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* [svn-r19481] I'm backing out my fix for bug 1707 because there're some ↵Raymond Lu2010-09-271-3/+0
| | | | | | | | | | | unresolved issues - r19441 and 19467. Bug 1707 is that H5Eset_auto causes a seg fault when an application uses -DH5_USE_16_API with the 1.8 library to compile. I created a branch off the trunk called set_auto to continue working on the problem. Tested on jam - backing out, simple.
* [svn-r19461] Purpose: Fix bug 1864Neil Fortner2010-09-211-1/+4
| | | | | | | | | | | Description: Library versions 1.6.3 and earlier contain a bug which causes them to be unable to perform certain operations on a group if that group's symbol table information is not cached in the parent group's symbol table. Versions 1.8.0 to 1.8.5 did not cache this information. Modified library to cache this information. Tested: jam, amani, heiwa (h5committest)
* [svn-r19457] Bug fix for 1707 - H5Eset_auto causes a seg fault when an ↵Raymond Lu2010-09-211-0/+3
| | | | | | | | | | | | | application uses -DH5_USE_16_API with the 1.8 library to compile. The cause is from the mismatch of H5Eprint1 and H5Eprint2 set through H5Eset_auto. I changed the union in the structure H5E_auto_t. Another change is to make H5Eget_auto fail if H5Eset_auto is called to set the printing function. I'll write a document for it. Tested on heiwa, jam, and amani. The property change in configure.in, config, and Makefile.am came from the merge of the 1.8 library change.
* [svn-r19437] add missing -C optionsAllen Byrne2010-09-201-1/+1
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* [svn-r19435] remove source package command - not neededAllen Byrne2010-09-201-1/+0
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* [svn-r19431] Updated configuration section with optional command line usage. ↵Allen Byrne2010-09-201-24/+100
| | | | Also added section on CPack.
* [svn-r19406] Purpose:Jonathan Kim2010-09-161-0/+4
| | | | | | | | | | | Add --exclude-path option Description: Specified path to an object will be excluded from comparing the two files or two groups. If group is specified all the member objects will be excluded. Related to "1890: h5diff excluding object for file comparison via command line" Tested: jam, amani and heiwa
* [svn-r19400] Purpose:Jonathan Kim2010-09-161-0/+3
| | | | | | | | | | Fix for Bug1975 h5diff - support recursive comparison on group when specified as an object Description: Compare member objects and groups recursively when two files or groups are specified to be compared. Support parallel diff and handling symbolic links accordingly. Tested: jam, amani, heiwa
* [svn-r19389] Purpose:Jonathan Kim2010-09-151-0/+2
| | | | | | | | | | Fix for Bug1896 h5repack - changing layout to COMPACT does not work Description: Make h5repack be able to convert a layout to COMPACT for small size dataset as default. Also add verifying layout changes in our test script. Tested: jam, amani, heiwa
* [svn-r19386] Purpose: Fix assertion failure caused by fractal heap header ↵Neil Fortner2010-09-151-0/+3
| | | | | | | | | | | | | | file pointer Description: The fractal heap header structure keeps a pointer to the file associated with it. However, it is possible for that file pointer to be closed while the header is still in cache (through the shared file pointer). Previously, the header's file pointer was not updated and subsequently pointed to an invalid file structure. Modified fractal heap code to update the file pointer every time the header is accessed. Tested: jam, linew, amani (h5committest)
* [svn-r19377] Added bug 1938 resolutionAllen Byrne2010-09-131-0/+3
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* [svn-r19367] Purpose:Mike McGreevy2010-09-101-0/+4
| | | | | | | | | | | | | | | | | | | Add windows threads support to HDF5. Description: Added calls to the windows threads library to the H5TS layer, and wrapped most calls to either pthreads or windows threads library with portable H5TS-style defines. Modified tests to use portable function definitions as well. This can be configured via CMake with the HDF5_ENABLE_THREADSAFE option, and should work on windows vista and later operating systems. Tested: h5committest, plus threadsafe with pthreads on jam and amani, and tested on a Windows Vista VM with threadsafe using windows threads.
