-1.4.0.tar.gz | tar xf - - -5.1.4. Bzip'd tar archive (*.tar.bz2) - - $ bunzip2 < hdf5-1.2.0.tar.bz2 | tar xf - - -5.2. Source vs. Build Directories - On most systems the build can occur in a directory other than the - source directory, allowing multiple concurrent builds and/or - read-only source code. In order to accomplish this, one should - create a build directory, cd into that directory, and run the - `configure' script found in the source directory (configure - details are below). - - Unfortunately, this does not work on recent Irix platforms (6.5? - and later) because that `make' doesn't understand the VPATH - variable. However, hdf5 also supports Irix `pmake' which has a - .PATH target which serves a similar purpose. Here's what the man - pages say about VPATH, which is the facility used by HDF5 - makefiles for this feature: - - The VPATH facility is a derivation of the undocumented VPATH - feature in the System V Release 3 version of make. System V - Release 4 has a new VPATH implementation, much like the - pmake(1) .PATH feature. This new feature is also undocumented - in the standard System V Release 4 manual pages. For this - reason it is not available in the IRIX version of make. The - VPATH facility should not be used with the new parallel make - option. - -5.3. Configuring - HDF5 uses the GNU autoconf system for configuration, which - detects various features of the host system and creates the - Makefiles. On most systems it should be sufficient to say: - - $ ./configure OR - $ sh configure - - The configuration process can be controlled through environment - variables, command-line switches, and host configuration files. - For a complete list of switches type: - - $ ./configure --help - - The host configuration files are located in the `config' - directory and are based on architecture name, vendor name, and/or - operating system which are displayed near the beginning of the - `configure' output. The host config file influences the behavior - of configure by setting or augmenting shell variables. - -5.3.1. Specifying the installation directories - Typing `make install' will install the HDF5 library, header - files, and support programs in /usr/local/lib, - /usr/local/include, and /usr/local/bin. To use a path other than - /usr/local specify the path with the `--prefix=PATH' switch: - - $ ./configure --prefix=$HOME - - If shared libraries are being built (the default) then the final - home of the shared library must be specified with this switch - before the library and executables are built. - -5.3.2. Using an alternate C compiler - By default, configure will look for the C compiler by trying - `gcc' and `cc'. However, if the environment variable "CC" is set - then its value is used as the C compiler (users of csh and - derivatives will need to prefix the commands below with `env'). - For instance, to use the native C compiler on a system which also - has the GNU gcc compiler: - - $ CC=cc ./configure - - A parallel version of hdf5 can be built by specifying `mpicc' as - the C compiler (the `--enable-parallel' flag documented below is - optional). Using the `mpicc' compiler will insure that the - correct MPI and MPI-IO header files and libraries are used. - - $ CC=/usr/local/mpi/bin/mpicc ./configure - - On Irix64 the default compiler is `cc'. To use an alternate - compiler specify it with the CC variable: - - $ CC='cc -o32' ./configure - - One may also use various environment variables to change the - behavior of the compiler. E.g., to ask for -n32 ABI: - - $ SGI_ABI=-n32 - $ export SGI_ABI - $ ./configure - - Similarly, users compiling on a Solaris machine and desiring to - build the distribution with 64-bit support should specify the - correct flags with the CC variable: - - $ CC='cc -xarch=v9' ./configure - - Specifying these machine architecture flags in the CFLAGS variable - (see below) will not work correctly. - -5.3.3. Additional compilation flags - If addtional flags must be passed to the compilation commands - then specify those flags with the CFLAGS variable. For instance, - to enable symbolic debugging of a production version of HDF5 one - might say: - - $ CFLAGS=-g ./configure --enable-production - -5.3.4. Compiling HDF5 wrapper libraries - One can optionally build the Fortran and/or C++ interface to the - HDF5 C library. By default, both options are disabled. To build - them, specify `--enable-fortran' and `--enable-cxx' respectively. - - $ ./configure --enable-fortran - $ ./configure --enable-cxx - - Configuration will halt if a working Fortran 90 or 95 compiler or - C++ compiler is not found. Currently, the Fortran configure tests - for these compilers in order: f90, pgf90, f95. To use an - alternative compiler specify it with the F9X variable: - - $ F9X=/usr/local/bin/g95 ./configure --enable-fortran - - Note: The Fortran and C++ interfaces are not supported on all the - platforms the main HDF5 library supports. Also, the Fortran - interface supports parallel HDF5 while the C++ interface does - not. - - Note: On T3E and J90 the following files should be modified before - building the Fortran Library: - fortran/src/H5Dff.f90 - fortran/src/H5Aff.f90 - fortran/src/H5Pff.f90 - Check for "Comment if on T3E ..." comment and comment out - specified lines. - - -5.3.5. Specifying other programs - The build system has been tuned for use with GNU make but works - also with other versions of make. If the `make' command runs a - non-GNU version but a GNU version is available under a different - name (perhaps `gmake') then HDF5 can be configured to use it by - setting the MAKE variable. Note that whatever value is used for - MAKE must also be used as the make command when building the - library: - - $ MAKE=gmake ./configure - $ gmake - - The `AR' and `RANLIB' variables can also be set to the names of - the `ar' and `ranlib' (or `:') commands to override values - detected by configure. - - The HDF5 library, include files, and utilities are installed - during `make install' (described below) with a BSD-compatible - install program detected automatically by configure. If none is - found then the shell script bin/install-sh is used. Configure - doesn't check that the install script actually works, but if a - bad install is detected on your system (e.g., on the ASCI blue - machine as of March 2, 1999) you have two choices: - - 1. Copy the bin/install-sh program to your $HOME/bin - directory, name it `install', and make sure that $HOME/bin - is searched before the system bin directories. - - 2. Specify the full path name of the `install-sh' program - as the value of the INSTALL environment variable. Note: do - not use `cp' or some other program in place of install - because the HDF5 makefiles also use the install program to - also change file ownership and/or access permissions. - -5.3.6. Specifying other libraries and headers - Configure searches the standard places (those places known by the - systems compiler) for include files and header files. However, - additional directories can be specified by using the CPPFLAGS - and/or LDFLAGS variables: - - $ CPPFLAGS=-I/home/robb/include \ - LDFLAGS=-L/home/robb/lib \ - ./configure - - HDF5 uses the zlib library for two purposes: it provides support - for the HDF5 deflate data compression filter, and it is used by - the h5toh4 converter and the h4toh5 converter in support of - HDF4. Configure searches the standard places (plus those - specified above with CPPFLAGS and LDFLAGS variables) for the zlib - headers and library. The search can be disabled by specifying - `--without-zlib' or alternate directories can be specified with - `--with-zlib=INCDIR,LIBDIR' or through the CPPFLAGS and LDFLAGS - variables: - - $ ./configure --with-zlib=/usr/unsup/include,/usr/unsup/lib - - $ CPPFLAGS=-I/usr/unsup/include \ - LDFLAGS=-L/usr/unsup/lib \ - ./configure - - The HDF5-to-HDF4 and HDF4-to-HDF5 conversion tool requires the - HDF4 library and header files which are detected the same way as - zlib. The switch to give to configure is `--with-hdf4'. Note - that HDF5 requires a newer version of zlib than the one shipped - with some versions of HDF4. Also, unless you have the "correct" - version of hdf4 the confidence testing will fail in the tools - directory. - -5.3.7. Static versus shared linking - The build process will create static libraries on all systems and - shared libraries on systems that support dynamic linking to a - sufficient degree. Either form of library may be suppressed by - saying `--disable-static' or `--disable-shared'. - - $ ./configure --disable-shared - - The C++ and Fortran libraries are currently only available in the - static format. - - To build only statically linked executables on platforms which - support shared libraries, use the `--enable-static-exec' flag. - - $ ./configure --enable-static-exec - -5.3.8. Optimization versus symbolic debugging - The library can be compiled to provide symbolic debugging support - so it can be debugged with gdb, dbx, ddd, etc or it can be - compiled with various optimizations. To compile for symbolic - debugging (the default for snapshots) say `--disable-production'; - to compile with optimizations (the default for supported public - releases) say `--enable-production'. On some systems the library - can also be compiled for profiling with gprof by saying - `--enable-production=profile'. - - $ ./configure --disable-production #symbolic debugging - $ ./configure --enable-production #optimized code - $ ./configure --enable-production=profile #for use with gprof - - Regardless of whether support for symbolic debugging is enabled, - the library also is able to perform runtime debugging of certain - packages (such as type conversion execution times, and extensive - invariant condition checking). To enable this debugging supply a - comma-separated list of package names to to the `--enable-debug' - switch (see Debugging.html for a list of package names). - Debugging can be disabled by saying `--disable-debug'. The - default debugging level for snapshots is a subset of the - available packages; the default for supported releases is no - debugging (debugging can incur a significant runtime penalty). - - $ ./configure --enable-debug=s,t #debug only H5S and H5T - $ ./configure --enable-debug #debug normal packages - $ ./configure --enable-debug=all #debug all packages - $ ./configure --disable-debug #no debugging - - HDF5 is also able to print a trace of all API function calls, - their arguments, and the return values. To enable or disable the - ability to trace the API say `--enable-trace' (the default for - snapthots) or `--disable-trace' (the default for public - releases). The tracing must also be enabled at runtime to see any - output (see Debugging.html). - -5.3.9. Large (>2GB) vs. small (<2GB) file capability - In order to read or write files that could potentially be larger - than 2GB it is necessary to use the non-ANSI `long long' data - type on some platforms. However, some compilers (e.g., GNU gcc - versions before 2.8.1 on Intel platforms) are unable to produce - correct machine code for this data type. To disable use of the - `long long' type on these machines say: - - $ ./configure --disable-hsizet - -5.3.10. Parallel vs. serial library - The HDF5 library can be configured to use MPI and MPI-IO for - parallelizm on a distributed multi-processor system. Read the - file INSTALL_parallel for detailed explanations. - -5.3.11. Threadsafe capability - The HDF5 library can be configured to be thread-safe (on a very - large scale) with the with the `--enable-threadsafe' flag to - configure. Read the file doc/TechNotes/ThreadSafeLibrary.html for - further details. - -5.3.12. Backward compatibility - The 1.4 version of the HDF5 library can be configured to operate - identically to the v1.2 library with the `--enable-hdf5v1_2' - configure flag. This allows existing code to be compiled with the - v1.4 library without requiring immediate changes to the - application source code. This flag will only be supported in the - v1.4 branch of the library, it will not be available in v1.5+. - -5.3.13. Network stream capability - The HDF5 library can be configured with a network stream file - driver with the `--enable-stream-vfd' configure flag. This option - compiles the "stream" Virtual File Driver into the main library. - See the documentation on the Virtual File Layer for more details - about the use of this driver. - - -5.4. Building - The library, confidence tests, and programs can be build by - saying just: - - $ make - - Note that if you supplied some other make command via the MAKE - variable during the configuration step then that same command - must be used here. - - When using GNU make you can add `-j -l6' to the make command to - compile in parallel on SMP machines. Do not give a number after - th `-j' since GNU make will turn it off for recursive invocations - of make. - - $ make -j -l6 - -5.5. Testing - HDF5 comes with various test suites, all of which can be run by - saying - - $ make check - - To run only the tests for the library change to the `test' - directory before issuing the command. Similarly, tests for the - parallel aspects of the library are in `testpar' and tests for - the support programs are in `tools'. - - Temporary files will be deleted by each test when it complets, - but may continue to exist in an incomplete state if the test - fails. To prevent deletion of the files define the HDF5_NOCLEANUP - environment variable. - -5.6. Installing - The HDF5 library, include files, and support programs can be - installed in a (semi-)public place by saying `make install'. The - files are installed under the directory specified with - `--prefix=DIR' (or '/usr/local') in directories named `lib', - `include', and `bin'. The prefix directory must exist prior to - `make install', but its subdirectories are created automatically. - - If `make install' fails because the install command at your site - somehow fails, you may use the install-sh that comes with the - source. You need to run ./configure again. - - $ INSTALL="$PWD/bin/install-sh -c" ./configure ... - $ make install - - The library can be used without installing it by pointing the - compiler at the `src' directory for both include files and - libraries. However, the minimum which must be installed to make - the library publically available is: - - The library: - ./src/libhdf5.a - - The public header files: - ./src/H5*public.h - - The main header file: - ./src/hdf5.h - - The configuration information: - ./src/H5pubconf.h - - The support programs that are useful are: - ./tools/h5ls (list file contents) - ./tools/h5dump (dump file contents) - ./tools/h5repart (repartition file families) - ./tools/h5toh4 (hdf5 to hdf4 file converter) - ./tools/h5debug (low-level file debugging) - ./tools/h5import (a demo) - ./tools/h4toh5 (hdf4 to hdf5 file converter) - -6. Using the Library - Please see the User Manual in the doc/html directory. - - Most programs will include and link with -lhdf5. - Additional libraries may also be necessary depending on whether - support for compression, etc. was compiled into the hdf5 library. - - A summary of the hdf5 installation can be found in the - libhdf5.settings file in the same directory as the static and/or - shared hdf5 libraries. - -7. Support - Support is described in the README file. diff --git a/INSTALL_TFLOPS b/INSTALL_TFLOPS deleted file mode 100644 index a05ef7f..0000000 --- a/INSTALL_TFLOPS +++ /dev/null @@ -1,163 +0,0 @@ - -FOR THE INTEL TFLOPS MACHINE: - -Below are the step-by-step procedures for building, testing, and -installing both the sequential and parallel versions of the HDF5 library. - ------------------ -Software locations ------------------- -The zlib compression library is installed in /usr/community/hdf5/ZLIB. -The mpich library, including mpi-io support, is in -/usr/community/mpich/mpich-1.2.0. - ---------------- -Sequential HDF5: ---------------- - -The setup process for building the sequential HDF5 library for the -ASCI Red machine is done by a coordination of events from sasn100 and -janus. Though janus can do compiling, it is better to build it -from sasn100 which has more complete building tools and runs faster. -It is also anti-social to tie up janus with compiling. The HDF5 building -requires the use of janus because one of steps is to execute a program -to find out the run-time characteristics of the TFLOPS machine. - -Assuming you have already unpacked the HDF5 tar-file into the -directory , follow the steps below: - -FROM SASN100, - -1) cd - -2) ./configure tflop - Due to a bug, you need to patch up two Makefile, src/Makefile and - test/Makefile, before the next step. You can use the following - shell commands. - -# Patch up various Makefile's. -# patch up src/Makefile -echo "patching src/Makefile" -ed - src/Makefile <<'EOF' -/^LT_RUN=.*/s//LT_RUN=$(RUNTEST)/ -w -q -EOF - -# patch up test/Makefile -echo "patching test/Makefile" -ed - test/Makefile <<'EOF' -/^RUNTEST=$(LT_RUN)/s/^/#/ -w -q -EOF - -3) make H5detect - - -FROM JANUS, - -4) cd - -5) make H5Tinit.c - - -FROM SASN100, - -6) make - - -When everything is finished compiling and linking, -you can run the tests by -FROM JANUS, - -7) make check - Sometimes the "make check" fails in the sub-directories of test - or tools with a message as "print not found". This is due to the - "make" of Janus thinking some binary code needs to be recompiled. - The easiest way to fix it is - FROM SASN100 - cd /test # or cd /tools - make clean; make # re-make all binary - - -Once satisfied with the test results, you can install -the software by -FROM SASN100, - -8) make install - - ---------------- -Parallel HDF5: ---------------- - -The setup process for building the parallel version of the HDF5 library for the -ASCI Red machine is very similar to the sequential version. Since TFLOPS -does not support MPIO, we have prepared a shell-script file that configures -with the appropriate MPI library. - -Assuming you have already unpacked the HDF5 tar-file into the -directory , follow the steps below: -FROM SASN100, - -1) cd - -2) CC=/usr/community/mpich/mpich-1.2.0/bin/mpicc ./configure tflop - Due to a bug, you need to patch up two Makefile, src/Makefile and - test/Makefile, before the next step. You can use the following - shell commands. - -# Patch up various Makefile's. -# patch up src/Makefile -echo "patching src/Makefile" -ed - src/Makefile <<'EOF' -/^LT_RUN=.