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* [svn-r14933] Purpose: Updating HDF5 to use automake 1.10.1 and libtool 2.2.2Mike McGreevy2008-05-052-17/+25
| | | | | | | | | | | | | | | | | | Description: Applying update to autotools that was applied to 1.8 a couple of weeks ago to the trunk. Updated bin/reconfigure script to reflect the new versions of libtool and automake in the /home1/packages/ directory. Rearranged configure.in script. When using libtool 2.2.2, the libtool script doesn't generate until later in the configuration process, so I had to move a test that parsed through the libtool script to a point after where it was actually being generated. Ran libtoolize on the project, and ran bin/reconfigure to regenerate configure and Makefile.in's throughout. Tested: kagiso, smirom, linew (h5committest)
* [svn-r14903] Undoing change committed in r14902.Scot Breitenfeld2008-04-3045-5936/+5634
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* [svn-r14902] Merged fortran_1_8 branch changes r14505:14901 into the trunk. ↵Scot Breitenfeld2008-04-3045-5634/+5936
| | | | New fortran wrappers added.
* [svn-r14864] Snapshot version 1.9 release 4HDF Tester2008-04-272-16/+17
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* [svn-r14860] Description:Quincey Koziol2008-04-2427-5871/+5200
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | Omnibus raw data I/O revisions, with wide-ranging changes and refactoring, in order to prepare for implementing "fast append" feature. These changes remove the majority of the code duplication for raw data I/O which has crept in over the last ten years and introduces a more object- oriented design for operating on different types of dataset storage. Chunked storage no longer has it's own I/O routines, it is now handled as either contiguous (if chunk is not pulled into the cache) or compact (if the chunk is cached in memory). No bug or feature changes, at least intentionally... :-) Tested on: FreeBSD/32 6.2 (duty) in debug mode FreeBSD/64 6.2 (liberty) w/C++ & FORTRAN, in debug mode Linux/32 2.6 (kagiso) w/PGI compilers, w/C++ & FORTRAN, w/threadsafe, in debug mode Linux/64-amd64 2.6 (smirom) w/default API=1.6.x, w/C++ & FORTRAN, in production mode Linux/64-ia64 2.6 (cobalt) w/Intel compilers, w/C++ & FORTRAN, in production mode Solaris/32 2.10 (linew) w/deprecated symbols disabled, w/C++ & FORTRAN, w/szip filter, in production mode Mac OS X/32 10.5.2 (amazon) in debug mode Linux/64-ia64 2.4 (tg-login3) w/parallel, w/FORTRAN, in production mode
* [svn-r14849] Snapshot version 1.9 release 3HDF Tester2008-04-202-3/+3
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* [svn-r14847] 1. test/links.c: add tests specific for windowsVailin Choi2008-04-161-1/+0
| | | | | | | | | remove HDputenv() from external_link_env() test (will add script later to set HDF5_EXT_PREFIX for running the test) modify and add more comments 2. src/H5private.h: remove #define for HDputenv() Tested on kagiso, linew and smirom.
* [svn-r14832] Snapshot version 1.9 release 2HDF Tester2008-04-132-3/+3
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* [svn-r14822] 1. src/H5private.h: fixed a bug in CHECK_ABSOLUTE() for windows.Vailin Choi2008-04-091-2/+1
| | | | 2. test/links.c: fixed one external link test to be the same as in 1.8.