* [svn-r19363] When mandatory filter failed to write data chunks, the datasetRaymond Lu2010-09-091-0/+3
| | | | | | | couldn't close (bug 1260). The fix releases all resources and closes the dataset but returns a failure. Tested with h5committest - jam, heiwa, amani.
* [svn-r19354] Quincey and I made H5Eset_current_stack also close the stack to ↵Raymond Lu2010-09-071-0/+3
| | | | | | | | be set. This is to avoid H5Eclose_stack clearing the default stack. Please see bug 1799. Tested on jam - simple change.
* [svn-r19334] Update CMake referenceAllen Byrne2010-09-011-6/+6
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* [svn-r19288] Bug 1934 - I added support of all data types for H5Tget_order. ↵Raymond Lu2010-08-241-2/+3
| | | | | | | | | | | | I added a new byte order H5T_ORDER_MIXED specifically for compound types and its derived types. They report mixed orders if they have members of different orders. There is no change to configure.in, config, and Makefile.am in the top directory. They have some property changes when I merged the code from 1.8. Tested on jam. I tested the same change for 1.8 with h5committest.
* [svn-r19251] New feature(bug #1934): I made H5Tset_order support all data ↵Raymond Lu2010-08-191-0/+2
| | | | | | | | | | | | | | | | | | types with some restictions: 1. For enum type, members shouldn't be defined yet. 2. H5T_ORDER_NONE only works for reference and fixed-length string. 3. For opaque type, the order will be ignored. 4. For compound type, all restrictions above apply to the members. I'll change H5Tget_order and do another commit. There is no change to configure.in, config, and Makefile.am. There is some property change for these files when I did a merge from 1.8. Tested on jam. But I tested the 1.8 on heiwa, and amani.
* [svn-r19176] Bug fix for #1239 - The filter's public function CAN_APPLY ↵Raymond Lu2010-08-051-0/+2
| | | | | | | | | | | | should return htri_t not herr_t. To minimize the change of the library's behavior, in the function H5Z_prelude_callback of H5Z.c, if the return value of can_apply is FALSE and the filter is MANDATE, this function returns a FAILURE. If the return value is FALSE but the filter is OPTIONAL, this function returns a SUCCEED. During the IO, the filter will fail and return a size of zero. But the pipeline will skip this filter. Tested the same change for 1.8 on jam, linew, and amani. Tested on jam with szip.
* [svn-r19148] Maintenance: Removed misleading information about the ↵Elena Pourmal2010-07-291-16/+6
| | | | | | | HDF4-to-HDF5 tools. The tools became a part of the h4h5tools distribution long time ago, but the INSTALL file was not updated in the development branch and slipped into 1.8 releases and current trunk.
* [svn-r19146] Purpose: Fix bug in direct IO driverNeil Fortner2010-07-281-0/+3
| | | | | | | | | | | Description: In certain circumstances, the direct I/O driver did not perform correctly when data was unaligned. The driver has been patched to fix this. Also added some potential performance improvements for the unaligned case, and strengthened the test for whether the data needs to be aligned. Tested: cobalt
* [svn-r19144] Update for bug fix #1956.Raymond Lu2010-07-281-0/+3
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* [svn-r19107] Move Resources folder to config/cmakeAllen Byrne2010-07-201-1/+1
| | | | Tested: Local Linux
* [svn-r19086] Snapshot version 1.9 release 74HDF Tester2010-07-181-1/+1
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* [svn-r19076] Purpose: Fix bug 1951Neil Fortner2010-07-161-0/+4
| | | | | | | | | | | | Description: A bug introduced in 1.8.5 causes local heap data blocks to be mis-aligned when sizeof_offsets + 2*sizeof_lengths is not a multiple of 8. In this case, the address of the data block as stored in the heap prefix is aligned but the actual data block is not. This causes files created with these sizes to be corrupted, and prevents uncorrupted files with these sizes to be unreadable. Modified local heap code to account for alignment. Tested: jam, amani, linew (h5committest)
* [svn-r19070] Document update: ID 1921 change mpirun to mpiexecAlbert Cheng2010-07-142-15/+78
| | | | | | Changed the use of mpirun to mpiexec which is the MPI-2 official standard. INSTALL_parallel: Also bring in previous update of Red Storm support.