*/s//LT_RUN=$(RUNTEST)/ -w -q -EOF - -# patch up test/Makefile -echo "patching test/Makefile" -ed - test/Makefile <<'EOF' -/^RUNTEST=$(LT_RUN)/s/^/#/ -w -q -EOF - - -3) make H5detect - - -FROM JANUS, - -4) cd - -5) make H5Tinit.c - - -FROM SASN100, - -6) make - - -When everything is finished compiling and linking, -FROM JANUS, - -7) make check - Sometimes the "make check" fails in the sub-directories of test - or tools with a message as "print not found". This is due to the - "make" of Janus thinking some binary code needs to be recompiled. - The easiest way to fix it is - FROM SASN100 - cd /test # or cd /tools - make clean; make # re-make all binary - - -Once satisfied with the parallel test results, as long as you -have the correct permission, -FROM SASN100, - -8) make install - - diff --git a/INSTALL_VFL b/INSTALL_VFL deleted file mode 100644 index d0466a3..0000000 --- a/INSTALL_VFL +++ /dev/null @@ -1,130 +0,0 @@ - Installation Instructions for HDF5 - with Different Virtual File Layer - - * * * - -This file contains installation instructions for HDF5 with certain Virtual File -Layer to handle file I/O. We currently have documented SRB and Globus-GASS. - - - - --- Part I. SRB --- -I. Overview ------------ -This part contains instructions for remote-accessing HDF5 through SRB. The -SRB version 1.1.7 on Sun Solaris 2.7 platform has been tested. If you have -difficulties installing the software in your system, please send mails to me -(Raymond Lu) at - - slu@ncsa.uiuc.edu - -First, you must obtain and unpack the HDF5 source as described in the file -INSTALL. You need the SRB library(client part) installed. You should also -have access to SRB server. - - -The Storage Resource Broker(SRB) from San Diego Supercomputer Center is client- -server middleware that provides a uniform interface for connecting to -heterogeneous data resources over a network and accessig replicated data sets. -SRB, in conjunction with the Metadata Catalog(MCAT), provides a way to access -data sets and resources based on their attributes rather than their names or -physical locations. Their webpage is at http://www.npaci.edu/Research/DI/srb. - -HDF5 is built on the top of SRB as a client to remotely access files on SRB -server through SRB. Right now, HDF-SRB only support low-level file transfer of -SRB. The MCAT part is not supported yet. Low-level file transfer means files -are treated just like Unix type files. Files can be read, written and -appended. Partial access(read and write to a chunk of file without transferrig -the whole) is also supported. - - -II. Installation Steps ----------------------- -The installation steps are similar to the ones in INSTALL file: - -1. Run 'configure' file with SRB options: - configure --with-srb=$SRB/include,$SRB/lib - where $SRB is your SRB installed library directory. - - For example, below is a script file to run 'configure': - #! /bin/sh - # how to configure to use the SRB - - SRB_DIR=/afs/ncsa.uiuc.edu/projects/hdf/users/slu/srb_install - configure --with-srb=$SRB_DIR/include,$SRB_DIR/lib - -2. Run 'make' - -3. Run 'make check' - -4. Run 'make install' - -5. Run testing program(Optional): - Go to the testing directory(cd test) and run srb_write, srb_read, - srb_append. Actually, these tests have been run in step 3. - - srb_write: Connect to SRB server, write an HDF5 file with an integer - dataset to SRB server. - srb_read: Connect to SRB server, read part of HDF5 file on the SRB server. - srb_append: Connect to SRB server, append an integer dataset to an existent - HDF5 file on the SRB server. - -6. For using HDF-SRB, please read comments in srb_write.c, srb_read.c, - srb_append.c in the hdf5/test directory. - - - - --- Part II. Globus-GASS --- - -I. Overview ------------ -This part contains instructions for remote-accessing HDF5 through Globus-GASS. -The SGI IRIX64(and IRIX) 6.5 platform have been tested. If you have -difficulties installing the software in your system, please send mails to me -(Raymond Lu) at - slu@ncsa.uiuc.edu - -First, you must obtain and unpack the HDF5 source as described in the file -INSTALL. You need the Globus 1.1.x and SSL(should have come with Globus) -packages. - -HDF5 is built on the top of Globus-GASS(1.1.x) to handle remote access. -Globus-GASS(1.1.x) only supports HTTP and HTTPS protocals for 'whole file -read and write'. More features may be added in the future. - -II. Installation Steps ----------------------- -The installation steps are similar to the ones in INSTALL file: - -1. Run 'configure' file with SSL and GASS options: - configure --with-ssl=$SSL/lib --with-gass=$GASS/include,$GASS/lib - where $SSL is your SSL directory, and $GASS is your Globus directory. - - For example, below is a script file to run 'configure': - #! /bin/sh - # how to configure to use the Globus-GASS(1.1.x) - - GASS_DIR=/usr/local/globus-install-1.1.1/development/mips-sgi-irix6.5-64_nothreads_standard_debug - SSL_LIB=/usr/local/ssl/lib - - configure --with-ssl=$SSL_LIB --with-gass=$GASS_DIR/include,$GASS_DIR/lib - -2. Run 'make' - -3. Run 'make check' - -4. Run 'make install' - -5. Run testing program: - There is one read testing program called 'gass_read' in the 'test' - directory. It does whole file read through HTTP protocal. The URL is - hard coded as - http://hdf.ncsa.uiuc.edu/GLOBUS/a.h5 - - The writing really depends on your web server. You have to set up your - server in right way to accept writing in files. We have tested it using - Apache Server(1.3.12) without authentication. If you need more details - about our testing, please contact us. Globus suggests using their GASS - server. - - There is another program called 'gass_append' used for experiments. diff --git a/INSTALL_Windows.txt b/INSTALL_Windows.txt deleted file mode 100644 index 8d7636f..0000000 --- a/INSTALL_Windows.txt +++ /dev/null @@ -1,916 +0,0 @@ -HDF5 Build and Install Instructions for Windows 2000/NT/98. ----------------------------------------------------------- - -The instructions which follow assume that you will be using the -source code release 'zip' file (hdf5-1_4_0.zip). - -***************************WARNINGS**************************** -Please read CAREFULLY about Preconditions before you go to the -following sections - -Preconditions - - 1. Installed MicroSoft Developer Studio,Visual C++ 6.0 and - WinZip. - - 2. Set up a directory structure to unpack the library. - For example: - - c:\ (any drive) - MyHDFstuff\ (any folder name) - - 3. Run WinZip on hdf5-1_4_0.zip (the entire source tree) and - extract hdf5 package into c:\MyHDFstuff(or whatever drive - and folder name you would like to choose). This creates a - directory called 'hdf5'under MyHDFstuff which contains - several files and directories. - - 4. HDF5 uses zlib for compression and zlib is distributed - with hdf5 lib. If you have your own version read section - VI about the zlib library. - - 5. You do need hdf4 (hdf and mfhdf) static and dll libraries - to generate hdf4-related tools. - - 6. Currently you can build and test either hdf5 libraries - and non-hdf4 related tools or hdf5 libraries and hdf4 - related tools;but not BOTH.In other words,you may either - follow Section II or Section III but NOT both Sections to - build HDF5 libraries and related tools. - ---------------------------------------------------------------- - -The following sections discuss installation procedures in detail: - - Section I: What do we build and install - Section II: Building and testing hdf5 libraries and non-hdf4 - related hdf5 tools - Section III: Building and testing hdf5 libraries and all hdf5 - tools - Section IV: Building an application using the HDF5 library or - DLL - Section V: Some more helpful pointers - Section VI: ZLIB library - removing or changing the path - -*************************************************************** - -Section I: - -What do we build and install? - - HDF5 static library: - debug and release version - - HDF5 Dynamic Link Library(DLL): - debug and release version as well as export libraries for - DLL - - HDF5 tool library: - debug and release version - - HDF5 tool export library for DLL: - debug and release version - - HDF5 tools: - non-hdf4 related tools and hdf4 related tools - - HDF5 library testing programs: - hdf5 library related comprehensive tests - - HDF5 related tools testing programs: - hdf5 tools testing programs - - HDF5 examples: - simple HDF5 examples - -************************************************************** - -Section II: - - Building and testing hdf5 libraries and non-hdf4 related tools - - ================================================== - -STEP 1: Building hdf5 libraries and non-hdf4 related tools - - - 1. Unpack all.zip in 'hdf5' and move the zlib.dll from - c:\myHDFstuff\hdf5\src\zlib\dll to the Windows system - directory. - - The system directory can usually be found under the path - C:\WINNT\system or C:\WINDOWS\system - - 2. Invoke Microsoft Visual C++, go to "File" and select - the "Open Workspace" option. - - Then open the c:\myHDFstuff\hdf5\proj\all\all.dsw - workspace. - - 3. If you don't want to build and test backward - compatibility with hdf5 1.2, you may skip this part and - go to part 4. - - To build and test backward compatibility with hdf5 1.2, - a) go to "Project" and select "Settings" - b) A window called "Project Settings" should be - popped up,on the upper-left corner is a small box - "Settings For". Set the option to - "Win32 Release". - c) Go to the the right side of "Project Settings" - window,choose C/C++ on the menu. - d) Go to the "Category" box below menu bar, choose - Preprocessor. - e) Go to "Preprocessor definitions" box below - "Category". Inside the box, type - "WANT_H5_V1_2_COMPAT". Note: don't type double - quote for "WANT_H5_V1_2_COMPAT" and add a comma - between "WANT_H5_V1_2_COMPAT" and the last - preprocessor definations(WIN32). - f) click OK at the bottom of "Project Settings" - window. - g) repeat a)-f) and choose the option as - "win32 Debug" on step b). - - 4. Select "Build", then Select "Set Active Configuration". - - On Windows platform select as the active configuration - - "all -- Win32 Debug" to build debug versions of - single-threaded static libraries, Debug multithreaded - DLLs and tests. - or - - "all -- Win32 Release" to build release versions of - single-threaded static libraries, multithreaded DLLs - and tests. - - - NOTE : "all" is a dummy target. You will get a link - error when "all.exe." is built: - - LINK: error LNK2001: unresolved external symbol - _mainCRTStartup..... - all.exe - 2 error(s), .... - - Warning messages can be ignored. The "all.exe" is never - created, so it is OK. - - When the debug or release build is done the directories - listed below will contain the following files: - - c:\MyHDFstuff\hdf5\proj\hdf5\debug - - c:\MyHDFstuff\hdf5\proj\hdf5\release - - - hdf5.lib- the hdf5 library - - c:\MyHDFstuff\hdf5\proj\hdf5dll\debug - - - hdf5ddll.dll- the hdf5 library - hdf5ddll.lib- the dll export library - - c:\MyHDFstuff\hdf5\proj\hdf5dll\release - - - hdf5dll.dll- the hdf5 library - hdf5dll.lib- the dll export library - - c:\MyHDFstuff\hdf5\test\"test directory"- - - where test directory is one of the following: - - big(dll) - - bittests(dll) - - chunk(dll) - - cmpd_dset(dll) - - dsets(dll) - - dtypes(dll) - - enum(dll) - - extend(dll) - - external(dll) - - fillval(dll) - - flush1(dll) - - flush2(dll) - - gheap(dll) - - hyperslab(dll) - - iopipe(dll) - - istore(dll) - - links(dll) - - mount(dll) - - mtime(dll) - - ohdr(dll) - - overhead(dll) - - stab(dll) - - testhdf5(dll) - - unlink(dll) - - - c:\MyHDFstuff\hdf5\tools\toolslib\debug - c:\MyHDFstuff\hdf5\tools\toolslib\release - - toolslib.lib- the tools library - - c:\MyHDFstuff\hdf5\tools\toolslibD\debug - c:\MyHDFstuff\hdf5\tools\toolslibD\release - - toolslibD.lib- the dll export library - - c:\MyHDFstuff\hdf5\tools\"tools directory"- - where non-hdf4 related tools directory is one of the - following: - - h5dump(dll) - - h5ls(dll) - - h5debug(dll) - - h5import(dll) - - h5repart(dll) - - - Test and tool directory contains debug and release - subdirectories with the corresponding tests and tools. - - -STEP 2: testing hdf5 libraries and non-hdf4 related tools - -In a command prompt window run the test batch file which resides in -the hdf5\test directory(for example: C:\MyHDFstuff\hdf5\test)to make -sure that the library was built correctly. - -You can possibily test four versions of hdf5 library and tools. They are: - - release version - release dll version - debug version - debug dll version - -NOTE: The hdf5ddll.dll and hdf5dll.dll should be placed into -the C:\WINNT\system or C:\WINDOWS\system directory before using the dlls. - -We strongly suggest you to redirect your testing results into -an output file and you can easily check the testing results. -You may use either NotePad or NoteTab Light or whatever other -windows tools to check the results. For the purpose of printing, -please choose font less than 14 for better alignment of the text. - - 1. hdf5 library testing - - cd into the hdf5\test directory. - - (1) basic tests - - Go to a) b) c) or d) to test your chosen version - - a) release static version - type: - hdf5test release >"Your output filename" - - b) release dll version - type: - hdf5test release dll > "Your output filename" - - c) debug static version - type: - hdf5test debug >"Your output filename" - - d) debug dll version - type: - hdf5test debug dll >"Your output filename" - - (2) timing tests - - Go to a) b) c) or d) to test your chosen version - - a) release static version - type: - hdf5timingtest release >"Your output filename" - - b) release dll version - type: - hdf5timingtest release dll >"Your output filename" - - c) debug static version - type: - hdf5timingtest debug >"Your output filename" - - d) debug dll version - type: - hdf5timingtest debug dll >"Your output filename" - - - Use notepad or notetab light to check results. You should -not find any FAILED marks in your output files. - - Note: big test is currently not working for windows, we are -still investigating this. - - 2. hdf5 tools testing - - Currently we are only supporting h5dump test. We are -investigating h5ls test now. - - 1) h5dump test - - cd back into hdf5 directory and then cd into tools -directory(...\hdf5\tools) - - Go to a) b) c) or d) to test your chosen version - - a) release static version - type: - dumptest release >"Your output filename" - - b) release dll version - type: - dumptest release dll > "Your output filename" - - c) debug static version - type: - dumptest debug >"Your output filename" - - d) debug dll version - type: - dumptest debug dll >"Your output filename" - - - We are using "fc" command to compare whether dumper -generates correct results. Supposedly you should find -"FC: no differences encountered" in your output file. -However, since we are comparing the actual dumper output -with the expected dumper output under different directory, -you may see something like: - -" -***** ..\TESTFILES\tall-1.ddl -############################# -Expected output for 'h5dump tall.h5' -############################# -HDF5 "tall.h5" { -GROUP "/" { -***** TALL-1.RESULTS -HDF5 "..\..\testfiles\tall.h5" { -GROUP "/" { -***** -" - - The actual dumper output is correct. The difference showing -here is the different representations of filename of the same -file. - -STEP 3: BUILDING THE EXAMPLES - - 1. Invoke Microsoft Visual C++, go to "File" and select - the "Open Workspace" option. - Then open the workspace - c:\myHDFstuff\hdf5\examples\allexamples\allexamples.dsw. - - 2. Select "Build", then Select "Set Active Configuration". - - On Windows platform select as the active configuration - - "allexamples -- Win32 Debug" to build debug versions - of the examples. - - or - - "allexamples -- Win32 Release" to build release - versions the examples. - - When the debug build or release build is done - there should be the following subdirectories in - C:\myHDFstuff\hdf5\examples\ - - attributetest - - chunkread - - compoundtest - - extendwritetest - - grouptest - - readtest - - selecttest - - writetest - - - - 3. Run the batch file "InstallExamples.bat" which - resides in the top level directory(C:\MyHDFSTUFF\hdf5). - This file creates 2 new directories,examplesREL and - examplesDBG,in the examples directory and places - all the executables in it. Both the release and debug - versions of the examples should be built before this - step is done. The examples should be tested in these 2 - new directories due to some dependencies between the - examples. Especially writetest.exe and extendwritetest.exe - should be executed before chunkread.exe and readtest.exe - due to dependencies among these files. - -************************************************************** - -Section III: BUILDING AND TESTING HDF5 LIBRARIES AND ALL HDF5 TOOLS - -------------------WARNINGS--------------------------------- - -1. This section is specifically for building HDF5 tools that needs to call HDF4 library. - -Currently we are supporting two hdf4-relatedtools: H4toh5 converter -and H5toh4 converter. If you are not using these tools, please go -back to Section II for building and installing information. - -2. This section builds and tests all versions of hdf5 libraries, -testing programs and tools covered in section II. -Additionally, it also builds and tests hdf4-related tools. We may refer some duplicated parts of this section to section II. - -3. In case - a) you don't install hdf libraries and related tools in - your machine, - b) or if the top directory of your hdf4 libraries and - tools are not under C:\hdf41r4 and you are not familar - on how to change settings of VC++ projects. - - you may get binary distribution from -ftp://ftp.ncsa.uiuc.edu/HDF/HDF/HDF4.1r4/windows_precompiled_code/HDF41r4.zip -and use Winzip to unpack HDF41r4.zip into C:\hdf41r4. - -4. We assume that you've installed hdf4(mfhdf and hdf) -libraries into drive C. The top level path should be -C:\HDF41r4. Under C:\HDF41r4 it should at least -include the following six directories: - -C:\HDF41r4\bin where hdf4 utilities are stored - -C:\HDF41r4\dlllib where release dll versions of hdf and mfhdf -libraries and export libraries of dlls are stored - -C:\HDF41r4\dlllibdbg where debug dll versions of hdf and mfhdf -libraries and export libraries of dlls are stored - -C:\HDF41r4\lib where release versions of hdf and mfhdf -libraries are stored - -C:\HDF41r4\libdbg where debug versions of hdf and mfhdf -libraries are stored - -C:\HDF41r4\include where header files are included - -Make sure that you copy all *.dll files under C:\HDF41r4 into Windows -system directory before the next step. - -If your path of hdf libraries and mfhdf libraries is different -from the default assumption, please DO follow No.4 of Step 1 on -the following: - - -Step 1. - - 1. Unpack all_withhdf4.zip in 'hdf5' and move the zlib.dll - from c:\myHDFstuff\hdf5\src\zlib\dll to the Windows - system directory. - - The system directory can usually be found under the path - C:\WINNT\system or C:\WIN98\system - - 2. Invoke Microsoft Visual C++, go to "File" and select the - "Open Workspace" option. - - Then open the c:\myHDFstuff\hdf5\proj\all\all.dsw - workspace. - - 3. If you don't want to build and test backward - compatibility with hdf5 1.2, you may skip this part and - go to part 4. - - To build and test backward compatibility with hdf5 1.2, - a) go to "Project" and select "Settings" - b) A window called "Project Settings" should be - popped up,on the upper-left corner is a small box - "Settings For" Choose the option to - "Win32 Release". - c) Go to the the right side of "Project Settings" - window, choose C/C++ on the menu. - d) Go to the "Category" box below menu bar, choose - Preprocessor. - e) Go to "Preprocessor definitions" box below - "Category". Inside the box, type - "WANT_H5_V1_2_COMPAT". Note: don't type - double quote for "WANT_H5_V1_2_COMPAT" and add a - comma between "WANT_H5_V1_2_COMPAT" and the last - preprocessor defination(WIN32). - f) click OK at the bottom of "Project Settings" - window. - g) repeat a)-f) and set the option to "win32 Debug" - on step b). - - 4. This part is for users who are familar with handling - settings of VC++ project and store their hdf4 libraries - not under C:\hdf41r4. Other users can skip this part. - - 4.1 Change the path where hdf4 library header files are - located - - a) On the View menu, click Workspace, you may see a - pop-up window with names of projects in all.dsw. - b) click FileView on the bottom of this window if you - are not seeing "all files big files ......." - c) You need to modify settings of four projects: h4toh5, - h4toh5dll,h5toh4 and h5toh4dll. - You also need to modify both debug and release - versions. - - You may do as follows: - c1)Right click the selected project and then click - "Settings" - c2)A dialog box called "Project Settings" will be - poped up - c3)On the upper-left part of the "Project Settings" - box, you may find a small window "Settings for". - Make sure inside this "Settings for" box is either - "Win32 Debug" or "Win32 Release". Change contents - into "Win32 Debug" or "Win32 Release" otherwise. - Remember the version(Win32 Release or Debug) you - chose. - c4)On the upper-right menu of the "Project Settings" - window, find C/C++ and click it. - c5)Just below the upper-right menu, find a small - window called category, make sure that - "Preprocessor" appear in this window. - c6)In the middle of "Project Settings" windows, you - may find a box called - "Additional include directories:" . You may notice - "C:\hdf41r4\include" inside this box. This is the - path where the default hdf4 header files is - included. Replace only this path - (C:\hdf41r4\include) with your own path that - includes your hdf4 header files. Don't touch any - other paths. - c7)After you've done this, click OK at the bottom of - "Project Settings" window. - c8)Repeat c1)-c7)but change contents of "settings - for" in c3) from "Win32 Release" to "Win32 Debug" - or vice versa. - d) repeat step c) for the other three projects. - - 4.2 Replace the user's hdf and mfhdf libraries, export - libraries of hdf and mfhdf DLLs - - You also need to modify four projects: h4toh5, - h4toh5dll, h5toh4 and h5toh4dll: - a) select project h4toh5 following instruction 4.1 a) - and b). - b) click h4toh5, you may find four libraries: - hm414d.lib,hd414d.lib and hm414.lib,hd414.lib - attached under the project h4toh5. hm414d.lib and - hd414d.lib are debug versions of mfhdf and hdf - libraries. hm414.lib and hd414.lib are release - versions of mfhdf and hdf libraries. - c) select these four libraries; go back to Edit menu and - choose "delete" option to delete template of these - libraries. - d) select project h4toh5 and right click the mouse, find - "Add Files to Projects", follow the instructions on - the pop-up box, to insert your own hm414d.lib, - hd414d.lib,hm414.lib and hd414.lib. You must know - their paths at first. - e) select project h4toh5dll following instruction 4.1 a) - and b). - f) click h4toh5dll, you may also find four libraries: - hd414m.lib,hd414md.lib and hm414m.lib,hd414m.lib - attached under the project h4toh5dll. These libraries - are debug and release versions of Export libraries of - mfhdf and hdf DLLs. - g) select these four libraries; go back to Edit menu and - choose "delete" option to delete template of these - libraries. - h) select project h4toh5dll and right click the mouse, - find "Add Files to Projects", follow the instructions - on the pop-up box, to insert your own hd414m.lib, - hd414md.lib,hm414m.lib and hd414m.lib. You must know - their paths at first. - i) repeat a)-h) for h5toh4 and h5toh4dll. - - 5. Select "Build", then Select "Set Active Configuration". - - On Windows platform select as the active configuration - - "all -- Win32 Debug" to build debug versions - single-threaded static libraries, - and tests. - or - - "all -- Win32 Release" to build release versions of - single-threaded static - libraries, and tests. - - - NOTE : "all" is a dummy target. You will get a link - error when "all.exe." is built: - - LINK: error LNK2001: unresolved external symbol - _mainCRTStartup..... - all.exe - 2 error(s), .... - - Warning messages can be ignored. The "all.exe" is never - created, so it is OK. - - You should see hdf5 libraries, tests and tools under - section II Step 1. - In addtion, under c:\MyHDFstuff\hdf5\tools\ - - You may also find: - h4toh5 - h5toh4 - h4toh5dll - h5toh4dll - for both the debug and release versions. - -STEP 2: testing hdf5 libraries and all hdf5 tools - - 1. hdf5 library testing - Follow all instructions of the same part in Section II - STEP 2 - - 2. non-hdf4 related tools testing - Follow all instructions of the same part in Section II - STEP 2 - - 3. hdf4-related tools testing - - 1) h4toh5 converter tool testing - - First cd into hdf5\tools - - Go to a) b) c) or d) to test your chosen version - - a) release static version - type: - h4toh5testrun release >"Your output filename" - - b) release dll version - type: - h4toh5testrun release dll > "Your output filename" - - c) debug static version - type: - h4toh5testrun debug >"Your output filename" - - d) debug dll version - type: - h4toh5testrun debug dll >"Your output filename" - - We are using "fc" command to compare whether h4toh5 - converter converts the hdf4 file into the correct hdf5 - file.In your output files, Please only pay attention to - those lines which start with - "FC:",you should find "FC: no differences encountered" - for all tested hdf4 files in your output. - - 2) h5toh4 converter tool testing - - To test the h5toh4 utility, you need to have hdf4 - dumper utility "hdp" in your system. - - Note: Currently h5toh4 release dll doesn't work - for all test cases possibly due to windows dealing - with "free memory" conventions for dll versions. - - 1) If your hdp utility is located at C:\hdf41r4\bin, - you may skip this part. Otherwise, copy your hdp.exe - file into the directory where your hdf5 tools are - located. For example, if your hdf5 tools directory is - C:\myHDFstuff\hdf5\tools; please copy hdp.exe into - this directory. - - 2) cd into \...