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* [svn-r19005] Purpose:Mike McGreevy2010-06-1556-188/+5383
| | | | | | | | | | | | | | | | | | | | | | | Commit metadata tagging framework. Description: This check-in contains a new framework whose goal is to apply a tag value to each new entry in the metadata cache as it is created. This tag value is such that it relates each piece of metadata to the HDF5 object that it belongs to (dataset, group, et cetera). This changeset includes the framework that applies the tags as well as a suite of tests to verify correct tag application, though does not yet make use of the tag values to flush/evict individual objects. Please refer to the "flush/evict individual objects" RFC for further discussion of these changes. Tested: jam, amani, linew (h5committest) liberty, abe, blue print
* [svn-r19001] Corrected large file optionAllen Byrne2010-06-141-1/+3
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* [svn-r18999] Removed and added files in CMake Resources folderAllen Byrne2010-06-141-1/+3
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* [svn-r18996] Updated config files and install commands per external ↵Allen Byrne2010-06-147-68/+193
| | | | | | developers recommendations. Tested: local linux
* [svn-r18992] Bug Fix: (ID 1921)Albert Cheng2010-06-113-34/+37
| | | | | | | | | | | | 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-r18987] Description:Frank Baker2010-06-081-0/+6
| | | | Add acknowledgment of LBNL contractual support.
* [svn-r18985] Test feature: (bugs 1919)Albert Cheng2010-06-084-5/+37
| | | | | | | | | | | | | | | | Problem: some launching command like yod (and sometimes mpirun), do not pass back the exit code of the executables back to the shell. It always returns 0 if it can launch the executable. This cause tests that expect non-zero exit code to fail incorrectly. Short term Solution: Added the feature that if $RUNSERIAL_NOEXITCODE is defined, do not test conditions that rely on non-zero exit code. Tests: dove-linux using RUNSERIAL=thgyod to see the failures and using $RUNSERIAL_NOEXITCODE=yes to bypass the errors. Also h5committested.
* [svn-r18984] Description:Albert Cheng2010-06-071-3/+9
| | | | | | | Fixed exit code (sometimes return code in Main) to follow the HDF5 standards. Tested: Tested in Dove-linux only since change is trivial and has passed in v1.8.
* [svn-r18976] Added comments regarding the -D_POSIX_SOURCE flag including a ↵Larry Knox2010-06-041-1/+12
| | | | | | reference to a discussion of the _POSIX_SOURCE, BSD_SOURCE, and _POSIX_C_SOURCE Macros and their intersaction at http://www.gnu.org/s/libc/manual/html_node/Feature-Test-Macros.html. Comment text only - not tested.
* [svn-r18965] Windows use of VC_EXTRALEAN no longer did anything. It has been ↵Allen Byrne2010-06-035-11/+8
| | | | | | | | replaced by WIN32_LEAN_AND_MEAN macro. This was the cause of a define conflict causing the use of grp1 and grp2 to be replaced with constants in the h5dumpgentest.c file. This also affected the use of the #include <winsock.h> needed by gethostname. The new include: winsock2.h has been added to h5private.h and either removed or updated in the other files. Tested: Windows
* [svn-r18963] Purpose:Mike McGreevy2010-06-032-0/+16
| | | | Add acknowledgments file to top level of hdf5 trunk distribution.
* [svn-r18958] Purpose:Jonathan Kim2010-06-031-12/+12
| | | | | | Fixed Windows compile error. Renamed to use 'gid1' and 'gid2' instead of 'grp1' and 'grp2'. Description: There is variable name confliction with 'grp1' ~ 'grp9' in Windows system. It occurs if H5private.h is included in the code.
* [svn-r18956] Corrected name of external librariesAllen Byrne2010-06-031-2/+2
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* [svn-r18950] Correct version numbers for trunkAllen Byrne2010-06-021-3/+3
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* [svn-r18949] Corrected where the static *.mod files are installed toAllen Byrne2010-06-021-6/+6
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* [svn-r18947] Purpose:Jonathan Kim2010-06-021-6/+22
| | | | | | | | Update Windows testing for h5ls according to the updates for Support follow symbolic links. Description: Sync with hdf5 trunk SVN r18943
* [svn-r18943] Purpose:Jonathan Kim2010-06-0226-218/+842
| | | | | | | | | | | | 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-r18942] Allen Byrne2010-06-011-1/+0
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* [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-r18930] Enabled mf test since it is fixed.Allen Byrne2010-06-011-2/+1
| | | | Tested: windows
* [svn-r18929] New feature:Albert Cheng2010-06-013-12/+79
| | | | | | | | | | Added ibm-flags to display the IBM XL compilers version information so that configure can report them in the configure summary and the libhdf5.settings file. For now, only the C compiler (xlc) versions are displayed. Also moved the C compiler options setting from ibm-aix to ibm-flags. Tested: NCSA Blue-print, both 32 and 64 bit modes.
