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* [svn-r15707] I changed the return values of H5Fget_obj_ids and ↵Raymond Lu2008-09-263-39/+69
| | | | | | | | H5Fget_obj_count to ssize_t and modified C++ and Fortran API functions. This is for bug #1245. Tested on kagiso - I've tested the same change using h5committest.
* [svn-r15702] Description:Quincey Koziol2008-09-251-12/+4
| | | | | | | | | Bring back r15701 from trunk: Remove some unused variables Tested on: Mac OS X/32 10.5.5 (amazon) Too minor to require h5committest
* [svn-r15683] Purpose: fix bug 1298Neil Fortner2008-09-227-42/+61
| | | | | | | | | | | Description: The optimized "subset" compound conversion function would improperly copy the "blank" space at the end of compound types. Modified H5T_conv_struct_init to detect when the subset type has extra space at the end, and calculate the size of the data that should be copied into the conversion buffer for each element. Changes to the functions that implement these conversions. Tested: kagiso, linew, smirom (h5committest)
* [svn-r15677] Description:Quincey Koziol2008-09-2226-135/+129
| | | | | | | | | | | | Bring r15676 back from trunk: Centralize all macros for declaring "magic numbers"/signatures for objects in the file into src/H5Fprivate.h, so it's easier to know what values have already been defined, etc. Tested on: Mac OS X/32 10.5.5 (amazon) Too minor to require h5committest
* [svn-r15657] Purpose: fix bug 1286Neil Fortner2008-09-182-49/+157
| | | | | | Description: Added configure test to see if pointer alignment restrictions are enforced (as in dereferencing an unaligned pointer causes an error). Added code in H5Tvlen.c to avoid dereferencing unaligned pointers, conditionally compiled based on the configure test. Added test case in dtypes.c which would previously cause such machines to fail. Tested: kagiso, smirom, linew (h5committest); linew64
* [svn-r15638] Bug 710: partial fix.Albert Cheng2008-09-161-144/+144
| | | | | | | | | | | Temporary removed b2 from the --enable-debug=all list so that this option will pass. "configure --help" lists the --enable-debug=all and users tend to use it and end up with compile failures in the b2 debug code. Since this bug will not be fixed soon, this is a temporary fix to let the configure and build work. Tested: h5committest plus "--enable-debu=all" test in kagiso.
* [svn-r15629] Description:Quincey Koziol2008-09-1694-872/+872
| | | | | | | | | | | | | Remove trailing whitespace from C/C++ source files, with the following script: foreach f (*.[ch] *.cpp) sed 's/[[:blank:]]*$//' $f > sed.out && mv sed.out $f end Tested on: Mac OS X/32 10.5.5 (amazon) No need for h5committest, just whitespace changes...
* [svn-r15624] This check-in fixes a bug inside parallel HDF5 testsuite.MuQun Yang2008-09-152-2/+32
| | | | | | When enable-debug is turned on, a special macro block H5_HAVE_INSTRUMENTED_LIBRARY inside HDF5 will be executed to check if some collective chunk IO test cases are being run with the correct settings(one link, multiple chunk etc.). However,when complicated derived datatype in some mpi-io packages are not supported, the library has to switch one link IO with/without the optimization to multiple chunk IO with/without the optimization. The current testsuite doesn't know this and generates a false assertion failure message. This check-in fix this problem by providing a second property to avoid the false faiure message.