* [svn-r14821] Having this signature Pedro Vicente Nunes2008-04-081-1/+1
| | | | | | | | | | | | | | | | H5_DLL herr_t H5_build_extpath(const char *, char **/*out*/); makes this stupid warning in windows that gets repeated in every source file c:\_pvn\hdf5\src\h5private.h(958) : warning C4138: '*/' found outside of comment changed signature to H5_DLL herr_t H5_build_extpath(const char *, char ** /*out*/ ); compiler is happy now tested: windows, linux
* [svn-r14799] Snapshot version 1.9 release 1HDF Tester2008-04-062-3/+3
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* [svn-r14794] Use putenv() instead of setenv() in test/links.c Vailin Choi2008-04-042-2/+3
| | | | (solaris did not support setenv() and unsetenv())
* [svn-r14789] Add handling for external link:Vailin Choi2008-04-027-31/+360
| | | | | | | 1. src/H5F.c, src/H5system.c: formulate path for mainfile 2. src/H5Lexternal.c: add search for target file 3. configure.in: add H5_HAVE_WINDOW_PATH 4. test/links.c: add tests for external link
* [svn-r14759] Snapshot version 1.9 release 0HDF Tester2008-03-202-3/+3
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* [svn-r14738] Description:Quincey Koziol2008-03-136-11/+44
| | | | | | | | | | Bring r14737 back from the 1.8 branch: Fix bug which would incorrectly encode the member offsets for compound datatypes whose size was between 256 & 511 bytes, when the "use the latest format" feature was enabled. Tested on: Mac OS X/32 10.5.2 (amazon) w/debug FreeBSD/32 6.2 (duty) w/production
* [svn-r14720] Description:Quincey Koziol2008-03-111-0/+2
| | | | | | | | | Minor bug fix to H5Aget_num_attrs() to return error when an invalid location ID is passed in. Tested on: Mac OS X/32 (amazon) Too minor to require h5committest
* [svn-r14709] Fixed the assert() failures (development mode) from Wed. daily ↵Vailin Choi2008-03-063-5/+6
| | | | | | | | | | tests: Add 2 more parameters to H5HF_man_iblock_size() (parent iblock and parent entry) for passing onto H5HF_iblock_man_iblock_protect(). This bug was there before but was revealed now by exercising the recursive part of the code from the new "h5stat_newgrat.h5". Tested on kagiso, smirom and linew with --disable-production.
* [svn-r14702] 1. H5HFiblock.c: fixed problem for uninitialized "u" for bug ↵Vailin Choi2008-03-042-3/+7
| | | | | | | | | | | | #1072 in H5HF_man_iblock_size(). 2. H5HFstat.c: Since H5HF_space_size() zeroed out fs_size, add "meta_size" to store free-space size before adding to "heap_size". 3. h5stat_gentest.c: increase # of groups to get "h5stat_newgrat.h5" that contains indirect block entries in fractal heap. This is for testing the recursive part of the code in H5HF_man_iblock_size(). 4. h5stat_newgrat.h5: the new .h5 file generated by h5stat_gentest.c. 5. h5stat_newgrat.ddl: expected output from new "h5stat_newgrat.h5".
* [svn-r14547] Maintenance: Changed version number to 1.9.0 as we agreed on ↵Elena Pourmal2008-02-111-2/+2
| | | | | | the HDF5 developers meeting on February 8, 2008; modified docs files to point to the documentation snapshots.
* [svn-r14526] Maintenance: Changed version number in the trunk to be 1.9.0-snap0hdf5-1_9-startElena Pourmal2008-02-072-4/+4
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* [svn-r14484] Maintenance: Changed version number to 1.8.0 in preparation for ↵Elena Pourmal2008-02-011-2/+2
| | | | | | the release.
* [svn-r14463] Purpose: Updating shared library version number for 1.8.0 release.Mike McGreevy2008-01-281-3/+3
| | | | | | | | | | | Description: config/lt_vers.am was updated as follows due to changes in API since last version update: LT_VERS_INTERFACE = 5 LT_VERS_REVISION = 0 LT_VERS_AGE = 0 Tested: kagiso
* [svn-r14460] Maintenance: Created rc2 tar ball and released to the ftp server;Elena Pourmal2008-01-271-2/+2
| | | | Changed version number to hdf501.8.0-rc3 using bin/h5vers script
* [svn-r14458] Fixed coredump under production 64-bit solaris.John Mainzer2008-01-251-13/+30
| | | | | | | | | | | | | | | | As best I can tell, H5C_make_space_in_cache() was accessing memory that had been deallocated -- however the bug was easy to mask, and jumped around even in different runs of the same executable. While I was never able to generate a definitive test case that exposed exactly where the core dump occured, I was able to generate print statement traces which made it clear that I was accessing freed memory. In any case, reworking the code to avoid the reference to freed cache entries seems to have fixed the problem. Tested serial production on Phoenix, and commit tested. Also, partial tests Linew.
* [svn-r14450] Fixed metadata cache performance bug introduced while adding ↵John Mainzer2008-01-231-11/+12
| | | | | | | | | | | code to detect and handle the case in which the skip list or LRU is modified out from under a scan of same by the flush callback of the entry under consideration. Test serial debug, serial production, and parallel debug on phoenix, and commit tested.