* [svn-r18926] Description:Quincey Koziol2010-05-314-93/+67
| | | | | | | | Get down to just one "resize_configs_are_equal" comparison routine. Tested on: Mac OS X/32 10.6.3 (amazon) (too minor to require h5committest)
* [svn-r18925] Updated install of fortran mod filesAllen Byrne2010-05-282-8/+30
| | | | Tested: local linux
* [svn-r18922] Fix for failures for test/mf.c on windows:Vailin Choi2010-05-282-1/+8
| | | | | 1. H5FD_stdio_truncate() windows code: need to do a rewind 2. Make sure fsinfo.fs_addr is initialized before creating the message.
* [svn-r18917] Description:Quincey Koziol2010-05-2732-1404/+1126
| | | | | | | | | | | | | | | | | | | | | | | | Bring r18911 (plus some adaptions to match the code on the trunk) from the metadata journaling "merging" branch to the trunk: More general changes to align trunk with eventual changes from metadata journaling branch. Tested on: FreeBSD/32 6.3 (duty) in debug mode FreeBSD/64 6.3 (liberty) w/C++ & FORTRAN, in debug mode Linux/32 2.6 (jam) w/PGI compilers, w/default API=1.8.x, w/C++ & FORTRAN, w/threadsafe, in debug mode Linux/64-amd64 2.6 (amani) w/Intel compilers, w/default API=1.6.x, w/C++ & FORTRAN, in production mode Solaris/32 2.10 (linew) w/deprecated symbols disabled, w/C++ & FORTRAN, w/szip filter, in production mode Linux/64-ia64 2.6 (cobalt) w/Intel compilers, w/C++ & FORTRAN, in production mode Linux/64-amd64 2.6 (abe) w/parallel, w/FORTRAN, in debug mode Mac OS X/32 10.6.3 (amazon) in debug mode Mac OS X/32 10.6.3 (amazon) w/C++ & FORTRAN, w/threadsafe, in production mode
* [svn-r18915] Description:Quincey Koziol2010-05-272-24/+28
| | | | | | | | Clean up a couple of compiler warnings (in Windows). Tested on: Mac OS X/32 10.6.3 (amazon) w/debug (too minor to require h5committest)
* [svn-r18914] Added fortran library to list of library links.Allen Byrne2010-05-271-9/+9
| | | | Tested: Windows, local linux
* [svn-r18908] Corrected name of cstub libraries (needed to be lowercase)Allen Byrne2010-05-261-5/+5
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* [svn-r18906] Updated with new name of CMake.txtAllen Byrne2010-05-261-1/+1
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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-r18898] Added fortran /dbglibs option to fortran compile flags for ↵Allen Byrne2010-05-252-1/+11
| | | | | | windows intel fortran case. Duplicated windows intel fortran flag block for hl/fortran
* [svn-r18894] Purpose: Improve allocation performance of filtered datasets ↵Neil Fortner2010-05-258-74/+95
| | | | | | | | | | | | | with non-default VL fill values. Description: Previously, H5D_chunk_allocate would, if a dataset were filtered and had a non-default VL fill value, allocate a new buffer for every chunk. Changed H5D_chunk_allocate to reuse the existing buffer if possible. Also other miscellaneous cleanup. Tested: jam, linew, amani (h5committest)
* [svn-r18890] Update CMake fortran configure/build with changes from community.Allen Byrne2010-05-255-14/+32
| | | | | | | | - Add an install rule to copy compiled fortran module files - Only build the xlatefile utility if testing and tools are enabled - Don't do MPI HAVE_XXX checks until MPI_FOUND is true - Install needs H5version.h & H5overflow.h to be copied - Add debug information flags to debug compile and link lines for win32 Intel compiler
* [svn-r18885] Add -C {Debug | Release} to ctest command lineAllen Byrne2010-05-241-1/+1
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* [svn-r18882] Maintenance: fixed a typo in email addressElena Pourmal2010-05-221-1/+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 Pourmal2010-05-223-44/+61
| | | | | | | | 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-r18877] Update testh5diff.bat for --follow-symlinks changeAllen Byrne2010-05-211-76/+76
