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* [svn-r13928] Purpose: 1) Moving H5_CXX_HAVE_OFFSETOF macro to ↵Mike McGreevy2007-06-292-8/+8
| | | | | | | | | | src/H5pubconf.h file. 2) Removing configuration of c++/src/H5cxx_pubconf.h file. Reasoning: the additional pubconf file caused compilation complications, this is cleaner. Tested: kagiso, smirom
* [svn-r13927] Description:Quincey Koziol2007-06-291-63/+64
| | | | | | | | Clean up the chunked storage "initialize by extent" routine, in preparation for fixing another VL-datatype fill value bug. Tested on: Mac OS X/32 10.4.10 (amazon)
* [svn-r13926] Description:Quincey Koziol2007-06-2918-587/+1178
| | | | | | | | | | | | Add small interface to "wrap" a static buffer (usually on the stack), but still allow for buffers larger than the static buffer to be allocated. This can eliminate _many_ short-lived buffer allocations in situations where the buffer is a predictable size (or at least a "very likely" size). Also, some minor code cleanups, particularly in the SOHM caching code. Tested on: Mac OS X/32 10.4.10 (amazon)
* [svn-r13925] Purpose: intermediate checkin for offsetof fix for PGI compiler.Mike McGreevy2007-06-282-10/+11
| | | | | | | | | | Description: added new configuration to generate a pubconf file in the c++/src directory, H5cxx_pubconf.h. When C++ compiler recognizes 'offsetof', the macro H5_CXX_HAVE_OFFSETOF is defined in the new pubconf file. tested: kagiso, smirom
* [svn-r13919] Description:Quincey Koziol2007-06-261-57/+14
| | | | | | | | | Clean up more redundant code for reading SOHM messages. Tested on: Mac OS X/32 10.4.10 (amazon) Linux/32 2.6 (chicago) Linux/64 2.6 (chicago2)
* [svn-r13918] Description:Quincey Koziol2007-06-268-786/+872
| | | | | | | | | | Refactor fill value buffer code into one location, for better long-term maintenance. Tested on: Mac OS X/32 10.4.10 (amazon) Linux/32 2.6 (chicago) Linux/64 2.6 (chicago2)
* [svn-r13917] Description:Quincey Koziol2007-06-263-4/+5
| | | | | | | | | Code & warning cleanups Tested on: Mac OS X/32 10.4.10 (amazon) Linux/32 2.6 (chicago) Linux/64 2.6 (chicago2)
* [svn-r13916] Purpose: Fix MinGW inconsistencyScott Wegner2007-06-261-0/+4
| | | | | | | | | | Description: Windows does not accept the buffer size parameter of setvbuf to be less than 2. Previously, we had our fix split between two files, H5private.h and the Windows H5pubconf.h. This was a problem for MinGW, because it generates its own H5private.h. This moves the fix out of H5pubconf.h and into H5private.h. This shouldn't affect other platforms. Tested: MinGW on WinXP
* [svn-r13915] Description:Quincey Koziol2007-06-262-68/+78
| | | | | | | | | Clean up SOHM code, to copy message in H5HF_op call instead of separate calls to H5HF_get_obj_len() and H5HF_read(). Tested on: Mac OS X/32 10.4.9 (amazon) Linux/32 2.6 (chicago)
* [svn-r13913] Maintenance after beta2 release: used bin/h5vers script to ↵Elena Pourmal2007-06-251-2/+2
| | | | change version number to 1.8.0-beta2poat1
* [svn-r13909] Mainetnance before createing beta2 tar ballhdf5-1_8_0-beta2Elena Pourmal2007-06-251-2/+2
| | | | Changed version number to 1.8.0-beta2
* [svn-r13893] Maintenance: Bump up version to beta2pre2 after creating a tar ↵Elena Pourmal2007-06-201-2/+2
| | | | ball for remote testing
* [svn-r13892] Maintenance: Changed library version to beta2pre1 in ↵Elena Pourmal2007-06-201-2/+2
| | | | | | | preparation for remote testing for the HDF5 1.8.0-beta2 release Platforms tested: kagiso (small change done by bin/h5vers script)
* [svn-r13885] Modify the comment from the checkin last round.Raymond Lu2007-06-192-9/+9
| | | | No test is needed.