\hdf5\tools. - Go to a) b) c) or d) to test your chosen version - - a) release static version - type: - h5toh4testrun release >"Your output filename" - - b) release dll version - type: - h5toh4testrun release dll > "Your output filename" - - c) debug static version - type: - h5toh4testrun debug >"Your output filename" - - d) debug dll version - type: - h5toh4testrun debug dll >"Your output filename" - - We are using "fc" command to compare whether h5toh4 - converter converts the hdf5 file into the correct hdf4 - file.In your output files, Please only pay attention to - those lines which start with - "FC:",you should find "FC: no differences encountered" - for all tested hdf4 files in your output. - Warnings appear on the prompt when testing h5toh4 converter - can be ignored. - - -STEP 3: BUILDING THE EXAMPLES - - Follow all instructions of SECTION II STEP 3. - -Section IV: -BUILDING AN APPLICATION USING THE HDF5 LIBRARY OR DLL- SOME HELPFUL -POINTERS -==================================================================== - -If you are building an application that uses the HDF5 library the -following locations will need to be specified for locating header files -and linking in the HDF libraries: - - \src - -where may be - - C:\MyHDFstuff\hdf5\ - -To specify this location in the settings for your VC++ project: - - 1. Open your VC project in Microsoft Visual C++ and make sure it is - the active project. - - 2. Go to the Project menu and chose the 'Settings' option. - - 3. Chose the build configuration you would like to modify in the - drop down menu labeled with 'Settings For:' - - 4. Chose the C/C++ tab - - 5. At the bottom of the window, there should be a text-area labeled - with 'Project Options:'. In this text-area, scroll until you - reach the end and type /I "\src" and - then click OK. - -To link the HDF5 library with your application: - - 1. Open your VC project in Microsoft Visual C++ and make sure it is - the active project. - - 2. Go to the Project menu and chose the 'Add to Project' option and - then 'Files' option. - - 3. Change the 'Files of type:' to 'Library Files (.lib)' - - 4. Navigate through the directories until you find the location of - the hdf5.lib. - - 5. Select hdf5.lib and click OK. - - -To use the DLL: - - 1. Follow the steps for specifing the location of the header files - as shown above. - - 2. Follow the steps for linking the HDF5 library as shown above - except now link the export library that is created with the DLL. - The export library is called hdf5dll.lib or hdf5ddll.lib for - debug version. - - 3. Place the DLL in a location that Windows will be able to locate - it. The search path and order for DLL's is - - a) The directory where the executable module for the current - process is located. - b) The current directory. - c} The Windows system directory. The GetSystemDirectory function - retrieves the path of this directory. - d) The Windows directory. The GetWindowsDirectory function - retrieves the path of this directory. - e) The directories listed in the PATH environment variable. - - -Section V: -MORE HELPFUL POINTERS -===================== - - -Here are some notes that may be of help if you are not familiar with -using the Visual C++ Development Environment. - -Project name and location issues: - - The files in all.zip must end up in the hdf5\ directory installed by - hdf5-1_4_0.zip - - If you must install all.dsw and all.dsp in another directory, - relative to hdf5\ , you will be asked to locate the sub-project - files, when you open the project all.dsw. - - If you want to rename all (the entire project), you will need to - modify two files all.dsw and all.dsp as text (contrary to the - explicit warnings in the files). - - You can also modify all.dsw and all.dsp as text, to allow these 2 - files to be installed in another directory. - - -Settings... details: - - If you create your own project, the necessary settings can be read - from the all.dsp file(as text), or from the Project Settings in the - Developer Studio project settings dialog. - - Project - Settings - C/C++ - Category - PreProcessor - Code Generation - Use run-time Library - These are all set to use - Single-Threaded - -DLL... hints: - - If you want to use DLL versions of hdf5 library in your application, - you should - 1) put hdf5 DLL into windows system directory - 2) add hdf5 DLL export library into your project - 3) Follow "Settings... details" into the last line: - change Single-Threaded into Multithreaded DLL or - Debug Multithreaded DLL - 4) Follow "Settings.. details" into PreProcessor: - Project - Settings - C/C++ - Category - PreProcessor - - Find PreProcessor definations and Add _HDF5USEDLL_ at the - end of the PreProcessor definations - - - - -Section VI: -ZLIB LIBRARY- REMOVING OR CHANGING THE PATH -============================================ - -If you would like to remove the zlib library from the hdf5 library or -use your own version of the zlib library then follow the steps below. - -Removing the zlib library completely: - - Open the all.dsw workspace file in Microsoft Visual C++. Go to the - hdf5 project. Select the zlib.lib file from this project and - delete(press the 'delete' key) it. Next open the H5config.h and - H5pubconf.h files from the src directory and remove the following - two lines: - - #define HAVE_LIBZ 1 - #define HAVE_COMPRESS2 - - then save the file. - - Next go to the hdf5dll project. Remove the zlib.lib from this - project too. Open the project settings for the hdf5dll project. - Go to the C/C++ settings tab and under the preprocessor definitions - remove the ZLIB_DLL in both the debug and the release settings. - Recompile the all project and then save the workspace. - - -Replacing the zlib library: - - Open the all.dsw workspace and go to the hdf5 project. Delete the - zlib.lib file from the file listing. Then select the hdf5 project - and richt click to get a menu. Pick the "add files to project..." - option and find the version of the zlib that you would like to use. - Then click OK in the file chooser dialog. Repeat the steps for the - hdf5dll project. You may also want to replace the zlib.h and zconf.h - files which are in the src directory with your own versions of these - files. Then recompile the all project. diff --git a/INSTALL_parallel b/INSTALL_parallel deleted file mode 100644 index e2a0709..0000000 --- a/INSTALL_parallel +++ /dev/null @@ -1,177 +0,0 @@ - Installation instructions for Parallel HDF5 - ------------------------------------------- - - -1. Overview ------------ - -This file contains instructions for the installation of parallel -HDF5. Platforms supported by this release are SGI Origin 2000, IBM SP2, -Intel TFLOPs, and Linux version 2.4 and greater. The steps are kind of -unnatural and will be more automized in the next release. If you have -difficulties installing the software in your system, please send mail to - - hdfparallel@ncsa.uiuc.edu - -In your mail, please include the output of "uname -a". Also attach the -content of "config.log" if you ran the "configure" command. - -First, you must obtain and unpack the HDF5 source as described in the -INSTALL file. You also need to obtain the information of the include and -library paths of MPI and MPIO software installed in your system since the -parallel HDF5 library uses them for parallel I/O access. - - -2. Quick Instruction for known systems --------------------------------------- - -The following shows particular steps to run the parallel HDF5 -configure for a few machines we've tested. If your particular platform -is not shown or somehow the steps do not work for yours, please go -to the next section for more detailed explanations. - ------- -TFLOPS ------- - -Follow the instuctions in INSTALL_TFLOPS. - -------- -IBM SP2 -------- - -First of all, make sure your environment variables are set correctly -to compile and execute a single process mpi applications for the SP2 -machine. They should be similar to the following: - - setenv CC mpcc_r - setenv MP_PROCS 1 - setenv MP_NODES 1 - setenv MP_LABELIO no - setenv MP_RMPOOL 0 - setenv RUNPARALLEL "MP_PROCS=2 MP_TASKS_PER_NODE=2 poe" - setenv LLNL_COMPILE_SINGLE_THREADED TRUE - -The shared library configuration for this version is broken. So, only -static library is supported. - -An error for powerpc-ibm-aix4.3.2.0's (LLNL Blue) install method was -discovered after the code freeze. You need to remove the following line -from config/powerpc-ibm-aix4.3.2.0 before configuration: - - ac_cv_path_install=${ac_cv_path_install='cp -r'} - -Then do the following steps: - - $ ./configure --disable-shared --prefix= - $ make # build the library - $ make check # verify the correctness - $ make install - - ---------------- -SGI Origin 2000 -Cray T3E -(where MPI-IO is part of system MPI library such as mpt 1.3) ---------------- - -#!/bin/sh - -RUNPARALLEL="mpirun -np 3" -export RUNPARALLEL -LIBS="-lmpi" -export LIBS -./configure --enable-parallel --disable-shared --prefix=$PWD/installdir -make -make check -make install - - ---------------- -SGI Origin 2000 -Cray T3E -(where MPI-IO is not part of system MPI library or I want to use my own - version of MPIO) ---------------- - -mpi1_inc="" #mpi-1 include -mpi1_lib="" #mpi-1 library -mpio_inc=-I$HOME/ROMIO/include #mpio include -mpio_lib="-L$HOME/ROMIO/lib/IRIX64" #mpio library - -MPI_INC="$mpio_inc $mpi1_inc" -MPI_LIB="$mpio_lib $mpi1_lib" - -#for version 1.1 -CPPFLAGS=$MPI_INC -export CPPFLAGS -LDFLAGS=$MPI_LIB -export LDFLAGS -RUNPARALLEL="mpirun -np 3" -export RUNPARALLEL -LIBS="-lmpio -lmpi" -export LIBS - -./configure --enable-parallel --disable-shared --prefix=$PWD/installdir -make -make check -make install - - ---------------------- -Linux 2.4 and greater ---------------------- - -Be sure that your installation of MPICH was configured with the following -configuration command-line option: - - -cflags="-D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64" - -This allows for >2GB sized files on Linux systems and is only available -with Linux kernels 2.4 and greater. - - ------------------- -HP V2500 and N4000 ------------------- - -Follow the instructions in section 3. - - -3. Detail explanation ---------------------- - -The HDF5 library can be configured to use MPI and MPI-IO for parallelism -on a distributed multi-processor system. The easiest way to do this is to -have a properly installed parallel compiler (e.g., MPICH's mpicc or IBM's -mpcc) and supply that executable as the value of the CC environment -variable: - - $ CC=mpcc ./configure - $ CC=/usr/local/mpi/bin/mpicc ./configure - -If no such wrapper script is available then you must specify your normal -C compiler along with the distribution of MPI/MPI-IO which is to be used -(values other than `mpich' will be added at a later date): - - $ ./configure --enable-parallel=mpich - -If the MPI/MPI-IO include files and/or libraries cannot be found by the -compiler then their directories must be given as arguments to CPPFLAGS -and/or LDFLAGS: - - $ CPPFLAGS=-I/usr/local/mpi/include \ - LDFLAGS=-L/usr/local/mpi/lib/LINUX/ch_p4 \ - ./configure --enable-parallel=mpich - -If a parallel library is being built then configure attempts to determine -how to run a parallel application on one processor and on many -processors. If the compiler is `mpicc' and the user hasn't specified -values for RUNSERIAL and RUNPARALLEL then configure chooses `mpirun' from -the same directory as `mpicc': - - RUNSERIAL: /usr/local/mpi/bin/mpirun -np 1 - RUNPARALLEL: /usr/local/mpi/bin/mpirun -np $${NPROCS:=3} - -The `$${NPROCS:=3}' will be substituted with the value of the NPROCS -environment variable at the time `make check' is run (or the value 3). diff --git a/MANIFEST b/MANIFEST index 48994a1..f3294a3 100644 --- a/MANIFEST +++ b/MANIFEST @@ -6,24 +6,14 @@ #------------------------------------------------------------------------------ ./COPYING -./INSTALL -./INSTALL_TFLOPS -./INSTALL_VFL -./INSTALL_parallel -./INSTALL_Windows.txt -./HISTORY.txt ./MANIFEST ./Makefile.dist ./Makefile.in -./README -./RELEASE.txt +./README.txt ./acconfig.h ./aclocal.m4 ./configure ./configure.in -./all.zip -./all_withf90.zip -./all_withhdf4.zip ./bin/checkapi _DO_NOT_DISTRIBUTE_ ./bin/checkposix _DO_NOT_DISTRIBUTE_ @@ -752,6 +742,15 @@ ./pablo/ProcTrace.h ./pablo/READ_ME + +./release_docs/INSTALL +./release_docs/INSTALL_TFLOPS +./release_docs/INSTALL_VFL +./release_docs/INSTALL_parallel +./release_docs/INSTALL_Windows.txt +./release_docs/HISTORY.txt +./release_docs/RELEASE.txt + ./src/.indent.pro _DO_NOT_DISTRIBUTE_ ./src/Dependencies ./src/H5.c @@ -1225,3 +1224,7 @@ ./tools/testfiles/tvldtypes1.h5.xml ./tools/testfiles/tvldtypes2.h5.xml ./tools/testfiles/tvldtypes3.h5.xml + +./windows/all.zip +./windows/all_withf90.zip +./windows/all_withhdf4.zip diff --git a/README b/README deleted file mode 100644 index e253fbf..0000000 --- a/README +++ /dev/null @@ -1,44 +0,0 @@ -This is hdf5-1.4.1-post4 currently under development -Please refer to the INSTALL file for installation instructions. ------------------------------------------------------------------------------- - -This release is almost fully functional for the entire API defined in the -documentation, see the RELEASE.txt file in this directory for information -specific to this release of the library. The INSTALL file contains -instructions on compiling and installing the library. The INSTALL_parallel -file contains instructions on installing the parallel version of the -library. - -Documentation for this release is in the html directory. Start with the -"index.html" in that dictectory. - -Four mailing lists are currently set up for use with the HDF5 -library. - - hdf5 - For general discussion of the HDF5 library with - other users. - - hdf5dev - For discussion of the HDF5 library development - with developers and other interested parties. - - hdf5announce - For announcements of HDF5 related developments, - not a discussion list. - - hdf5cvs - For checkin notices of code development on the library, - not a discussion list. - -To subscribe to a list, send mail to "majordomo@ncsa.uiuc.edu", -with "subscribe " in the _body_, not the Subject, of the message. -E.g., subscribe hdf5 - -Messages to be sent to the list should be sent to "@ncsa.uiuc.edu". - -Nearly daily code snapshots are now being provided at the following URL: - ftp://hdf.ncsa.uiuc.edu/pub/outgoing/hdf5/snapshots -Please read the readme file in that directory before working with a library -snapshot. - -The HDF5 website is located at http://hdf.ncsa.uiuc.edu/HDF5/ - -Bugs should be reported to hdfhelp@ncsa.uiuc.edu. - diff --git a/README.txt b/README.txt new file mode 100644 index 0000000..e253fbf --- /dev/null +++ b/README.txt @@ -0,0 +1,44 @@ +This is hdf5-1.4.1-post4 currently under development +Please refer to the INSTALL file for installation instructions. +------------------------------------------------------------------------------ + +This release is almost fully functional for the entire API defined in the +documentation, see the RELEASE.txt file in this directory for information +specific to this release of the library. The INSTALL file contains +instructions on compiling and installing the library. The INSTALL_parallel +file contains instructions on installing the parallel version of the +library. + +Documentation for this release is in the html directory. Start with the +"index.html" in that dictectory. + +Four mailing lists are currently set up for use with the HDF5 +library. + + hdf5 - For general discussion of the HDF5 library with + other users. + + hdf5dev - For discussion of the HDF5 library development + with developers and other interested parties. + + hdf5announce - For announcements of HDF5 related developments, + not a discussion list. + + hdf5cvs - For checkin notices of code development on the library, + not a discussion list. + +To subscribe to a list, send mail to "majordomo@ncsa.uiuc.edu", +with "subscribe " in the _body_, not the Subject, of the message. +E.g., subscribe hdf5 + +Messages to be sent to the list should be sent to "@ncsa.uiuc.edu". + +Nearly daily code snapshots are now being provided at the following URL: + ftp://hdf.ncsa.uiuc.edu/pub/outgoing/hdf5/snapshots +Please read the readme file in that directory before working with a library +snapshot. + +The HDF5 website is located at http://hdf.ncsa.uiuc.edu/HDF5/ + +Bugs should be reported to hdfhelp@ncsa.uiuc.edu. + diff --git a/RELEASE.txt b/RELEASE.txt deleted file mode 100644 index 3827029..0000000 --- a/RELEASE.txt +++ /dev/null @@ -1,144 +0,0 @@ -HDF5 library version 1.4.1-post4 currently under development -================================================================================ - - -INTRODUCTION - -This document describes the differences between HDF5-1.4.1 and -HDF5-1.4.2, and contains information on the platforms tested and -known problems in HDF5-1.4.2. 