* [svn-r14448] Maintenance: Released version hdf5-1.8.0-rc1 to the public fTP ↵Elena Pourmal2008-01-213-4/+4
| | | | | | | | server and changed the version to hdf5-1.8.0-rc2 using bin/h5vers script. Platforms tested: ran test for hdf5-1.8.0-rc1 source on kagiso after craeting public tar ball.
* [svn-r14445] Added code to detect the situation in which a metadata cache ↵John Mainzer2008-01-202-37/+532
| | | | | | | | | | | | | | entry flush callback functions modifies the skip list or LRU out from under a partial or complete flush of the cache. This is a test for a situation that should not occur, but we test anyway. Also added code to skip longer tests in cache_api in express tests. Tested serial and parallel on phoenix (debian --x86-32), and commit test. Elena commit tested as well, and ran a manual test under MacOS X.
* [svn-r14442] Modified metadata cache to adapt more quickly to the insertion of aJohn Mainzer2008-01-189-41/+648
| | | | | | | | | | | | | | | | | large entry, or to a large increases in the size of an existing entry. This required some additions to the cache configuration structure, and thus will require changes in the metadata cache documentation. The basic idea is to monitor the size of entries as they are loaded, inserted, or increased in size. If the size of the entry (or increase) exceeds some user selected fraction of the size of the cache, increase the size of the cache. Note that this fix was designed quickly -- while it deals with the use case that exposed the problem, we may have to revisit the issue later. Tested serial and parallel on Phoenix, and h5committest.
* [svn-r14422] Description:Quincey Koziol2008-01-151-3/+2
| | | | | | | Clean up thread safety code a bit more... Tested on: Mac OS X/32 10.5.1 (amazon) w/threadsafe
* [svn-r14421] Description:Quincey Koziol2008-01-158-15/+20
| | | | | | | Minor cleanups and clarifications to prototype information. Tested on: Mac OS X/32 10.5.1 (amazon)
* [svn-r14420] Description:Quincey Koziol2008-01-155-82/+78
| | | | | | | | Correct the prototype for H5Sselect_elements() to take an 'hsize_t *' for the coordinates, instead of 'hsize_t **'. Tested on: Mac OS X/32 10.5.1 (amazon)
* [svn-r14419] Description:Quincey Koziol2008-01-152-34/+21
| | | | | | | | Streamline threadsafety code to be simpler and reduce latency of holding locks. Tested on: Mac OS X/32 10.5.1 (amazon) w/threadsafe
* [svn-r14417] Description:Quincey Koziol2008-01-151-36/+40
| | | | | | | | Handled truncated files better, when the truncation falls in decoding a local heap. Tested on: Mac OS X/32 10.5.1 (amazon)
* [svn-r14413] Description:Quincey Koziol2008-01-144-34/+34
| | | | | | | | | | | | | | | | | | | Change H5P[gs]et_format_bounds() => H5P[gs]et_libver_bounds() and also enumerated values H5F_FORMAT_{EARLIEST, LATEST} => H5F_LIBVER_{EARLIEST, LATEST} Tested on: FreeBSD/32 6.2 (duty) in debug mode FreeBSD/64 6.2 (liberty) w/C++ & FORTRAN, in debug mode Linux/32 2.6 (kagiso) w/PGI compilers, w/C++ & FORTRAN, w/threadsafe, in debug mode Linux/64-amd64 2.6 (smirom) w/default API=1.6.x, w/C++ & FORTRAN, in production mode Linux/64-ia64 2.6 (cobalt) w/Intel compilers, w/C++ & FORTRAN, in production mode Solaris/32 2.10 (linew) w/deprecated symbols disabled, w/C++ & FORTRAN, w/szip filter, in production mode Mac OS X/32 10.4.10 (amazon) in debug mode Linux/64-ia64 2.4 (tg-login3) w/parallel, w/FORTRAN, in production mode
* [svn-r14402] Description:Quincey Koziol2008-01-136-1/+43