* [svn-r19064] Snapshot version 1.9 release 73HDF Tester2010-07-111-1/+1
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* [svn-r19051] Purpose:Jonathan Kim2010-07-071-0/+2
| | | | | | | | | | | Add --no-dangling-links option to h5ls. Description: Related to "Bug 1830 - Following an dangling external link in h5ls should set non-zero return code." If --no-dangling-links option is specified and any dangling link is found, return exit code 1 (error). Tested: jam, amani and heiwa
* [svn-r19047] Snapshot version 1.9 release 72HDF Tester2010-07-041-1/+1
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* [svn-r19034] Purpose:Jonathan Kim2010-06-281-0/+2
| | | | | | | | | | Change h5ls not to manipulate special characters in object name or attribute name for smart display. Description: Related to "But1784 h5ls has input and output issues with links that have '\' characters in them." Tested: jam, amani and linew
* [svn-r19031] Snapshot version 1.9 release 71HDF Tester2010-06-281-1/+1
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* [svn-r19022] Snapshot version 1.9 release 70HDF Tester2010-06-201-1/+1
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* [svn-r19006] Purpose: Improve performance of the the chunk cacheNeil Fortner2010-06-151-0/+2
| | | | | | | | | | Description: Previously, the chunk cache would, when looking for a chunk, alwaylook for the chunk in the b-tree before checking the cache. Reworked the functions that look up chunks to always check the cache first and avoid the b-tree lookup if the chunk is in cache. Tested: jam, linew, amani (h5committest)
* [svn-r18992] Bug Fix: (ID 1921)Albert Cheng2010-06-111-0/+3
| | | | | | | | | | | | PHDF5 changed to use "mpiexec", instead of mpirun, as the default MPI applications startup command as defined in the MPI-2 definition, section 4.1. Note that only mpich related (using mpicc command) definitions are changed to mpiexec. Other favors like hcc, AIX, champion, are not changed since I don't have a way to verify them yet. Tested: jam and amani, using both current and new mpich. Did not h5committested since this affects PHDF5 configure only.
* [svn-r18956] Corrected name of external librariesAllen Byrne2010-06-031-2/+2
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* [svn-r18943] Purpose:Jonathan Kim2010-06-021-0/+2
| | | | | | | | | | | | Support follow symbolic links. Description: Add '--follow-symlinks' option to follow symbolic links (soft and external). Update help page according to RM. Remove some warning messages from compiler. Tested: jam, amani and linew
* [svn-r18940] Update Cygwin and Windows referencesAllen Byrne2010-06-012-277/+16
| | | | Removed support for MinGW
* [svn-r18933] Update Cygwin install instructionsAllen Byrne2010-06-011-23/+14
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* [svn-r18903] Renamed Cmake specific document, making more general for all ↵Allen Byrne2010-05-264-97/+113
| | | | platforms. Updated references in other files.