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 -- Bug Fixes since HDF5-1.4.1 -- Documentation -- Platforms Tested -- Supported Configuration Features -- Known Problems - - -New Features -============ - - * File sizes greater than 2GB are now supported on Linux systems with - version 2.4.x or higher kernels. - * Added a global string variable H5_lib_vers_info_g which holds the - HDF5 library version information. This can be used to identify - an hdf5 library or hdf5 application binary. - Also added a verification of the consistency between H5_lib_vers_info_g - and other version information in the source code. - * Parallel HDF5 now runs on the HP V2500 and HP N4000 machines. - * F90 API: - - Added aditional parameter "dims" to the h5dread/h5dwrite and - h5aread/h5awrite subroutines. This parameter is 1D array of size - 7 and contains the sizes of the data buffer dimensions. - * F90 static library is available on Windows platforms. See - INSTALL_Windows.txt for details. - * F90 APIs are available on HPUX 11.00 and IBM SP platforms. - * H5 <-> GIF convertor has been added. This is available under - tools/gifconv. The convertor supports the ability to create animated - gifs as well. - * Verified correct operation of library on Solaris 2.8 in both 64-bit and - 32-bit compilation modes. See INSTALL document for instructions on - compiling the distribution with 64-bit support. - * Added support for the Metrowerks Code Warrior compiler for Windows. - -Bug Fixes since HDF5-1.4.1 Release -================================== - - * Fixed bug with non-zero userblock sizes causing raw data to not - write correctly. - * Fixed problems with Pablo build and linking with non-standard MPI I/O. - * Fixed build on Linux systems with --enable-static-exec flag. It now - works correctly. - * IMPORTANT: Fixed file metadata corruption bug which could cause metadata - data loss in certain situations. - * The allocation by alignment (H5Pset_alignment) feature code somehow - got dropped in some 1.3.x version. Re-implemented it with "new and - improved" algorithm. It keeps track of "wasted" file-fragment in - the free-list too. - * H5 <-> GIF convertor has been added. This is available under - tools/gifconv. The convertor supports the ability to create animated - gifs as well. - * Removed limitation that the data transfer buffer size needed to be - set for datasets whose dimensions were too large for the 'all' selection - code to handle. Any size dimensioned datasets should be handled - correctly now. - -Documentation -============= - - -Platforms Tested -================ - - - AIX 4.3.3.0 (IBM SP powerpc) xlc 3.6.6 - mpcc_r 3.6.6 - Cray T3E sn6711 2.0.5.47 Cray Standard C Version 6.5.0.0 - Cray SV1 10.0.0.8 Cray Standard C Version 6.5.0.0 - FreeBSD 4.3 gcc 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.11.01.20 - IRIX 6.5 MIPSpro cc 7.30 - IRIX64 6.5 (64 & n32) MIPSpro cc 7.3.1m - Linux 2.4.4 gcc-2.95.3 - g++ 2.95.3 - Linux 2.2.18smp gcc-2.95.2 - g++ 2.95.2 - 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) - - SunOS 5.7 WorkShop Compilers 5.0 98/12/15 C 5.0 - (Solaris 2.7) Workshop Compilers 5.0 98/12/15 C++ 5.0 - 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 -======================================== - - * See "Supported Configuration Features Summary" section for the HDF5 - 1.4.0 release in the HISTORY.txt file. - - -Known Problems -============== - - * The h5dump tests may fail to match the expected output in some - platforms (e.g. SP2 parallel, Windows) where the error messages - directed to "stderr" do not appear in the "right order" with output - from stdout. This is not an error. - - * The --enable-static-exec configure flag fails to compile for HP-UX - 11.00 platforms. - - * The executable are always dynamic on IRIX64 6.5(64 and n32) and - IRIX 6.5 even if they are configured with --enable-static-exec. - - * The shared library failed compilation on IRIX 6.5. - - * After "make install" or "make install-doc" one may need to reload - the source from the tar file before doing another build. - - * See "Known problems" section for the HDF5 1.4.0 release in the - HISTORY.txt file. diff --git a/all.zip b/all.zip deleted file mode 100644 index e987ed5..0000000 Binary files a/all.zip and /dev/null differ diff --git a/all_withf90.zip b/all_withf90.zip deleted file mode 100644 index 85f6bda..0000000 Binary files a/all_withf90.zip and /dev/null differ diff --git a/all_withhdf4.zip b/all_withhdf4.zip deleted file mode 100644 index 0d7ae1d..0000000 Binary files a/all_withhdf4.zip and /dev/null differ diff --git a/release_docs/HISTORY.txt b/release_docs/HISTORY.txt new file mode 100644 index 0000000..ebf460a --- /dev/null +++ b/release_docs/HISTORY.txt @@ -0,0 +1,1751 @@ +HDF5 HISTORY +============ + +CONTENTS +I. Release Information for hdf5-1.4.1 +II. Release Information for hdf5-1.4.0 +III. Release Information for hdf5-1.2.2 +IV. Release Information for hdf5-1.2.1 +V. Release Information for hdf5-1.2.0 + A. Platforms Supported + B. Known Problems + C. Changes Since Version 1.0.1 + 1. Documentation + 2. Configuration + 3. Debugging + 4. Datatypes + 5. Dataspaces + 6. Persistent Pointers + 7. Parallel Support + 8. New API Functions + a. Property List Interface + b. Dataset Interface + c. Dataspace Interface + d. Datatype Interface + e. Identifier Interface + f. Reference Interface + g. Ragged Arrays + 9. Tools + +VI. Changes from Release 1.0.0 to Release 1.0.1 +VII. Changes from the Beta 1.0.0 Release to Release 1.0.0 +VIII. Changes from the Second Alpha 1.0.0 Release to the Beta 1.0.0 Release +IX. 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.] + +----------------------------------------------------------------------- + + +%%%%1.4.1%%%% Release Information for hdf5-1.4.1 (April/01) + + + + + HDF5 Release 1.4.1 + + +INTRODUCTION + +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 +(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 +- Bug Fixes since HDF5-1.4.0 +- Documentation +- Platforms Tested +- Supported Configuration Features +- Known Problems + + +New Features +============ + + * 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 + + The XML output is suitable for use with other tools, including the + Java Tools: + + http://hdf.ncsa.uiuc.edu/java-hdf5-html + + +Bug Fixes since HDF5-1.4.0 Release +================================== + + * h4toh5 utility: conversion of images is fixed + + 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 + + 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 + + * 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 + * The RCSID string in H5public.h was causing the C++ compiling problem + because when it was included multiple times, C++ did not like + multiple definitions of the same static variable. All occurance of + RCSID definition are removed since we have not used it consistently + before. + + +Documentation +============= + + PDF and Postscript versions of the following documents are available + for this release: + Document Filename + -------- -------- + Introduction to HDF5 H5-R141-Introduction.pdf + HDF5 Reference Manual H5-R141-RefManual.pdf + C++ APIs to HDF5 documents H5-R141-Cplusplus.pdf + Fortran90 APIs to HDF5 documents H5-R141-Fortran90.pdf + + PDF and Postscript files containing H5-R141-DocSet.pdf + all of the above H5-R141-DocSet.ps + + These files are not included in this distribution, but are available + via the Web or FTP at the following locations: + http://hdf.ncsa.uiuc.edu/HDF5/doc/PSandPDF/ + ftp://ftp.ncsa.uiuc.edu/HDF/HDF5/docs/ + + While these documents are labeled Release 1.4.1, they describe + Release 1.4.0 as well. + + +Platforms Tested +================ + +Due to the nature of this release only C, C++ libraries and tools were tested. + + AIX 4.3.3.0 (IBM SP powerpc) xlc 3.6.6 + mpcc_r 3.6.6 + Cray T3E sn6711 2.0.5.47 Cray Standard C Version 6.5.0.0 + Cray SV1 10.0.0.8 Cray Standard C Version 6.5.0.0 + FreeBSD 4.3 gcc 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.11.01.20 + IRIX 6.5 MIPSpro cc 7.30 + IRIX64 6.5 (64 & n32) MIPSpro cc 7.3.1m + Linux 2.2.18smp gcc-2.95.2 + g++ 2.95.2 + 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) + + SunOS 5.7 WorkShop Compilers 5.0 98/12/15 C 5.0 + (Solaris 2.7) Workshop Compilers 5.0 98/12/15 C++ 5.0 + 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 +======================================== + + * See "Supported Configuration Features Summary" section for the HDF5 + 1.4.0 release in the HISTORY.txt file. + +Known Problems +============== + + * The h5dump tests may fail to match the expected output in some + platforms (e.g. SP2 parallel, Windows) where the error messages + directed to "stderr" do not appear in the "right order" with output + from stdout. This is not an error. + + * The --enable-static-exec configure flag fails to compile for HP-UX + 11.00 platforms. + + * The executable are always dynamic on IRIX64 6.5(64 and n32) and + IRIX 6.5 even if they are configured with --enable-static-exec. + + * The shared library failed compilation on IRIX 6.5. + + * After "make install" or "make install-doc" one may need to reload the source + from the tar file before doing another build. + + * See "Known problems" section for the HDF5 1.4.0 release in the + HISTORY.txt file. + +%%%%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) + +II. Release Information for hdf5-1.2.2 + +INTRODUCTION + +This document describes the differences between HDF5-1.2.1 and +HDF5-1.2.2, and contains information on the platforms where HDF5-1.2.2 +was tested and known problems in HDF5-1.2.2. + +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 + +- Features Added since HDF5-1.2.1 +- Bug Fixes since HDF5-1.2.1 +- Known Problems +- Platforms Tested + + +Features Added since HDF5-1.2.1 +=============================== + * Added internal free-lists to reduce memory required by the library and + H5garbage_collect API function. + * h5dump displays opaque and bitfield types. + * 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. + +Bug Fixes since HDF5-1.2.1 +========================== + * h5dump correctly displays compound datatypes, including simple and + nested compound types. + * h5dump correctly displays the committed copy of predefined types. + * Corrected an error in h5toh4 which did not convert the 32-bit + int from HDF5 to HDF4 correctly for the T3E platform. + * Corrected a floating point number conversion error for the + Cray J90 platform. The error did not convert the value 0.0 + correctly. + * 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 caused 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 without the same dimension being unlimited. + * Improved metadata hashing & caching algorithms to avoid + many hash flushes and also removed some redundant I/O when moving metadata + blocks in the file. + * The libhdf5.settings file shows the correct machine byte-sex. + * 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. + +Known Problems +============== + +o SunOS 5.6 with C WorkShop Compilers 4.2: hyperslab selections will + fail if library is compiled using optimization of any level. +o TFLOPS: dsets test fails if compiled with optimization turned on. +o J90: tools fail to dispay data for the datasets with a compound datatype. + +Platforms Tested +================ + + AIX 4.3.3 (IBM SP) 3.6.6 | binaries + mpicc using mpich 1.1.2 | are not + mpicc_r using IBM MPI-IO prototype | available + AIX 4.3.2.0 (IBM SP) xlc 5.0.1.0 + Cray J90 10.0.0.7 cc 6.3.0.2 + Cray T3E 2.0.5.29 cc 6.3.0.2 + mpt.1.3 + FreeBSD 4.0 gcc 2.95.2 + HP-UX B.10.20 HP C HP92453-01 A.10.32 + HP-UX B.11.00 HP92453-01 A.11.00.13 HP C Compiler + (static library only, h5toh4 tool is not available) + IRIX 6.5 MIPSpro cc 7.30 + IRIX64 6.5 (64 & n32) MIPSpro cc 7.3.1m + mpt.1.4 + + Linux 2.2.10 SMP gcc 2.95.1 + mpicc(gcc-2.95.1) + gcc (egcs-2.91.66) + mpicc (egcs-2.91.66) + Linux 2.2.16 (RedHat 6.2) gcc 2.95.2 + + OSF1 V4.0 DEC-V5.2-040 + SunOS 5.6 cc WorkShop Compilers 5.0 no optimization + SunOS 5.7 cc WorkShop Compilers 5.0 + SolarisX86 SunOS 5.5.1 gcc version 2.7.2 with --disable-hsizet + TFLOPS 3.2.1 pgcc Rel 3.1-3i + mpich-1.1.2 with local changes + Windows NT4.0 sp5 MSVC++ 6.0 + Windows 98 MSVC++ 6.0 + Windows 2000 MSVC++ 6.0 + + + +%%%%1.2.1%%%% Release Information for hdf5-1.2.1 + +III. Release Information for hdf5-1.2.1 + +Bug fixes since HDF5-1.2.0 +========================== + +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. + +Library +------- + + * Error was fixed which was not allowing dataset region references to have + their regions retrieved correctly. + * 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. + +Tests +------ + + * Added additional tests for group and attribute iteration. + * Added additional test for staggered hyperslab iteration. + * Added additional test for random 5-D hyperslab selection. + +Tools +------ + + * 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. + +Documentation +------------- + + * User's Guide and Reference Manual were updated. + See doc/html/PSandPDF/index.html for more details. + + +Platforms Tested: +================ +Note: Due to the nature of bug fixes, only static versions of the library and tools were tested. + + + AIX 4.3.2 (IBM SP) 3.6.6 + Cray T3E 2.0.4.81 cc 6.3.0.1 + mpt.1.3 + FreeBSD 3.3-STABLE gcc 2.95.2 + HP-UX B.10.20 HP C HP92453-01 A.10.32 + IRIX 6.5 MIPSpro cc 7.30 + IRIX64 6.5 (64 & n32) MIPSpro cc 7.3.1m + mpt.1.3 (SGI MPI 3.2.0.0) + + Linux 2.2.10 SuSE egcs-2.91.66 configured with + (i686-pc-linux-gnu) --disable-hsizet + mpich-1.2.0 egcs-2.91.66 19990314/Linux + + OSF1 V4.0 DEC-V5.2-040 + SunOS 5.6 cc WorkShop Compilers 4.2 no optimization + SunOS 5.7 cc WorkShop Compilers 5.0 + TFLOPS 2.8 cicc (pgcc Rel 3.0-5i) + mpich-1.1.2 with local changes + Windows NT4.0 sp5 MSVC++ 6.0 + +Known Problems: +============== + +o SunOS 5.6 with C WorkShop Compilers 4.2: Hyperslab selections will + fail if library is compiled using optimization of any level. + + + +%%%%1.2.0%%%% Release Information for hdf5-1.2.0 + +IV. Release Information for hdf5-1.2.0 + +A. Platforms Supported + ------------------- + +Operating systems listed below with compiler information and MPI library, if +applicable, are systems that HDF5 1.2.0 was tested on. + + Compiler & libraries + Platform Information Comment + -------- ---------- -------- + + AIX 4.3.2 (IBM SP) 3.6.6 + + Cray J90 10.0.0.6 cc 6.3.0.0 + + Cray T3E 2.0.4.61 cc 6.2.1.0 + mpt.1.3 + + FreeBSD 3.2 gcc 2.95.1 + + HP-UX B.10.20 HP C HP92453-01 A.10.32 + gcc 2.8.1 + + IRIX 6.5 MIPSpro cc 7.30 + + IRIX64 6.5 (64 & n32) MIPSpro cc 7.3.1m + mpt.1.3 (SGI MPI 3.2.0.0) + + Linux 2.2.10 egcs-2.91.66 configured with + --disable-hsizet + lbraries: glibc2 + + OSF1 V4.0 DEC-V5.2-040 + + SunOS 5.6 cc WorkShop Compilers 4.2 + no optimization + gcc 2.8.1 + + SunOS 5.7 cc WorkShop Compilers 5.0 + gcc 2.8.1 + + TFLOPS 2.7.1 cicc (pgcc Rel 3.0-4i) + mpich-1.1.2 with local changes + + Windows NT4.0 intel MSVC++ 5.0 and 6.0 + + Windows NT alpha 4.0 MSVC++ 5.0 + + Windows 98 MSVC++ 5.0 + + +B. Known Problems + -------------- + +* NT alpha 4.0 + Dumper utiliy h5dump fails if linked with DLL. + +* SunOS 5.6 with C WorkShop Compilers 4.2 + Hyperslab selections will fail if library is compiled using optimization + of any level. + + +C. Changes Since Version 1.0.1 + --------------------------- + +1. Documentation + ------------- + +* More examples + +* Updated user guide, reference manual, and format specification. + +* Self-contained documentation for installations isolated from the + Internet. + +* HDF5 Tutorial was added to the documentation + +2. Configuration + ------------- + +* Better detection and support for MPI-IO. + +* Recognition of compilers with known code generation problems. + +* Support for various compilers on a single architecture (e.g., the + native compiler and the GNU compilers). + +* Ability to build from read-only media and with different compilers + and/or options concurrently. + +* Added a libhdf5.settings file which summarizes the configuration + information and is installed along with the library. + +* Builds a shared library on most systems that support it. + +* Support for Cray T3E, J90 and Windows/NT. + +3. Debugging + --------- + +* Improved control and redirection of debugging and tracing messages. + +4. Datatypes + --------- + +* Optimizations to compound datatype conversions and I/O operations. + +* Added nearly 100 optimized conversion functions for native datatypes + including support for non-aligned data. + +* Added support for bitfield, opaque, and enumeration types. + +* Added distinctions between signed and unsigned char types to the + list of predefined native hdf5 datatypes. + +* Added HDF5 type definitions for C9x types like int32_t. + +* Application-defined type conversion functions can handle non-packed + data. + +* Changed the H5Tunregister() function to use wildcards when matching + conversion functions. H5Tregister_hard() and H5Tregister_soft() + were combined into H5Tregister(). + +* Support for variable-length datatypes (arrays of varying length per + dataset element). Variable length strings currently supported only + as variable length arrays of 1-byte integers. + +5. Dataspaces + ---------- + +* New query functions for selections. + +* I/O operations bypass the stripmining loop and go directly to + storage for certain contiguous selections in the absense of type + conversions. In other cases the stripmining buffers are used more + effectively. + +* Reduced the number of I/O requests under certain circumstances, + improving performance on systems with high I/O latency. + +6. Persistent Pointers + ------------------- + +* Object (serial and parallel) and dataset region (serial only) + references are implemented. + +7. Parallel Support + ---------------- + +* Improved parallel I/O performance. + +* Supported new platforms: Cray T3E, Linux, DEC Cluster. + +* Use vendor supported version of MPIO on SGI O2K and Cray platforms. + +* Improved the algorithm that translates an HDF5 hyperslab selection + into an MPI type for better collective I/O performance. + +8. New API functions + ----------------- + + a. Property List Interface: + ------------------------ + + H5Pset_xfer - set data transfer properties + H5Pset_preserve - set dataset transfer property list status + H5Pget_preserve - get dataset transfer property list status + H5Pset_hyper_cache - indicates whether to cache hyperslab blocks during I/O + H5Pget_hyper_cache - returns information regarding the caching of + hyperslab blocks during I/O + H5Pget_btree_ratios - sets B-tree split ratios for a dataset + transfer property list + H5Pset_btree_ratios - gets B-tree split ratios for a dataset + transfer property list + H5Pset_vlen_mem_manager - sets the memory manager for variable-length + datatype allocation + H5Pget_vlen_mem_manager - sets the memory manager for variable-length + datatype allocation + + b. Dataset Interface: + ------------------ + + H5Diterate - iterate over all selected elements in a dataspace + H5Dget_storage_size - return the amount of storage required for a dataset + H5Dvlen_reclaim - reclaim VL datatype memory buffers + + c. Dataspace Interface: + -------------------- + H5Sget_select_hyper_nblocks - get number of hyperslab blocks + H5Sget_select_hyper_blocklist - get the list of hyperslab blocks + currently selected + H5Sget_select_elem_npoints - get the number of element points + in the current selection + H5Sget_select_elem_pointlist - get the list of element points + currently selected + H5Sget_select_bounds - gets the bounding box containing + the current selection + + d. Datatype Interface: + ------------------- + H5Tget_super - return the base datatype from which a + datatype is derived + H5Tvlen_create - creates a new variable-length dataype + H5Tenum_create - creates a new enumeration datatype + H5Tenum_insert - inserts a new enumeration datatype member + H5Tenum_nameof - returns the symbol name corresponding to a + specified member of an enumeration datatype + H5Tvalueof - return the value corresponding to a + specified member of an enumeration datatype + H5Tget_member_value - return the value of an enumeration datatype member + H5Tset_tag - tags an opaque datatype + H5Tget_tag - gets the tag associated with an opaque datatype + + e. Identifier Interface: + --------------------- + H5Iget_type - retrieve the type of an object + + f. Reference Interface: + -------------------- + H5Rcreate - creates a reference + H5Rdereference - open the HDF5 object referenced + H5Rget_region - retrieve a dataspace with the specified region selected + H5Rget_object_type - retrieve the type of object that an + object reference points to + + g. Ragged Arrays (alpha) (names of those API functions were changed): + ------------------------------------------------------------------ + H5RAcreate - create a new ragged array (old name was H5Rcreate) + H5RAopen - open an existing array (old name was H5Ropen) + H5RAclose - close a ragged array (old name was H5Rclose) + H5RAwrite - write to an array (old name was H5Rwrite) + H5RAread - read from an array (old name was H5Rread) + + +9. Tools + ----- + +* Enhancements to the h5ls tool including the ability to list objects + from more than one file, to display raw hexadecimal data, to + show file addresses for raw data, to format output more reasonably, + to show object attributes, and to perform a recursive listing, + +* Enhancements to h5dump: support new data types added since previous + versions. + +* h5toh4: An hdf5 to hdf4 converter. + + + +%%%%1.0.1%%%% Release Information for hdf5-1.0.1 + +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. + +* [Bug-Fix]: Configure failed for all IRIX versions other than 6.3. + It now configures correctly for all IRIX 6.x version. + +* Released Parallel HDF5 + + Supported Features: + ------------------ + + HDF5 files are accessed according to the communicator and INFO + object defined in the property list set by H5Pset_mpi. + + Independent read and write accesses to fixed and extendable dimension + datasets. + + Collective read and write accesses to fixed dimension datasets. + + Supported Platforms: + ------------------- + + Intel Red + IBM SP2 + SGI Origin 2000 + + Changes In This Release: + ----------------------- + + o Support of Access to Extendable Dimension Datasets. + Extendable dimension datasets must use chunked storage methods. + A new function, H5Dextend, is created to extend the current + dimensions of a dataset. The current release requires the + MPI application must make a collective call to extend the + dimensions of an extendable dataset before writing to the + newly extended area. (The serial does not require the + call of H5Dextend. The dimensions of an extendable + dataset is increased when data is written to beyond the + current dimensions but within the maximum dimensions.) + The required collective call of H5Dextend may be relaxed + in future release. + + This release only support independent read and write accesses + to extendable datasets. Collective accesses to extendable + datasets will be implemented in future releases. + + o Collective access to fixed dimension datasets. + Collective access to a dataset can be specified in the transfer + property list argument in H5Dread and H5Dwrite. The current + release supports collective access to fixed dimension datasets. + Collective access to extendable datasets