| | | | Tested: windows
* [svn-r18873] Purpose:Jonathan Kim2010-05-2116-143/+143
| | | | | | | | | | | 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-r18871] Description:Quincey Koziol2010-05-211-8/+8
| | | | | | | | | Clean up compiler warnings (on Windows, I hope) by marking some routines as taking 'volatile' parameters. Tested on: Mac OS X/32 10.6.3 (amazon) w/debug (too minor for h5committest)
* [svn-r18868] Purpose: Fix bug in dataset shrinking algorithmNeil Fortner2010-05-204-262/+384
| | | | | | | | | | | | | | | | 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-r18864] Description:Quincey Koziol2010-05-2020-1279/+254
| | | | | | | | | | | | | | | | | | | | General cleanups to align metadata journaling branch and trunk Tested on: FreeBSD/32 6.3 (duty) in debug mode FreeBSD/64 6.3 (liberty) w/C++ & FORTRAN, in debug mode Linux/32 2.6 (jam) w/PGI compilers, w/default API=1.8.x, w/C++ & FORTRAN, w/threadsafe, in debug mode Linux/64-amd64 2.6 (amani) w/Intel compilers, w/default API=1.6.x, w/C++ & FORTRAN, in production mode Solaris/32 2.10 (linew) w/deprecated symbols disabled, w/C++ & FORTRAN, w/szip filter, in production mode Linux/64-ia64 2.6 (cobalt) w/Intel compilers, w/C++ & FORTRAN, in production mode Linux/64-amd64 2.6 (abe) w/parallel, w/FORTRAN, in debug mode Mac OS X/32 10.6.3 (amazon) in debug mode Mac OS X/32 10.6.3 (amazon) w/C++ & FORTRAN, w/threadsafe, in production mode
* [svn-r18859] pull r18858 from 185;Allen Byrne2010-05-191-10/+5
| | | | Cange allocation of buffer to use the specified dimensions to calculate the size of a data buffer. Also removed any initialized values.
* [svn-r18856] Added CPack commands for installtion programAllen Byrne2010-05-1918-21/+161
| | | | Tested: local linux and Windows
* [svn-r18837] Description:Quincey Koziol2010-05-1817-1895/+1229
| | | | | | | | | | | | | | | | | | | | | | Remove the size parameter from H5[A]C_unprotect() and the H5[A]C__SIZE_CHANGED_FLAG, switching all clients & tests over to using H5[A]C_resize_entry appropriately. Tested on: FreeBSD/32 6.3 (duty) in debug mode FreeBSD/64 6.3 (liberty) w/C++ & FORTRAN, in debug mode Linux/32 2.6 (jam) w/PGI compilers, w/default API=1.8.x, w/C++ & FORTRAN, w/threadsafe, in debug mode Linux/64-amd64 2.6 (amani) w/Intel compilers, w/default API=1.6.x, w/C++ & FORTRAN, in production mode Solaris/32 2.10 (linew) w/deprecated symbols disabled, w/C++ & FORTRAN, w/szip filter, in production mode Linux/64-ia64 2.6 (cobalt) w/Intel compilers, w/C++ & FORTRAN, in production mode Linux/64-amd64 2.6 (abe) w/parallel, w/FORTRAN, in production mode Mac OS X/32 10.6.3 (amazon) in debug mode Mac OS X/32 10.6.3 (amazon) w/C++ & FORTRAN, w/threadsafe, in production mode
* [svn-r18834] Description:Quincey Koziol2010-05-171-1/+2
| | | | | | | | | Correct function enter macro and add 'done' label, for routine that is only invoked when configured with --enable-debug=all. Tested on: Mac OS X/32 10.6.3 (amazon) w/debug & production (too minor to require h5committest)
* [svn-r18832] Description:Quincey Koziol2010-05-171-1/+1
| | | | | | | | Correct error where variable didn't always get initialized correctly. Tested on: Mac OS X/32 10.6.3 (amazon) w/debug & prod Windows w/debug & prod
* [svn-r18831] Purpose:Jonathan Kim2010-05-171-5/+4
| | | | | | | Resolve build issue on Windows due to the location of variable definition. Tested: jam
* [svn-r18827] Description:Quincey Koziol2010-05-171-1/+1
| | | | | | | | Correct error where variable didn't always get initialized correctly. Tested on: Mac OS X/32 10.6.3 (amazon) w/debug & prod Windows w/debug & prod
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