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | Add work-around to allow reading files that were produced with a buggy earlier version of the library, which could create objects with the wrong object header message count. There is now a configure flag "--enable-strict-format-checks" which triggers a failure on reading a file with this sort of corruption (when enabled) and allows the object to be read (when disabled). The default value for the "strict-format-checks" flag is yes when the "debug" flag is enabled and no when the "debug" flag is disabled. Note that if strict format checks are disabled (allowing objects with this particular kind of corruption to be read) and the file is opened with write access, the library will re-write the object header for the corrupt object with the correct # of object header messages. This closes bugzilla bug #1010. Tested on: FreeBSD/32 6.2 (duty) in debug mode FreeBSD/64 6.2 (liberty) w/C++ & FORTRAN, in debug mode Linux/32 2.6 (kagiso) w/PGI compilers, w/C++ & FORTRAN, w/threadsafe, in debug mode Linux/64-amd64 2.6 (smirom) w/default API=1.6.x, w/C++ & FORTRAN, in production mode Linux/64-ia64 2.6 (cobalt) w/Intel compilers, w/C++ & FORTRAN, in production mode Solaris/32 2.10 (linew) w/deprecated symbols disabled, w/C++ & FORTRAN, w/szip filter, in production mode Mac OS X/32 10.4.10 (amazon) in debug mode Linux/64-ia64 2.4 (tg-login3) w/parallel, w/FORTRAN, in production mode
* [svn-r14379] add check of some values for the nbit and scale offest filters ↵Pedro Vicente Nunes2008-01-073-2/+5
| | | | | | | | on the h5repack verify function note: some sybols were made public tested: windows, linux
* [svn-r14376] moved a couple more private filter symbols to the public side, ↵Pedro Vicente Nunes2008-01-043-5/+5
| | | | | | needed by h5repack tested: windows, linux
* [svn-r14374] Description:Quincey Koziol2008-01-044-7/+32
| | | | | | | | | Updates from running bin/reconfigure on recent changes, in preparation for making private snapshot. Also updated tracing information for recent types added to public API routines. Tested on: Linux/32 2.6.x (kagiso)
* [svn-r14372] Description:Quincey Koziol2008-01-036-59/+60
| | | | | | | | Further cleanups & simplifications to prepare for next phase of work. Tested on: FreeBSD/32 6.2 (duty) Mac OS X/32 10.5.1 (amazon)
* [svn-r14371] Description:Quincey Koziol2008-01-031-80/+92
| | | | | | | Code cleanups in preparation for larger changes. Tested on: Mac OS X/32 (amazon)
* [svn-r14365] Add szip filter check of client data values for has_filters.Pedro Vicente Nunes2008-01-032-9/+11
| | | | | | NOTE: szip client symbols were made public Tested: windows, linux, solaris
* [svn-r14364] Description:Quincey Koziol2008-01-033-65/+83
| | | | | | | | | | | | | | | | | | | Avoid creating free space manager for fractal heap when just performing queries. Tested on: FreeBSD/32 6.2 (duty) in debug mode FreeBSD/64 6.2 (liberty) w/C++ & FORTRAN, in debug mode Linux/32 2.6 (kagiso) w/PGI compilers, w/C++ & FORTRAN, w/threadsafe, in debug mode Linux/64-amd64 2.6 (smirom) w/default API=1.6.x, w/C++ & FORTRAN, in production mode Linux/64-ia64 2.6 (cobalt) w/Intel compilers, w/C++ & FORTRAN, in production mode Solaris/32 2.10 (linew) w/deprecated symbols disabled, w/C++ & FORTRAN, w/szip filter, in production mode Mac OS X/32 10.4.10 (amazon) in debug mode Linux/64-ia64 2.4 (tg-login3) w/parallel, w/FORTRAN, in production mode
* [svn-r14363] Description:Quincey Koziol2008-01-035-1659/+1877
| | | | | | | | Refactor file space allocation routines into separate source module. Tested on: FreeBSD/32 6.2 (duty) in debug mode Mac OS X/32 10.4.10 (amazon) in debug mode
* [svn-r14362] Description:Quincey Koziol2008-01-033-26/+119
| | | | | | | | | | | | | | | | | | Switched from "H5P[gs]et_latest_format" to "H5P[gs]et_format_bounds". Tested on: FreeBSD/32 6.2 (duty) in debug mode FreeBSD/64 6.2 (liberty) w/C++ & FORTRAN, in debug mode Linux/32 2.6 (kagiso) w/PGI compilers, w/C++ & FORTRAN, w/threadsafe, in debug mode Linux/64-amd64 2.6 (smirom) w/default API=1.6.x, w/C++ & FORTRAN, in production mode Linux/64-ia64 2.6 (cobalt) w/Intel compilers, w/C++ & FORTRAN, in production mode Solaris/32 2.10 (linew) w/deprecated symbols disabled, w/C++ & FORTRAN, w/szip filter, in production mode Mac OS X/32 10.4.10 (amazon) in debug mode Linux/64-ia64 2.4 (tg-login3) w/parallel, w/FORTRAN, in production mode