* [svn-r15621] Snapshot version 1.8 release 1 (snap4)HDF Tester2008-09-141-2/+2
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* [svn-r15613] Description:Quincey Koziol2008-09-114-12/+11
| | | | | | | | | Bring back r15612 from trunk: Minor cleanups of formatting, etc. Tested on: Mac OS X/32 10.5.4. (amazon) Too minor to require h5committest
* [svn-r15610] Description:Quincey Koziol2008-09-1056-2304/+2559
| | | | | | | | | Bring r15609 back from trunk: Omnibus compiler warning cleanup & some formatting happiness. Tested on: Mac OS X/32 10.5.4 (amazon) Too minor to require h5committest
* [svn-r15597] Snapshot version 1.8 release 1 (snap3)HDF Tester2008-09-081-2/+2
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* [svn-r15567] Snapshot version 1.8 release 1 (snap2)HDF Tester2008-09-014-2/+10
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* [svn-r15553] Fix potential memory leak in H5E_close_msg_cb.Neil Fortner2008-08-281-1/+4
| | | | Tested: kagiso
* [svn-r15516] Fix faulty error checking in call to H5I_remove().Neil Fortner2008-08-211-1/+1
| | | | | | Add prototype to the top of app_ref.c to suppress warning. Tested: kagiso
* [svn-r15513] Description:Quincey Koziol2008-08-2198-1535/+1544
| | | | | | | | | | Bring back r15510 & r15512 from trunk: Fix compiler warnings and formatting. Tested on: Mac OS X/32 10.5.4 (amazon) More tests upcoming
* [svn-r15489] Description:Quincey Koziol2008-08-191-1/+1
| | | | | | | | | | | Bring rev. 15488 back from trunk: Fix bug where library could core dump when an invalid location ID was passed to H5Giterate() (and add test for this case). Tested on: Mac OS X/32 10.5.4 (amazon) Too minor to require h5committest
* [svn-r15486] Purpose: Allow library to shut down properly when objects have ↵Neil Fortner2008-08-1961-518/+558
| | | | | | | | | | | | | | | | reference count > 1. Description: Added a new field 'app_count' to H5I_id_info_t struct, to track the reference count on an id due to the application. the old 'count' field tracks the total. Generally any id visible to the application gets placed in app_count. Added app_ref boolean parameter to H5I_inc_ref, H5I_dec_ref, H5I_register, H5I_clear_type, and a few other functions, to specify whether the operation(s) being performed on the id(s) are due to the application (TRUE) or not (FALSE). Test added for this case. Tested: kagiso, smirom, linew (h5committest)
* [svn-r15480] Snapshot version 1.8 release 1 (snap1)HDF Tester2008-08-171-2/+2
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* [svn-r15478] Removed vestigal code from H5SM_delete_from_index() which would ↵Neil Fortner2008-08-171-11/+0
| | | | | | | | | have dereferenced an uninitialized pointer if it had been reachable. Closes bz #1280. Tested: kagiso, smirom, linew (h5committest)
* [svn-r15471] Snapshot version 1.8 release 1 (snap0)HDF Tester2008-08-141-2/+2
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* [svn-r15463] Description:Quincey Koziol2008-08-122-2/+4
| | | | | | | | Bring revision 15462 (compiler warnings) back from trunk. Tested on: Mac OS X/32 10.5.4 (amazon) w/FORTRAN & C++ (Too minor to require h5committest)
* [svn-r15459] Purpose: Modify the library to take the proper action when ↵Neil Fortner2008-08-1131-100/+218
| | | | | | | | | | | | | | | files with incorrect datatype versions are encountered. Description: The library now recognizes some problems with datatype versions in H5O_decode_helper(), and, if not performing strict format checks, automatically corrects them. Framework added for other message decode routines to automatically correct file errors. Datatype version information added to h5debug. Resolves bz#1236, 1266. Test files with incorrect datatype versions corrected. Tested: kagiso, smirom, linew (h5committest)
* [svn-r15450] Purpose: Fix various problems that were occurring when using ↵Neil Fortner2008-08-077-131/+128
| | | | | | | | | | | | | | mounted files. Description: Moved mount table from top file structure to shared file structure. Moved parent out of mount table and back into top file structure. mounted files can now be accessed from any handle of the parent file. Changes to how files are closed. Stricter cycle checking on mounted files. Removed unused function H5F_has_mount(). Tested: kagiso, smirom, linew (h5committest)
* [svn-r15390] Last round of checkin introduced a bug. This checkin corrected ↵Raymond Lu2008-07-214-58/+70
| | | | | | | | | | | | | | it and made a few minor changes. Last round of check in fixed the problem when an attribute was opened twice and data was written with one of the handles, the file didn't have the data. It happened because each handle had its own object structure, and the empty one overwrote the data with fill value. This is fixed by making some attribute information like the data be shared in the attribute structure. Tested on smirom, kagiso, and linew.