will be implemented in + future releases. + + o HDF5 files are opened according to Communicator and INFO object. + H5Dopen now records the communicator and INFO setup by H5Pset_mmpi + and pass them to the corresponding MPIO open file calls for + processing. + + o This release has been tested on IBM SP2, Intel Red and SGI Origin 2000 + systems. It uses the ROMIO version of MPIO interface for parallel + I/O supports. + + + +%%%%1.0.0%%%% Release Information for hdf5-1.0.0 + +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 + entire dataset when the dataset is created. This will be remedied + in a future version. Chunked datasets using fill values do not + incur any additional overhead. See H5Pset_fill_value(). + +* Multiple hdf5 files can be "mounted" on one another to create a + larger virtual file. See H5Fmount(). + +* Object names can be removed or changed but objects are never + actually removed from the file yet. See H5Gunlink() and H5Gmove(). + +* Added a tuning mechanism for B-trees to insure that sequential + writes to chunked datasets use less overhead. See H5Pset_btree_ratios(). + +* Various optimizations and bug fixes. + + + +%%%%1.0.0 Beta%%%% Release Information for hdf5-1.0.0 Beta + +VII. Changes from the Second Alpha 1.0.0 Release to the Beta 1.0.0 Release + +* Strided hyperslab selections in dataspaces now working. + +* The compression API has been replaced with a more general filter + API. See doc/html/Filters.html for details. + +* Alpha-quality 2d ragged arrays are implemented as a layer built on + top of other hdf5 objects. The API and storage format will almost + certainly change. + +* More debugging support including API tracing. See Debugging.html. + +* C and Fortran style 8-bit fixed-length character string types are + supported with space or null padding or null termination and + translations between them. + +* Added function H5Fflush() to write all cached data immediately to + the file. + +* Datasets maintain a modification time which can be retrieved with + H5Gstat(). + +* The h5ls tool can display much more information, including all the + values of a dataset. + + + +%%%%1.0.0 Alpha 2%%%% Release Information for hdf5-1.0.0 Alpha 2 + +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 + renamed from `H5P' to `H5S' and the property list (template) API has + been renamed from `H5C' to `H5P'. + +* The new attribute API `H5A' has been added. An attribute is a small + dataset which can be attached to some other object (for instance, a + 4x4 transformation matrix attached to a 3-dimensional dataset, or an + English abstract attached to a group). + +* The error handling API `H5E' has been completed. By default, when an + API function returns failure an error stack is displayed on the + standard error stream. The H5Eset_auto() controls the automatic + printing and H5E_BEGIN_TRY/H5E_END_TRY macros can temporarily + disable the automatic error printing. + +* Support for large files and datasets (>2GB) has been added. There + is an html document that describes how it works. Some of the types + for function arguments have changed to support this: all arguments + pertaining to sizes of memory objects are `size_t' and all arguments + pertaining to file sizes are `hsize_t'. + +* More data type conversions have been added although none of them are + fine tuned for performance. There are new converters from integer + to integer and float to float, but not between integers and floating + points. A bug has been fixed in the converter between compound + types. + +* The numbered types have been removed from the API: int8, uint8, + int16, uint16, int32, uint32, int64, uint64, float32, and float64. + Use standard C types instead. Similarly, the numbered types were + removed from the H5T_NATIVE_* architecture; use unnumbered types + which correspond to the standard C types like H5T_NATIVE_INT. + +* More debugging support was added. If tracing is enabled at + configuration time (the default) and the HDF5_TRACE environment + variable is set to a file descriptor then all API calls will emit + the function name, argument names and values, and return value on + that file number. There is an html document that describes this. + If appropriate debugging options are enabled at configuration time, + some packages will display performance information on stderr. + +* Data types can be stored in the file as independent objects and + multiple datasets can share a data type. + +* The raw data I/O stream has been implemented and the application can + control meta and raw data caches, so I/O performance should be + improved from the first alpha release. + +* Group and attribute query functions have been implemented so it is + now possible to find out the contents of a file with no prior + knowledge. + +* External raw data storage allows datasets to be written by other + applications or I/O libraries and described and accessed through + HDF5. + +* Hard and soft (symbolic) links are implemented which allow groups to + share objects. Dangling and recursive symbolic links are supported. + +* User-defined data compression is implemented although we may + generalize the interface to allow arbitrary user-defined filters + which can be used for compression, checksums, encryption, + performance monitoring, etc. The publicly-available `deflate' + method is predefined if the GNU libz.a can be found at configuration + time. + +* The configuration scripts have been modified to make it easier to + build debugging vs. production versions of the library. + +* The library automatically checks that the application was compiled + with the correct version of header files. + + + Parallel HDF5 Changes + +* Parallel support for fixed dimension datasets with contiguous or + chunked storages. Also, support unlimited dimension datasets which + must use chunk storage. No parallel support for compressed datasets. + +* Collective data transfer for H5Dread/H5Dwrite. Collective access + support for datasets with contiguous storage only, thus only fixed + dimension datasets for now. + +* H5Pset_mpi and H5Pget_mpi no longer have the access_mode + argument. It is taken over by the data-transfer property list + of H5Dread/H5Dwrite. + +* New functions H5Pset_xfer and H5Pget_xfer to handle the + specification of independent or collective data transfer_mode + in the dataset transfer properties list. The properties + list can be used to specify data transfer mode in the H5Dwrite + and H5Dread function calls. + +* Added parallel support for datasets with chunked storage layout. + When a dataset is extend in a PHDF5 file, all processes that open + the file must collectively call H5Dextend with identical new dimension + sizes. + + + LIST OF API FUNCTIONS + +The following functions are implemented. Errors are returned if an +attempt is made to use some feature which is not implemented and +printing the error stack will show `not implemented yet'. + +Library + H5check - check that lib version matches header version + H5open - initialize library (happens automatically) + H5close - shut down the library (happens automatically) + H5dont_atexit - don't call H5close on exit + H5get_libversion - retrieve library version info + H5check_version - check for specific library version + +Property Lists + H5Pclose - release template resources + H5Pcopy - copy a template + H5Pcreate - create a new template + H5Pget_chunk - get chunked storage properties + H5Pset_chunk - set chunked storage properties + H5Pget_class - get template class + H5Pget_istore_k - get chunked storage properties + H5Pset_istore_k - set chunked storage properties + H5Pget_layout - get raw data layout class + H5Pset_layout - set raw data layout class + H5Pget_sizes - get address and size sizes + H5Pset_sizes - set address and size sizes + H5Pget_sym_k - get symbol table storage properties + H5Pset_sym_k - set symbol table storage properties + H5Pget_userblock - get user-block size + H5Pset_userblock - set user-block size + H5Pget_version - get file version numbers + H5Pget_alignment - get data alignment properties + H5Pset_alignment - set data alignment properties + H5Pget_external_count- get count of external data files + H5Pget_external - get information about an external data file + H5Pset_external - add a new external data file to the list + H5Pget_driver - get low-level file driver class + H5Pget_stdio - get properties for stdio low-level driver + H5Pset_stdio - set properties for stdio low-level driver + H5Pget_sec2 - get properties for sec2 low-level driver + H5Pset_sec2 - set properties for sec2 low-level driver + H5Pget_core - get properties for core low-level driver + H5Pset_core - set properties for core low-level driver + H5Pget_split - get properties for split low-level driver + H5Pset_split - set properties for split low-level driver + H5P_get_family - get properties for family low-level driver + H5P_set_family - set properties for family low-level driver + H5Pget_cache - get meta- and raw-data caching properties + H5Pset_cache - set meta- and raw-data caching properties + H5Pget_buffer - get raw-data I/O pipe buffer properties + H5Pset_buffer - set raw-data I/O pipe buffer properties + H5Pget_preserve - get type conversion preservation properties + H5Pset_preserve - set type conversion preservation properties + H5Pget_nfilters - get number of raw data filters + H5Pget_filter - get raw data filter properties + H5Pset_filter - set raw data filter properties + H5Pset_deflate - set deflate compression filter properties + H5Pget_mpi - get MPI-IO properties + H5Pset_mpi - set MPI-IO properties + H5Pget_xfer - get data transfer properties + + H5Pset_xfer - set data transfer properties + + H5Pset_preserve - set dataset transfer property list status + + H5Pget_preserve - get dataset transfer property list status + + H5Pset_hyper_cache - indicates whether to cache hyperslab blocks during I/O + + H5Pget_hyper_cache - returns information regarding the caching of + hyperslab blocks during I/O + + H5Pget_btree_ratios - sets B-tree split ratios for a dataset + transfer property list + + H5Pset_btree_ratios - gets B-tree split ratios for a dataset + transfer property list + + H5Pset_vlen_mem_manager - sets the memory manager for variable-length + datatype allocation + + H5Pget_vlen_mem_manager - sets the memory manager for variable-length + datatype allocation + +Datasets + H5Dclose - release dataset resources + H5Dcreate - create a new dataset + H5Dget_space - get data space + H5Dget_type - get data type + H5Dget_create_plist - get dataset creation properties + H5Dopen - open an existing dataset + H5Dread - read raw data + H5Dwrite - write raw data + H5Dextend - extend a dataset + + H5Diterate - iterate over all selected elements in a dataspace + + H5Dget_storage_size - return the amount of storage required for a dataset + + H5Dvlen_reclaim - reclaim VL datatype memory buffers + +Attributes + H5Acreate - create a new attribute + H5Aopen_name - open an attribute by name + H5Aopen_idx - open an attribute by number + H5Awrite - write values into an attribute + H5Aread - read values from an attribute + H5Aget_space - get attribute data space + H5Aget_type - get attribute data type + H5Aget_name - get attribute name + H5Anum_attrs - return the number of attributes for an object + H5Aiterate - iterate over an object's attributes + H5Adelete - delete an attribute + H5Aclose - close an attribute + +Errors + H5Eclear - clear the error stack + H5Eprint - print an error stack + H5Eget_auto - get automatic error reporting settings + H5Eset_auto - set automatic error reporting + H5Ewalk - iterate over the error stack + H5Ewalk_cb - the default error stack iterator function + H5Eget_major - get the message for the major error number + H5Eget_minor - get the message for the minor error number + +Files + H5Fclose - close a file and release resources + H5Fcreate - create a new file + H5Fget_create_plist - get file creation property list + H5Fget_access_plist - get file access property list + H5Fis_hdf5 - determine if a file is an hdf5 file + H5Fopen - open an existing file + H5Freopen - reopen an HDF5 file + H5Fmount - mount a file + H5Funmount - unmount a file + H5Fflush - flush all buffers associated with a file to disk + +Groups + H5Gclose - close a group and release resources + H5Gcreate - create a new group + H5Gopen - open an existing group + H5Giterate - iterate over the contents of a group + H5Gmove - change the name of some object + H5Glink - create a hard or soft link to an object + H5Gunlink - break the link between a name and an object + H5Gget_objinfo - get information about a group entry + H5Gget_linkval - get the value of a soft link + H5Gget_comment - get the comment string for an object + H5Gset_comment - set the comment string for an object + +Dataspaces + H5Screate - create a new data space + H5Scopy - copy a data space + H5Sclose - release data space + H5Screate_simple - create a new simple data space + H5Sset_space - set simple data space extents + H5Sis_simple - determine if data space is simple + H5Sset_extent_simple - set simple data space dimensionality and size + H5Sget_simple_extent_npoints - get number of points in simple extent + H5Sget_simple_extent_ndims - get simple data space dimensionality + H5Sget_simple_extent_dims - get simple data space size + H5Sget_simple_extent_type - get type of simple extent + H5Sset_extent_none - reset extent to be empty + H5Sextent_copy - copy the extent from one data space to another + H5Sget_select_npoints - get number of points selected for I/O + H5Sselect_hyperslab - set hyperslab dataspace selection + H5Sselect_elements - set element sequence dataspace selection + H5Sselect_all - select entire extent for I/O + H5Sselect_none - deselect all elements of extent + H5Soffset_simple - set selection offset + H5Sselect_valid - determine if selection is valid for extent + + H5Sget_select_hyper_nblocks - get number of hyperslab blocks + + H5Sget_select_hyper_blocklist - get the list of hyperslab blocks + currently selected + + H5Sget_select_elem_npoints - get the number of element points + in the current selection + + H5Sget_select_elem_pointlist - get the list of element points + currently selected + + H5Sget_select_bounds - gets the bounding box containing + the current selection + +Datatypes + H5Tclose - release data type resources + H5Topen - open a named data type + H5Tcommit - name a data type + H5Tcommitted - determine if a type is named + H5Tcopy - copy a data type + H5Tcreate - create a new data type + H5Tequal - compare two data types + H5Tlock - lock type to prevent changes + H5Tfind - find a data type conversion function + H5Tconvert - convert data from one type to another + H5Tregister - register a conversion function + H5Tunregister - remove a conversion function + H5Tget_overflow - get function that handles overflow conv. cases + H5Tset_overflow - set function to handle overflow conversion cases + H5Tget_class - get data type class + H5Tget_cset - get character set + H5Tget_ebias - get exponent bias + H5Tget_fields - get floating point fields + H5Tget_inpad - get inter-field padding + H5Tget_member_dims - get struct member dimensions + H5Tget_member_name - get struct member name + H5Tget_member_offset - get struct member byte offset + H5Tget_member_type - get struct member type + H5Tget_nmembers - get number of struct members + H5Tget_norm - get floating point normalization + H5Tget_offset - get bit offset within type + H5Tget_order - get byte order + H5Tget_pad - get padding type + H5Tget_precision - get precision in bits + H5Tget_sign - get integer sign type + H5Tget_size - get size in bytes + H5Tget_strpad - get string padding + H5Tinsert - insert scalar struct member + H5Tinsert_array - insert array struct member + H5Tpack - pack struct members + H5Tset_cset - set character set + H5Tset_ebias - set exponent bias + H5Tset_fields - set floating point fields + H5Tset_inpad - set inter-field padding + H5Tset_norm - set floating point normalization + H5Tset_offset - set bit offset within type + H5Tset_order - set byte order + H5Tset_pad - set padding type + H5Tset_precision - set precision in bits + H5Tset_sign - set integer sign type + H5Tset_size - set size in bytes + H5Tset_strpad - set string padding + + H5Tget_super - return the base datatype from which a + datatype is derived + + H5Tvlen_create - creates a new variable-length dataype + + H5Tenum_create - creates a new enumeration datatype + + H5Tenum_insert - inserts a new enumeration datatype member + + H5Tenum_nameof - returns the symbol name corresponding to a + specified member of an enumeration datatype + + H5Tvalueof - return the value corresponding to a + specified member of an enumeration datatype + + H5Tget_member_value - return the value of an enumeration datatype member + + H5Tset_tag - tags an opaque datatype + + H5Tget_tag - gets the tag associated with an opaque datatype + + - H5Tregister_hard - register specific type conversion function + - H5Tregister_soft - register general type conversion function + +Filters + H5Tregister - register a conversion function + +Compression + H5Zregister - register new compression and uncompression + functions for a method specified by a method number + +Identifiers + + H5Iget_type - retrieve the type of an object + +References + + H5Rcreate - creates a reference + + H5Rdereference - open the HDF5 object referenced + + H5Rget_region - retrieve a dataspace with the specified region selected + + H5Rget_object_type - retrieve the type of object that an + object reference points to + +Ragged Arrays (alpha) + H5RAcreate - create a new ragged array + H5RAopen - open an existing array + H5RAclose - close a ragged array + H5RAwrite - write to an array + H5RAread - read from an array + + diff --git a/release_docs/INSTALL b/release_docs/INSTALL new file mode 100644 index 0000000..20ce060 --- /dev/null +++ b/release_docs/INSTALL @@ -0,0 +1,538 @@ + + Instructions for the Installation of HDF5 Software + ================================================== + + CONTENTS + -------- + 1. Obtaining HDF5 + + 2. Warnings about compilers + 2.1. GNU (Intel platforms) + 2.2. DEC + 2.3. SGI (Irix64 6.2) + 2.4. Windows/NT + + 3. Quick installation + 3.1. TFLOPS + 3.2. Windows + 3.3. Certain Virtual File Layer(VFL) + + 4. HDF5 dependencies + 4.1. Zlib + 4.2. MPI and MPI-IO + + 5. Full installation instructions for source distributions + 5.1. Unpacking the distribution + 5.1.1. Non-compressed tar archive (*.tar) + 5.1.2. Compressed tar archive (*.tar.Z) + 5.1.3. Gzip'd tar archive (*.tar.gz) + 5.1.4. Bzip'd tar archive (*.tar.bz2) + 5.2. Source vs. Build Directories + 5.3. Configuring + 5.3.1. Specifying the installation directories + 5.3.2. Using an alternate C compiler + 5.3.3. Additional compilation flags + 5.3.4. Compiling HDF5 wrapper libraries + 5.3.5. Specifying other programs + 5.3.6. Specifying other libraries and headers + 5.3.7. Static versus shared linking + 5.3.8. Optimization versus symbolic debugging + 5.3.9. Large (>2GB) vs. small (<2GB) file capability + 5.3.10. Parallel vs. serial library + 5.4. Building + 5.5. Testing + 5.6. Installing + + 6. Using the Library + + 7. Support + +***************************************************************************** + +1. Obtaining HDF5 + The latest supported public release of HDF5 is available from + ftp://hdf.ncsa.uiuc.edu/pub/dist/HDF5. For Unix platforms, it is + available in tar format uncompressed or compressed with compress, + gzip, or bzip2. For Microsoft Windows, it is in ZIP format. + + The HDF team also makes snapshots of the source code available on + a regular basis. These snapshots are unsupported (that is, the + HDF team will not release a bug-fix on a particular snapshot; + rather any bug fixes will be rolled into the next snapshot). + Furthermore, the snapshots have only been tested on a few + machines and may not test correctly for parallel applications. + Snapshots can be found at + ftp://hdf.ncsa.uiuc.edu/pub/outgoing/hdf5/snapshots in a limited + number of formats. + +2. Warnings about compilers + OUTPUT FROM THE FOLLOWING COMPILERS SHOULD BE EXTREMELY SUSPECT + WHEN USED TO COMPILE THE HDF5 LIBRARY, ESPECIALLY IF + OPTIMIZATIONS ARE ENABLED. IN ALL CASES, HDF5 ATTEMPTS TO WORK + AROUND THE COMPILER BUGS BUT THE HDF5 DEVELOPMENT TEAM MAKES NO + GUARANTEES THAT THERE ARE OTHER CODE GENERATION PROBLEMS. + +2.1. GNU (Intel platforms) + Versions before 2.8.1 have serious problems allocating registers + when functions contain operations on `long long' data types. + Supplying the `--disable-hsizet' switch to configure (documented + below) will prevent hdf5 from using `long long' data types in + situations that are known not to work, but it limits the hdf5 + address space to 2GB. + +2.2. DEC + The V5.2-038 compiler (and possibly others) occasionally + generates incorrect code for memcpy() calls when optimizations + are enabled, resulting in unaligned access faults. HDF5 works + around the problem by casting the second argument to `char *'. + +2.3. SGI (Irix64 6.2) + The Mongoose 7.00 compiler has serious optimization bugs and + should be upgraded to MIPSpro 7.2.1.2m. Patches are available + from SGI. + +2.4. Windows/NT + The MicroSoft Win32 5.0 compiler