* [svn-r13884] The second step of optimization for compound data for the ChicagoRaymond Lu2007-06-195-73/+508
| | | | | | | | | | | | | | | | | | | | | | | | | | company. The I/O is optimized when the source and destination members are a subset of each other one way or another, and the order is the same, and no conversion is needed. For example: struct source { struct destination { TYPE1 A; --> TYPE1 A; TYPE2 B; --> TYPE2 B; TYPE3 C; --> TYPE3 C; }; TYPE4 D; TYPE5 E; }; or struct destination { struct source { TYPE1 A; --> TYPE1 A; TYPE2 B; --> TYPE2 B; TYPE3 C; --> TYPE3 C; }; TYPE4 D; TYPE5 E; }; The optimization is simply moving data from the source to the appropriate places in the buffer and bypass the reading of the background data and data conversion. Tested on smirom, liberty, sol, and copper.
* [svn-r13883] Description:Quincey Koziol2007-06-191-89/+309
| | | | | | | | | | | Fixed bugs w/VL-datatype fill values for chunked dataset storage. Tested on: Mac OS X/32 10.4.9 (amazon) FreeBSD/32 6.2 (duty) FreeBSD/64 6.2 (liberty) Linux/32 2.6 (chicago) Linux/64 2.6 (chicago2)
* [svn-r13878] Description:Quincey Koziol2007-06-191-11/+16
| | | | | | | | | Improve efficiency of writing VL-datatype fill values. Tested on: Mac OS X/32 10.4.9 (amazon) Linux/32 2.6 (chicago) Linux/64 2.6 (chicago2)
* [svn-r13873] Purpose: Code cleanupScott Wegner2007-06-181-9/+4
| | | | | | | | | | Description: Changed a macro in H5FDwindows.c from IO_BUF_SIZE to a more specific WINDOWS_MAX_BUF, and moved it to our H5pubconf.h, where users can customize it to their own preference. This value is needed because of a bug in the Windows _write function, it is unsafe to write buffers larger than 2GB-1 bytes in one write. Tested: VS2005 on WinXP.
* [svn-r13872] WinXP x64 does not define the error code EWOULDBLOCK, but ↵Scott Wegner2007-06-181-0/+10
| | | | | | | | instead uses its own WSAEWOULDBLOCK. Although the stream vfd isn't supported on Windows, this was requested by a user via bug #890. This won't affect any other platforms, but should help, should we ever decide to support stream vfd on Windows. Tested: kagiso, linew, smirom (via h5committest) NOT tested on Windows, as it is unsupported.
* [svn-r13870] Description:Quincey Koziol2007-06-154-85/+205
| | | | | | | | | | Fix writing variable-length datatype fill values for contiguous dataset storage Tested on: Mac OS X/32 10.4.9 (amazon) Linux/32 2.6 (chicago) Linux/64 2.6 (chicago2)
* [svn-r13866] Updated the open command to add the _O_BINARY flag, which ↵Scott Wegner2007-06-141-27/+31
| | | | | | | Windows needs for reading and seeking. Tested: VS.NET and VS2005 on WinXP 32-bit and x64
* [svn-r13865] Purpose: Adding a new macro, H5_HAVE_OFFSETOF.Mike McGreevy2007-06-142-2/+5
| | | | | | | | Description: When the compiler has the __offsetof__ extension, the H5_HAVE_OFFSETOF macro will be defined. When the compiler does not have the extension, the macro will remain undefined. Tested: kagiso
* [svn-r13862] Although still not completely ready, this fixes many problems ↵Scott Wegner2007-06-131-47/+64
| | | | | | | in the new Windows file driver related to writing large buffers (4GB+). sec2 is still set as the default driver on Windows. Tested: .NET on WinXP and 2005 on WinXP x64
* [svn-r13856] H5FDwindows.h is included in the hdf5.h but we didn't put it ↵MuQun Yang2007-06-124-0/+8
