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* [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.
* [svn-r18687] Description:Binh-Minh Ribler2010-05-031-0/+4
| | | | | | Added notes about new functions: CommonFG::getObjTypeByIdx CommonFG::getObjnameByIdx
* [svn-r18684] Snapshot version 1.9 release 68HDF Tester2010-05-021-1/+1
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* [svn-r18589] Snapshot version 1.9 release 67HDF Tester2010-04-181-1/+1
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* [svn-r18579] Purpose:Mike McGreevy2010-04-151-0/+3
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | Autotool Upgrade / Libtool Bug Fix Description: Updated autotools referenced in bin/reconfigure as follows: Autoconf 2.64 --> Autoconf 2.65 Automake 1.11 --> Automake 1.11.1 Libtool 2.2.6a --> Libtool 2.2.6b-mcg The referenced libtool version is a custom version of 2.2.6b. It has been tweaked to fix a bug in libtool that occurs when using PGI 10.0 compilers. A check incorrectly categorizes the C++ compiler as version 1.0 instead of 10.0, and the link line is subsequently set up incorrectly and fails to compile. A patch has been made available and will be included in the next release of libtool, but in the meantime I've applied the patch to a custom installation as indicated above. This bin/reconfigure now references the custom installation, and the resulting configure script will correctly categorize the PGI 10.0 C++ compiler. Ran bin/reconfigure to regenerate configure and makefiles. Tested: jam and amani with PGI 10.0 compilers. h5committest
* [svn-r18545] Snapshot version 1.9 release 66HDF Tester2010-04-111-1/+1
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* [svn-r18535] Purpose: Fix bug 1815Neil Fortner2010-04-081-0/+2
| | | | | | | | | | | Description: Attempting to copy an object with NULL references (all bytes zero) with the H5O_COPY_EXPAND_REFERENCE_FLAG flag set would cause a failure or an assertion (depending on whether it was in debug mode). Changed copy routine to detect NULL references (object and region) and avoid attempting to expand the reference in this case. Tested: jam, linew, amani (h5committest)
* [svn-r18508] Snapshot version 1.9 release 65HDF Tester2010-04-041-1/+1
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* [svn-r18465] Snapshot version 1.9 release 64HDF Tester2010-03-281-1/+1
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* [svn-r18445] Purpose: Fix bug 1637Neil Fortner2010-03-241-0/+2
| | | | | | | | | | Description: Modified algorithm for extending a dataset with early allocation so it only deals with the new chunks. Formerly, it would loop over all chunks, checking to see if each existed in cache and on disk, causing major performance issues with large numbers of chunks. Tested: jam, linew, amani (h5committest)
* [svn-r18432] Snapshot version 1.9 release 63HDF Tester2010-03-211-1/+1
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* [svn-r18406] Snapshot version 1.9 release 62HDF Tester2010-03-141-1/+1
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* [svn-r18395] Purpose: Fix links.c failureNeil Fortner2010-03-091-0/+2
| | | | | | | | | | | | | | | | Description: The core file driver previously matched files only based on the name used to open them, even when a backing store is used. This caused problems in the failing test when it traversed an external link to itself, and did not recognize that it was the same file. Similar tests in links.c were skipped when the core file driver was used. The failure was previously masked by inappropriate file flushes caused by external link traversal. Added code to the core file driver to keep track of low level file information of the backings store to allow for accurate recognition of duplicate files. Also re-enabled all links.c tests for the core file driver. Tested: Fedora (core and sec2 drivers; no time for full commit test, will monitor daily tests)
* [svn-r18376] Purpose: Fix bug 1733Neil Fortner2010-03-051-0/+3
| | | | | | | | | Description: Support for expanding external links was not implemented in H5Ocopy, even though a flag existed for H5Pset_copy_object to enable this. This patch implements this feature. Tested: jam, amani, linew (h5committest); Fedora
* [svn-r18374] Purpose: Fix bugs involving external linksNeil Fortner2010-03-051-0/+2
| | | | | | | | | | | | Description: Previously, the library would reopen the source file when traversing an external link if unable to find the target file otherwise. This has been corrected. Also moved the call to H5F_flush from H5F_try_close to H5F_dest, so the file is only flushed when the last identifier for the file is closed. This prevernts situations where the library could attempt to flush a file with protected metadata. Tested: jam, amani, linew (h5committest); Fedora
* [svn-r18362] Test commit from windowsAllen Byrne2010-03-031-0/+2
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* [svn-r18360] Updated project files and release docs to VS2008 and IVF101 based.Allen Byrne2010-03-033-235/+47
| | | | | | Made change to cpp version of testhdf5 for the elimination of dsets standalone. Tested: Windows
* [svn-r18350] Snapshot version 1.9 release 61HDF Tester2010-02-281-1/+1
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* [svn-r18273] Purpose:Jonathan Kim2010-02-181-0/+2
| | | | | | | | | | | | | | | | | | bugzilla 1754: h5diff: support comparing through links. Description: Fix incorrect (or hanging) behavior in parallel mode when specifying invalid combination of command options. (ex: -v and -q , --no-dangling-links without --follow-links) Add relate test case Update h5diffgentest.c due to add test files this and previous time Note: svn #18266 (prior to this) svn #18164 (original check-in) Tested: h5committest (jam, amani and linew)