is unable to cast unsigned long + long values to doubles. HDF5 works around this bug by first + casting to signed long long and then to double. + A link warning: defaultlib "LIBC" conflicts with use of other + libs appears for debug version of VC++ 6.0. This warning will + not affect building and testing hdf5 libraries. + + +3. Quick installation + For those that don't like to read ;-) the following steps can be + used to configure, build, test, and install the HDF5 library, + header files, and support programs. + + $ gunzip < hdf5-1.4.0.tar.gz | tar xf - + $ cd hdf5-1.4.0 + $ make check + $ make install + +3.1. TFLOPS + Users of the Intel TFLOPS machine, after reading this file, + should see the INSTALL_TFLOPS for more instructions. + +3.2. Windows + Users of Microsoft Windows should see the INSTALL_Windows for + detailed instructions. + +3.3. Certain Virtual File Layer(VFL) + If users want to install with special Virtual File Layer(VFL), + please go to read INSTALL_VFL file. SRB and Globus-GASS have + been documented. + + +4. HDF5 dependencies +4.1. Zlib + The HDF5 library has a predefined compression filter that uses + the "deflate" method for chunked datatsets. If zlib-1.1.2 or + later is found then HDF5 will use it, otherwise HDF5's predefined + compression method will degenerate to a no-op (the compression + filter will succeed but the data will not be compressed). + +4.2. MPI and MPI-IO + The parallel version of the library is built upon the foundation + provided by MPI and MPI-IO. If these libraries are not available + when HDF5 is configured then only a serial version of HDF5 can be + built. + +5. Full installation instructions for source distributions +5.1. Unpacking the distribution + The HDF5 source code is distributed in a variety of formats which + can be unpacked with the following commands, each of which + creates an `hdf5-1.2.0' directory. + +5.1.1. Non-compressed tar archive (*.tar) + + $ tar xf hdf5-1.4.0.tar + +5.1.2. Compressed tar archive (*.tar.Z) + + $ uncompress -c < hdf5-1.4.0.tar.Z | tar xf - + +5.1.3. Gzip'd tar archive (*.tar.gz) + + $ gunzip < hdf5-1.4.0.tar.gz | tar xf - + +5.1.4. Bzip'd tar archive (*.tar.bz2) + + $ bunzip2 < hdf5-1.2.0.tar.bz2 | tar xf - + +5.2. Source vs. Build Directories + On most systems the build can occur in a directory other than the + source directory, allowing multiple concurrent builds and/or + read-only source code. In order to accomplish this, one should + create a build directory, cd into that directory, and run the + `configure' script found in the source directory (configure + details are below). + + Unfortunately, this does not work on recent Irix platforms (6.5? + and later) because that `make' doesn't understand the VPATH + variable. However, hdf5 also supports Irix `pmake' which has a + .PATH target which serves a similar purpose. Here's what the man + pages say about VPATH, which is the facility used by HDF5 + makefiles for this feature: + + The VPATH facility is a derivation of the undocumented VPATH + feature in the System V Release 3 version of make. System V + Release 4 has a new VPATH implementation, much like the + pmake(1) .PATH feature. This new feature is also undocumented + in the standard System V Release 4 manual pages. For this + reason it is not available in the IRIX version of make. The + VPATH facility should not be used with the new parallel make + option. + +5.3. Configuring + HDF5 uses the GNU autoconf system for configuration, which + detects various features of the host system and creates the + Makefiles. On most systems it should be sufficient to say: + + $ ./configure OR + $ sh configure + + The configuration process can be controlled through environment + variables, command-line switches, and host configuration files. + For a complete list of switches type: + + $ ./configure --help + + The host configuration files are located in the `config' + directory and are based on architecture name, vendor name, and/or + operating system which are displayed near the beginning of the + `configure' output. The host config file influences the behavior + of configure by setting or augmenting shell variables. + +5.3.1. Specifying the installation directories + Typing `make install' will install the HDF5 library, header + files, and support programs in /usr/local/lib, + /usr/local/include, and /usr/local/bin. To use a path other than + /usr/local specify the path with the `--prefix=PATH' switch: + + $ ./configure --prefix=$HOME + + If shared libraries are being built (the default) then the final + home of the shared library must be specified with this switch + before the library and executables are built. + +5.3.2. Using an alternate C compiler + By default, configure will look for the C compiler by trying + `gcc' and `cc'. However, if the environment variable "CC" is set + then its value is used as the C compiler (users of csh and + derivatives will need to prefix the commands below with `env'). + For instance, to use the native C compiler on a system which also + has the GNU gcc compiler: + + $ CC=cc ./configure + + A parallel version of hdf5 can be built by specifying `mpicc' as + the C compiler (the `--enable-parallel' flag documented below is + optional). Using the `mpicc' compiler will insure that the + correct MPI and MPI-IO header files and libraries are used. + + $ CC=/usr/local/mpi/bin/mpicc ./configure + + On Irix64 the default compiler is `cc'. To use an alternate + compiler specify it with the CC variable: + + $ CC='cc -o32' ./configure + + One may also use various environment variables to change the + behavior of the compiler. E.g., to ask for -n32 ABI: + + $ SGI_ABI=-n32 + $ export SGI_ABI + $ ./configure + + Similarly, users compiling on a Solaris machine and desiring to + build the distribution with 64-bit support should specify the + correct flags with the CC variable: + + $ CC='cc -xarch=v9' ./configure + + Specifying these machine architecture flags in the CFLAGS variable + (see below) will not work correctly. + +5.3.3. Additional compilation flags + If addtional flags must be passed to the compilation commands + then specify those flags with the CFLAGS variable. For instance, + to enable symbolic debugging of a production version of HDF5 one + might say: + + $ CFLAGS=-g ./configure --enable-production + +5.3.4. Compiling HDF5 wrapper libraries + One can optionally build the Fortran and/or C++ interface to the + HDF5 C library. By default, both options are disabled. To build + them, specify `--enable-fortran' and `--enable-cxx' respectively. + + $ ./configure --enable-fortran + $ ./configure --enable-cxx + + Configuration will halt if a working Fortran 90 or 95 compiler or + C++ compiler is not found. Currently, the Fortran configure tests + for these compilers in order: f90, pgf90, f95. To use an + alternative compiler specify it with the F9X variable: + + $ F9X=/usr/local/bin/g95 ./configure --enable-fortran + + Note: The Fortran and C++ interfaces are not supported on all the + platforms the main HDF5 library supports. Also, the Fortran + interface supports parallel HDF5 while the C++ interface does + not. + + Note: On T3E and J90 the following files should be modified before + building the Fortran Library: + fortran/src/H5Dff.f90 + fortran/src/H5Aff.f90 + fortran/src/H5Pff.f90 + Check for "Comment if on T3E ..." comment and comment out + specified lines. + + +5.3.5. Specifying other programs + The build system has been tuned for use with GNU make but works + also with other versions of make. If the `make' command runs a + non-GNU version but a GNU version is available under a different + name (perhaps `gmake') then HDF5 can be configured to use it by + setting the MAKE variable. Note that whatever value is used for + MAKE must also be used as the make command when building the + library: + + $ MAKE=gmake ./configure + $ gmake + + The `AR' and `RANLIB' variables can also be set to the names of + the `ar' and `ranlib' (or `:') commands to override values + detected by configure. + + The HDF5 library, include files, and utilities are installed + during `make install' (described below) with a BSD-compatible + install program detected automatically by configure. If none is + found then the shell script bin/install-sh is used. Configure + doesn't check that the install script actually works, but if a + bad install is detected on your system (e.g., on the ASCI blue + machine as of March 2, 1999) you have two choices: + + 1. Copy the bin/install-sh program to your $HOME/bin + directory, name it `install', and make sure that $HOME/bin + is searched before the system bin directories. + + 2. Specify the full path name of the `install-sh' program + as the value of the INSTALL environment variable. Note: do + not use `cp' or some other program in place of install + because the HDF5 makefiles also use the install program to + also change file ownership and/or access permissions. + +5.3.6. Specifying other libraries and headers + Configure searches the standard places (those places known by the + systems compiler) for include files and header files. However, + additional directories can be specified by using the CPPFLAGS + and/or LDFLAGS variables: + + $ CPPFLAGS=-I/home/robb/include \ + LDFLAGS=-L/home/robb/lib \ + ./configure + + HDF5 uses the zlib library for two purposes: it provides support + for the HDF5 deflate data compression filter, and it is used by + the h5toh4 converter and the h4toh5 converter in support of + HDF4. Configure searches the standard places (plus those + specified above with CPPFLAGS and LDFLAGS variables) for the zlib + headers and library. The search can be disabled by specifying + `--without-zlib' or alternate directories can be specified with + `--with-zlib=INCDIR,LIBDIR' or through the CPPFLAGS and LDFLAGS + variables: + + $ ./configure --with-zlib=/usr/unsup/include,/usr/unsup/lib + + $ CPPFLAGS=-I/usr/unsup/include \ + LDFLAGS=-L/usr/unsup/lib \ + ./configure + + The HDF5-to-HDF4 and HDF4-to-HDF5 conversion tool requires the + HDF4 library and header files which are detected the same way as + zlib. The switch to give to configure is `--with-hdf4'. Note + that HDF5 requires a newer version of zlib than the one shipped + with some versions of HDF4. Also, unless you have the "correct" + version of hdf4 the confidence testing will fail in the tools + directory. + +5.3.7. Static versus shared linking + The build process will create static libraries on all systems and + shared libraries on systems that support dynamic linking to a + sufficient degree. Either form of library may be suppressed by + saying `--disable-static' or `--disable-shared'. + + $ ./configure --disable-shared + + The C++ and Fortran libraries are currently only available in the + static format. + + To build only statically linked executables on platforms which + support shared libraries, use the `--enable-static-exec' flag. + + $ ./configure --enable-static-exec + +5.3.8. Optimization versus symbolic debugging + The library can be compiled to provide symbolic debugging support + so it can be debugged with gdb, dbx, ddd, etc or it can be + compiled with various optimizations. To compile for symbolic + debugging (the default for snapshots) say `--disable-production'; + to compile with optimizations (the default for supported public + releases) say `--enable-production'. On some systems the library + can also be compiled for profiling with gprof by saying + `--enable-production=profile'. + + $ ./configure --disable-production #symbolic debugging + $ ./configure --enable-production #optimized code + $ ./configure --enable-production=profile #for use with gprof + + Regardless of whether support for symbolic debugging is enabled, + the library also is able to perform runtime debugging of certain + packages (such as type conversion execution times, and extensive + invariant condition checking). To enable this debugging supply a + comma-separated list of package names to to the `--enable-debug' + switch (see Debugging.html for a list of package names). + Debugging can be disabled by saying `--disable-debug'. The + default debugging level for snapshots is a subset of the + available packages; the default for supported releases is no + debugging (debugging can incur a significant runtime penalty). + + $ ./configure --enable-debug=s,t #debug only H5S and H5T + $ ./configure --enable-debug #debug normal packages + $ ./configure --enable-debug=all #debug all packages + $ ./configure --disable-debug #no debugging + + HDF5 is also able to print a trace of all API function calls, + their arguments, and the return values. To enable or disable the + ability to trace the API say `--enable-trace' (the default for + snapthots) or `--disable-trace' (the default for public + releases). The tracing must also be enabled at runtime to see any + output (see Debugging.html). + +5.3.9. Large (>2GB) vs. small (<2GB) file capability + In order to read or write files that could potentially be larger + than 2GB it is necessary to use the non-ANSI `long long' data + type on some platforms. However, some compilers (e.g., GNU gcc + versions before 2.8.1 on Intel platforms) are unable to produce + correct machine code for this data type. To disable use of the + `long long' type on these machines say: + + $ ./configure --disable-hsizet + +5.3.10. Parallel vs. serial library + The HDF5 library can be configured to use MPI and MPI-IO for + parallelizm on a distributed multi-processor system. Read the + file INSTALL_parallel for detailed explanations. + +5.3.11. Threadsafe capability + The HDF5 library can be configured to be thread-safe (on a very + large scale) with the with the `--enable-threadsafe' flag to + configure. Read the file doc/TechNotes/ThreadSafeLibrary.html for + further details. + +5.3.12. Backward compatibility + The 1.4 version of the HDF5 library can be configured to operate + identically to the v1.2 library with the `--enable-hdf5v1_2' + configure flag. This allows existing code to be compiled with the + v1.4 library without requiring immediate changes to the + application source code. This flag will only be supported in the + v1.4 branch of the library, it will not be available in v1.5+. + +5.3.13. Network stream capability + The HDF5 library can be configured with a network stream file + driver with the `--enable-stream-vfd' configure flag. This option + compiles the "stream" Virtual File Driver into the main library. + See the documentation on the Virtual File Layer for more details + about the use of this driver. + + +5.4. Building + The library, confidence tests, and programs can be build by + saying just: + + $ make + + Note that if you supplied some other make command via the MAKE + variable during the configuration step then that same command + must be used here. + + When using GNU make you can add `-j -l6' to the make command to + compile in parallel on SMP machines. Do not give a number after + th `-j' since GNU make will turn it off for recursive invocations + of make. + + $ make -j -l6 + +5.5. Testing + HDF5 comes with various test suites, all of which can be run by + saying + + $ make check + + To run only the tests for the library change to the `test' + directory before issuing the command. Similarly, tests for the + parallel aspects of the library are in `testpar' and tests for + the support programs are in `tools'. + + Temporary files will be deleted by each test when it complets, + but may continue to exist in an incomplete state if the test + fails. To prevent deletion of the files define the HDF5_NOCLEANUP + environment variable. + +5.6. Installing + The HDF5 library, include files, and support programs can be + installed in a (semi-)public place by saying `make install'. The + files are installed under the directory specified with + `--prefix=DIR' (or '/usr/local') in directories named `lib', + `include', and `bin'. The prefix directory must exist prior to + `make install', but its subdirectories are created automatically. + + If `make install' fails because the install command at your site + somehow fails, you may use the install-sh that comes with the + source. You need to run ./configure again. + + $ INSTALL="$PWD/bin/install-sh -c" ./configure ... + $ make install + + The library can be used without installing it by pointing the + compiler at the `src' directory for both include files and + libraries. However, the minimum which must be installed to make + the library publically available is: + + The library: + ./src/libhdf5.a + + The public header files: + ./src/H5*public.h + + The main header file: + ./src/hdf5.h + + The configuration information: + ./src/H5pubconf.h + + The support programs that are useful are: + ./tools/h5ls (list file contents) + ./tools/h5dump (dump file contents) + ./tools/h5repart (repartition file families) + ./tools/h5toh4 (hdf5 to hdf4 file converter) + ./tools/h5debug (low-level file debugging) + ./tools/h5import (a demo) + ./tools/h4toh5 (hdf4 to hdf5 file converter) + +6. Using the Library + Please see the User Manual in the doc/html directory. + + Most programs will include and link with -lhdf5. + Additional libraries may also be necessary depending on whether + support for compression, etc. was compiled into the hdf5 library. + + A summary of the hdf5 installation can be found in the + libhdf5.settings file in the same directory as the static and/or + shared hdf5 libraries. + +7. Support + Support is described in the README file. diff --git a/release_docs/INSTALL_TFLOPS b/release_docs/INSTALL_TFLOPS new file mode 100644 index 0000000..a05ef7f --- /dev/null +++ b/release_docs/INSTALL_TFLOPS @@ -0,0 +1,163 @@ + +FOR THE INTEL TFLOPS MACHINE: + +Below are the step-by-step procedures for building, testing, and +installing both the sequential and parallel versions of the HDF5 library. + +----------------- +Software locations +------------------ +The zlib compression library is installed in /usr/community/hdf5/ZLIB. +The mpich library, including mpi-io support, is in +/usr/community/mpich/mpich-1.2.0. + +--------------- +Sequential HDF5: +--------------- + +The setup process for building the sequential HDF5 library for the +ASCI Red machine is done by a coordination of events from sasn100 and +janus. Though janus can do compiling, it is better to build it +from sasn100 which has more complete building tools and runs faster. +It is also anti-social to tie up janus with compiling. The HDF5 building +requires the use of janus because one of steps is to execute a program +to find out the run-time characteristics of the TFLOPS machine. + +Assuming you have already unpacked the HDF5 tar-file into the +directory , follow the steps below: + +FROM SASN100, + +1) cd + +2) ./configure tflop + Due to a bug, you need to patch up two Makefile, src/Makefile and + test/Makefile, before the next step. You can use the following + shell commands. + +# Patch up various Makefile's. +# patch up src/Makefile +echo "patching src/Makefile" +ed - src/Makefile <<'EOF' +/^LT_RUN=.*/s//LT_RUN=$(RUNTEST)/ +w +q +EOF + +# patch up test/Makefile +echo "patching test/Makefile" +ed - test/Makefile <<'EOF' +/^RUNTEST=$(LT_RUN)/s/^/#/ +w +q +EOF + +3) make H5detect + + +FROM JANUS, + +4) cd + +5) make H5Tinit.c + + +FROM SASN100, + +6) make + + +When everything is finished compiling and linking, +you can run the tests by +FROM JANUS, + +7) make check + Sometimes the "make check" fails in the sub-directories of test + or tools with a message as "print not found". This is due to the + "make" of Janus thinking some binary code needs to be recompiled. + The easiest way to fix it is + FROM SASN100 + cd /test # or cd /tools + make clean; make # re-make all binary + + +Once satisfied with the test results, you can install +the software by +FROM SASN100, + +8) make install + + +--------------- +Parallel HDF5: +--------------- + +The setup process for building the parallel version of the HDF5 library for the +ASCI Red machine is very similar to the sequential version. Since TFLOPS +does not support MPIO, we have prepared a shell-script file that configures +with the appropriate MPI library. + +Assuming you have already unpacked the HDF5 tar-file into the +directory , follow the steps below: +FROM SASN100, + +1) cd + +2) CC=/usr/community/mpich/mpich-1.2.0/bin/mpicc ./configure tflop + Due to a bug, you need to patch up two Makefile, src/Makefile and + test/Makefile, before the next step. You can use the following + shell commands. + +# Patch up various Makefile's. +# patch up src/Makefile +echo "patching src/Makefile" +ed - src/Makefile <<'EOF' +/^LT_RUN=.