| | | | | | | | | | | | | | | | into Makefile.am un der /src. So when gmake check-install is run for HDF5 examples, it will fail. Th e fix is to include a macro #ifdef H5_HAVE_WINDOW around #include H5FDwindows.h so that H5FDwindows.h will only be included on windows, not on other platforms. We've fixed with the same way for other source code that includes H5FDwindows.h. This has been tested with h5committest. However, it takes a few hours to test all tests and except kagiso. Tests on linew and smirom cannot finish. It takes forever for the fheap test. And for parallel test at kagiso, ph5diff test seems to be hanged. I think all of our changes will only affect windows. So in order not to block other developers to check in their code, we just go ahead to check our changes. Kent Yang
* [svn-r13852] Added includes in various places to make it possible to set ↵Scott Wegner2007-06-116-1/+1055
| | | | | | | windows as the default vfd. Although sec2 is still default on Windows, it should now be possible to switch by simply changing H5pubconf.h . Tested: .NET 2003 on WinXP
* [svn-r13850] Description:Quincey Koziol2007-06-111-2/+2
| | | | | | | | | | | Hook "default VFD" configure macros into library. Also, make "default VFD" default to sec2 instead of nothing. Tested on: FreeBSD/32 6.2 (duty) FreeBSD/64 6.2 (liberty) Mac OS X/32 10.4.9 (amazon)
* [svn-r13849] Purpose: adding a --with-default-vfd= flag to configuration.Mike McGreevy2007-06-111-0/+3
| | | | | | | | Description: this flag will define the macro H5_DEFAULT_VFD in src/pubconf.h and set it to be either H5FD_SEC2 or H5FD_STDIO, depending on the value set with the configuration flag (either sec2 or stdio). Tested: kagiso, smirom, linew
* [svn-r13846] Purpose: To remove changes from version #13839 (regarding ↵Mike McGreevy2007-06-081-1/+0
| | | | | | | | DEFAULT_VFD). Description: Changes made during this checkin need to be greatly modified, so I'm removing them now rather than leaving them in and fixing them later.
* [svn-r13842] Description:Quincey Koziol2007-06-085-37/+155
| | | | | | | | | | | | Fix compact dataset storage to initialize VL datatype fill values correctly. Also, fix bug in global heap code when the fix action on a global heap is to delete an object in a heap with no free space. Tested on: Mac OS X/32 10.4.9 (amazon) FreeBSD/32 6.2 (duty)
* [svn-r13841] Description:Quincey Koziol2007-06-082-6/+32
| | | | | | | | | | Add a little more information to the debugging routine, for VL datatypes. Minor code cleanups Tested on: Mac OS X/32 10.4.9 (duty) Too minor to require h5committest
* [svn-r13839] Purpose: creation of a DEFAULT_VFD macro in the ↵Mike McGreevy2007-06-071-0/+1
| | | | | | | | | | | test/Makefile. Description: a new configure flag has been created that will now set a macro in the test/Makefile. The flag is with-default-vfd=. When set to a virtual file driver (e.g. "--with-default-vfd=sec2"), the macro DEFAULT_VFD will hold this value. Tested: kagiso, smirom, linew
* [svn-r13836] Description:Quincey Koziol2007-06-051-18/+17
| | | | | | | Minor code cleanups Tested on: Mac OS X/32 10.4.9 (amazon)
* [svn-r13829] Some systems (only SGI Altix ProPack 4 discovered so far) ↵Raymond Lu2007-06-023-2/+18
| | | | | | | | | | | | doesn't return correct file size from MPI_File_get_size. Bypass this problem by replacing it with stat. Add an option --disable-mpi-size in configure to indicate this function doesn't work properly. Add a test in testpar/t_mpi.c, too. If it returns wrong file size, print out a warning. Tested on kagiso (parallel) because already tested the same change to v1.6 on several platforms (kagiso, cobalt, copper, and sol).