* [svn-r18885] Add -C {Debug | Release} to ctest command lineAllen Byrne2010-05-241-1/+1
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* [svn-r18881] Maintenance: Fixed a typo in the bug number (should be 1851 ↵Elena Pourmal2010-05-221-1/+1
| | | | instead of 1855)
* [svn-r18880] Bug fix: Elena Pourmal2010-05-221-0/+5
| | | | | | | | Fixed a bug (1855) in H5DSattach_scale, H5DSis_attached and H5DSdetach_scale caused by using H5Tget_native_type function to determine the native type for reading REFERENCE_LIST attribute. The bug was exposed on Mac PPC. Platforms tested: juniper (Mac PPC), jam, amani, linew
* [svn-r18873] Purpose:Jonathan Kim2010-05-211-1/+1
| | | | | | | | | | | Rename '--follow-links' to '--follow-symlinks' Description: The '--follow-links' option is to follow symbolic links (soft and external). Make the name more intuitive and specific to the feature. Tested: jam, amani and linew
* [svn-r18868] Purpose: Fix bug in dataset shrinking algorithmNeil Fortner2010-05-201-0/+2
| | | | | | | | | | | | | | | | Description: Previously, it was possible for a chunk to be flushed due to chunk operations in the callback from H5B_iterate in H5D_chunk_prune_by_extent. Because flushing the chunk can force it to be reallocated if it is filtered, this can change the contents of the chunk b-tree in the middle of H5B_iterate. Because H5B_iterate uses a locally cached copy of the b-tree, this causes subsequent operations to be passed incorrect data. Rewrote H5D_chunk_prune_by_extent to avoid H5B_iterate entirely. Also fixed a bug in the dataset expand algorithm that could cause extra chunks to be created. Tested: jam, linew, smirom (h5committest)
* [svn-r18823] Snapshot version 1.9 release 69HDF Tester2010-05-161-1/+1
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* [svn-r18818] Bug fix: Elena Pourmal2010-05-151-0/+7
| | | | | | | | | | | Fixed a bug in the H5DSdetach_scale function when 0 bytes were allocated after the last reference to a dim. scale was removed from the list of references in a VL element of the DIMENSION_LIST attribute; modified the function to comply with the Spec: DIMENSION_LIST attribute is deleted now when no dimension scales left attached. Platforms tested: jam with electric fence, amani amd linew
* [svn-r18813] Purpose:Jonathan Kim2010-05-141-0/+8
| | | | | | | | | | | | | | | Add bug fixes for Tools. Description: Added list: 1726 - NPOESS: h5repack loses attributes for datasets of type H5T_REFERENCE 1814 - NPOESS: h5repack doesn't handle references to the groups as an element of a dataset 1817 - h5copy fail to copy dangling link by specifying link path directly 1793 - h5ls on a non-existent file gives 0 return code Tested: no, just text update.
* [svn-r18804] Purpose:Mike McGreevy2010-05-141-0/+2
| | | | | | | | | | | | | Fix memory leaks Description Added a routine to free memory which addresses a memory leak when variable length strings are used as fill values. Tested: h5committest and valgrind (on jam/amani) to confirm freed memory.
* [svn-r18803] Description:Binh-Minh Ribler2010-05-141-4/+16
| | | | | | | | | Added notes about + PropList::PropList(id) pclass id/plist id + new DataSet::getInMemDataSize + CommonFG::getLinkval and CommonFG::getComment take default values + bugzilla 1061 + read/write methods of DataSet and Attribute
* [svn-r18793] Add files to support building library with CMakeAllen Byrne2010-05-134-56/+361
| | | | Tested: Local linux
* [svn-r18709] Purpose:Mike McGreevy2010-05-051-0/+6
| | | | | | | | | | | | | | | | | | | | | | | | | Improve configure's large-file support control. Description: Modified configure to now attempt to add defines necessary for supporting largefiles on all systems, instead of solely on linux. This is in response to user requests to enable largefile support on Solaris by default, as well as to give extra control on AIX (instead of just jamming the necessary flag into the config files). The old --enable-linux-lfs flag has been removed in favor of the --enable-largefile flag (enabled by default), which can be used on all platforms. On systems where large files cannot be supported in this manner, configure will report as such. Tested: h5committest AIX (NCSA's blue_print machine) duty, liberty, and linew.
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