*/s//LT_RUN=$(RUNTEST)/ +w +q +EOF + +# patch up test/Makefile +echo "patching test/Makefile" +ed - test/Makefile <<'EOF' +/^RUNTEST=$(LT_RUN)/s/^/#/ +w +q +EOF + + +3) make H5detect + + +FROM JANUS, + +4) cd + +5) make H5Tinit.c + + +FROM SASN100, + +6) make + + +When everything is finished compiling and linking, +FROM JANUS, + +7) make check + Sometimes the "make check" fails in the sub-directories of test + or tools with a message as "print not found". This is due to the + "make" of Janus thinking some binary code needs to be recompiled. + The easiest way to fix it is + FROM SASN100 + cd /test # or cd /tools + make clean; make # re-make all binary + + +Once satisfied with the parallel test results, as long as you +have the correct permission, +FROM SASN100, + +8) make install + + diff --git a/release_docs/INSTALL_VFL b/release_docs/INSTALL_VFL new file mode 100644 index 0000000..d0466a3 --- /dev/null +++ b/release_docs/INSTALL_VFL @@ -0,0 +1,130 @@ + Installation Instructions for HDF5 + with Different Virtual File Layer + + * * * + +This file contains installation instructions for HDF5 with certain Virtual File +Layer to handle file I/O. We currently have documented SRB and Globus-GASS. + + + + --- Part I. SRB --- +I. Overview +----------- +This part contains instructions for remote-accessing HDF5 through SRB. The +SRB version 1.1.7 on Sun Solaris 2.7 platform has been tested. If you have +difficulties installing the software in your system, please send mails to me +(Raymond Lu) at + + slu@ncsa.uiuc.edu + +First, you must obtain and unpack the HDF5 source as described in the file +INSTALL. You need the SRB library(client part) installed. You should also +have access to SRB server. + + +The Storage Resource Broker(SRB) from San Diego Supercomputer Center is client- +server middleware that provides a uniform interface for connecting to +heterogeneous data resources over a network and accessig replicated data sets. +SRB, in conjunction with the Metadata Catalog(MCAT), provides a way to access +data sets and resources based on their attributes rather than their names or +physical locations. Their webpage is at http://www.npaci.edu/Research/DI/srb. + +HDF5 is built on the top of SRB as a client to remotely access files on SRB +server through SRB. Right now, HDF-SRB only support low-level file transfer of +SRB. The MCAT part is not supported yet. Low-level file transfer means files +are treated just like Unix type files. Files can be read, written and +appended. Partial access(read and write to a chunk of file without transferrig +the whole) is also supported. + + +II. Installation Steps +---------------------- +The installation steps are similar to the ones in INSTALL file: + +1. Run 'configure' file with SRB options: + configure --with-srb=$SRB/include,$SRB/lib + where $SRB is your SRB installed library directory. + + For example, below is a script file to run 'configure': + #! /bin/sh + # how to configure to use the SRB + + SRB_DIR=/afs/ncsa.uiuc.edu/projects/hdf/users/slu/srb_install + configure --with-srb=$SRB_DIR/include,$SRB_DIR/lib + +2. Run 'make' + +3. Run 'make check' + +4. Run 'make install' + +5. Run testing program(Optional): + Go to the testing directory(cd test) and run srb_write, srb_read, + srb_append. Actually, these tests have been run in step 3. + + srb_write: Connect to SRB server, write an HDF5 file with an integer + dataset to SRB server. + srb_read: Connect to SRB server, read part of HDF5 file on the SRB server. + srb_append: Connect to SRB server, append an integer dataset to an existent + HDF5 file on the SRB server. + +6. For using HDF-SRB, please read comments in srb_write.c, srb_read.c, + srb_append.c in the hdf5/test directory. + + + + --- Part II. Globus-GASS --- + +I. Overview +----------- +This part contains instructions for remote-accessing HDF5 through Globus-GASS. +The SGI IRIX64(and IRIX) 6.5 platform have been tested. If you have +difficulties installing the software in your system, please send mails to me +(Raymond Lu) at + slu@ncsa.uiuc.edu + +First, you must obtain and unpack the HDF5 source as described in the file +INSTALL. You need the Globus 1.1.x and SSL(should have come with Globus) +packages. + +HDF5 is built on the top of Globus-GASS(1.1.x) to handle remote access. +Globus-GASS(1.1.x) only supports HTTP and HTTPS protocals for 'whole file +read and write'. More features may be added in the future. + +II. Installation Steps +---------------------- +The installation steps are similar to the ones in INSTALL file: + +1. Run 'configure' file with SSL and GASS options: + configure --with-ssl=$SSL/lib --with-gass=$GASS/include,$GASS/lib + where $SSL is your SSL directory, and $GASS is your Globus directory. + + For example, below is a script file to run 'configure': + #! /bin/sh + # how to configure to use the Globus-GASS(1.1.x) + + GASS_DIR=/usr/local/globus-install-1.1.1/development/mips-sgi-irix6.5-64_nothreads_standard_debug + SSL_LIB=/usr/local/ssl/lib + + configure --with-ssl=$SSL_LIB --with-gass=$GASS_DIR/include,$GASS_DIR/lib + +2. Run 'make' + +3. Run 'make check' + +4. Run 'make install' + +5. Run testing program: + There is one read testing program called 'gass_read' in the 'test' + directory. It does whole file read through HTTP protocal. The URL is + hard coded as + http://hdf.ncsa.uiuc.edu/GLOBUS/a.h5 + + The writing really depends on your web server. You have to set up your + server in right way to accept writing in files. We have tested it using + Apache Server(1.3.12) without authentication. If you need more details + about our testing, please contact us. Globus suggests using their GASS + server. + + There is another program called 'gass_append' used for experiments. diff --git a/release_docs/INSTALL_Windows.txt b/release_docs/INSTALL_Windows.txt new file mode 100644 index 0000000..8d7636f --- /dev/null +++ b/release_docs/INSTALL_Windows.txt @@ -0,0 +1,916 @@ +HDF5 Build and Install Instructions for Windows 2000/NT/98. +---------------------------------------------------------- + +The instructions which follow assume that you will be using the +source code release 'zip' file (hdf5-1_4_0.zip). + +***************************WARNINGS**************************** +Please read CAREFULLY about Preconditions before you go to the +following sections + +Preconditions + + 1. Installed MicroSoft Developer Studio,Visual C++ 6.0 and + WinZip. + + 2. Set up a directory structure to unpack the library. + For example: + + c:\ (any drive) + MyHDFstuff\ (any folder name) + + 3. Run WinZip on hdf5-1_4_0.zip (the entire source tree) and + extract hdf5 package into c:\MyHDFstuff(or whatever drive + and folder name you would like to choose). This creates a + directory called 'hdf5'under MyHDFstuff which contains + several files and directories. + + 4. HDF5 uses zlib for compression and zlib is distributed + with hdf5 lib. If you have your own version read section + VI about the zlib library. + + 5. You do need hdf4 (hdf and mfhdf) static and dll libraries + to generate hdf4-related tools. + + 6. Currently you can build and test either hdf5 libraries + and non-hdf4 related tools or hdf5 libraries and hdf4 + related tools;but not BOTH.In other words,you may either + follow Section II or Section III but NOT both Sections to + build HDF5 libraries and related tools. + +--------------------------------------------------------------- + +The following sections discuss installation procedures in detail: + + Section I: What do we build and install + Section II: Building and testing hdf5 libraries and non-hdf4 + related hdf5 tools + Section III: Building and testing hdf5 libraries and all hdf5 + tools + Section IV: Building an application using the HDF5 library or + DLL + Section V: Some more helpful pointers + Section VI: ZLIB library - removing or changing the path + +*************************************************************** + +Section I: + +What do we build and install? + + HDF5 static library: + debug and release version + + HDF5 Dynamic Link Library(DLL): + debug and release version as well as export libraries for + DLL + + HDF5 tool library: + debug and release version + + HDF5 tool export library for DLL: + debug and release version + + HDF5 tools: + non-hdf4 related tools and hdf4 related tools + + HDF5 library testing programs: + hdf5 library related comprehensive tests + + HDF5 related tools testing programs: + hdf5 tools testing programs + + HDF5 examples: + simple HDF5 examples + +************************************************************** + +Section II: + + Building and testing hdf5 libraries and non-hdf4 related tools + + ================================================== + +STEP 1: Building hdf5 libraries and non-hdf4 related tools + + + 1. Unpack all.zip in 'hdf5' and move the zlib.dll from + c:\myHDFstuff\hdf5\src\zlib\dll to the Windows system + directory. + + The system directory can usually be found under the path + C:\WINNT\system or C:\WINDOWS\system + + 2. Invoke Microsoft Visual C++, go to "File" and select + the "Open Workspace" option. + + Then open the c:\myHDFstuff\hdf5\proj\all\all.dsw + workspace. + + 3. If you don't want to build and test backward + compatibility with hdf5 1.2, you may skip this part and + go to part 4. + + To build and test backward compatibility with hdf5 1.2, + a) go to "Project" and select "Settings" + b) A window called "Project Settings" should be + popped up,on the upper-left corner is a small box + "Settings For". Set the option to + "Win32 Release". + c) Go to the the right side of "Project Settings" + window,choose C/C++ on the menu. + d) Go to the "Category" box below menu bar, choose + Preprocessor. + e) Go to "Preprocessor definitions" box below + "Category". Inside the box, type + "WANT_H5_V1_2_COMPAT". Note: don't type double + quote for "WANT_H5_V1_2_COMPAT" and add a comma + between "WANT_H5_V1_2_COMPAT" and the last + preprocessor definations(WIN32). + f) click OK at the bottom of "Project Settings" + window. + g) repeat a)-f) and choose the option as + "win32 Debug" on step b). + + 4. Select "Build", then Select "Set Active Configuration". + + On Windows platform select as the active configuration + + "all -- Win32 Debug" to build debug versions of + single-threaded static libraries, Debug multithreaded + DLLs and tests. + or + + "all -- Win32 Release" to build release versions of + single-threaded static libraries, multithreaded DLLs + and tests. + + + NOTE : "all" is a dummy target. You will get a link + error when "all.exe." is built: + + LINK: error LNK2001: unresolved external symbol + _mainCRTStartup..... + all.exe - 2 error(s), .... + + Warning messages can be ignored. The "all.exe" is never + created, so it is OK. + + When the debug or release build is done the directories + listed below will contain the following files: + + c:\MyHDFstuff\hdf5\proj\hdf5\debug - + c:\MyHDFstuff\hdf5\proj\hdf5\release - + + hdf5.lib- the hdf5 library + + c:\MyHDFstuff\hdf5\proj\hdf5dll\debug - + + hdf5ddll.dll- the hdf5 library + hdf5ddll.lib- the dll export library + + c:\MyHDFstuff\hdf5\proj\hdf5dll\release - + + hdf5dll.dll- the hdf5 library + hdf5dll.lib- the dll export library + + c:\MyHDFstuff\hdf5\test\"test directory"- + + where test directory is one of the following: + + big(dll) + + bittests(dll) + + chunk(dll) + + cmpd_dset(dll) + + dsets(dll) + + dtypes(dll) + + enum(dll) + + extend(dll) + + external(dll) + + fillval(dll) + + flush1(dll) + + flush2(dll) + + gheap(dll) + + hyperslab(dll) + + iopipe(dll) + + istore(dll) + + links(dll) + + mount(dll) + + mtime(dll) + + ohdr(dll) + + overhead(dll) + + stab(dll) + + testhdf5(dll) + + unlink(dll) + + + c:\MyHDFstuff\hdf5\tools\toolslib\debug + c:\MyHDFstuff\hdf5\tools\toolslib\release + + toolslib.lib- the tools library + + c:\MyHDFstuff\hdf5\tools\toolslibD\debug + c:\MyHDFstuff\hdf5\tools\toolslibD\release + + toolslibD.lib- the dll export library + + c:\MyHDFstuff\hdf5\tools\"tools directory"- + where non-hdf4 related tools directory is one of the + following: + + h5dump(dll) + + h5ls(dll) + + h5debug(dll) + + h5import(dll) + + h5repart(dll) + + + Test and tool directory contains debug and release + subdirectories with the corresponding tests and tools. + + +STEP 2: testing hdf5 libraries and non-hdf4 related tools + +In a command prompt window run the test batch file which resides in +the hdf5\test directory(for example: C:\MyHDFstuff\hdf5\test)to make +sure that the library was built correctly. + +You can possibily test four versions of hdf5 library and tools. They are: + + release version + release dll version + debug version + debug dll version + +NOTE: The hdf5ddll.dll and hdf5dll.dll should be placed into +the C:\WINNT\system or C:\WINDOWS\system directory before using the dlls. + +We strongly suggest you to redirect your testing results into +an output file and you can easily check the testing results. +You may use either NotePad or NoteTab Light or whatever other +windows tools to check the results. For the purpose of printing, +please choose font less than 14 for better alignment of the text. + + 1. hdf5 library testing + + cd into the hdf5\test directory. + + (1) basic tests + + Go to a) b) c) or d) to test your chosen version + + a) release static version + type: + hdf5test release >"Your output filename" + + b) release dll version + type: + hdf5test release dll > "Your output filename" + + c) debug static version + type: + hdf5test debug >"Your output filename" + + d) debug dll version + type: + hdf5test debug dll >"Your output filename" + + (2) timing tests + + Go to a) b) c) or d) to test your chosen version + + a) release static version + type: + hdf5timingtest release >"Your output filename" + + b) release dll version + type: + hdf5timingtest release dll >"Your output filename" + + c) debug static version + type: + hdf5timingtest debug >"Your output filename" + + d) debug dll version + type: + hdf5timingtest debug dll >"Your output filename" + + + Use notepad or notetab light to check results. You should +not find any FAILED marks in your output files. + + Note: big test is currently not working for windows, we are +still investigating this. + + 2. hdf5 tools testing + + Currently we are only supporting h5dump test. We are +investigating h5ls test now. + + 1) h5dump test + + cd back into hdf5 directory and then cd into tools +directory(...\hdf5\tools) + + Go to a) b) c) or d) to test your chosen version + + a) release static version + type: + dumptest release >"Your output filename" + + b) release dll version + type: + dumptest release dll > "Your output filename" + + c) debug static version + type: + dumptest debug >"Your output filename" + + d) debug dll version + type: + dumptest debug dll >"Your output filename" + + + We are using "fc" command to compare whether dumper +generates correct results. Supposedly you should find +"FC: no differences encountered" in your output file. +However, since we are comparing the actual dumper output +with the expected dumper output under different directory, +you may see something like: + +" +***** ..\TESTFILES\tall-1.ddl +############################# +Expected output for 'h5dump tall.h5' +############################# +HDF5 "tall.h5" { +GROUP "/" { +***** TALL-1.RESULTS +HDF5 "..\..\testfiles\tall.h5" { +GROUP "/" { +***** +" + + The actual dumper output is correct. The difference showing +here is the different representations of filename of the same +file. + +STEP 3: BUILDING THE EXAMPLES + + 1. Invoke Microsoft Visual C++, go to "File" and select + the "Open Workspace" option. + Then open the workspace + c:\myHDFstuff\hdf5\examples\allexamples\allexamples.dsw. + + 2. Select "Build", then Select "Set Active Configuration". + + On Windows platform select as the active configuration + + "allexamples -- Win32 Debug" to build debug versions + of the examples. + + or + + "allexamples -- Win32 Release" to build release + versions the examples. + + When the debug build or release build is done + there should be the following subdirectories in + C:\myHDFstuff\hdf5\examples\ + + attributetest + + chunkread + + compoundtest + + extendwritetest + + grouptest + + readtest + + selecttest + + writetest + + + + 3. Run the batch file "InstallExamples.bat" which + resides in the top level directory(C:\MyHDFSTUFF\hdf5). + This file creates 2 new directories,examplesREL and + examplesDBG,in the examples directory and places + all the executables in it. Both the release and debug + versions of the examples should be built before this + step is done. The examples should be tested in these 2 + new directories due to some dependencies between the + examples. Especially writetest.exe and extendwritetest.exe + should be executed before chunkread.exe and readtest.exe + due to dependencies among these files. + +************************************************************** + +Section III: BUILDING AND TESTING HDF5 LIBRARIES AND ALL HDF5 TOOLS + +------------------WARNINGS--------------------------------- + +1. This section is specifically for building HDF5 tools that needs to call HDF4 library. + +Currently we are supporting two hdf4-relatedtools: H4toh5 converter +and H5toh4 converter. If you are not using these tools, please go +back to Section II for building and installing information. + +2. This section builds and tests all versions of hdf5 libraries, +testing programs and tools covered in section II. +Additionally, it also builds and tests hdf4-related tools. We may refer some duplicated parts of this section to section II. + +3. In case + a) you don't install hdf libraries and related tools in + your machine, + b) or if the top directory of your hdf4 libraries and + tools are not under C:\hdf41r4 and you are not familar + on how to change settings of VC++ projects. + + you may get binary distribution from +ftp://ftp.ncsa.uiuc.edu/HDF/HDF/HDF4.1r4/windows_precompiled_code/HDF41r4.zip +and use Winzip to unpack HDF41r4.zip into C:\hdf41r4. + +4. We assume that you've installed hdf4(mfhdf and hdf) +libraries into drive C. The top level path should be +C:\HDF41r4. Under C:\HDF41r4 it should at least +include the following six directories: + +C:\HDF41r4\bin where hdf4 utilities are stored + +C:\HDF41r4\dlllib where release dll versions of hdf and mfhdf +libraries and export libraries of dlls are stored + +C:\HDF41r4\dlllibdbg where debug dll versions of hdf and mfhdf +libraries and export libraries of dlls are stored + +C:\HDF41r4\lib where release versions of hdf and mfhdf +libraries are stored + +C:\HDF41r4\libdbg where debug versions of hdf and mfhdf +libraries are stored + +C:\HDF41r4\include where header files are included + +Make sure that you copy all *.dll files under C:\HDF41r4 into Windows +system directory before the next step. + +If your path of hdf libraries and mfhdf libraries is different +from the default assumption, please DO follow No.4 of Step 1 on +the following: + + +Step 1. + + 1. Unpack all_withhdf4.zip in 'hdf5' and move the zlib.dll + from c:\myHDFstuff\hdf5\src\zlib\dll to the Windows + system directory. + + The system directory can usually be found under the path + C:\WINNT\system or C:\WIN98\system + + 2. Invoke Microsoft Visual C++, go to "File" and select the + "Open Workspace" option. + + Then open the c:\myHDFstuff\hdf5\proj\all\all.dsw + workspace. + + 3. If you don't want to build and test backward + compatibility with hdf5 1.2, you may skip this part and + go to part 4. + + To build and test backward compatibility with hdf5 1.2, + a) go to "Project" and select "Settings" + b) A window called "Project Settings" should be + popped up,on the upper-left corner is a small box + "Settings For" Choose the option to + "Win32 Release". + c) Go to the the right side of "Project Settings" + window, choose C/C++ on the menu. + d) Go to the "Category" box below menu bar, choose + Preprocessor. + e) Go to "Preprocessor definitions" box below + "Category". Inside the box, type + "WANT_H5_V1_2_COMPAT". Note: don't type + double quote for "WANT_H5_V1_2_COMPAT" and add a + comma between "WANT_H5_V1_2_COMPAT" and the last + preprocessor defination(WIN32). + f) click OK at the bottom of "Project Settings" + window. + g) repeat a)-f) and set the option to "win32 Debug" + on step b). + + 4. This part is for users who are familar with handling + settings of VC++ project and store their hdf4 libraries + not under C:\hdf41r4. Other users can skip this part. + + 4.1 Change the path where hdf4 library header files are + located + + a) On the View menu, click Workspace, you may see a + pop-up window with names of projects in all.dsw. + b) click FileView on the bottom of this window if you + are not seeing "all files big files ......." + c) You need to modify settings of four projects: h4toh5, + h4toh5dll,h5toh4 and h5toh4dll. + You also need to modify both debug and release + versions. + + You may do as follows: + c1)Right click the selected project and then click + "Settings" + c2)A dialog box called "Project Settings" will be + poped up + c3)On the upper-left part of the "Project Settings" + box, you may find a small window "Settings for". + Make sure inside this "Settings for" box is either + "Win32 Debug" or "Win32 Release". Change contents + into "Win32 Debug" or "Win32 Release" otherwise. + Remember the version(Win32 Release or Debug) you + chose. + c4)On the upper-right menu of the "Project Settings" + window, find C/C++ and click it. + c5)Just below the upper-right menu, find a small + window called category, make sure that + "Preprocessor" appear in this window. + c6)In the middle of "Project Settings" windows, you + may find a box called + "Additional include directories:" . You may notice + "C:\hdf41r4\include" inside this box. This is the + path where the default hdf4 header files is + included. Replace only this path + (C:\hdf41r4\include) with your own path that + includes your hdf4 header