* [svn-r15385] Description:Quincey Koziol2008-07-181-1/+1
| | | | | | | Correct return value for error condition to avoid compiler warning Tested on: Just eyeballed, very minor
* [svn-r15376] Description:Quincey Koziol2008-07-161-2/+2
| | | | Bump shared library version # for change to H5G_info_t struct
* [svn-r15373] Description:Quincey Koziol2008-07-161-3/+3
| | | | | | | Correct wrong error return value to avoid compiler warning Tested on: Just eyeballed, extremely minor
* [svn-r15368] Description:Quincey Koziol2008-07-155-1/+61
| | | | | | | | | | | | | | | Bring back r15367 from the trunk: Add check to avoid mounting a file on a group twice, when the mounts are done on the same HDF5 file, but opened with separate H5Fopen queries. Also add new 'mounted' flag to the H5G_info_t struct, queried with the H5Gget_info() API call, to allow applications to detect and avoid this situation. Tested on: Mac OS X/32 10.5.4 (amazon) Linux/64 10.5.4 (chicago)
* [svn-r15336] Fixed incorrect error message in H5Pset_fletcher32:Neil Fortner2008-07-081-1/+1
| | | | | | | | "unable to add deflate filter to pipeline" -> "unable to add fletcher32 filter to pipeline" Tested: kagiso
* [svn-r15330] When an attribute was opened twice and data was written with ↵Raymond Lu2008-07-079-384/+608
| | | | | | | | | | | one of the handles, the file didn't have the data. It happened because each handle had its own object structure, and the empty one overwrote the data with fill value. This is fixed by making some attribute information like the data be shared in the attribute structure. Tested on smirom, kagiso, and linew.
* [svn-r15297] Bug fix for H5Tpack. The problem was that H5Tpack didn't act ↵Raymond Lu2008-06-301-1/+5
| | | | | | | | | correctly with nested compound datatype. The size of compound type's member type wasn't updated. It's fixed in this commit. Tested on smirom. The same change was tested on three systems for v1.9.
* [svn-r15228] Description:Quincey Koziol2008-06-177-11/+13
| | | | | | | | | | | | | | | | | | | | Bring back revision 15227 from trunk: Small cleanups to copying datatypes 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 10.5.3 (amazon) in debug mode Linux/64-ia64 2.4 (tg-login3) w/parallel, w/FORTRAN, in production mode
* [svn-r15212] Description:Quincey Koziol2008-06-1313-48/+108
| | | | | | | | | | | Bring back revision 15211 from trunk: Update the gcc flags for version 4.3 Clean up warnings Tested on: Mac OS X/32 10.5.3 (amazon)
* [svn-r15209] Description:Quincey Koziol2008-06-122-6/+9
| | | | | | | | | | | Bring back revision 15208 from trunk: Add a "HDcompile_assert" macro for assertions that can/should be checked at compile time, as opposed to run time. (And used it for a couple of simple cases, to begin) Tested on: Mac OS X/32 10.5.3 (amazon)
* [svn-r15189] Description:Quincey Koziol2008-06-101-7/+8
| | | | | | | | | | Bring revision 15188 back from trunk: Avoid leaking memory when copying the internal "shared" struct for a named datatype when it's already been opened earlier. Tested on: Linux/64 2.6 (chicago)
* [svn-r15181] Purpose: _WIN32 macro cleanupScott Wegner2008-06-091-23/+1
| | | | | | | | | | Description: As part of our Windows cleanup, we try to remove windows-specific tweaks in the source code. There are many instances where Windows code is introduces via ifdef's. We re-evaluate whether they are still required, and found that many of them are not. Others we change to "feature"-specific code, rather than Windows-specific. Tested: VS2005 on WinXP VS.NET on WinXP h5committest (kagisopp, smirom, linew)
* [svn-r15163] Purpose: Create new HDpthread_self and HDpthread_self_ulong macrosScott Wegner2008-06-065-17/+20
| | | | | | | | | Description: On Windows, the pthread_self function cannot be used to print the returned thread ID for debugging. Instead, we need a separate function, GetCurrentThreadId. To eliminate some Windows ifdef's in the code, we create two new function macros which can be used by all platforms. It is conditionally defined in H5win32defs.h, and globally in H5private.h. Tested: VS2005 w/ pthreads on WinXP kagiso w/ pthreads