* [svn-r13827] Description:Quincey Koziol2007-06-012-1/+56
| | | | | | | | | Close another memory leak for VL fill values, and clean up some temporary data structures on error. Tested on: FreeBSD/32 6.2 (duty) Mac OS X/32 10.4.9 (amazon)
* [svn-r13825] Description:Quincey Koziol2007-05-319-37/+157
| | | | | | | | | Incremental step forward in fixing problems with fill values that have a variable-length daattype. This set of changes fixes problems with the copying the property list values. tested Tn: Mac OS X/32 10.4.9 (amazon)
* [svn-r13823] Description:Quincey Koziol2007-05-311-1/+1
| | | | | | | Minor code cleanup to reduce initialization overhead. Tested on: Mac OS X/32 10.4.9 (amazon)
* [svn-r13822] Description:Quincey Koziol2007-05-311-0/+1
| | | | | | | | Undef the "post copy file" macro for "new style" fill values before defining it again. Tested on: FreeBSD/32 6.2 (duty) w/gcc 4.2
* [svn-r13821] Peter Cao2007-05-3010-4/+131
| | | | | | | | | | | | | | | | | | | | | Fixed a bug at copying shared reg_ref attribute. The ref values of an attribute was not writen in file. The post_copy_file() at H5Oattr.c only updates the value in memory. To fix the problem, we added H5O_shared_post_copy_file(), which delete the attribute in file (with the incorrect value) and create an new attribute with the correct values. I added the following functions: H5Oshared.c:H5O_shared_post_copy_file(H5F_t *f, hid_t dxpl_id, H5O_t *oh, void *mesg); H5Oshared.h: H5O_SHARED_POST_COPY_FILE and modified the following files to include shared_post_copy_file() H5Oattr.c H5Odtype.c H5Ofill.c H5Opline.c H5Osdspace.c
* [svn-r13816] Description:Quincey Koziol2007-05-291-29/+33
| | | | | | | | Fix a few typos and a small memory leak. Tested on: FreeBSD/32 6.2 (duty) Linux/64 2.6 (chicago2)
* [svn-r13815] Description:Quincey Koziol2007-05-292-0/+11
| | | | Regenerate configuration files after latest checkin
* [svn-r13814] Description:Quincey Koziol2007-05-2913-57/+60
| | | | | | | | | | | | | | Change back to clearing memory buffers by default, but give users option to disable this, for performance reasons (--disable-clear-file-buffers). Also, add configure option (--enable-using-memchecker) to conveniently control making the library "play nice" with memory checking tools like valgrind and purify. Tested on: Mac OS X/32 10.4.9 (amazon) FreeBSD/32 6.2 (duty) Linux/32 2.6 (kagiso)
* [svn-r13811] Description:Quincey Koziol2007-05-291-1/+1
| | | | | | | | Update information printed when the file module's debugging is enabled and file memory is leaked. Tested on: Linux/32 2.6 (chicago)
* [svn-r13808] Description:Quincey Koziol2007-05-242-11/+19
| | | | | | | | | | | | | Fix possible file corruption when using "new" format object headers and the size of chunk #0 for an object header transitions between needing 1->2->4->8- byte encoding for the size and there are "clean" messages in the object header already. (Usually triggered by flushing the file while adding attributes to an object) Tested on: Mac OS X/32 10.4.9 (amazon) Linux/32 2.6 (chicago) Linux/64 2.6 (chicago2)
* [svn-r13807] Description:Quincey Koziol2007-05-241-35/+2
| | | | | | | | | | | Fix error which attempted to allocate space for attribute that has a 'null' dataspace. Tested on: Mac OS X/32 10.4.9 (amazon) FreeBSD/32 6.2 (duty) Linux/32 2.6 (chicago) Linux/64 2.6 (chicago2)
* [svn-r13806] Description:Quincey Koziol2007-05-241-1/+1
| | | | | | | | | | Correct prototype for H5Sextent_equal() Tested on: Mac OS X/32 10.4.9 (amazon) FreeBSD/32 6.2 (duty) Linux/32 2.6 (chicago) Linux/64 2.6 (chicago2)
* [svn-r13803] Optimization of reading compound data.Raymond Lu2007-05-231-59/+139
| | | | | | | | | | | | | | | | | Optimize a special case when the source members are a subset of destination, and the order is the same, and no conversion is needed. For example: struct source { struct destination { TYPE1 A; --> TYPE1 A; TYPE2 B; --> TYPE2 B; TYPE3 C; --> TYPE3 C; }; TYPE4 D; TYPE5 E; }; The optimization is simply moving data to the appropriate places in the buffer. This optimization work is for the Chicago company. Tested on sol, copper, smirom, liberty.
* [svn-r13798] Description:Quincey Koziol2007-05-231-8/+4
| | | | | | | Clean up compiler warnings Tested on: Mac OS X/32 10.4.9 (amazon)
* [svn-r13797] Description:Quincey Koziol2007-05-231-80/+0
| | | | | | | | Re-enable fast attribute comparisons "in place" in the fractal heap. Tested on: FreeBSD/32 6.2 (duty) Mac OS X/32 10.4.9 (amazon)
* [svn-r13796] Description:Quincey Koziol2007-05-239-204/+242
| | | | | | | | | Clean up ISOHM code further and get rid of several non-optimal ways of working with object headers. Tested on: FreeBSD/32 6.2 (duty) Mac OS X/32 10.4.9 (amazon)
* [svn-r13794] Description:Quincey Koziol2007-05-222-3/+3
| | | | | | | Add 'const' to some pointers in internal routines. Tested on: Linux/32 2.6 (chicago)
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