* [svn-r14360] New function has_filters (replace has_filters for each object ↵Pedro Vicente Nunes2008-01-022-1/+4
| | | | | | | | | and for global filters): verify if all requested filters in the array FILTER obtained from user input are present in the property list PID obtained from the output file. All the filter comparison of client data values is done here instead of the previous filtcmp TO DO: szip, nbit and scale offset NOTE: the symbol H5Z_SHUFFLE_TOTAL_NPARMS was made public Tested: windows, teragrid with icc 8.1, linux (kagiso), solaris (linew)
* [svn-r14359] Description:Quincey Koziol2007-12-241-1/+1
| | | | | | | | | Corrected a compiler warning in the local heap code. Fixed the shared message flag symbols from the recent switchover. Tested on: FreeBSD 6.2/32 (duty)
* [svn-r14358] Description:Quincey Koziol2007-12-233-22/+18
| | | | | | | | | | | | | | | | | | | Tweak the constants for the shared message flags to be equal to the other flags useds for the underlying messages. Tested on: FreeBSD/32 6.2 (duty) in debug mode FreeBSD/64 6.2 (liberty) w/C++ & FORTRAN, in debug mode Linux/32 2.6 (kagiso) w/PGI compilers, w/C++ & FORTRAN, w/threadsafe, in debug mode Linux/64-amd64 2.6 (smirom) w/default API=1.6.x, w/C++ & FORTRAN, in production mode Linux/64-ia64 2.6 (cobalt) w/Intel compilers, w/C++ & FORTRAN, in production mode Solaris/32 2.10 (linew) w/deprecated symbols disabled, w/C++ & FORTRAN, w/szip filter, in production mode Mac OS X/32 10.4.10 (amazon) in debug mode Linux/64-ia64 2.4 (tg-login3) w/parallel, w/FORTRAN, in production mode
* [svn-r14357] Description:Quincey Koziol2007-12-222-10/+44
| | | | | | | | | | | | | | | | | | | | Add a hack to the local heap code to resize the metadata cache when the heap block will be too large for the cache. This should be removed when the metadata cache handles "too large" object insertions (or resizes) correctly. Tested on: FreeBSD/32 6.2 (duty) in debug mode FreeBSD/64 6.2 (liberty) w/C++ & FORTRAN, in debug mode Linux/32 2.6 (kagiso) w/PGI compilers, w/C++ & FORTRAN, w/threadsafe, in debug mode Linux/64-amd64 2.6 (smirom) w/default API=1.6.x, w/C++ & FORTRAN, in production mode Linux/64-ia64 2.6 (cobalt) w/Intel compilers, w/C++ & FORTRAN, in production mode Solaris/32 2.10 (linew) w/deprecated symbols disabled, w/C++ & FORTRAN, w/szip filter, in production mode Mac OS X/32 10.4.10 (amazon) in debug mode Linux/64-ia64 2.4 (tg-login3) w/parallel, w/FORTRAN, in production mode
* [svn-r14356] Description:Quincey Koziol2007-12-203-77/+58
| | | | | | | | | | | | | | | | | | | Refactor work for bug #956 to simplify a bit and to cover some corner cases. Tested on: FreeBSD/32 6.2 (duty) in debug mode FreeBSD/64 6.2 (liberty) w/C++ & FORTRAN, in debug mode Linux/32 2.6 (kagiso) w/PGI compilers, w/C++ & FORTRAN, w/threadsafe, in debug mode Linux/64-amd64 2.6 (smirom) w/default API=1.6.x, w/C++ & FORTRAN, in production mode Linux/64-ia64 2.6 (cobalt) w/Intel compilers, w/C++ & FORTRAN, in production mode Solaris/32 2.10 (linew) w/deprecated symbols disabled, w/C++ & FORTRAN, w/szip filter, in production mode Mac OS X/32 10.4.10 (amazon) in debug mode Linux/64-ia64 2.4 (tg-login3) w/parallel, w/FORTRAN, in production mode
* [svn-r14354] Bug fix for #956 where the element coordinates went wrong for ↵Raymond Lu2007-12-203-1/+61
| | | | | | | | dataspace selection. Added a test for it, too. This round of checkin isn't well tarnished yet. I'll come back to work on Jan. 8. I'll revise it then. Tested it on kagiso, smirom, linew.
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