* [svn-r15160] Purpose: Separate Windows function macro definitions to win32defs.hScott Wegner2008-06-053-386/+880
| | | | | | | | | | | | | | Description: In library code, we try not to use system calls directly, but instead use the HD{function} macro instead. This way, we can map special versions of the call on particular systems. Previously, it was all done in H5private.h. However, in an effort to clean up platform-specific definitions, we move all of the Windows macros into a separate file, win32defs.h. This way, we can use the non-Posix versions that Visual Studio sends warnings about. Some macros are set specifically in the platform-specific header files. Then, any macros left unset will be set by the "default" implementation in H5private.h. This checkin also cleans up various source files to use the HD* macros when possible. Tested: VS2005 on WinXP VS.NET on WinXP h5committest (kagiso, linew, smirom)
* [svn-r15148] Description:Quincey Koziol2008-06-051-1/+4
| | | | | | | | | | | | Bring back revision 15146 from the trunk: Correct the definition of the 'nbytes' variable in the in-memory version of the B-tree key for chunks from 'size_t' to 'uint32_t', to match the definitions everywhere else. Tested on: Mac OS X/32 10.5.3 (amazon) debug & production Linux/64 2.6 (chicago) production
* [svn-r15132] Description:Quincey Koziol2008-06-0327-3515/+4287
| | | | | | | | | | | | | | Bring back revision 15131 from trunk: Finish omnibus chunked dataset I/O refactoring, to separate general actions on chunked datasets from actions that are specific to using the v1 B-tree index. Cleaned up a few bugs and added some additional tests also. Tested on: Mac OS X/32 10.5.3 (amazon) Linux/32 2.4 (chicago)
* [svn-r15127] Purpose: Make Windows threadsafe debug message more usefulScott Wegner2008-06-021-2/+6
| | | | | | | | | | Description: On Linux-like systems, we can get the ID of the current thread through a pthread_self. However on Windows, the return cannot be cast as a threadID, so we simply couldn't get the ID. Previously we simply gave up and printed a message that we couldn't get an ID. Instead, though, we can use the Windows-specific call to GetCurrentThreadId(), which achieves the same goal. This way we can provide better debug output with threadsafe features. Tested: VS2005 on WinXP VS.NET on WinXP (other platforms not tested because change is within _WIN32 ifdef)
* [svn-r15118] Purpose: Backport Windows project cleanup from trunk: remove ↵Scott Wegner2008-06-021-6/+0
| | | | | | | | | | | | | | | | | ignored system library, standardize program debug information, and unify Windows h5tinit Description: These changes are made via a user's suggestion, bugzilla bug #1164. These have all been tested in the trunk, and are stable/favorable changes. In many of our project files on Windows, we have our linker setting set to ignore old link libraries-- either libc.lib or libcd.lib. This is a relic from converting project files from old versions of Visual Studio to newer ones, and is unnecessary. We remove the ignored library from the project files. This actually makes no difference in the output binaries. In our debug project configurations, many of the projects were generating debug information for "Program Database and Edit & Continue". Other projects were using different settings, or none at all. We standardize to use "Program Database" setting, because it generates much smaller .obj files and cuts out unnecessary debug information. Previously, there was Windows-dependent code inside H5detect.c, because not all projects could access the gethostname() function. However, we standardize our project-files to link with WS2_32.lib, so now this function is available. Thus, the Windows-specific code has been removed from H5detect.c. Tested: VS2005 on WinXP VS.NET on WinXP
* [svn-r15105] Maintenance: Modified version to 1.8.1-snap0, and updated ↵Elena Pourmal2008-05-301-2/+2
| | | | | | HISTORY-1_8.txt and RELEASE.txt for the further development in the branch.