files. Don't touch any + other paths. + c7)After you've done this, click OK at the bottom of + "Project Settings" window. + c8)Repeat c1)-c7)but change contents of "settings + for" in c3) from "Win32 Release" to "Win32 Debug" + or vice versa. + d) repeat step c) for the other three projects. + + 4.2 Replace the user's hdf and mfhdf libraries, export + libraries of hdf and mfhdf DLLs + + You also need to modify four projects: h4toh5, + h4toh5dll, h5toh4 and h5toh4dll: + a) select project h4toh5 following instruction 4.1 a) + and b). + b) click h4toh5, you may find four libraries: + hm414d.lib,hd414d.lib and hm414.lib,hd414.lib + attached under the project h4toh5. hm414d.lib and + hd414d.lib are debug versions of mfhdf and hdf + libraries. hm414.lib and hd414.lib are release + versions of mfhdf and hdf libraries. + c) select these four libraries; go back to Edit menu and + choose "delete" option to delete template of these + libraries. + d) select project h4toh5 and right click the mouse, find + "Add Files to Projects", follow the instructions on + the pop-up box, to insert your own hm414d.lib, + hd414d.lib,hm414.lib and hd414.lib. You must know + their paths at first. + e) select project h4toh5dll following instruction 4.1 a) + and b). + f) click h4toh5dll, you may also find four libraries: + hd414m.lib,hd414md.lib and hm414m.lib,hd414m.lib + attached under the project h4toh5dll. These libraries + are debug and release versions of Export libraries of + mfhdf and hdf DLLs. + g) select these four libraries; go back to Edit menu and + choose "delete" option to delete template of these + libraries. + h) select project h4toh5dll and right click the mouse, + find "Add Files to Projects", follow the instructions + on the pop-up box, to insert your own hd414m.lib, + hd414md.lib,hm414m.lib and hd414m.lib. You must know + their paths at first. + i) repeat a)-h) for h5toh4 and h5toh4dll. + + 5. Select "Build", then Select "Set Active Configuration". + + On Windows platform select as the active configuration + + "all -- Win32 Debug" to build debug versions + single-threaded static libraries, + and tests. + or + + "all -- Win32 Release" to build release versions of + single-threaded static + libraries, and tests. + + + NOTE : "all" is a dummy target. You will get a link + error when "all.exe." is built: + + LINK: error LNK2001: unresolved external symbol + _mainCRTStartup..... + all.exe - 2 error(s), .... + + Warning messages can be ignored. The "all.exe" is never + created, so it is OK. + + You should see hdf5 libraries, tests and tools under + section II Step 1. + In addtion, under c:\MyHDFstuff\hdf5\tools\ + + You may also find: + h4toh5 + h5toh4 + h4toh5dll + h5toh4dll + for both the debug and release versions. + +STEP 2: testing hdf5 libraries and all hdf5 tools + + 1. hdf5 library testing + Follow all instructions of the same part in Section II + STEP 2 + + 2. non-hdf4 related tools testing + Follow all instructions of the same part in Section II + STEP 2 + + 3. hdf4-related tools testing + + 1) h4toh5 converter tool testing + + First cd into hdf5\tools + + Go to a) b) c) or d) to test your chosen version + + a) release static version + type: + h4toh5testrun release >"Your output filename" + + b) release dll version + type: + h4toh5testrun release dll > "Your output filename" + + c) debug static version + type: + h4toh5testrun debug >"Your output filename" + + d) debug dll version + type: + h4toh5testrun debug dll >"Your output filename" + + We are using "fc" command to compare whether h4toh5 + converter converts the hdf4 file into the correct hdf5 + file.In your output files, Please only pay attention to + those lines which start with + "FC:",you should find "FC: no differences encountered" + for all tested hdf4 files in your output. + + 2) h5toh4 converter tool testing + + To test the h5toh4 utility, you need to have hdf4 + dumper utility "hdp" in your system. + + Note: Currently h5toh4 release dll doesn't work + for all test cases possibly due to windows dealing + with "free memory" conventions for dll versions. + + 1) If your hdp utility is located at C:\hdf41r4\bin, + you may skip this part. Otherwise, copy your hdp.exe + file into the directory where your hdf5 tools are + located. For example, if your hdf5 tools directory is + C:\myHDFstuff\hdf5\tools; please copy hdp.exe into + this directory. + + 2) cd into \...\hdf5\tools. + Go to a) b) c) or d) to test your chosen version + + a) release static version + type: + h5toh4testrun release >"Your output filename" + + b) release dll version + type: + h5toh4testrun release dll > "Your output filename" + + c) debug static version + type: + h5toh4testrun debug >"Your output filename" + + d) debug dll version + type: + h5toh4testrun debug dll >"Your output filename" + + We are using "fc" command to compare whether h5toh4 + converter converts the hdf5 file into the correct hdf4 + file.In your output files, Please only pay attention to + those lines which start with + "FC:",you should find "FC: no differences encountered" + for all tested hdf4 files in your output. + Warnings appear on the prompt when testing h5toh4 converter + can be ignored. + + +STEP 3: BUILDING THE EXAMPLES + + Follow all instructions of SECTION II STEP 3. + +Section IV: +BUILDING AN APPLICATION USING THE HDF5 LIBRARY OR DLL- SOME HELPFUL +POINTERS +==================================================================== + +If you are building an application that uses the HDF5 library the +following locations will need to be specified for locating header files +and linking in the HDF libraries: + + \src + +where may be + + C:\MyHDFstuff\hdf5\ + +To specify this location in the settings for your VC++ project: + + 1. Open your VC project in Microsoft Visual C++ and make sure it is + the active project. + + 2. Go to the Project menu and chose the 'Settings' option. + + 3. Chose the build configuration you would like to modify in the + drop down menu labeled with 'Settings For:' + + 4. Chose the C/C++ tab + + 5. At the bottom of the window, there should be a text-area labeled + with 'Project Options:'. In this text-area, scroll until you + reach the end and type /I "\src" and + then click OK. + +To link the HDF5 library with your application: + + 1. Open your VC project in Microsoft Visual C++ and make sure it is + the active project. + + 2. Go to the Project menu and chose the 'Add to Project' option and + then 'Files' option. + + 3. Change the 'Files of type:' to 'Library Files (.lib)' + + 4. Navigate through the directories until you find the location of + the hdf5.lib. + + 5. Select hdf5.lib and click OK. + + +To use the DLL: + + 1. Follow the steps for specifing the location of the header files + as shown above. + + 2. Follow the steps for linking the HDF5 library as shown above + except now link the export library that is created with the DLL. + The export library is called hdf5dll.lib or hdf5ddll.lib for + debug version. + + 3. Place the DLL in a location that Windows will be able to locate + it. The search path and order for DLL's is + + a) The directory where the executable module for the current + process is located. + b) The current directory. + c} The Windows system directory. The GetSystemDirectory function + retrieves the path of this directory. + d) The Windows directory. The GetWindowsDirectory function + retrieves the path of this directory. + e) The directories listed in the PATH environment variable. + + +Section V: +MORE HELPFUL POINTERS +===================== + + +Here are some notes that may be of help if you are not familiar with +using the Visual C++ Development Environment. + +Project name and location issues: + + The files in all.zip must end up in the hdf5\ directory installed by + hdf5-1_4_0.zip + + If you must install all.dsw and all.dsp in another directory, + relative to hdf5\ , you will be asked to locate the sub-project + files, when you open the project all.dsw. + + If you want to rename all (the entire project), you will need to + modify two files all.dsw and all.dsp as text (contrary to the + explicit warnings in the files). + + You can also modify all.dsw and all.dsp as text, to allow these 2 + files to be installed in another directory. + + +Settings... details: + + If you create your own project, the necessary settings can be read + from the all.dsp file(as text), or from the Project Settings in the + Developer Studio project settings dialog. + + Project + Settings + C/C++ + Category + PreProcessor + Code Generation + Use run-time Library + These are all set to use + Single-Threaded + +DLL... hints: + + If you want to use DLL versions of hdf5 library in your application, + you should + 1) put hdf5 DLL into windows system directory + 2) add hdf5 DLL export library into your project + 3) Follow "Settings... details" into the last line: + change Single-Threaded into Multithreaded DLL or + Debug Multithreaded DLL + 4) Follow "Settings.. details" into PreProcessor: + Project + Settings + C/C++ + Category + PreProcessor + + Find PreProcessor definations and Add _HDF5USEDLL_ at the + end of the PreProcessor definations + + + + +Section VI: +ZLIB LIBRARY- REMOVING OR CHANGING THE PATH +============================================ + +If you would like to remove the zlib library from the hdf5 library or +use your own version of the zlib library then follow the steps below. + +Removing the zlib library completely: + + Open the all.dsw workspace file in Microsoft Visual C++. Go to the + hdf5 project. Select the zlib.lib file from this project and + delete(press the 'delete' key) it. Next open the H5config.h and + H5pubconf.h files from the src directory and remove the following + two lines: + + #define HAVE_LIBZ 1 + #define HAVE_COMPRESS2 + + then save the file. + + Next go to the hdf5dll project. Remove the zlib.lib from this + project too. Open the project settings for the hdf5dll project. + Go to the C/C++ settings tab and under the preprocessor definitions + remove the ZLIB_DLL in both the debug and the release settings. + Recompile the all project and then save the workspace. + + +Replacing the zlib library: + + Open the all.dsw workspace and go to the hdf5 project. Delete the + zlib.lib file from the file listing. Then select the hdf5 project + and richt click to get a menu. Pick the "add files to project..." + option and find the version of the zlib that you would like to use. + Then click OK in the file chooser dialog. Repeat the steps for the + hdf5dll project. You may also want to replace the zlib.h and zconf.h + files which are in the src directory with your own versions of these + files. Then recompile the all project. diff --git a/release_docs/INSTALL_parallel b/release_docs/INSTALL_parallel new file mode 100644 index 0000000..e2a0709 --- /dev/null +++ b/release_docs/INSTALL_parallel @@ -0,0 +1,177 @@ + Installation instructions for Parallel HDF5 + ------------------------------------------- + + +1. Overview +----------- + +This file contains instructions for the installation of parallel +HDF5. Platforms supported by this release are SGI Origin 2000, IBM SP2, +Intel TFLOPs, and Linux version 2.4 and greater. The steps are kind of +unnatural and will be more automized in the next release. If you have +difficulties installing the software in your system, please send mail to + + hdfparallel@ncsa.uiuc.edu + +In your mail, please include the output of "uname -a". Also attach the +content of "config.log" if you ran the "configure" command. + +First, you must obtain and unpack the HDF5 source as described in the +INSTALL file. You also need to obtain the information of the include and +library paths of MPI and MPIO software installed in your system since the +parallel HDF5 library uses them for parallel I/O access. + + +2. Quick Instruction for known systems +-------------------------------------- + +The following shows particular steps to run the parallel HDF5 +configure for a few machines we've tested. If your particular platform +is not shown or somehow the steps do not work for yours, please go +to the next section for more detailed explanations. + +------ +TFLOPS +------ + +Follow the instuctions in INSTALL_TFLOPS. + +------- +IBM SP2 +------- + +First of all, make sure your environment variables are set correctly +to compile and execute a single process mpi applications for the SP2 +machine. They should be similar to the following: + + setenv CC mpcc_r + setenv MP_PROCS 1 + setenv MP_NODES 1 + setenv MP_LABELIO no + setenv MP_RMPOOL 0 + setenv RUNPARALLEL "MP_PROCS=2 MP_TASKS_PER_NODE=2 poe" + setenv LLNL_COMPILE_SINGLE_THREADED TRUE + +The shared library configuration for this version is broken. So, only +static library is supported. + +An error for powerpc-ibm-aix4.3.2.0's (LLNL Blue) install method was +discovered after the code freeze. You need to remove the following line +from config/powerpc-ibm-aix4.3.2.0 before configuration: + + ac_cv_path_install=${ac_cv_path_install='cp -r'} + +Then do the following steps: + + $ ./configure --disable-shared --prefix= + $ make # build the library + $ make check # verify the correctness + $ make install + + +--------------- +SGI Origin 2000 +Cray T3E +(where MPI-IO is part of system MPI library such as mpt 1.3) +--------------- + +#!/bin/sh + +RUNPARALLEL="mpirun -np 3" +export RUNPARALLEL +LIBS="-lmpi" +export LIBS +./configure --enable-parallel --disable-shared --prefix=$PWD/installdir +make +make check +make install + + +--------------- +SGI Origin 2000 +Cray T3E +(where MPI-IO is not part of system MPI library or I want to use my own + version of MPIO) +--------------- + +mpi1_inc="" #mpi-1 include +mpi1_lib="" #mpi-1 library +mpio_inc=-I$HOME/ROMIO/include #mpio include +mpio_lib="-L$HOME/ROMIO/lib/IRIX64" #mpio library + +MPI_INC="$mpio_inc $mpi1_inc" +MPI_LIB="$mpio_lib $mpi1_lib" + +#for version 1.1 +CPPFLAGS=$MPI_INC +export CPPFLAGS +LDFLAGS=$MPI_LIB +export LDFLAGS +RUNPARALLEL="mpirun -np 3" +export RUNPARALLEL +LIBS="-lmpio -lmpi" +export LIBS + +./configure --enable-parallel --disable-shared --prefix=$PWD/installdir +make +make check +make install + + +--------------------- +Linux 2.4 and greater +--------------------- + +Be sure that your installation of MPICH was configured with the following +configuration command-line option: + + -cflags="-D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64" + +This allows for >2GB sized files on Linux systems and is only available +with Linux kernels 2.4 and greater. + + +------------------ +HP V2500 and N4000 +------------------ + +Follow the instructions in section 3. + + +3. Detail explanation +--------------------- + +The HDF5 library can be configured to use MPI and MPI-IO for parallelism +on a distributed multi-processor system. The easiest way to do this is to +have a properly installed parallel compiler (e.g., MPICH's mpicc or IBM's +mpcc) and supply that executable as the value of the CC environment +variable: + + $ CC=mpcc ./configure + $ CC=/usr/local/mpi/bin/mpicc ./configure + +If no such wrapper script is available then you must specify your normal +C compiler along with the distribution of MPI/MPI-IO which is to be used +(values other than `mpich' will be added at a later date): + + $ ./configure --enable-parallel=mpich + +If the MPI/MPI-IO include files and/or libraries cannot be found by the +compiler then their directories must be given as arguments to CPPFLAGS +and/or LDFLAGS: + + $ CPPFLAGS=-I/usr/local/mpi/include \ + LDFLAGS=-L/usr/local/mpi/lib/LINUX/ch_p4 \ + ./configure --enable-parallel=mpich + +If a parallel library is being built then configure attempts to determine +how to run a parallel application on one processor and on many +processors. If the compiler is `mpicc' and the user hasn't specified +values for RUNSERIAL and RUNPARALLEL then configure chooses `mpirun' from +the same directory as `mpicc': + + RUNSERIAL: /usr/local/mpi/bin/mpirun -np 1 + RUNPARALLEL: /usr/local/mpi/bin/mpirun -np $${NPROCS:=3} + +The `$${NPROCS:=3}' will be substituted with the value of the NPROCS +environment variable at the time `make check' is run (or the value 3). diff --git a/release_docs/RELEASE.txt b/release_docs/RELEASE.txt new file mode 100644 index 0000000..3827029 --- /dev/null +++ b/release_docs/RELEASE.txt @@ -0,0 +1,144 @@ +HDF5 library version 1.4.1-post4 currently under development +================================================================================ + + +INTRODUCTION + +This document describes the differences between HDF5-1.4.1 and +HDF5-1.4.2, and contains information on the platforms tested and +known problems in HDF5-1.4.2. 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 +- Bug Fixes since HDF5-1.4.1 +- Documentation +- Platforms Tested +- Supported Configuration Features +- Known Problems + + +New Features +============ + + * File sizes greater than 2GB are now supported on Linux systems with + version 2.4.x or higher kernels. + * Added a global string variable H5_lib_vers_info_g which holds the + HDF5 library version information. This can be used to identify + an hdf5 library or hdf5 application binary. + Also added a verification of the consistency between H5_lib_vers_info_g + and other version information in the source code. + * Parallel HDF5 now runs on the HP V2500 and HP N4000 machines. + * F90 API: + - Added aditional parameter "dims" to the h5dread/h5dwrite and + h5aread/h5awrite subroutines. This parameter is 1D array of size + 7 and contains the sizes of the data buffer dimensions. + * F90 static library is available on Windows platforms. See + INSTALL_Windows.txt for details. + * F90 APIs are available on HPUX 11.00 and IBM SP platforms. + * H5 <-> GIF convertor has been added. This is available under + tools/gifconv. The convertor supports the ability to create animated + gifs as well. + * Verified correct operation of library on Solaris 2.8 in both 64-bit and + 32-bit compilation modes. See INSTALL document for instructions on + compiling the distribution with 64-bit support. + * Added support for the Metrowerks Code Warrior compiler for Windows. + +Bug Fixes since HDF5-1.4.1 Release +================================== + + * Fixed bug with non-zero userblock sizes causing raw data to not + write correctly. + * Fixed problems with Pablo build and linking with non-standard MPI I/O. + * Fixed build on Linux systems with --enable-static-exec flag. It now + works correctly. + * IMPORTANT: Fixed file metadata corruption bug which could cause metadata + data loss in certain situations. + * The allocation by alignment (H5Pset_alignment) feature code somehow + got dropped in some 1.3.x version. Re-implemented it with "new and + improved" algorithm. It keeps track of "wasted" file-fragment in + the free-list too. + * H5 <-> GIF convertor has been added. This is available under + tools/gifconv. The convertor supports the ability to create animated + gifs as well. + * Removed limitation that the data transfer buffer size needed to be + set for datasets whose dimensions were too large for the 'all' selection + code to handle. Any size dimensioned datasets should be handled + correctly now. + +Documentation +============= + + +Platforms Tested +================ + + + AIX 4.3.3.0 (IBM SP powerpc) xlc 3.6.6 + mpcc_r 3.6.6 + Cray T3E sn6711 2.0.5.47 Cray Standard C Version 6.5.0.0 + Cray SV1 10.0.0.8 Cray Standard C Version 6.5.0.0 + FreeBSD 4.3 gcc 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.11.01.20 + IRIX 6.5 MIPSpro cc 7.30 + IRIX64 6.5 (64 & n32) MIPSpro cc 7.3.1m + Linux 2.4.4 gcc-2.95.3 + g++ 2.95.3 + Linux 2.2.18smp gcc-2.95.2 + g++ 2.95.2 + 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) + + SunOS 5.7 WorkShop Compilers 5.0 98/12/15 C 5.0 + (Solaris 2.7) Workshop Compilers 5.0 98/12/15 C++ 5.0 + 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 +======================================== + + * See "Supported Configuration Features Summary" section for the HDF5 + 1.4.0 release in the HISTORY.txt file. + + +Known Problems +============== + + * The h5dump tests may fail to match the expected output in some + platforms (e.g. SP2 parallel, Windows) where the error messages + directed to "stderr" do not appear in the "right order" with output + from stdout. This is not an error. + + * The --enable-static-exec configure flag fails to compile for HP-UX + 11.00 platforms. + + * The executable are always dynamic on IRIX64 6.5(64 and n32) and + IRIX 6.5 even if they are configured with --enable-static-exec. + + * The shared library failed compilation on IRIX 6.5. + + * After "make install" or "make install-doc" one may need to reload + the source from the tar file before doing another build. + + * See "Known problems" section for the HDF5 1.4.0 release in the + HISTORY.txt file. diff --git a/windows/all.zip b/windows/all.zip new file mode 100755 index 0000000..e987ed5 Binary files /dev/null and b/windows/all.zip differ diff --git a/windows/all_withf90.zip b/windows/all_withf90.zip new file mode 100755 index 0000000..85f6bda Binary files /dev/null and b/windows/all_withf90.zip differ diff --git a/windows/all_withhdf4.zip b/windows/all_withhdf4.zip new file mode 100644 index 0000000..0d7ae1d Binary files /dev/null and b/windows/all_withhdf4.zip differ -- cgit v0.12