* [svn-r15085] Updated version number to 1.8.1 to prepare for official release ↵Albert Cheng2008-05-281-2/+2
| | | | of v1.8.1.
* [svn-r15068] Maintenance: used h5vers script to change version number to ↵Elena Pourmal2008-05-222-4/+4
| | | | | | 1.8.1-rc1 before creating a tar ball for remote testing
* [svn-r15042] Bug fix.Albert Cheng2008-05-201-4/+4
| | | | | | | | | | | | | | | | | | | Description: The fortran Makefile.am used HDF_FORTRAN to indicate it is part of the Fortran API source so that conclude.am will give fortran api prefix in the test output. The symbox HDF_FORTRAN is also used in configure for a different purpose (indicated --enable-fortran). They conflicted. Similar problem for the symbol HDF_CXX. Solution: Changed all the involved Makefile.am to use "FORTRAN_API" instead. It is a more appropriate name. Same for CXX_API. Along the way, discovered that the Makefile.am of hl/fortran/test and hl/cxx/test did not have those symbols at all. Added them in. Platform tested: Kagiso serial and h5committested (kagisopp, smirom, linew).
* [svn-r15038] Description:Quincey Koziol2008-05-191-2/+6
| | | | | | | | | Bring revision 15037 from trunk: Better cleanup of internal structures when no szip encoder. Tested on: Linux/32 2.6 (kagiso) w/szip-no encoder
* [svn-r15035] Description:Quincey Koziol2008-05-192-4/+5
| | | | | | | | | | Backport revision 15034 from trunk: Correct another case of using 'size_t' for chunk sizes where 'uint32_t' was necessary. Tested on: FreeBSD/64 6.2 (liberty) w/C++ & FORTRAN
* [svn-r15033] Purpose:Albert Cheng2008-05-192-18/+77
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | Improvement. Description: src/libhdf5.settings was the initial configure summary and is installed. Then configure is changed to dump a summary of the configure settings to the output and also append it to src/libhdf5.settings. That created two different output formats and duplicated information. This is the initial attempt to clean up this confusion and unify the output format. It is decided to use the src/libhdf5.settings template as the unified means. This requires more macros symbols be defined. The following symbols are all related to generating the src/libhdf5.settings file. AC_SUBST(EXTERNAL_FILTERS) AC_SUBST(MPE) MPE=no AC_SUBST(STATIC_EXEC) STATIC_EXEC=no AC_SUBST(HDF_FORTRAN) HDF_FORTRAN=no AC_SUBST(FC) HDF_FORTRAN=no AC_SUBST(HDF_CXX) HDF_CXX=no AC_SUBST(CXX) HDF_CXX=no AC_SUBST(HDF5_HL) HDF5_HL=yes AC_SUBST(GPFS) GPFS=no AC_SUBST(LINUX_LFS) LINUX_LFS=no AC_SUBST(INSTRUMENT) INSTRUMENT=no AC_SUBST(CODESTACK) CODESTACK=no AC_SUBST(HAVE_DMALLOC) HAVE_DMALLOC=no AC_SUBST(DIRECT_VFD) DIRECT_VFD=no AC_SUBST(THREADSAFE) THREADSAFE=no AC_SUBST(STATIC_SHARED) AC_SUBST(enable_shared) AC_SUBST(enable_static) AC_SUBST(UNAME_INFO) UNAME_INFO=`uname -a` The src/libhdf5.settings.in has CONDITIONAL's added to it too. The untrue conditions turned into a "#" and these lines are cleaned by the post processing script. Platform tested: h5committest on kagiso, smirom and linew. (smirom had failures not due to my changes.)
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